https://launchpad.net/ubuntu/+source/relion/3.1.3-3build1/+build/25549282 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos01-ppc64el-019 5.4.0-137-generic #154-Ubuntu SMP Thu Jan 5 17:03:14 UTC 2023 ppc64le Buildd toolchain package versions: launchpad-buildd_229~619~ubuntu20.04.1 python3-lpbuildd_229~619~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.8 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1. Syncing the system clock with the buildd NTP service... 4 Feb 12:59:10 ntpdate[1893]: adjust time server 10.211.37.1 offset 0.000907 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=lunar --arch=ppc64el PACKAGEBUILD-25549282 --image-type chroot /home/buildd/filecache-default/7984b9498478de1d58b749dc057a3cf5e3226d68 Creating target for build PACKAGEBUILD-25549282 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=lunar --arch=ppc64el PACKAGEBUILD-25549282 Starting target for build PACKAGEBUILD-25549282 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=lunar --arch=ppc64el PACKAGEBUILD-25549282 'deb http://ftpmaster.internal/ubuntu lunar main universe' 'deb http://ftpmaster.internal/ubuntu lunar-security main universe' 'deb http://ftpmaster.internal/ubuntu lunar-updates main universe' 'deb http://ftpmaster.internal/ubuntu lunar-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-25549282 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=lunar --arch=ppc64el PACKAGEBUILD-25549282 Updating target for build PACKAGEBUILD-25549282 Get:1 http://ftpmaster.internal/ubuntu lunar InRelease [267 kB] Get:2 http://ftpmaster.internal/ubuntu lunar-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu lunar-updates InRelease [90.7 kB] Get:4 http://ftpmaster.internal/ubuntu lunar-proposed InRelease [118 kB] Get:5 http://ftpmaster.internal/ubuntu lunar/main ppc64el Packages [1335 kB] Get:6 http://ftpmaster.internal/ubuntu lunar/main Translation-en [508 kB] Get:7 http://ftpmaster.internal/ubuntu lunar/universe ppc64el Packages [14.1 MB] Get:8 http://ftpmaster.internal/ubuntu lunar/universe Translation-en [5893 kB] Get:9 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el Packages [90.9 kB] Get:10 http://ftpmaster.internal/ubuntu lunar-proposed/main Translation-en [34.0 kB] Get:11 http://ftpmaster.internal/ubuntu lunar-proposed/universe ppc64el Packages [293 kB] Get:12 http://ftpmaster.internal/ubuntu lunar-proposed/universe Translation-en [136 kB] Fetched 23.0 MB in 5s (4643 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: adduser advancecomp apt bash binutils binutils-common binutils-powerpc64le-linux-gnu coreutils cpp-12 debconf diffutils dpkg dpkg-dev fakeroot g++-12 gcc-12 gcc-12-base gpg gpg-agent gpgconf gpgv grep libacl1 libapt-pkg6.0 libasan8 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libc-bin libc-dev-bin libc6 libc6-dev libcap2 libcc1-0 libcrypt-dev libcrypt1 libctf-nobfd0 libctf0 libdb5.3 libdpkg-perl libfakeroot libgcc-12-dev libgcc-s1 libgcrypt20 libgnutls30 libgomp1 libitm1 liblsan0 liblzma5 libmpfr6 libncurses6 libncursesw6 libp11-kit0 libpcre2-8-0 libperl5.36 libquadmath0 libreadline8 libselinux1 libsemanage-common libsemanage2 libsqlite3-0 libssl3 libstdc++-12-dev libstdc++6 libsystemd-shared libsystemd0 libtinfo6 libtsan2 libubsan1 libudev1 libzstd1 linux-libc-dev lsb-base ncurses-base ncurses-bin openssl perl perl-base perl-modules-5.36 pkgbinarymangler readline-common sed sensible-utils systemd systemd-sysv sysvinit-utils tzdata xz-utils zlib1g 91 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 100 MB of archives. After this operation, 4309 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu lunar/main ppc64el bash ppc64el 5.2.15-2ubuntu1 [956 kB] Get:2 http://ftpmaster.internal/ubuntu lunar/main ppc64el coreutils ppc64el 9.1-1ubuntu2 [1508 kB] Get:3 http://ftpmaster.internal/ubuntu lunar/main ppc64el diffutils ppc64el 1:3.8-3 [196 kB] Get:4 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libc-bin ppc64el 2.37-0ubuntu1 [736 kB] Get:5 http://ftpmaster.internal/ubuntu lunar/main ppc64el libcrypt-dev ppc64el 1:4.4.33-2 [143 kB] Get:6 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libc6-dev ppc64el 2.37-0ubuntu1 [2057 kB] Get:7 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libc-dev-bin ppc64el 2.37-0ubuntu1 [20.9 kB] Get:8 http://ftpmaster.internal/ubuntu lunar/main ppc64el libcrypt1 ppc64el 1:4.4.33-2 [106 kB] Get:9 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el linux-libc-dev ppc64el 6.1.0-14.14 [1461 kB] Get:10 http://ftpmaster.internal/ubuntu lunar/main ppc64el libcc1-0 ppc64el 12.2.0-14ubuntu1 [48.9 kB] Get:11 http://ftpmaster.internal/ubuntu lunar/main ppc64el libctf0 ppc64el 2.40-2ubuntu1 [110 kB] Get:12 http://ftpmaster.internal/ubuntu lunar/main ppc64el libctf-nobfd0 ppc64el 2.40-2ubuntu1 [109 kB] Get:13 http://ftpmaster.internal/ubuntu lunar/main ppc64el binutils-powerpc64le-linux-gnu ppc64el 2.40-2ubuntu1 [2446 kB] Get:14 http://ftpmaster.internal/ubuntu lunar/main ppc64el libbinutils ppc64el 2.40-2ubuntu1 [728 kB] Get:15 http://ftpmaster.internal/ubuntu lunar/main ppc64el binutils-common ppc64el 2.40-2ubuntu1 [226 kB] Get:16 http://ftpmaster.internal/ubuntu lunar/main ppc64el binutils ppc64el 2.40-2ubuntu1 [3082 B] Get:17 http://ftpmaster.internal/ubuntu lunar/main ppc64el gcc-12-base ppc64el 12.2.0-14ubuntu1 [19.3 kB] Get:18 http://ftpmaster.internal/ubuntu lunar/main ppc64el libgcc-s1 ppc64el 12.2.0-14ubuntu1 [34.0 kB] Get:19 http://ftpmaster.internal/ubuntu lunar/main ppc64el libgomp1 ppc64el 12.2.0-14ubuntu1 [139 kB] Get:20 http://ftpmaster.internal/ubuntu lunar/main ppc64el libitm1 ppc64el 12.2.0-14ubuntu1 [32.6 kB] Get:21 http://ftpmaster.internal/ubuntu lunar/main ppc64el libatomic1 ppc64el 12.2.0-14ubuntu1 [10.6 kB] Get:22 http://ftpmaster.internal/ubuntu lunar/main ppc64el libasan8 ppc64el 12.2.0-14ubuntu1 [2450 kB] Get:23 http://ftpmaster.internal/ubuntu lunar/main ppc64el liblsan0 ppc64el 12.2.0-14ubuntu1 [1082 kB] Get:24 http://ftpmaster.internal/ubuntu lunar/main ppc64el libtsan2 ppc64el 12.2.0-14ubuntu1 [2568 kB] Get:25 http://ftpmaster.internal/ubuntu lunar/main ppc64el libubsan1 ppc64el 12.2.0-14ubuntu1 [992 kB] Get:26 http://ftpmaster.internal/ubuntu lunar/main ppc64el libquadmath0 ppc64el 12.2.0-14ubuntu1 [155 kB] Get:27 http://ftpmaster.internal/ubuntu lunar/main ppc64el g++-12 ppc64el 12.2.0-14ubuntu1 [11.4 MB] Get:28 http://ftpmaster.internal/ubuntu lunar/main ppc64el libstdc++-12-dev ppc64el 12.2.0-14ubuntu1 [2289 kB] Get:29 http://ftpmaster.internal/ubuntu lunar/main ppc64el libgcc-12-dev ppc64el 12.2.0-14ubuntu1 [1512 kB] Get:30 http://ftpmaster.internal/ubuntu lunar/main ppc64el gcc-12 ppc64el 12.2.0-14ubuntu1 [19.8 MB] Get:31 http://ftpmaster.internal/ubuntu lunar/main ppc64el cpp-12 ppc64el 12.2.0-14ubuntu1 [10.0 MB] Get:32 http://ftpmaster.internal/ubuntu lunar/main ppc64el libstdc++6 ppc64el 12.2.0-14ubuntu1 [787 kB] Get:33 http://ftpmaster.internal/ubuntu lunar/main ppc64el zlib1g ppc64el 1:1.2.13.dfsg-1ubuntu4 [70.1 kB] Get:34 http://ftpmaster.internal/ubuntu lunar/main ppc64el libmpfr6 ppc64el 4.2.0-1 [343 kB] Get:35 http://ftpmaster.internal/ubuntu lunar/main ppc64el libzstd1 ppc64el 1.5.2+dfsg2-3 [354 kB] Get:36 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libc6 ppc64el 2.37-0ubuntu1 [3178 kB] Get:37 http://ftpmaster.internal/ubuntu lunar/main ppc64el liblzma5 ppc64el 5.4.1-0.0 [154 kB] Get:38 http://ftpmaster.internal/ubuntu lunar/main ppc64el libgcrypt20 ppc64el 1.10.1-3ubuntu1 [718 kB] Get:39 http://ftpmaster.internal/ubuntu lunar/main ppc64el libacl1 ppc64el 2.3.1-3 [20.4 kB] Get:40 http://ftpmaster.internal/ubuntu lunar/main ppc64el libaudit-common all 1:3.0.7-1.1 [5108 B] Get:41 http://ftpmaster.internal/ubuntu lunar/main ppc64el libaudit1 ppc64el 1:3.0.7-1.1 [50.8 kB] Get:42 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libcap2 ppc64el 1:2.66-3ubuntu1 [33.2 kB] Get:43 http://ftpmaster.internal/ubuntu lunar/main ppc64el libpcre2-8-0 ppc64el 10.42-1 [256 kB] Get:44 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libselinux1 ppc64el 3.4-1build3 [96.4 kB] Get:45 http://ftpmaster.internal/ubuntu lunar/main ppc64el libperl5.36 ppc64el 5.36.0-7 [4848 kB] Get:46 http://ftpmaster.internal/ubuntu lunar/main ppc64el perl ppc64el 5.36.0-7 [235 kB] Get:47 http://ftpmaster.internal/ubuntu lunar/main ppc64el perl-base ppc64el 5.36.0-7 [1855 kB] Get:48 http://ftpmaster.internal/ubuntu lunar/main ppc64el perl-modules-5.36 all 5.36.0-7 [2984 kB] Get:49 http://ftpmaster.internal/ubuntu lunar/main ppc64el libdb5.3 ppc64el 5.3.28+dfsg2-1 [847 kB] Get:50 http://ftpmaster.internal/ubuntu lunar/main ppc64el debconf all 1.5.82 [125 kB] Get:51 http://ftpmaster.internal/ubuntu lunar/main ppc64el libssl3 ppc64el 3.0.7-1ubuntu1 [2133 kB] Get:52 http://ftpmaster.internal/ubuntu lunar/main ppc64el systemd-sysv ppc64el 252.4-1ubuntu1 [11.4 kB] Get:53 http://ftpmaster.internal/ubuntu lunar/main ppc64el systemd ppc64el 252.4-1ubuntu1 [3199 kB] Get:54 http://ftpmaster.internal/ubuntu lunar/main ppc64el libsystemd-shared ppc64el 252.4-1ubuntu1 [1964 kB] Get:55 http://ftpmaster.internal/ubuntu lunar/main ppc64el libp11-kit0 ppc64el 0.24.1-2ubuntu1 [258 kB] Get:56 http://ftpmaster.internal/ubuntu lunar/main ppc64el libsystemd0 ppc64el 252.4-1ubuntu1 [406 kB] Get:57 http://ftpmaster.internal/ubuntu lunar/main ppc64el libudev1 ppc64el 252.4-1ubuntu1 [111 kB] Get:58 http://ftpmaster.internal/ubuntu lunar/main ppc64el libapt-pkg6.0 ppc64el 2.5.5 [1016 kB] Get:59 http://ftpmaster.internal/ubuntu lunar/main ppc64el dpkg ppc64el 1.21.19ubuntu3 [1416 kB] Get:60 http://ftpmaster.internal/ubuntu lunar/main ppc64el grep ppc64el 3.8-5 [170 kB] Get:61 http://ftpmaster.internal/ubuntu lunar/main ppc64el ncurses-bin ppc64el 6.4-2 [196 kB] Get:62 http://ftpmaster.internal/ubuntu lunar/main ppc64el sed ppc64el 4.9-1 [208 kB] Get:63 http://ftpmaster.internal/ubuntu lunar/main ppc64el ncurses-base all 6.4-2 [21.3 kB] Get:64 http://ftpmaster.internal/ubuntu lunar/main ppc64el sysvinit-utils ppc64el 3.05-7ubuntu2 [28.5 kB] Get:65 http://ftpmaster.internal/ubuntu lunar/main ppc64el lsb-base all 11.5 [4296 B] Get:66 http://ftpmaster.internal/ubuntu lunar/main ppc64el adduser all 3.129ubuntu1 [59.0 kB] Get:67 http://ftpmaster.internal/ubuntu lunar/main ppc64el gpgv ppc64el 2.2.40-1ubuntu2 [171 kB] Get:68 http://ftpmaster.internal/ubuntu lunar/main ppc64el libgnutls30 ppc64el 3.7.8-4ubuntu1 [1038 kB] Get:69 http://ftpmaster.internal/ubuntu lunar/main ppc64el apt ppc64el 2.5.5 [1417 kB] Get:70 http://ftpmaster.internal/ubuntu lunar/main ppc64el libattr1 ppc64el 1:2.5.1-4 [13.2 kB] Get:71 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libsemanage-common all 3.4-1build3 [9808 B] Get:72 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libsemanage2 ppc64el 3.4-1build3 [113 kB] Get:73 http://ftpmaster.internal/ubuntu lunar/main ppc64el libncurses6 ppc64el 6.4-2 [144 kB] Get:74 http://ftpmaster.internal/ubuntu lunar/main ppc64el libncursesw6 ppc64el 6.4-2 [179 kB] Get:75 http://ftpmaster.internal/ubuntu lunar/main ppc64el libtinfo6 ppc64el 6.4-2 [124 kB] Get:76 http://ftpmaster.internal/ubuntu lunar/main ppc64el sensible-utils all 0.0.17+nmu1 [19.3 kB] Get:77 http://ftpmaster.internal/ubuntu lunar/main ppc64el readline-common all 8.2-1.3 [55.7 kB] Get:78 http://ftpmaster.internal/ubuntu lunar/main ppc64el libreadline8 ppc64el 8.2-1.3 [175 kB] Get:79 http://ftpmaster.internal/ubuntu lunar/main ppc64el libsqlite3-0 ppc64el 3.40.1-1 [749 kB] Get:80 http://ftpmaster.internal/ubuntu lunar/main ppc64el openssl ppc64el 3.0.7-1ubuntu1 [1195 kB] Get:81 http://ftpmaster.internal/ubuntu lunar/main ppc64el tzdata all 2022g-2ubuntu1 [397 kB] Get:82 http://ftpmaster.internal/ubuntu lunar/main ppc64el xz-utils ppc64el 5.4.1-0.0 [246 kB] Get:83 http://ftpmaster.internal/ubuntu lunar/main ppc64el advancecomp ppc64el 2.5-1 [235 kB] Get:84 http://ftpmaster.internal/ubuntu lunar/main ppc64el dpkg-dev all 1.21.19ubuntu3 [1067 kB] Get:85 http://ftpmaster.internal/ubuntu lunar/main ppc64el libdpkg-perl all 1.21.19ubuntu3 [247 kB] Get:86 http://ftpmaster.internal/ubuntu lunar/main ppc64el libfakeroot ppc64el 1.30.1-1.1ubuntu1 [32.8 kB] Get:87 http://ftpmaster.internal/ubuntu lunar/main ppc64el fakeroot ppc64el 1.30.1-1.1ubuntu1 [62.1 kB] Get:88 http://ftpmaster.internal/ubuntu lunar/main ppc64el gpg ppc64el 2.2.40-1ubuntu2 [646 kB] Get:89 http://ftpmaster.internal/ubuntu lunar/main ppc64el gpgconf ppc64el 2.2.40-1ubuntu2 [103 kB] Get:90 http://ftpmaster.internal/ubuntu lunar/main ppc64el gpg-agent ppc64el 2.2.40-1ubuntu2 [253 kB] Get:91 http://ftpmaster.internal/ubuntu lunar/main ppc64el pkgbinarymangler all 151 [16.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 100 MB in 5s (20.0 MB/s) (Reading database ... 13031 files and directories currently installed.) 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Setting up libstdc++-12-dev:ppc64el (12.2.0-14ubuntu1) ... Setting up binutils (2.40-2ubuntu1) ... Setting up dpkg-dev (1.21.19ubuntu3) ... Setting up gcc-12 (12.2.0-14ubuntu1) ... Setting up g++-12 (12.2.0-14ubuntu1) ... Processing triggers for debianutils (5.7-0.4) ... Processing triggers for libc-bin (2.37-0ubuntu1) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-25549282 ppc64el lunar-proposed -c chroot:build-PACKAGEBUILD-25549282 --arch=ppc64el --dist=lunar-proposed --nolog relion_3.1.3-3build1.dsc Initiating build PACKAGEBUILD-25549282 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-137-generic #154-Ubuntu SMP Thu Jan 5 17:03:14 UTC 2023 ppc64le sbuild (Debian sbuild) 0.79.0 (05 February 2020) on bos01-ppc64el-019.buildd +==============================================================================+ | relion 3.1.3-3build1 (ppc64el) Sat, 04 Feb 2023 12:59:38 +0000 | +==============================================================================+ Package: relion Version: 3.1.3-3build1 Source Version: 3.1.3-3build1 Distribution: lunar-proposed Machine Architecture: ppc64el Host Architecture: ppc64el Build Architecture: ppc64el Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-25549282/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/relion-yZ7FbN/resolver-cNfDje' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- relion_3.1.3-3build1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/relion-yZ7FbN/relion-3.1.3' with '<>' I: NOTICE: Log filtering will replace 'build/relion-yZ7FbN' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: cmake, debhelper-compat (= 13), libfftw3-dev, libfltk1.3-dev, libopenmpi-dev, libtiff-dev, fluid, build-essential, fakeroot Filtered Build-Depends: cmake, debhelper-compat (= 13), libfftw3-dev, libfltk1.3-dev, libopenmpi-dev, libtiff-dev, fluid, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [405 B] Get:5 copy:/<>/apt_archive ./ Packages [487 B] Fetched 1849 B in 0s (154 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils cmake cmake-data debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file fluid fontconfig-config fonts-dejavu-core gettext gettext-base gfortran-12 groff-base ibverbs-providers intltool-debian libarchive-zip-perl libarchive13 libbrotli1 libbsd0 libcairo2 libcbor0.8 libcurl4 libdebhelper-perl libdeflate-dev libdeflate0 libdrm-amdgpu1 libdrm-common libdrm-nouveau2 libdrm-radeon1 libdrm2 libdw1 libedit2 libelf1 libevent-2.1-7a libevent-core-2.1-7a libevent-dev libevent-extra-2.1-7 libevent-openssl-2.1-7 libevent-pthreads-2.1-7 libexpat1 libfabric1 libfftw3-bin libfftw3-dev libfftw3-double3 libfftw3-long3 libfftw3-single3 libfido2-1 libfile-stripnondeterminism-perl libfltk-cairo1.3 libfltk-forms1.3 libfltk-gl1.3 libfltk-images1.3 libfltk1.3 libfltk1.3-dev libfontconfig1 libfreetype6 libgfortran-12-dev libgfortran5 libgl1 libgl1-mesa-dri libglapi-mesa libglvnd0 libglx-mesa0 libglx0 libhwloc-dev libhwloc-plugins libhwloc15 libibverbs-dev libibverbs1 libicu71 libjbig-dev libjbig0 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev libjs-jquery libjs-jquery-ui libjsoncpp25 libldap2 liblerc-dev liblerc4 libllvm15 libltdl-dev libltdl7 liblzma-dev libmagic-mgc libmagic1 libmunge2 libnghttp2-14 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi3 libpciaccess0 libpipeline1 libpixman-1-0 libpmix-dev libpmix2 libpsl5 libpthread-stubs0-dev librdmacm1 librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libssh-4 libsub-override-perl libtiff-dev libtiff6 libtiffxx6 libtool libuchardet0 libucx0 libuv1 libwebp-dev libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libx11-dev libx11-xcb1 libxau-dev libxau6 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcb1 libxcb1-dev libxcursor1 libxdmcp-dev libxdmcp6 libxext6 libxfixes3 libxft2 libxinerama1 libxml2 libxnvctrl0 libxrender1 libxshmfence1 libxxf86vm1 libzstd-dev m4 man-db ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client po-debconf sgml-base x11proto-dev xorg-sgml-doctools xtrans-dev zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc cmake-doc cmake-format elpa-cmake-mode ninja-build dh-make gettext-doc libasprintf-dev libgettextpo-dev gfortran-12-doc libcoarrays-dev groff lrzip libfftw3-doc fltk1.3-doc libcairo2-dev libpng-dev libxext-dev libxft-dev libxinerama-dev libjs-jquery-ui-docs libtool-doc liblzma-doc openmpi-doc pciutils lm-sensors gcj-jdk libx11-doc libxcb-doc m4-doc apparmor less www-browser opencl-icd gfortran | fortran-compiler keychain libpam-ssh monkeysphere ssh-askpass libmail-box-perl sgml-base-doc Recommended packages: fltk1.3-doc curl | wget | lynx libarchive-cpio-perl libgl-dev libglu1-mesa-dev | libglu-dev libgl1-amber-dri javascript-common libldap-common libcoarrays-openmpi-dev publicsuffix libsasl2-modules xauth libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils cmake cmake-data debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file fluid fontconfig-config fonts-dejavu-core gettext gettext-base gfortran-12 groff-base ibverbs-providers intltool-debian libarchive-zip-perl libarchive13 libbrotli1 libbsd0 libcairo2 libcbor0.8 libcurl4 libdebhelper-perl libdeflate-dev libdeflate0 libdrm-amdgpu1 libdrm-common libdrm-nouveau2 libdrm-radeon1 libdrm2 libdw1 libedit2 libelf1 libevent-2.1-7a libevent-core-2.1-7a libevent-dev libevent-extra-2.1-7 libevent-openssl-2.1-7 libevent-pthreads-2.1-7 libexpat1 libfabric1 libfftw3-bin libfftw3-dev libfftw3-double3 libfftw3-long3 libfftw3-single3 libfido2-1 libfile-stripnondeterminism-perl libfltk-cairo1.3 libfltk-forms1.3 libfltk-gl1.3 libfltk-images1.3 libfltk1.3 libfltk1.3-dev libfontconfig1 libfreetype6 libgfortran-12-dev libgfortran5 libgl1 libgl1-mesa-dri libglapi-mesa libglvnd0 libglx-mesa0 libglx0 libhwloc-dev libhwloc-plugins libhwloc15 libibverbs-dev libibverbs1 libicu71 libjbig-dev libjbig0 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev libjs-jquery libjs-jquery-ui libjsoncpp25 libldap2 liblerc-dev liblerc4 libllvm15 libltdl-dev libltdl7 liblzma-dev libmagic-mgc libmagic1 libmunge2 libnghttp2-14 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi3 libpciaccess0 libpipeline1 libpixman-1-0 libpmix-dev libpmix2 libpsl5 libpthread-stubs0-dev librdmacm1 librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libssh-4 libsub-override-perl libtiff-dev libtiff6 libtiffxx6 libtool libuchardet0 libucx0 libuv1 libwebp-dev libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libx11-dev libx11-xcb1 libxau-dev libxau6 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcb1 libxcb1-dev libxcursor1 libxdmcp-dev libxdmcp6 libxext6 libxfixes3 libxft2 libxinerama1 libxml2 libxnvctrl0 libxrender1 libxshmfence1 libxxf86vm1 libzstd-dev m4 man-db ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client po-debconf sbuild-build-depends-main-dummy sgml-base x11proto-dev xorg-sgml-doctools xtrans-dev zlib1g-dev 0 upgraded, 175 newly installed, 0 to remove and 0 not upgraded. Need to get 105 MB of archives. After this operation, 444 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [720 B] Get:2 http://ftpmaster.internal/ubuntu lunar/main ppc64el sgml-base all 1.31 [11.4 kB] Get:3 http://ftpmaster.internal/ubuntu lunar/main ppc64el libbsd0 ppc64el 0.11.7-2 [60.1 kB] Get:4 http://ftpmaster.internal/ubuntu lunar/main ppc64el libelf1 ppc64el 0.188-2.1 [63.2 kB] Get:5 http://ftpmaster.internal/ubuntu lunar/main ppc64el libexpat1 ppc64el 2.5.0-1 [95.3 kB] Get:6 http://ftpmaster.internal/ubuntu lunar/main ppc64el libicu71 ppc64el 71.1-3ubuntu1 [10.9 MB] Get:7 http://ftpmaster.internal/ubuntu lunar/main ppc64el libxml2 ppc64el 2.9.14+dfsg-1.1 [820 kB] Get:8 http://ftpmaster.internal/ubuntu lunar/main ppc64el bsdextrautils ppc64el 2.38.1-4ubuntu1 [76.4 kB] Get:9 http://ftpmaster.internal/ubuntu lunar/main ppc64el libmagic-mgc ppc64el 1:5.44-3 [293 kB] Get:10 http://ftpmaster.internal/ubuntu lunar/main ppc64el libmagic1 ppc64el 1:5.44-3 [104 kB] Get:11 http://ftpmaster.internal/ubuntu lunar/main ppc64el file ppc64el 1:5.44-3 [22.4 kB] Get:12 http://ftpmaster.internal/ubuntu lunar/main ppc64el gettext-base ppc64el 0.21-11 [40.7 kB] Get:13 http://ftpmaster.internal/ubuntu lunar/main ppc64el libuchardet0 ppc64el 0.0.7-1build2 [80.4 kB] Get:14 http://ftpmaster.internal/ubuntu lunar/main ppc64el groff-base ppc64el 1.22.4-9 [1004 kB] Get:15 http://ftpmaster.internal/ubuntu lunar/main ppc64el libcbor0.8 ppc64el 0.8.0-2ubuntu1 [26.6 kB] Get:16 http://ftpmaster.internal/ubuntu lunar/main ppc64el libdrm-common all 2.4.114-1 [5940 B] Get:17 http://ftpmaster.internal/ubuntu lunar/main ppc64el libdrm2 ppc64el 2.4.114-1 [47.2 kB] Get:18 http://ftpmaster.internal/ubuntu lunar/main ppc64el libedit2 ppc64el 3.1-20221030-2 [122 kB] Get:19 http://ftpmaster.internal/ubuntu lunar/main ppc64el libfido2-1 ppc64el 1.12.0-2 [110 kB] Get:20 http://ftpmaster.internal/ubuntu lunar/main ppc64el libnghttp2-14 ppc64el 1.51.0-1 [87.1 kB] Get:21 http://ftpmaster.internal/ubuntu lunar/main ppc64el libnuma1 ppc64el 2.0.16-1 [26.7 kB] Get:22 http://ftpmaster.internal/ubuntu lunar/main ppc64el libpipeline1 ppc64el 1.5.7-1 [25.8 kB] Get:23 http://ftpmaster.internal/ubuntu lunar/main ppc64el libpsl5 ppc64el 0.21.0-1.2build2 [60.3 kB] Get:24 http://ftpmaster.internal/ubuntu lunar/main ppc64el libuv1 ppc64el 1.44.2-1 [106 kB] Get:25 http://ftpmaster.internal/ubuntu lunar/main ppc64el libxau6 ppc64el 1:1.0.9-1build5 [8028 B] Get:26 http://ftpmaster.internal/ubuntu lunar/main ppc64el libxdmcp6 ppc64el 1:1.1.3-0ubuntu5 [12.3 kB] Get:27 http://ftpmaster.internal/ubuntu lunar/main ppc64el libxcb1 ppc64el 1.15-1 [55.5 kB] Get:28 http://ftpmaster.internal/ubuntu lunar/main ppc64el libx11-data all 2:1.8.3-3 [118 kB] Get:29 http://ftpmaster.internal/ubuntu lunar/main ppc64el libx11-6 ppc64el 2:1.8.3-3 [737 kB] Get:30 http://ftpmaster.internal/ubuntu lunar/main ppc64el libxext6 ppc64el 2:1.3.4-1build1 [40.0 kB] Get:31 http://ftpmaster.internal/ubuntu lunar/main ppc64el man-db ppc64el 2.11.2-1 [1256 kB] Get:32 http://ftpmaster.internal/ubuntu lunar/main ppc64el openssh-client ppc64el 1:9.0p1-1ubuntu8 [1027 kB] Get:33 http://ftpmaster.internal/ubuntu lunar/main ppc64el m4 ppc64el 1.4.19-2 [275 kB] Get:34 http://ftpmaster.internal/ubuntu lunar/main ppc64el autoconf all 2.71-3 [339 kB] Get:35 http://ftpmaster.internal/ubuntu lunar/main ppc64el autotools-dev all 20220109.1 [44.9 kB] Get:36 http://ftpmaster.internal/ubuntu lunar/main ppc64el automake all 1:1.16.5-1.3 [558 kB] Get:37 http://ftpmaster.internal/ubuntu lunar/main ppc64el autopoint all 0.21-11 [420 kB] Get:38 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libarchive13 ppc64el 3.6.2-1ubuntu1 [525 kB] Get:39 http://ftpmaster.internal/ubuntu lunar/main ppc64el libbrotli1 ppc64el 1.0.9-2build7 [369 kB] Get:40 http://ftpmaster.internal/ubuntu lunar/main ppc64el libsasl2-modules-db ppc64el 2.1.28+dfsg-10 [22.7 kB] Get:41 http://ftpmaster.internal/ubuntu lunar/main ppc64el libsasl2-2 ppc64el 2.1.28+dfsg-10 [69.2 kB] Get:42 http://ftpmaster.internal/ubuntu lunar/main ppc64el libldap2 ppc64el 2.6.3+dfsg-1~exp1ubuntu1 [217 kB] Get:43 http://ftpmaster.internal/ubuntu lunar/main ppc64el librtmp1 ppc64el 2.4+20151223.gitfa8646d.1-2build4 [65.5 kB] Get:44 http://ftpmaster.internal/ubuntu lunar/main ppc64el libssh-4 ppc64el 0.10.4-2 [235 kB] Get:45 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libcurl4 ppc64el 7.87.0-2ubuntu1 [358 kB] Get:46 http://ftpmaster.internal/ubuntu lunar/main ppc64el libjsoncpp25 ppc64el 1.9.5-4 [89.4 kB] Get:47 http://ftpmaster.internal/ubuntu lunar/main ppc64el librhash0 ppc64el 1.4.3-3 [144 kB] Get:48 http://ftpmaster.internal/ubuntu lunar/main ppc64el cmake-data all 3.25.1-1 [2049 kB] Get:49 http://ftpmaster.internal/ubuntu lunar/main ppc64el cmake ppc64el 3.25.1-1 [9432 kB] Get:50 http://ftpmaster.internal/ubuntu lunar/main ppc64el libdebhelper-perl all 13.11.4ubuntu3 [66.1 kB] Get:51 http://ftpmaster.internal/ubuntu lunar/main ppc64el libtool all 2.4.7-5 [166 kB] Get:52 http://ftpmaster.internal/ubuntu lunar/main ppc64el dh-autoreconf all 20 [16.1 kB] Get:53 http://ftpmaster.internal/ubuntu lunar/main ppc64el libarchive-zip-perl all 1.68-1 [90.2 kB] Get:54 http://ftpmaster.internal/ubuntu lunar/main ppc64el libsub-override-perl all 0.09-4 [8706 B] Get:55 http://ftpmaster.internal/ubuntu lunar/main ppc64el libfile-stripnondeterminism-perl all 1.13.1-1 [18.1 kB] Get:56 http://ftpmaster.internal/ubuntu lunar/main ppc64el dh-strip-nondeterminism all 1.13.1-1 [5362 B] Get:57 http://ftpmaster.internal/ubuntu lunar/main ppc64el libdw1 ppc64el 0.188-2.1 [284 kB] Get:58 http://ftpmaster.internal/ubuntu lunar/main ppc64el debugedit ppc64el 1:5.0-5 [51.1 kB] Get:59 http://ftpmaster.internal/ubuntu lunar/main ppc64el dwz ppc64el 0.15-1 [139 kB] Get:60 http://ftpmaster.internal/ubuntu lunar/main ppc64el gettext ppc64el 0.21-11 [970 kB] Get:61 http://ftpmaster.internal/ubuntu lunar/main ppc64el intltool-debian all 0.35.0+20060710.6 [23.2 kB] Get:62 http://ftpmaster.internal/ubuntu lunar/main ppc64el po-debconf all 1.0.21+nmu1 [233 kB] Get:63 http://ftpmaster.internal/ubuntu lunar/main ppc64el debhelper all 13.11.4ubuntu3 [925 kB] Get:64 http://ftpmaster.internal/ubuntu lunar/main ppc64el libfreetype6 ppc64el 2.12.1+dfsg-4 [521 kB] Get:65 http://ftpmaster.internal/ubuntu lunar/main ppc64el fonts-dejavu-core all 2.37-2build2 [1137 kB] Get:66 http://ftpmaster.internal/ubuntu lunar/main ppc64el fontconfig-config ppc64el 2.14.1-3ubuntu1 [32.5 kB] Get:67 http://ftpmaster.internal/ubuntu lunar/main ppc64el libfontconfig1 ppc64el 2.14.1-3ubuntu1 [182 kB] Get:68 http://ftpmaster.internal/ubuntu lunar/main ppc64el libxfixes3 ppc64el 1:6.0.0-2 [11.6 kB] Get:69 http://ftpmaster.internal/ubuntu lunar/main ppc64el libxrender1 ppc64el 1:0.9.10-1.1 [23.3 kB] Get:70 http://ftpmaster.internal/ubuntu lunar/main ppc64el libxcursor1 ppc64el 1:1.2.1-1 [26.9 kB] Get:71 http://ftpmaster.internal/ubuntu lunar/main ppc64el libxft2 ppc64el 2.3.6-1 [59.8 kB] Get:72 http://ftpmaster.internal/ubuntu lunar/main ppc64el libxinerama1 ppc64el 2:1.1.4-3 [7658 B] Get:73 http://ftpmaster.internal/ubuntu lunar/universe ppc64el libfltk1.3 ppc64el 1.3.8-5 [683 kB] Get:74 http://ftpmaster.internal/ubuntu lunar/universe ppc64el libfltk-forms1.3 ppc64el 1.3.8-5 [14.6 kB] Get:75 http://ftpmaster.internal/ubuntu lunar/main ppc64el libjpeg-turbo8 ppc64el 2.1.2-0ubuntu1 [214 kB] Get:76 http://ftpmaster.internal/ubuntu lunar/main ppc64el libjpeg8 ppc64el 8c-2ubuntu10 [2266 B] Get:77 http://ftpmaster.internal/ubuntu lunar/universe ppc64el libfltk-images1.3 ppc64el 1.3.8-5 [29.6 kB] Get:78 http://ftpmaster.internal/ubuntu lunar/universe ppc64el fluid ppc64el 1.3.8-5 [231 kB] Get:79 http://ftpmaster.internal/ubuntu lunar/main ppc64el libgfortran5 ppc64el 12.2.0-14ubuntu1 [546 kB] Get:80 http://ftpmaster.internal/ubuntu lunar/main ppc64el libgfortran-12-dev ppc64el 12.2.0-14ubuntu1 [594 kB] Get:81 http://ftpmaster.internal/ubuntu lunar/main ppc64el gfortran-12 ppc64el 12.2.0-14ubuntu1 [10.5 MB] Get:82 http://ftpmaster.internal/ubuntu lunar/main ppc64el libnl-3-200 ppc64el 3.7.0-0.2 [71.5 kB] Get:83 http://ftpmaster.internal/ubuntu lunar/main ppc64el libnl-route-3-200 ppc64el 3.7.0-0.2 [203 kB] Get:84 http://ftpmaster.internal/ubuntu lunar/main ppc64el libibverbs1 ppc64el 44.0-2 [71.2 kB] Get:85 http://ftpmaster.internal/ubuntu lunar/main ppc64el ibverbs-providers ppc64el 44.0-2 [403 kB] Get:86 http://ftpmaster.internal/ubuntu lunar/main ppc64el libpixman-1-0 ppc64el 0.42.2-1 [300 kB] Get:87 http://ftpmaster.internal/ubuntu lunar/main ppc64el libxcb-render0 ppc64el 1.15-1 [17.2 kB] Get:88 http://ftpmaster.internal/ubuntu lunar/main ppc64el libxcb-shm0 ppc64el 1.15-1 [5896 B] Get:89 http://ftpmaster.internal/ubuntu lunar/main ppc64el libcairo2 ppc64el 1.16.0-7 [672 kB] Get:90 http://ftpmaster.internal/ubuntu lunar/main ppc64el libdeflate0 ppc64el 1.14-1 [53.8 kB] Get:91 http://ftpmaster.internal/ubuntu lunar/main ppc64el libdeflate-dev ppc64el 1.14-1 [49.2 kB] Get:92 http://ftpmaster.internal/ubuntu lunar/main ppc64el libdrm-amdgpu1 ppc64el 2.4.114-1 [23.8 kB] Get:93 http://ftpmaster.internal/ubuntu lunar/main ppc64el libdrm-nouveau2 ppc64el 2.4.114-1 [20.5 kB] Get:94 http://ftpmaster.internal/ubuntu lunar/main ppc64el libdrm-radeon1 ppc64el 2.4.114-1 [25.8 kB] Get:95 http://ftpmaster.internal/ubuntu lunar/main ppc64el libevent-2.1-7a ppc64el 2.1.12-stable-5ubuntu1 [169 kB] Get:96 http://ftpmaster.internal/ubuntu lunar/main ppc64el libevent-core-2.1-7a ppc64el 2.1.12-stable-5ubuntu1 [106 kB] Get:97 http://ftpmaster.internal/ubuntu lunar/main ppc64el libevent-extra-2.1-7 ppc64el 2.1.12-stable-5ubuntu1 [74.6 kB] Get:98 http://ftpmaster.internal/ubuntu lunar/main ppc64el libevent-pthreads-2.1-7 ppc64el 2.1.12-stable-5ubuntu1 [7830 B] Get:99 http://ftpmaster.internal/ubuntu lunar/main ppc64el libevent-openssl-2.1-7 ppc64el 2.1.12-stable-5ubuntu1 [16.7 kB] Get:100 http://ftpmaster.internal/ubuntu lunar/main ppc64el libevent-dev ppc64el 2.1.12-stable-5ubuntu1 [329 kB] Get:101 http://ftpmaster.internal/ubuntu lunar/main ppc64el librdmacm1 ppc64el 44.0-2 [78.6 kB] Get:102 http://ftpmaster.internal/ubuntu lunar/universe ppc64el libfabric1 ppc64el 1.17.0-3 [677 kB] Get:103 http://ftpmaster.internal/ubuntu lunar/main ppc64el libfftw3-double3 ppc64el 3.3.8-2ubuntu8 [383 kB] Get:104 http://ftpmaster.internal/ubuntu lunar/main ppc64el libfftw3-long3 ppc64el 3.3.8-2ubuntu8 [593 kB] Get:105 http://ftpmaster.internal/ubuntu lunar/main ppc64el libfftw3-single3 ppc64el 3.3.8-2ubuntu8 [392 kB] Get:106 http://ftpmaster.internal/ubuntu lunar/main ppc64el libfftw3-bin ppc64el 3.3.8-2ubuntu8 [32.3 kB] Get:107 http://ftpmaster.internal/ubuntu lunar/main ppc64el libfftw3-dev ppc64el 3.3.8-2ubuntu8 [1089 kB] Get:108 http://ftpmaster.internal/ubuntu lunar/universe ppc64el libfltk-cairo1.3 ppc64el 1.3.8-5 [6870 B] Get:109 http://ftpmaster.internal/ubuntu lunar/main ppc64el libglvnd0 ppc64el 1.6.0-1 [82.8 kB] Get:110 http://ftpmaster.internal/ubuntu lunar/main ppc64el libglapi-mesa ppc64el 22.2.5-0ubuntu1 [34.6 kB] Get:111 http://ftpmaster.internal/ubuntu lunar/main ppc64el libx11-xcb1 ppc64el 2:1.8.3-3 [7836 B] Get:112 http://ftpmaster.internal/ubuntu lunar/main ppc64el libxcb-dri2-0 ppc64el 1.15-1 [7444 B] Get:113 http://ftpmaster.internal/ubuntu lunar/main ppc64el libxcb-dri3-0 ppc64el 1.15-1 [7392 B] Get:114 http://ftpmaster.internal/ubuntu lunar/main ppc64el libxcb-glx0 ppc64el 1.15-1 [26.2 kB] Get:115 http://ftpmaster.internal/ubuntu lunar/main ppc64el libxcb-present0 ppc64el 1.15-1 [5814 B] Get:116 http://ftpmaster.internal/ubuntu lunar/main ppc64el libxcb-sync1 ppc64el 1.15-1 [9720 B] Get:117 http://ftpmaster.internal/ubuntu lunar/main ppc64el libxcb-xfixes0 ppc64el 1.15-1 [10.6 kB] Get:118 http://ftpmaster.internal/ubuntu lunar/main ppc64el libxshmfence1 ppc64el 1.3-1build4 [5566 B] Get:119 http://ftpmaster.internal/ubuntu lunar/main ppc64el libxxf86vm1 ppc64el 1:1.1.4-1build3 [11.8 kB] Get:120 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libllvm15 ppc64el 1:15.0.7-1 [26.3 MB] Get:121 http://ftpmaster.internal/ubuntu lunar/main ppc64el libsensors-config all 1:3.6.0-7ubuntu1 [5274 B] Get:122 http://ftpmaster.internal/ubuntu lunar/main ppc64el libsensors5 ppc64el 1:3.6.0-7ubuntu1 [32.3 kB] Get:123 http://ftpmaster.internal/ubuntu lunar/main ppc64el libgl1-mesa-dri ppc64el 22.2.5-0ubuntu1 [6093 kB] Get:124 http://ftpmaster.internal/ubuntu lunar/main ppc64el libglx-mesa0 ppc64el 22.2.5-0ubuntu1 [175 kB] Get:125 http://ftpmaster.internal/ubuntu lunar/main ppc64el libglx0 ppc64el 1.6.0-1 [42.2 kB] Get:126 http://ftpmaster.internal/ubuntu lunar/main ppc64el libgl1 ppc64el 1.6.0-1 [109 kB] Get:127 http://ftpmaster.internal/ubuntu lunar/universe ppc64el libfltk-gl1.3 ppc64el 1.3.8-5 [46.5 kB] Get:128 http://ftpmaster.internal/ubuntu lunar/main ppc64el xorg-sgml-doctools all 1:1.11-1.1 [10.9 kB] Get:129 http://ftpmaster.internal/ubuntu lunar/main ppc64el x11proto-dev all 2022.1-1 [605 kB] Get:130 http://ftpmaster.internal/ubuntu lunar/main ppc64el libxau-dev ppc64el 1:1.0.9-1build5 [10.3 kB] Get:131 http://ftpmaster.internal/ubuntu lunar/main ppc64el libxdmcp-dev ppc64el 1:1.1.3-0ubuntu5 [28.1 kB] Get:132 http://ftpmaster.internal/ubuntu lunar/main ppc64el xtrans-dev all 1.4.0-1 [68.9 kB] Get:133 http://ftpmaster.internal/ubuntu lunar/main ppc64el libpthread-stubs0-dev ppc64el 0.4-1build2 [5510 B] Get:134 http://ftpmaster.internal/ubuntu lunar/main ppc64el libxcb1-dev ppc64el 1.15-1 [96.0 kB] Get:135 http://ftpmaster.internal/ubuntu lunar/main ppc64el libx11-dev ppc64el 2:1.8.3-3 [830 kB] Get:136 http://ftpmaster.internal/ubuntu lunar/universe ppc64el libfltk1.3-dev ppc64el 1.3.8-5 [1014 kB] Get:137 http://ftpmaster.internal/ubuntu lunar/universe ppc64el libhwloc15 ppc64el 2.9.0-1 [204 kB] Get:138 http://ftpmaster.internal/ubuntu lunar/main ppc64el libjpeg-turbo8-dev ppc64el 2.1.2-0ubuntu1 [337 kB] Get:139 http://ftpmaster.internal/ubuntu lunar/main ppc64el libjpeg8-dev ppc64el 8c-2ubuntu10 [1476 B] Get:140 http://ftpmaster.internal/ubuntu lunar/main ppc64el libjpeg-dev ppc64el 8c-2ubuntu10 [1476 B] Get:141 http://ftpmaster.internal/ubuntu lunar/main ppc64el libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] Get:142 http://ftpmaster.internal/ubuntu lunar/universe ppc64el libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] Get:143 http://ftpmaster.internal/ubuntu lunar/main ppc64el liblerc4 ppc64el 4.0.0+ds-2ubuntu2 [268 kB] Get:144 http://ftpmaster.internal/ubuntu lunar/main ppc64el liblerc-dev ppc64el 4.0.0+ds-2ubuntu2 [273 kB] Get:145 http://ftpmaster.internal/ubuntu lunar/main ppc64el libltdl7 ppc64el 2.4.7-5 [47.7 kB] Get:146 http://ftpmaster.internal/ubuntu lunar/main ppc64el libltdl-dev ppc64el 2.4.7-5 [178 kB] Get:147 http://ftpmaster.internal/ubuntu lunar/main ppc64el libnl-3-dev ppc64el 3.7.0-0.2 [128 kB] Get:148 http://ftpmaster.internal/ubuntu lunar/main ppc64el libnl-route-3-dev ppc64el 3.7.0-0.2 [254 kB] Get:149 http://ftpmaster.internal/ubuntu lunar/universe ppc64el libmunge2 ppc64el 0.5.15-2 [16.6 kB] Get:150 http://ftpmaster.internal/ubuntu lunar/main ppc64el libpciaccess0 ppc64el 0.17-2 [20.5 kB] Get:151 http://ftpmaster.internal/ubuntu lunar/main ppc64el libxnvctrl0 ppc64el 510.47.03-0ubuntu1 [11.7 kB] Get:152 http://ftpmaster.internal/ubuntu lunar/universe ppc64el ocl-icd-libopencl1 ppc64el 2.3.1-1 [42.2 kB] Get:153 http://ftpmaster.internal/ubuntu lunar/universe ppc64el libhwloc-plugins ppc64el 2.9.0-1 [17.5 kB] Get:154 http://ftpmaster.internal/ubuntu lunar/universe ppc64el libpmix2 ppc64el 4.2.2-1 [744 kB] Get:155 http://ftpmaster.internal/ubuntu lunar/universe ppc64el libucx0 ppc64el 1.13.1-1 [957 kB] Get:156 http://ftpmaster.internal/ubuntu lunar/universe ppc64el libopenmpi3 ppc64el 4.1.4-3ubuntu2 [2667 kB] Get:157 http://ftpmaster.internal/ubuntu lunar/main ppc64el libnuma-dev ppc64el 2.0.16-1 [43.9 kB] Get:158 http://ftpmaster.internal/ubuntu lunar/universe ppc64el libhwloc-dev ppc64el 2.9.0-1 [305 kB] Get:159 http://ftpmaster.internal/ubuntu lunar/main ppc64el zlib1g-dev ppc64el 1:1.2.13.dfsg-1ubuntu4 [901 kB] Get:160 http://ftpmaster.internal/ubuntu lunar/universe ppc64el libpmix-dev ppc64el 4.2.2-1 [1117 kB] Get:161 http://ftpmaster.internal/ubuntu lunar/main ppc64el libjbig0 ppc64el 2.1-6ubuntu1 [34.4 kB] Get:162 http://ftpmaster.internal/ubuntu lunar/main ppc64el libjbig-dev ppc64el 2.1-6ubuntu1 [32.6 kB] Get:163 http://ftpmaster.internal/ubuntu lunar/main ppc64el liblzma-dev ppc64el 5.4.1-0.0 [203 kB] Get:164 http://ftpmaster.internal/ubuntu lunar/main ppc64el libzstd-dev ppc64el 1.5.2+dfsg2-3 [450 kB] Get:165 http://ftpmaster.internal/ubuntu lunar/main ppc64el libwebp7 ppc64el 1.2.4-0.1 [290 kB] Get:166 http://ftpmaster.internal/ubuntu lunar/main ppc64el libwebpmux3 ppc64el 1.2.4-0.1 [25.2 kB] Get:167 http://ftpmaster.internal/ubuntu lunar/main ppc64el libwebpdemux2 ppc64el 1.2.4-0.1 [11.2 kB] Get:168 http://ftpmaster.internal/ubuntu lunar/main ppc64el libwebp-dev ppc64el 1.2.4-0.1 [414 kB] Get:169 http://ftpmaster.internal/ubuntu lunar/main ppc64el libtiff6 ppc64el 4.5.0-4ubuntu1 [253 kB] Get:170 http://ftpmaster.internal/ubuntu lunar/main ppc64el libtiffxx6 ppc64el 4.5.0-4ubuntu1 [5870 B] Get:171 http://ftpmaster.internal/ubuntu lunar/main ppc64el libtiff-dev ppc64el 4.5.0-4ubuntu1 [414 kB] Get:172 http://ftpmaster.internal/ubuntu lunar/universe ppc64el openmpi-common all 4.1.4-3ubuntu2 [163 kB] Get:173 http://ftpmaster.internal/ubuntu lunar/universe ppc64el openmpi-bin ppc64el 4.1.4-3ubuntu2 [119 kB] Get:174 http://ftpmaster.internal/ubuntu lunar/main ppc64el libibverbs-dev ppc64el 44.0-2 [719 kB] Get:175 http://ftpmaster.internal/ubuntu lunar/universe ppc64el libopenmpi-dev ppc64el 4.1.4-3ubuntu2 [866 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 105 MB in 10s (11.0 MB/s) Selecting previously unselected package sgml-base. (Reading database ... 15079 files and directories currently installed.) Preparing to unpack .../000-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package libbsd0:ppc64el. Preparing to unpack .../001-libbsd0_0.11.7-2_ppc64el.deb ... Unpacking libbsd0:ppc64el (0.11.7-2) ... Selecting previously unselected package libelf1:ppc64el. Preparing to unpack .../002-libelf1_0.188-2.1_ppc64el.deb ... Unpacking libelf1:ppc64el (0.188-2.1) ... Selecting previously unselected package libexpat1:ppc64el. Preparing to unpack .../003-libexpat1_2.5.0-1_ppc64el.deb ... Unpacking libexpat1:ppc64el (2.5.0-1) ... Selecting previously unselected package libicu71:ppc64el. Preparing to unpack .../004-libicu71_71.1-3ubuntu1_ppc64el.deb ... Unpacking libicu71:ppc64el (71.1-3ubuntu1) ... Selecting previously unselected package libxml2:ppc64el. Preparing to unpack .../005-libxml2_2.9.14+dfsg-1.1_ppc64el.deb ... Unpacking libxml2:ppc64el (2.9.14+dfsg-1.1) ... 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Unpacking libfltk-images1.3:ppc64el (1.3.8-5) ... Selecting previously unselected package fluid. Preparing to unpack .../076-fluid_1.3.8-5_ppc64el.deb ... Unpacking fluid (1.3.8-5) ... Selecting previously unselected package libgfortran5:ppc64el. Preparing to unpack .../077-libgfortran5_12.2.0-14ubuntu1_ppc64el.deb ... Unpacking libgfortran5:ppc64el (12.2.0-14ubuntu1) ... Selecting previously unselected package libgfortran-12-dev:ppc64el. Preparing to unpack .../078-libgfortran-12-dev_12.2.0-14ubuntu1_ppc64el.deb ... Unpacking libgfortran-12-dev:ppc64el (12.2.0-14ubuntu1) ... Selecting previously unselected package gfortran-12. Preparing to unpack .../079-gfortran-12_12.2.0-14ubuntu1_ppc64el.deb ... Unpacking gfortran-12 (12.2.0-14ubuntu1) ... Selecting previously unselected package libnl-3-200:ppc64el. Preparing to unpack .../080-libnl-3-200_3.7.0-0.2_ppc64el.deb ... Unpacking libnl-3-200:ppc64el (3.7.0-0.2) ... Selecting previously unselected package libnl-route-3-200:ppc64el. 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Selecting previously unselected package libcairo2:ppc64el. Preparing to unpack .../087-libcairo2_1.16.0-7_ppc64el.deb ... Unpacking libcairo2:ppc64el (1.16.0-7) ... Selecting previously unselected package libdeflate0:ppc64el. Preparing to unpack .../088-libdeflate0_1.14-1_ppc64el.deb ... Unpacking libdeflate0:ppc64el (1.14-1) ... Selecting previously unselected package libdeflate-dev:ppc64el. Preparing to unpack .../089-libdeflate-dev_1.14-1_ppc64el.deb ... Unpacking libdeflate-dev:ppc64el (1.14-1) ... Selecting previously unselected package libdrm-amdgpu1:ppc64el. Preparing to unpack .../090-libdrm-amdgpu1_2.4.114-1_ppc64el.deb ... Unpacking libdrm-amdgpu1:ppc64el (2.4.114-1) ... Selecting previously unselected package libdrm-nouveau2:ppc64el. Preparing to unpack .../091-libdrm-nouveau2_2.4.114-1_ppc64el.deb ... Unpacking libdrm-nouveau2:ppc64el (2.4.114-1) ... Selecting previously unselected package libdrm-radeon1:ppc64el. 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Setting up libevent-core-2.1-7a:ppc64el (2.1.12-stable-5ubuntu1) ... Setting up libglvnd0:ppc64el (1.6.0-1) ... Setting up libcbor0.8:ppc64el (0.8.0-2ubuntu1) ... Setting up libdebhelper-perl (13.11.4ubuntu3) ... Setting up libbrotli1:ppc64el (1.0.9-2build7) ... Setting up libsensors-config (1:3.6.0-7ubuntu1) ... Setting up libnghttp2-14:ppc64el (1.51.0-1) ... Setting up libmagic1:ppc64el (1:5.44-3) ... Setting up libdeflate0:ppc64el (1.14-1) ... Setting up libevent-openssl-2.1-7:ppc64el (2.1.12-stable-5ubuntu1) ... Setting up libfftw3-long3:ppc64el (3.3.8-2ubuntu8) ... Setting up gettext-base (0.21-11) ... Setting up m4 (1.4.19-2) ... Setting up file (1:5.44-3) ... Setting up libpthread-stubs0-dev:ppc64el (0.4-1build2) ... Setting up libjbig0:ppc64el (2.1-6ubuntu1) ... Setting up libevent-2.1-7a:ppc64el (2.1.12-stable-5ubuntu1) ... Setting up libsasl2-modules-db:ppc64el (2.1.28+dfsg-10) ... Setting up xtrans-dev (1.4.0-1) ... Setting up autotools-dev (20220109.1) ... Setting up libuv1:ppc64el (1.44.2-1) ... Setting up libmunge2 (0.5.15-2) ... Setting up libfreetype6:ppc64el (2.12.1+dfsg-4) ... Setting up libx11-data (2:1.8.3-3) ... Setting up librtmp1:ppc64el (2.4+20151223.gitfa8646d.1-2build4) ... Setting up libhwloc15:ppc64el (2.9.0-1) ... Setting up autopoint (0.21-11) ... Setting up libjsoncpp25:ppc64el (1.9.5-4) ... Setting up fonts-dejavu-core (2.37-2build2) ... Setting up libsensors5:ppc64el (1:3.6.0-7ubuntu1) ... Setting up liblerc-dev:ppc64el (4.0.0+ds-2ubuntu2) ... Setting up libjpeg-turbo8:ppc64el (2.1.2-0ubuntu1) ... Setting up libltdl7:ppc64el (2.4.7-5) ... Setting up libfftw3-double3:ppc64el (3.3.8-2ubuntu8) ... Setting up libglapi-mesa:ppc64el (22.2.5-0ubuntu1) ... Setting up libsasl2-2:ppc64el (2.1.28+dfsg-10) ... Setting up libssh-4:ppc64el (0.10.4-2) ... Setting up libgfortran5:ppc64el (12.2.0-14ubuntu1) ... Setting up autoconf (2.71-3) ... Setting up libwebp7:ppc64el (1.2.4-0.1) ... Setting up liblzma-dev:ppc64el (5.4.1-0.0) ... Setting up zlib1g-dev:ppc64el (1:1.2.13.dfsg-1ubuntu4) ... Setting up libnuma1:ppc64el (2.0.16-1) ... Setting up ocl-icd-libopencl1:ppc64el (2.3.1-1) ... Setting up libxshmfence1:ppc64el (1.3-1build4) ... Setting up librhash0:ppc64el (1.4.3-3) ... Setting up libuchardet0:ppc64el (0.0.7-1build2) ... Setting up openmpi-common (4.1.4-3ubuntu2) ... Setting up libsub-override-perl (0.09-4) ... Setting up xorg-sgml-doctools (1:1.11-1.1) ... Setting up sgml-base (1.31) ... Setting up cmake-data (3.25.1-1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libfido2-1:ppc64el (1.12.0-2) ... Setting up libwebpmux3:ppc64el (1.2.4-0.1) ... Setting up libbsd0:ppc64el (0.11.7-2) ... Setting up libdeflate-dev:ppc64el (1.14-1) ... Setting up libdrm-common (2.4.114-1) ... Setting up libelf1:ppc64el (0.188-2.1) ... Setting up libxml2:ppc64el (2.9.14+dfsg-1.1) ... Setting up libldap2:ppc64el (2.6.3+dfsg-1~exp1ubuntu1) ... Setting up libevent-pthreads-2.1-7:ppc64el (2.1.12-stable-5ubuntu1) ... Setting up libjpeg8:ppc64el (8c-2ubuntu10) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up x11proto-dev (2022.1-1) ... Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libdw1:ppc64el (0.188-2.1) ... Setting up libjpeg-turbo8-dev:ppc64el (2.1.2-0ubuntu1) ... Setting up libxdmcp6:ppc64el (1:1.1.3-0ubuntu5) ... Setting up libevent-extra-2.1-7:ppc64el (2.1.12-stable-5ubuntu1) ... Setting up libxcb1:ppc64el (1.15-1) ... Setting up gettext (0.21-11) ... Setting up libxcb-xfixes0:ppc64el (1.15-1) ... Setting up libxau-dev:ppc64el (1:1.0.9-1build5) ... Setting up libtool (2.4.7-5) ... Setting up libarchive13:ppc64el (3.6.2-1ubuntu1) ... Setting up libxcb-render0:ppc64el (1.15-1) ... Setting up libfftw3-bin (3.3.8-2ubuntu8) ... Setting up fontconfig-config (2.14.1-3ubuntu1) ... Setting up libxcb-glx0:ppc64el (1.15-1) ... Setting up libwebpdemux2:ppc64el (1.2.4-0.1) ... Setting up libedit2:ppc64el (3.1-20221030-2) ... Setting up libjbig-dev:ppc64el (2.1-6ubuntu1) ... Setting up libgfortran-12-dev:ppc64el (12.2.0-14ubuntu1) ... Setting up libxcb-shm0:ppc64el (1.15-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnuma-dev:ppc64el (2.0.16-1) ... Setting up libxcb-present0:ppc64el (1.15-1) ... Setting up dh-autoreconf (20) ... Setting up libltdl-dev:ppc64el (2.4.7-5) ... Setting up libxdmcp-dev:ppc64el (1:1.1.3-0ubuntu5) ... Setting up gfortran-12 (12.2.0-14ubuntu1) ... Setting up libwebp-dev:ppc64el (1.2.4-0.1) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libxcb-sync1:ppc64el (1.15-1) ... Setting up libevent-dev (2.1.12-stable-5ubuntu1) ... Setting up libxcb-dri2-0:ppc64el (1.15-1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libdrm2:ppc64el (2.4.114-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-9) ... Setting up libtiff6:ppc64el (4.5.0-4ubuntu1) ... Setting up libllvm15:ppc64el (1:15.0.7-1) ... Setting up libnl-3-200:ppc64el (3.7.0-0.2) ... Setting up debugedit (1:5.0-5) ... Setting up libcurl4:ppc64el (7.87.0-2ubuntu1) ... Setting up libx11-6:ppc64el (2:1.8.3-3) ... Setting up libhwloc-dev:ppc64el (2.9.0-1) ... Setting up libfontconfig1:ppc64el (2.14.1-3ubuntu1) ... Setting up libjpeg8-dev:ppc64el (8c-2ubuntu10) ... Setting up libtiffxx6:ppc64el (4.5.0-4ubuntu1) ... Setting up libfftw3-dev:ppc64el (3.3.8-2ubuntu8) ... Setting up libdrm-amdgpu1:ppc64el (2.4.114-1) ... Setting up libxcb-dri3-0:ppc64el (1.15-1) ... Setting up libx11-xcb1:ppc64el (2:1.8.3-3) ... Setting up libdrm-nouveau2:ppc64el (2.4.114-1) ... Setting up libxcb1-dev:ppc64el (1.15-1) ... Setting up libxrender1:ppc64el (1:0.9.10-1.1) ... Setting up libdrm-radeon1:ppc64el (2.4.114-1) ... Setting up openssh-client (1:9.0p1-1ubuntu8) ... update-alternatives: using /usr/bin/ssh to provide /usr/bin/rsh (rsh) in auto mode update-alternatives: using /usr/bin/slogin to provide /usr/bin/rlogin (rlogin) in auto mode update-alternatives: using /usr/bin/scp to provide /usr/bin/rcp (rcp) in auto mode Setting up po-debconf (1.0.21+nmu1) ... Setting up libgl1-mesa-dri:ppc64el (22.2.5-0ubuntu1) ... Setting up libjpeg-dev:ppc64el (8c-2ubuntu10) ... Setting up libx11-dev:ppc64el (2:1.8.3-3) ... Setting up libxext6:ppc64el (2:1.3.4-1build1) ... Setting up man-db (2.11.2-1) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up libcairo2:ppc64el (1.16.0-7) ... Setting up libxxf86vm1:ppc64el (1:1.1.4-1build3) ... Setting up libnl-route-3-200:ppc64el (3.7.0-0.2) ... Setting up libxnvctrl0:ppc64el (510.47.03-0ubuntu1) ... Setting up libtiff-dev:ppc64el (4.5.0-4ubuntu1) ... Setting up libxfixes3:ppc64el (1:6.0.0-2) ... Setting up libxinerama1:ppc64el (2:1.1.4-3) ... Setting up libnl-3-dev:ppc64el (3.7.0-0.2) ... Setting up cmake (3.25.1-1) ... Setting up libibverbs1:ppc64el (44.0-2) ... Setting up libxft2:ppc64el (2.3.6-1) ... Setting up libglx-mesa0:ppc64el (22.2.5-0ubuntu1) ... Setting up libglx0:ppc64el (1.6.0-1) ... Setting up ibverbs-providers:ppc64el (44.0-2) ... Setting up libxcursor1:ppc64el (1:1.2.1-1) ... Setting up debhelper (13.11.4ubuntu3) ... Setting up libhwloc-plugins:ppc64el (2.9.0-1) ... Setting up libnl-route-3-dev:ppc64el (3.7.0-0.2) ... Setting up libgl1:ppc64el (1.6.0-1) ... Setting up librdmacm1:ppc64el (44.0-2) ... Setting up libucx0:ppc64el (1.13.1-1) ... Setting up libpmix2:ppc64el (4.2.2-1) ... Setting up libfltk1.3:ppc64el (1.3.8-5) ... Setting up libfltk-gl1.3:ppc64el (1.3.8-5) ... Setting up libfltk-cairo1.3:ppc64el (1.3.8-5) ... Setting up libibverbs-dev:ppc64el (44.0-2) ... Setting up libfltk-images1.3:ppc64el (1.3.8-5) ... Setting up libfltk-forms1.3:ppc64el (1.3.8-5) ... Setting up libpmix-dev:ppc64el (4.2.2-1) ... Setting up libfltk1.3-dev:ppc64el (1.3.8-5) ... Setting up libfabric1:ppc64el (1.17.0-3) ... Setting up libopenmpi3:ppc64el (4.1.4-3ubuntu2) ... Setting up fluid (1.3.8-5) ... Setting up openmpi-bin (4.1.4-3ubuntu2) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up libopenmpi-dev:ppc64el (4.1.4-3ubuntu2) ... update-alternatives: using /usr/lib/powerpc64le-linux-gnu/openmpi/include to provide /usr/include/powerpc64le-linux-gnu/mpi (mpi-powerpc64le-linux-gnu) in auto mode Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.37-0ubuntu1) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (ppc64el included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-137-generic #154-Ubuntu SMP Thu Jan 5 17:03:14 UTC 2023 ppc64el (ppc64le) Toolchain package versions: binutils_2.40-2ubuntu1 dpkg-dev_1.21.19ubuntu3 g++-12_12.2.0-14ubuntu1 gcc-12_12.2.0-14ubuntu1 libc6-dev_2.37-0ubuntu1 libstdc++-12-dev_12.2.0-14ubuntu1 libstdc++6_12.2.0-14ubuntu1 linux-libc-dev_6.1.0-14.14 Package versions: adduser_3.129ubuntu1 advancecomp_2.5-1 apt_2.5.5 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-11 autotools-dev_20220109.1 base-files_12.3ubuntu1 base-passwd_3.6.1 bash_5.2.15-2ubuntu1 binutils_2.40-2ubuntu1 binutils-common_2.40-2ubuntu1 binutils-powerpc64le-linux-gnu_2.40-2ubuntu1 bsdextrautils_2.38.1-4ubuntu1 bsdutils_1:2.38.1-4ubuntu1 build-essential_12.9ubuntu3 bzip2_1.0.8-5build1 ca-certificates_20211016ubuntu1 cmake_3.25.1-1 cmake-data_3.25.1-1 coreutils_9.1-1ubuntu2 cpp_4:12.2.0-1ubuntu1 cpp-12_12.2.0-14ubuntu1 dash_0.5.11+git20210903+057cd650a4ed-9ubuntu1 debconf_1.5.82 debhelper_13.11.4ubuntu3 debianutils_5.7-0.4 debugedit_1:5.0-5 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.8-3 dpkg_1.21.19ubuntu3 dpkg-dev_1.21.19ubuntu3 dwz_0.15-1 e2fsprogs_1.46.6~rc1-1ubuntu1 fakeroot_1.30.1-1.1ubuntu1 file_1:5.44-3 findutils_4.9.0-3ubuntu1 fluid_1.3.8-5 fontconfig-config_2.14.1-3ubuntu1 fonts-dejavu-core_2.37-2build2 g++_4:12.2.0-1ubuntu1 g++-12_12.2.0-14ubuntu1 gcc_4:12.2.0-1ubuntu1 gcc-12_12.2.0-14ubuntu1 gcc-12-base_12.2.0-14ubuntu1 gettext_0.21-11 gettext-base_0.21-11 gfortran-12_12.2.0-14ubuntu1 gpg_2.2.40-1ubuntu2 gpg-agent_2.2.40-1ubuntu2 gpgconf_2.2.40-1ubuntu2 gpgv_2.2.40-1ubuntu2 grep_3.8-5 groff-base_1.22.4-9 gzip_1.12-1ubuntu1 hostname_3.23ubuntu2 ibverbs-providers_44.0-2 init_1.65.2 init-system-helpers_1.65.2 intltool-debian_0.35.0+20060710.6 libacl1_2.3.1-3 libapparmor1_3.0.8-1ubuntu1 libapt-pkg6.0_2.5.5 libarchive-zip-perl_1.68-1 libarchive13_3.6.2-1ubuntu1 libargon2-1_0~20171227-0.3 libasan8_12.2.0-14ubuntu1 libassuan0_2.5.5-5 libatomic1_12.2.0-14ubuntu1 libattr1_1:2.5.1-4 libaudit-common_1:3.0.7-1.1 libaudit1_1:3.0.7-1.1 libbinutils_2.40-2ubuntu1 libblkid1_2.38.1-4ubuntu1 libbrotli1_1.0.9-2build7 libbsd0_0.11.7-2 libbz2-1.0_1.0.8-5build1 libc-bin_2.37-0ubuntu1 libc-dev-bin_2.37-0ubuntu1 libc6_2.37-0ubuntu1 libc6-dev_2.37-0ubuntu1 libcairo2_1.16.0-7 libcap-ng0_0.8.3-1build1 libcap2_1:2.66-3ubuntu1 libcbor0.8_0.8.0-2ubuntu1 libcc1-0_12.2.0-14ubuntu1 libcom-err2_1.46.6~rc1-1ubuntu1 libcrypt-dev_1:4.4.33-2 libcrypt1_1:4.4.33-2 libcryptsetup12_2:2.5.0-6ubuntu3 libctf-nobfd0_2.40-2ubuntu1 libctf0_2.40-2ubuntu1 libcurl4_7.87.0-2ubuntu1 libdb5.3_5.3.28+dfsg2-1 libdebconfclient0_0.264ubuntu1 libdebhelper-perl_13.11.4ubuntu3 libdeflate-dev_1.14-1 libdeflate0_1.14-1 libdevmapper1.02.1_2:1.02.185-1ubuntu1 libdpkg-perl_1.21.19ubuntu3 libdrm-amdgpu1_2.4.114-1 libdrm-common_2.4.114-1 libdrm-nouveau2_2.4.114-1 libdrm-radeon1_2.4.114-1 libdrm2_2.4.114-1 libdw1_0.188-2.1 libedit2_3.1-20221030-2 libelf1_0.188-2.1 libevent-2.1-7a_2.1.12-stable-5ubuntu1 libevent-core-2.1-7a_2.1.12-stable-5ubuntu1 libevent-dev_2.1.12-stable-5ubuntu1 libevent-extra-2.1-7_2.1.12-stable-5ubuntu1 libevent-openssl-2.1-7_2.1.12-stable-5ubuntu1 libevent-pthreads-2.1-7_2.1.12-stable-5ubuntu1 libexpat1_2.5.0-1 libext2fs2_1.46.6~rc1-1ubuntu1 libfabric1_1.17.0-3 libfakeroot_1.30.1-1.1ubuntu1 libfdisk1_2.38.1-4ubuntu1 libffi8_3.4.4-1 libfftw3-bin_3.3.8-2ubuntu8 libfftw3-dev_3.3.8-2ubuntu8 libfftw3-double3_3.3.8-2ubuntu8 libfftw3-long3_3.3.8-2ubuntu8 libfftw3-single3_3.3.8-2ubuntu8 libfido2-1_1.12.0-2 libfile-stripnondeterminism-perl_1.13.1-1 libfltk-cairo1.3_1.3.8-5 libfltk-forms1.3_1.3.8-5 libfltk-gl1.3_1.3.8-5 libfltk-images1.3_1.3.8-5 libfltk1.3_1.3.8-5 libfltk1.3-dev_1.3.8-5 libfontconfig1_2.14.1-3ubuntu1 libfreetype6_2.12.1+dfsg-4 libgcc-12-dev_12.2.0-14ubuntu1 libgcc-s1_12.2.0-14ubuntu1 libgcrypt20_1.10.1-3ubuntu1 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libgfortran-12-dev_12.2.0-14ubuntu1 libgfortran5_12.2.0-14ubuntu1 libgl1_1.6.0-1 libgl1-mesa-dri_22.2.5-0ubuntu1 libglapi-mesa_22.2.5-0ubuntu1 libglvnd0_1.6.0-1 libglx-mesa0_22.2.5-0ubuntu1 libglx0_1.6.0-1 libgmp10_2:6.2.1+dfsg1-1.1ubuntu1 libgnutls30_3.7.8-4ubuntu1 libgomp1_12.2.0-14ubuntu1 libgpg-error0_1.46-1 libgssapi-krb5-2_1.20.1-1build1 libhogweed6_3.8.1-2 libhwloc-dev_2.9.0-1 libhwloc-plugins_2.9.0-1 libhwloc15_2.9.0-1 libibverbs-dev_44.0-2 libibverbs1_44.0-2 libicu71_71.1-3ubuntu1 libidn2-0_2.3.3-1build1 libip4tc2_1.8.7-1ubuntu7 libisl23_0.25-1 libitm1_12.2.0-14ubuntu1 libjansson4_2.14-2 libjbig-dev_2.1-6ubuntu1 libjbig0_2.1-6ubuntu1 libjpeg-dev_8c-2ubuntu10 libjpeg-turbo8_2.1.2-0ubuntu1 libjpeg-turbo8-dev_2.1.2-0ubuntu1 libjpeg8_8c-2ubuntu10 libjpeg8-dev_8c-2ubuntu10 libjs-jquery_3.6.1+dfsg+~3.5.14-1 libjs-jquery-ui_1.13.2+dfsg-1 libjson-c5_0.16-2 libjsoncpp25_1.9.5-4 libk5crypto3_1.20.1-1build1 libkeyutils1_1.6.3-2 libkmod2_30+20220905-1ubuntu1 libkrb5-3_1.20.1-1build1 libkrb5support0_1.20.1-1build1 libldap2_2.6.3+dfsg-1~exp1ubuntu1 liblerc-dev_4.0.0+ds-2ubuntu2 liblerc4_4.0.0+ds-2ubuntu2 libllvm15_1:15.0.7-1 liblockfile-bin_1.17-1build2 liblockfile1_1.17-1build2 liblsan0_12.2.0-14ubuntu1 libltdl-dev_2.4.7-5 libltdl7_2.4.7-5 liblz4-1_1.9.4-1 liblzma-dev_5.4.1-0.0 liblzma5_5.4.1-0.0 libmagic-mgc_1:5.44-3 libmagic1_1:5.44-3 libmd0_1.0.4-2 libmount1_2.38.1-4ubuntu1 libmpc3_1.3.1-1 libmpfr6_4.2.0-1 libmunge2_0.5.15-2 libncurses6_6.4-2 libncursesw6_6.4-2 libnettle8_3.8.1-2 libnghttp2-14_1.51.0-1 libnl-3-200_3.7.0-0.2 libnl-3-dev_3.7.0-0.2 libnl-route-3-200_3.7.0-0.2 libnl-route-3-dev_3.7.0-0.2 libnpth0_1.6-3build2 libnsl-dev_1.3.0-2build2 libnsl2_1.3.0-2build2 libnuma-dev_2.0.16-1 libnuma1_2.0.16-1 libopenmpi-dev_4.1.4-3ubuntu2 libopenmpi3_4.1.4-3ubuntu2 libp11-kit0_0.24.1-2ubuntu1 libpam-modules_1.5.2-5ubuntu1 libpam-modules-bin_1.5.2-5ubuntu1 libpam-runtime_1.5.2-5ubuntu1 libpam0g_1.5.2-5ubuntu1 libpciaccess0_0.17-2 libpcre2-8-0_10.42-1 libperl5.36_5.36.0-7 libpipeline1_1.5.7-1 libpixman-1-0_0.42.2-1 libpmix-dev_4.2.2-1 libpmix2_4.2.2-1 libpng16-16_1.6.39-2 libprocps8_2:3.3.17-7ubuntu1 libpsl5_0.21.0-1.2build2 libpthread-stubs0-dev_0.4-1build2 libquadmath0_12.2.0-14ubuntu1 librdmacm1_44.0-2 libreadline8_8.2-1.3 librhash0_1.4.3-3 librtmp1_2.4+20151223.gitfa8646d.1-2build4 libsasl2-2_2.1.28+dfsg-10 libsasl2-modules-db_2.1.28+dfsg-10 libseccomp2_2.5.4-1ubuntu2 libselinux1_3.4-1build3 libsemanage-common_3.4-1build3 libsemanage2_3.4-1build3 libsensors-config_1:3.6.0-7ubuntu1 libsensors5_1:3.6.0-7ubuntu1 libsepol2_3.4-2 libsmartcols1_2.38.1-4ubuntu1 libsqlite3-0_3.40.1-1 libss2_1.46.6~rc1-1ubuntu1 libssh-4_0.10.4-2 libssl3_3.0.7-1ubuntu1 libstdc++-12-dev_12.2.0-14ubuntu1 libstdc++6_12.2.0-14ubuntu1 libsub-override-perl_0.09-4 libsystemd-shared_252.4-1ubuntu1 libsystemd0_252.4-1ubuntu1 libtasn1-6_4.19.0-2 libtiff-dev_4.5.0-4ubuntu1 libtiff6_4.5.0-4ubuntu1 libtiffxx6_4.5.0-4ubuntu1 libtinfo6_6.4-2 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtool_2.4.7-5 libtsan2_12.2.0-14ubuntu1 libubsan1_12.2.0-14ubuntu1 libuchardet0_0.0.7-1build2 libucx0_1.13.1-1 libudev1_252.4-1ubuntu1 libunistring2_1.0-2 libuuid1_2.38.1-4ubuntu1 libuv1_1.44.2-1 libwebp-dev_1.2.4-0.1 libwebp7_1.2.4-0.1 libwebpdemux2_1.2.4-0.1 libwebpmux3_1.2.4-0.1 libx11-6_2:1.8.3-3 libx11-data_2:1.8.3-3 libx11-dev_2:1.8.3-3 libx11-xcb1_2:1.8.3-3 libxau-dev_1:1.0.9-1build5 libxau6_1:1.0.9-1build5 libxcb-dri2-0_1.15-1 libxcb-dri3-0_1.15-1 libxcb-glx0_1.15-1 libxcb-present0_1.15-1 libxcb-render0_1.15-1 libxcb-shm0_1.15-1 libxcb-sync1_1.15-1 libxcb-xfixes0_1.15-1 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po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3.1 procps_2:3.3.17-7ubuntu1 readline-common_8.2-1.3 rpcsvc-proto_1.4.2-0ubuntu6 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-1 sensible-utils_0.0.17+nmu1 sgml-base_1.31 systemd_252.4-1ubuntu1 systemd-sysv_252.4-1ubuntu1 sysvinit-utils_3.05-7ubuntu2 tar_1.34+dfsg-1.1 tzdata_2022g-2ubuntu1 ubuntu-keyring_2021.03.26 usrmerge_33ubuntu1 util-linux_2.38.1-4ubuntu1 util-linux-extra_2.38.1-4ubuntu1 x11proto-dev_2022.1-1 xorg-sgml-doctools_1:1.11-1.1 xtrans-dev_1.4.0-1 xz-utils_5.4.1-0.0 zlib1g_1:1.2.13.dfsg-1ubuntu4 zlib1g-dev_1:1.2.13.dfsg-1ubuntu4 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: relion Binary: relion, relion-gui Architecture: any Version: 3.1.3-3build1 Maintainer: Debian Med Packaging Team Uploaders: Roland Fehrenbacher , Andreas Tille , Homepage: https://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/relion Vcs-Git: https://salsa.debian.org/med-team/relion.git Testsuite: autopkgtest Build-Depends: cmake, debhelper-compat (= 13), libfftw3-dev, libfltk1.3-dev, libopenmpi-dev, libtiff-dev, fluid Package-List: relion deb science optional arch=any relion-gui deb science optional arch=any Checksums-Sha1: c6ca397db6c711f87305bd803f672345f7487bae 2345487 relion_3.1.3.orig.tar.gz afb73aaa795f8036722da03d5f8c04e0b8f1b9c7 12044 relion_3.1.3-3build1.debian.tar.xz Checksums-Sha256: f10934058e0670807b7004899d7b5103c21ad77841219352c66a33f98586d42e 2345487 relion_3.1.3.orig.tar.gz aef5a85778b7f05fb4bf9d725a545487d90de1965d01130b1af14aa995e18fb6 12044 relion_3.1.3-3build1.debian.tar.xz Files: 5ddaf9afe51d743c5f58f625d9fd1cb7 2345487 relion_3.1.3.orig.tar.gz c9b1e561d8ef134a68b02f3bc776dc9d 12044 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signature: No public key dpkg-source: warning: cannot verify inline signature for ./relion_3.1.3-3build1.dsc: no acceptable signature found dpkg-source: info: extracting relion in /<> dpkg-source: info: unpacking relion_3.1.3.orig.tar.gz dpkg-source: info: unpacking relion_3.1.3-3build1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 0001-Repair-wrong-comment-sign-pointed-out-by-Alexey-Roma.patch dpkg-source: info: applying typos.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-25549282 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-25549282 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-25549282 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -mLaunchpad Build Daemon -B -rfakeroot dpkg-buildpackage: info: source package relion dpkg-buildpackage: info: source version 3.1.3-3build1 dpkg-buildpackage: info: source distribution lunar dpkg-source --before-build . dpkg-buildpackage: info: host architecture ppc64el debian/rules clean dh clean debian/rules override_dh_clean make[1]: Entering directory '/<>' dh_clean rm -rf build make[1]: Leaving directory '/<>' debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a debian/rules override_dh_auto_configure make[1]: Entering directory '/<>' mkdir /<>/build cd /<>/build; \ CC=gcc CXX=g++ cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_SKIP_RPATH=TRUE -DDoublePrec_GPU=ON -DGUI=ON -DCUDA=OFF /<> CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. CMake Warning (dev) at /usr/share/cmake-3.25/Modules/CMakeDetermineCompilerId.cmake:93 (if): Policy CMP0054 is not set: Only interpret if() arguments as variables or keywords when unquoted. Run "cmake --help-policy CMP0054" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Quoted variables like "CUDA" will no longer be dereferenced when the policy is set to NEW. Since the policy is not set the OLD behavior will be used. Call Stack (most recent call first): /usr/share/cmake-3.25/Modules/CMakeDetermineCCompiler.cmake:123 (CMAKE_DETERMINE_COMPILER_ID) CMakeLists.txt:6 (project) This warning is for project developers. Use -Wno-dev to suppress it. -- The C compiler identification is GNU 12.2.0 -- The CXX compiler identification is GNU 12.2.0 -- Detecting C compiler ABI info CMake Warning (dev) at /usr/share/cmake-3.25/Modules/CMakeDetermineCompilerABI.cmake:29 (if): Policy CMP0054 is not set: Only interpret if() arguments as variables or keywords when unquoted. Run "cmake --help-policy CMP0054" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Quoted variables like "CUDA" will no longer be dereferenced when the policy is set to NEW. Since the policy is not set the OLD behavior will be used. Call Stack (most recent call first): /usr/share/cmake-3.25/Modules/CMakeTestCCompiler.cmake:26 (CMAKE_DETERMINE_COMPILER_ABI) CMakeLists.txt:6 (project) This warning is for project developers. Use -Wno-dev to suppress it. -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- BUILD TYPE set to the default type: 'Release' -- Setting fallback CUDA_ARCH=35 -- ALLOW_CTF_IN_SAGD enabled - This build of RELION allows modulation of particle images by a contrast transfer function inside stochastic average gradient descent, as specified in Claim 1 of patent US10,282,513B2 -- Setting cpu precision to double -- Setting accelerated code precision to single -- Using non-cuda compilation.... -- Found MPI_C: /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi_cxx.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") -- MPI_INCLUDE_PATH : /usr/lib/powerpc64le-linux-gnu/openmpi/include;/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -- MPI_LIBRARIES : /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi_cxx.so;/usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -- MPI_CXX_INCLUDE_PATH : /usr/lib/powerpc64le-linux-gnu/openmpi/include;/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -- MPI_CXX_LIBRARIES : /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi_cxx.so;/usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -- CMAKE_C_COMPILER : /usr/bin/gcc -- CMAKE_CXX_COMPILER : /usr/bin/g++ -- MPI_C_COMPILER : /usr/bin/mpicc -- MPI_CXX_COMPILER : /usr/bin/mpicxx -- CMAKE_CXX_COMPILER_ID : GNU -- Found X11: /usr/include -- Looking for XOpenDisplay in /usr/lib/powerpc64le-linux-gnu/libX11.so -- Looking for XOpenDisplay in /usr/lib/powerpc64le-linux-gnu/libX11.so - found -- Looking for gethostbyname -- Looking for gethostbyname - found -- Looking for connect -- Looking for connect - found -- Looking for remove -- Looking for remove - found -- Looking for shmat -- Looking for shmat - found -- Found FLTK: fltk_images;fltk_forms;fltk -- X11 and FLTK were found -- FLTK_LIBRARIES: fltk_images;fltk_forms;fltk;/usr/lib/powerpc64le-linux-gnu/libX11.so;/usr/lib/powerpc64le-linux-gnu/libm.so -- Found FFTW -- FFTW_PATH: /usr/include -- FFTW_INCLUDES: /usr/include -- FFTW_LIBRARIES: /usr/lib/powerpc64le-linux-gnu/libfftw3f.so;/usr/lib/powerpc64le-linux-gnu/libfftw3.so -- Looking for sincos -- Looking for sincos - found -- Looking for __sincos -- Looking for __sincos - not found -- Found TIFF: /usr/lib/powerpc64le-linux-gnu/libtiff.so (found version "4.5.0") -- Found ZLIB: /usr/lib/powerpc64le-linux-gnu/libz.so (found version "1.2.13") -- Could NOT find PNG (missing: PNG_LIBRARY PNG_PNG_INCLUDE_DIR) BUILD_SHARED_LIBS = OFF -- Building static libs (larger build size and binaries) Running apps/CMakeLists.txt... -- CMAKE_BINARY_DIR:/<>/build -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: DoublePrec_GPU -- Build files have been written to: /<>/build make[1]: Leaving directory '/<>' debian/rules override_dh_auto_build make[1]: Entering directory '/<>' /usr/bin/make -j4 -C build make[2]: Entering directory '/<>/build' /usr/bin/cmake -S/<> -B/<>/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/build/CMakeFiles /<>/build//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/<>/build' /usr/bin/make -f CMakeFiles/copy_scripts.dir/build.make CMakeFiles/copy_scripts.dir/depend /usr/bin/make -f src/apps/CMakeFiles/relion_lib.dir/build.make src/apps/CMakeFiles/relion_lib.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<> /<>/build /<>/build /<>/build/CMakeFiles/copy_scripts.dir/DependInfo.cmake --color= make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/relion_lib.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f CMakeFiles/copy_scripts.dir/build.make CMakeFiles/copy_scripts.dir/build make[4]: Entering directory '/<>/build' /usr/bin/cmake -E copy /<>/scripts/star_printtable /<>/build/bin/relion_star_printtable make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/relion_lib.dir/build.make src/apps/CMakeFiles/relion_lib.dir/build /usr/bin/cmake -E copy /<>/scripts/star_plottable /<>/build/bin/relion_star_plottable make[4]: Entering directory '/<>/build' /usr/bin/cmake -E copy /<>/scripts/star_loopheader /<>/build/bin/relion_star_loopheader [ 1%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/__/macros.cpp.o [ 1%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/args.cpp.o [ 1%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/CPlot2D.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/CPlot2D.cpp.o -MF CMakeFiles/relion_lib.dir/__/CPlot2D.cpp.o.d -o CMakeFiles/relion_lib.dir/__/CPlot2D.cpp.o -c /<>/src/CPlot2D.cpp cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/__/macros.cpp.o -MF CMakeFiles/relion_lib.dir/__/__/macros.cpp.o.d -o CMakeFiles/relion_lib.dir/__/__/macros.cpp.o -c /<>/build/macros.cpp cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/args.cpp.o -MF CMakeFiles/relion_lib.dir/__/args.cpp.o.d -o CMakeFiles/relion_lib.dir/__/args.cpp.o -c /<>/src/args.cpp /usr/bin/cmake -E copy /<>/scripts/star_datablock_stack /<>/build/bin/relion_star_datablock_stack /usr/bin/cmake -E copy /<>/scripts/star_datablock_singlefiles /<>/build/bin/relion_star_datablock_singlefiles /usr/bin/cmake -E copy /<>/scripts/star_datablock_ctfdat /<>/build/bin/relion_star_datablock_ctfdat /usr/bin/cmake -E copy /<>/scripts/qsub.csh /<>/build/bin/relion_qsub.csh make[4]: Leaving directory '/<>/build' [ 1%] Built target copy_scripts [ 1%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/assembly.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/assembly.cpp.o -MF CMakeFiles/relion_lib.dir/__/assembly.cpp.o.d -o CMakeFiles/relion_lib.dir/__/assembly.cpp.o -c /<>/src/assembly.cpp [ 2%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/autopicker.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/autopicker.cpp.o -MF CMakeFiles/relion_lib.dir/__/autopicker.cpp.o.d -o CMakeFiles/relion_lib.dir/__/autopicker.cpp.o -c /<>/src/autopicker.cpp In file included from /<>/src/image.h:455, from /<>/src/autopicker.h:10, from /<>/src/autopicker.cpp:20: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 2%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o -c /<>/src/autopicker_mpi.cpp /<>/src/CPlot2D.cpp: In member function ‘CPlot2D::ComputeLabelTickSpacing(double, double, double*, double*, double*, int, std::__cxx11::basic_string, std::allocator >)’: /<>/src/CPlot2D.cpp:743:41: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] 743 | sprintf(m_cYAxisLabelFormat,"%%.%df",nfrac); | ^~ /<>/src/CPlot2D.cpp:743:37: note: directive argument in the range [0, 2147483647] 743 | sprintf(m_cYAxisLabelFormat,"%%.%df",nfrac); | ^~~~~~~~ In file included from /usr/include/stdio.h:906, from /usr/include/c++/12/cstdio:42, from /usr/include/c++/12/ext/string_conversions.h:43, from /usr/include/c++/12/bits/basic_string.h:3960, from /usr/include/c++/12/string:53, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /<>/src/CPlot2D.cpp:21: In function ‘sprintf’, inlined from ‘CPlot2D::ComputeLabelTickSpacing(double, double, double*, double*, double*, int, std::__cxx11::basic_string, std::allocator >)’ at /<>/src/CPlot2D.cpp:743:16: /usr/include/powerpc64le-linux-gnu/bits/stdio2.h:30:34: note: ‘__sprintf_chk’ output between 5 and 14 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /<>/src/CPlot2D.cpp: In member function ‘CPlot2D::ComputeLabelTickSpacing(double, double, double*, double*, double*, int, std::__cxx11::basic_string, std::allocator >)’: /<>/src/CPlot2D.cpp:733:41: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] 733 | sprintf(m_cXAxisLabelFormat,"%%.%df",nfrac); | ^~ /<>/src/CPlot2D.cpp:733:37: note: directive argument in the range [0, 2147483647] 733 | sprintf(m_cXAxisLabelFormat,"%%.%df",nfrac); | ^~~~~~~~ In function ‘sprintf’, inlined from ‘CPlot2D::ComputeLabelTickSpacing(double, double, double*, double*, double*, int, std::__cxx11::basic_string, std::allocator >)’ at /<>/src/CPlot2D.cpp:733:16: /usr/include/powerpc64le-linux-gnu/bits/stdio2.h:30:34: note: ‘__sprintf_chk’ output between 5 and 14 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 3%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/backprojector.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/backprojector.cpp.o -MF CMakeFiles/relion_lib.dir/__/backprojector.cpp.o.d -o CMakeFiles/relion_lib.dir/__/backprojector.cpp.o -c /<>/src/backprojector.cpp In file included from /<>/src/image.h:455, from /<>/src/autopicker.h:10, from /<>/src/autopicker_mpi.h:12, from /<>/src/autopicker_mpi.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /<>/src/image.h:455, from /<>/src/projector.h:25, from /<>/src/backprojector.h:33, from /<>/src/backprojector.cpp:27: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 3%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/complex.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/complex.cpp.o -MF CMakeFiles/relion_lib.dir/__/complex.cpp.o.d -o CMakeFiles/relion_lib.dir/__/complex.cpp.o -c /<>/src/complex.cpp [ 3%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctf.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/ctf.cpp.o -MF CMakeFiles/relion_lib.dir/__/ctf.cpp.o.d -o CMakeFiles/relion_lib.dir/__/ctf.cpp.o -c /<>/src/ctf.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/obs_model.h:24, from /<>/src/ctf.h:50, from /<>/src/ctf.cpp:45: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 4%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner.cpp.o -MF CMakeFiles/relion_lib.dir/__/ctffind_runner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/ctffind_runner.cpp.o -c /<>/src/ctffind_runner.cpp In file included from /<>/src/image.h:455, from /<>/src/ctffind_runner.h:31, from /<>/src/ctffind_runner.cpp:20: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 4%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner_mpi.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/ctffind_runner_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/ctffind_runner_mpi.cpp.o -c /<>/src/ctffind_runner_mpi.cpp In file included from /<>/src/image.h:455, from /<>/src/ctffind_runner.h:31, from /<>/src/ctffind_runner_mpi.h:25, from /<>/src/ctffind_runner_mpi.cpp:20: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 4%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/error.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/error.cpp.o -MF CMakeFiles/relion_lib.dir/__/error.cpp.o.d -o CMakeFiles/relion_lib.dir/__/error.cpp.o -c /<>/src/error.cpp [ 5%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/euler.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/euler.cpp.o -MF CMakeFiles/relion_lib.dir/__/euler.cpp.o.d -o CMakeFiles/relion_lib.dir/__/euler.cpp.o -c /<>/src/euler.cpp [ 5%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/exp_model.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/exp_model.cpp.o -MF CMakeFiles/relion_lib.dir/__/exp_model.cpp.o.d -o CMakeFiles/relion_lib.dir/__/exp_model.cpp.o -c /<>/src/exp_model.cpp In file included from /<>/src/image.h:455, from /<>/src/exp_model.h:24, from /<>/src/exp_model.cpp:20: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/fftw.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/fftw.cpp.o -MF CMakeFiles/relion_lib.dir/__/fftw.cpp.o.d -o CMakeFiles/relion_lib.dir/__/fftw.cpp.o -c /<>/src/fftw.cpp [ 6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/filename.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/filename.cpp.o -MF CMakeFiles/relion_lib.dir/__/filename.cpp.o.d -o CMakeFiles/relion_lib.dir/__/filename.cpp.o -c /<>/src/filename.cpp [ 6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/flex_analyser.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/flex_analyser.cpp.o -MF CMakeFiles/relion_lib.dir/__/flex_analyser.cpp.o.d -o CMakeFiles/relion_lib.dir/__/flex_analyser.cpp.o -c /<>/src/flex_analyser.cpp In file included from /<>/src/image.h:455, from /<>/src/exp_model.h:24, from /<>/src/flex_analyser.h:24, from /<>/src/flex_analyser.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 7%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/funcs.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/funcs.cpp.o -MF CMakeFiles/relion_lib.dir/__/funcs.cpp.o.d -o CMakeFiles/relion_lib.dir/__/funcs.cpp.o -c /<>/src/funcs.cpp [ 7%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/healpix_sampling.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/healpix_sampling.cpp.o -MF CMakeFiles/relion_lib.dir/__/healpix_sampling.cpp.o.d -o CMakeFiles/relion_lib.dir/__/healpix_sampling.cpp.o -c /<>/src/healpix_sampling.cpp In file included from /<>/src/image.h:455, from /<>/src/helix.h:30, from /<>/src/healpix_sampling.h:31, from /<>/src/healpix_sampling.cpp:20: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 7%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/helix.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/helix.cpp.o -MF CMakeFiles/relion_lib.dir/__/helix.cpp.o.d -o CMakeFiles/relion_lib.dir/__/helix.cpp.o -c /<>/src/helix.cpp In file included from /<>/src/image.h:455, from /<>/src/helix.h:30, from /<>/src/helix.cpp:22: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 8%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/helix_inimodel2d.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/helix_inimodel2d.cpp.o -MF CMakeFiles/relion_lib.dir/__/helix_inimodel2d.cpp.o.d -o CMakeFiles/relion_lib.dir/__/helix_inimodel2d.cpp.o -c /<>/src/helix_inimodel2d.cpp In file included from /<>/src/image.h:455, from /<>/src/helix_inimodel2d.h:29, from /<>/src/helix_inimodel2d.cpp:22: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 8%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/image.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/image.cpp.o -MF CMakeFiles/relion_lib.dir/__/image.cpp.o.d -o CMakeFiles/relion_lib.dir/__/image.cpp.o -c /<>/src/image.cpp In file included from /<>/src/image.h:455, from /<>/src/image.cpp:20: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 9%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/local_symmetry.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/local_symmetry.cpp.o -MF CMakeFiles/relion_lib.dir/__/local_symmetry.cpp.o.d -o CMakeFiles/relion_lib.dir/__/local_symmetry.cpp.o -c /<>/src/local_symmetry.cpp [ 9%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/local_symmetry_mpi.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/local_symmetry_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/local_symmetry_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/local_symmetry_mpi.cpp.o -c /<>/src/local_symmetry_mpi.cpp In file included from /<>/src/image.h:455, from /<>/src/local_symmetry.h:30, from /<>/src/local_symmetry.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /<>/src/image.h:455, from /<>/src/local_symmetry.h:30, from /<>/src/local_symmetry_mpi.h:5, from /<>/src/local_symmetry_mpi.cpp:1: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 9%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/mask.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/mask.cpp.o -MF CMakeFiles/relion_lib.dir/__/mask.cpp.o.d -o CMakeFiles/relion_lib.dir/__/mask.cpp.o -c /<>/src/mask.cpp [ 10%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/matrix1d.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/matrix1d.cpp.o -MF CMakeFiles/relion_lib.dir/__/matrix1d.cpp.o.d -o CMakeFiles/relion_lib.dir/__/matrix1d.cpp.o -c /<>/src/matrix1d.cpp [ 10%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/matrix2d.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/matrix2d.cpp.o -MF CMakeFiles/relion_lib.dir/__/matrix2d.cpp.o.d -o CMakeFiles/relion_lib.dir/__/matrix2d.cpp.o -c /<>/src/matrix2d.cpp [ 11%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/memory.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/memory.cpp.o -MF CMakeFiles/relion_lib.dir/__/memory.cpp.o.d -o CMakeFiles/relion_lib.dir/__/memory.cpp.o -c /<>/src/memory.cpp [ 11%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/metadata_container.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/metadata_container.cpp.o -MF CMakeFiles/relion_lib.dir/__/metadata_container.cpp.o.d -o CMakeFiles/relion_lib.dir/__/metadata_container.cpp.o -c /<>/src/metadata_container.cpp [ 11%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/metadata_label.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/metadata_label.cpp.o -MF CMakeFiles/relion_lib.dir/__/metadata_label.cpp.o.d -o CMakeFiles/relion_lib.dir/__/metadata_label.cpp.o -c /<>/src/metadata_label.cpp [ 12%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/metadata_table.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/metadata_table.cpp.o -MF CMakeFiles/relion_lib.dir/__/metadata_table.cpp.o.d -o CMakeFiles/relion_lib.dir/__/metadata_table.cpp.o -c /<>/src/metadata_table.cpp [ 12%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/micrograph_model.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/micrograph_model.cpp.o -MF CMakeFiles/relion_lib.dir/__/micrograph_model.cpp.o.d -o CMakeFiles/relion_lib.dir/__/micrograph_model.cpp.o -c /<>/src/micrograph_model.cpp In file included from /<>/src/image.h:455, from /<>/src/micrograph_model.cpp:23: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /usr/include/powerpc64le-linux-gnu/c++/12/bits/c++allocator.h:33, from /usr/include/c++/12/bits/allocator.h:46, from /usr/include/c++/12/bits/stl_tree.h:64, from /usr/include/c++/12/map:60, from /<>/src/metadata_table.h:32, from /<>/src/metadata_table.cpp:45: In member function ‘std::__new_allocator::deallocate(double*, unsigned long)’, inlined from ‘std::allocator_traits >::deallocate(std::allocator&, double*, unsigned long)’ at /usr/include/c++/12/bits/alloc_traits.h:496:23, inlined from ‘std::_Vector_base >::_M_deallocate(double*, unsigned long)’ at /usr/include/c++/12/bits/stl_vector.h:387:19, inlined from ‘std::_Vector_base >::~_Vector_base()’ at /usr/include/c++/12/bits/stl_vector.h:366:15, inlined from ‘std::vector >::~vector()’ at /usr/include/c++/12/bits/stl_vector.h:733:7, inlined from ‘removeDuplicatedParticles(MetaDataTable&, EMDLabel, double, double, FileName, bool)’ at /<>/src/metadata_table.cpp:1963:1: /usr/include/c++/12/bits/new_allocator.h:158:33: warning: ‘operator delete(void*)’ called on pointer ‘_647’ with nonzero offset [1, 9223372036854775807] [-Wfree-nonheap-object] 158 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In member function ‘std::__new_allocator::allocate(unsigned long, void const*)’, inlined from ‘std::allocator_traits >::allocate(std::allocator&, unsigned long)’ at /usr/include/c++/12/bits/alloc_traits.h:464:28, inlined from ‘std::_Vector_base >::_M_allocate(unsigned long)’ at /usr/include/c++/12/bits/stl_vector.h:378:33, inlined from ‘std::_Vector_base >::_M_create_storage(unsigned long)’ at /usr/include/c++/12/bits/stl_vector.h:395:44, inlined from ‘std::_Vector_base >::_Vector_base(unsigned long, std::allocator const&)’ at /usr/include/c++/12/bits/stl_vector.h:332:26, inlined from ‘std::vector >::vector(unsigned long, double const&, std::allocator const&)’ at /usr/include/c++/12/bits/stl_vector.h:566:47, inlined from ‘removeDuplicatedParticles(MetaDataTable&, EMDLabel, double, double, FileName, bool)’ at /<>/src/metadata_table.cpp:1876:52: /usr/include/c++/12/bits/new_allocator.h:137:55: note: returned from ‘operator new(unsigned long)’ 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ [ 12%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ml_model.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/ml_model.cpp.o -MF CMakeFiles/relion_lib.dir/__/ml_model.cpp.o.d -o CMakeFiles/relion_lib.dir/__/ml_model.cpp.o -c /<>/src/ml_model.cpp [ 13%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ml_optimiser.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/ml_optimiser.cpp.o -MF CMakeFiles/relion_lib.dir/__/ml_optimiser.cpp.o.d -o CMakeFiles/relion_lib.dir/__/ml_optimiser.cpp.o -c /<>/src/ml_optimiser.cpp In file included from /<>/src/image.h:455, from /<>/src/projector.h:25, from /<>/src/ml_model.h:23, from /<>/src/ml_model.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /<>/src/image.h:455, from /<>/src/projector.h:25, from /<>/src/ml_model.h:23, from /<>/src/ml_optimiser.h:35, from /<>/src/ml_optimiser.cpp:44: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 13%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ml_optimiser_mpi.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/ml_optimiser_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/ml_optimiser_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/ml_optimiser_mpi.cpp.o -c /<>/src/ml_optimiser_mpi.cpp In file included from /<>/src/image.h:455, from /<>/src/projector.h:25, from /<>/src/ml_model.h:23, from /<>/src/ml_optimiser.h:35, from /<>/src/ml_optimiser_mpi.h:24, from /<>/src/ml_optimiser_mpi.cpp:20: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 14%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/motioncorr_runner.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/motioncorr_runner.cpp.o -MF CMakeFiles/relion_lib.dir/__/motioncorr_runner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/motioncorr_runner.cpp.o -c /<>/src/motioncorr_runner.cpp [ 14%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/motioncorr_runner_mpi.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/motioncorr_runner_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/motioncorr_runner_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/motioncorr_runner_mpi.cpp.o -c /<>/src/motioncorr_runner_mpi.cpp In file included from /<>/src/image.h:455, from /<>/src/motioncorr_runner.h:32, from /<>/src/motioncorr_runner.cpp:22: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /<>/src/image.h:455, from /<>/src/motioncorr_runner.h:32, from /<>/src/motioncorr_runner_mpi.h:25, from /<>/src/motioncorr_runner_mpi.cpp:20: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 14%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/mpi.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/mpi.cpp.o -c /<>/src/mpi.cpp [ 15%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/multidim_array.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/multidim_array.cpp.o -MF CMakeFiles/relion_lib.dir/__/multidim_array.cpp.o.d -o CMakeFiles/relion_lib.dir/__/multidim_array.cpp.o -c /<>/src/multidim_array.cpp [ 15%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/numerical_recipes.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/numerical_recipes.cpp.o -MF CMakeFiles/relion_lib.dir/__/numerical_recipes.cpp.o.d -o CMakeFiles/relion_lib.dir/__/numerical_recipes.cpp.o -c /<>/src/numerical_recipes.cpp In file included from /<>/src/numerical_recipes.h:48, from /<>/src/numerical_recipes.cpp:49: In function ‘free_Tvector(double*&, int, int)void’, inlined from ‘brent(double, double, double, double (*)(double*, void*), void*, double, double*, int, double*, double*)’ at /<>/src/numerical_recipes.cpp:594:25: /<>/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object] 74 | free((char*)(v + nl)); | ~~~~^~~~~~~~~~~~~~~~~ /<>/src/numerical_recipes.cpp: In function ‘brent(double, double, double, double (*)(double*, void*), void*, double, double*, int, double*, double*)’: /<>/src/numerical_recipes.cpp:579:13: note: declared here 579 | RFLOAT *xt=NULL; | ^~ In function ‘free_Tvector(double*&, int, int)void’, inlined from ‘linmin(double*, double*, int, double&, double (*)(double*, void*), void*)’ at /<>/src/numerical_recipes.cpp:691:17: /<>/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] 74 | free((char*)(v + nl)); | ~~~~^~~~~~~~~~~~~~~~~ /<>/src/numerical_recipes.cpp: In function ‘linmin(double*, double*, int, double&, double (*)(double*, void*), void*)’: /<>/src/numerical_recipes.cpp:673:13: note: declared here 673 | RFLOAT *xicom=NULL; | ^~~~~ In function ‘free_Tvector(double*&, int, int)void’, inlined from ‘linmin(double*, double*, int, double&, double (*)(double*, void*), void*)’ at /<>/src/numerical_recipes.cpp:691:17: /<>/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] 74 | free((char*)(v + nl)); | ~~~~^~~~~~~~~~~~~~~~~ /<>/src/numerical_recipes.cpp: In function ‘linmin(double*, double*, int, double&, double (*)(double*, void*), void*)’: /<>/src/numerical_recipes.cpp:673:13: note: declared here 673 | RFLOAT *xicom=NULL; | ^~~~~ In function ‘free_Tvector(double*&, int, int)void’, inlined from ‘powell(double*, double*, int, double, int&, double&, double (*)(double*, void*), void*, bool)’ at /<>/src/numerical_recipes.cpp:767:25: /<>/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object] 74 | free((char*)(v + nl)); | ~~~~^~~~~~~~~~~~~~~~~ /<>/src/numerical_recipes.cpp: In function ‘powell(double*, double*, int, double, int&, double&, double (*)(double*, void*), void*, bool)’: /<>/src/numerical_recipes.cpp:703:24: note: declared here 703 | RFLOAT *pt, *ptt, *xit; | ^~~ In function ‘free_Tvector(double*&, int, int)void’, inlined from ‘powell(double*, double*, int, double, int&, double&, double (*)(double*, void*), void*, bool)’ at /<>/src/numerical_recipes.cpp:768:25: /<>/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object] 74 | free((char*)(v + nl)); | ~~~~^~~~~~~~~~~~~~~~~ /<>/src/numerical_recipes.cpp: In function ‘powell(double*, double*, int, double, int&, double&, double (*)(double*, void*), void*, bool)’: /<>/src/numerical_recipes.cpp:703:18: note: declared here 703 | RFLOAT *pt, *ptt, *xit; | ^~~ In function ‘free_Tvector(double*&, int, int)void’, inlined from ‘powell(double*, double*, int, double, int&, double&, double (*)(double*, void*), void*, bool)’ at /<>/src/numerical_recipes.cpp:769:25: /<>/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object] 74 | free((char*)(v + nl)); | ~~~~^~~~~~~~~~~~~~~~~ /<>/src/numerical_recipes.cpp: In function ‘powell(double*, double*, int, double, int&, double&, double (*)(double*, void*), void*, bool)’: /<>/src/numerical_recipes.cpp:703:13: note: declared here 703 | RFLOAT *pt, *ptt, *xit; | ^~ [ 15%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/parallel.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/parallel.cpp.o -MF CMakeFiles/relion_lib.dir/__/parallel.cpp.o.d -o CMakeFiles/relion_lib.dir/__/parallel.cpp.o -c /<>/src/parallel.cpp [ 16%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/particle_subtractor.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/particle_subtractor.cpp.o -MF CMakeFiles/relion_lib.dir/__/particle_subtractor.cpp.o.d -o CMakeFiles/relion_lib.dir/__/particle_subtractor.cpp.o -c /<>/src/particle_subtractor.cpp [ 16%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/pipeline_control.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/pipeline_control.cpp.o -MF CMakeFiles/relion_lib.dir/__/pipeline_control.cpp.o.d -o CMakeFiles/relion_lib.dir/__/pipeline_control.cpp.o -c /<>/src/pipeline_control.cpp In file included from /<>/src/image.h:455, from /<>/src/projector.h:25, from /<>/src/ml_model.h:23, from /<>/src/ml_optimiser.h:35, from /<>/src/particle_subtractor.h:24, from /<>/src/particle_subtractor.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 17%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/pipeline_jobs.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/pipeline_jobs.cpp.o -MF CMakeFiles/relion_lib.dir/__/pipeline_jobs.cpp.o.d -o CMakeFiles/relion_lib.dir/__/pipeline_jobs.cpp.o -c /<>/src/pipeline_jobs.cpp [ 17%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/pipeliner.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/pipeliner.cpp.o -MF CMakeFiles/relion_lib.dir/__/pipeliner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/pipeliner.cpp.o -c /<>/src/pipeliner.cpp [ 17%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/postprocessing.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/postprocessing.cpp.o -MF CMakeFiles/relion_lib.dir/__/postprocessing.cpp.o.d -o CMakeFiles/relion_lib.dir/__/postprocessing.cpp.o -c /<>/src/postprocessing.cpp In file included from /<>/src/image.h:455, from /<>/src/postprocessing.h:24, from /<>/src/postprocessing.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 18%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/preprocessing.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/preprocessing.cpp.o -MF CMakeFiles/relion_lib.dir/__/preprocessing.cpp.o.d -o CMakeFiles/relion_lib.dir/__/preprocessing.cpp.o -c /<>/src/preprocessing.cpp In file included from /<>/src/image.h:455, from /<>/src/preprocessing.h:29, from /<>/src/preprocessing.cpp:20: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 18%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/preprocessing_mpi.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/preprocessing_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/preprocessing_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/preprocessing_mpi.cpp.o -c /<>/src/preprocessing_mpi.cpp [ 18%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/projector.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/projector.cpp.o -MF CMakeFiles/relion_lib.dir/__/projector.cpp.o.d -o CMakeFiles/relion_lib.dir/__/projector.cpp.o -c /<>/src/projector.cpp In file included from /<>/src/image.h:455, from /<>/src/preprocessing.h:29, from /<>/src/preprocessing_mpi.h:24, from /<>/src/preprocessing_mpi.cpp:20: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /<>/src/image.h:455, from /<>/src/projector.h:25, from /<>/src/projector.cpp:20: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 19%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/reconstructor.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/reconstructor.cpp.o -MF CMakeFiles/relion_lib.dir/__/reconstructor.cpp.o.d -o CMakeFiles/relion_lib.dir/__/reconstructor.cpp.o -c /<>/src/reconstructor.cpp In file included from /<>/src/image.h:455, from /<>/src/projector.h:25, from /<>/src/backprojector.h:33, from /<>/src/reconstructor.h:23, from /<>/src/reconstructor.cpp:20: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 19%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/reconstructor_mpi.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/reconstructor_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/reconstructor_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/reconstructor_mpi.cpp.o -c /<>/src/reconstructor_mpi.cpp In file included from /<>/src/image.h:455, from /<>/src/projector.h:25, from /<>/src/backprojector.h:33, from /<>/src/reconstructor.h:23, from /<>/src/reconstructor_mpi.h:25, from /<>/src/reconstructor_mpi.cpp:20: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 20%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/renderEER.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/renderEER.cpp.o -MF CMakeFiles/relion_lib.dir/__/renderEER.cpp.o.d -o CMakeFiles/relion_lib.dir/__/renderEER.cpp.o -c /<>/src/renderEER.cpp In file included from /<>/src/image.h:455, from /<>/src/renderEER.cpp:10: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/renderEER.cpp: In member function ‘void EERRenderer::readLegacy(FILE*)’: /<>/src/renderEER.cpp:191:14: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 191 | fread(buf, sizeof(char), file_size, fh); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 20%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/scheduler.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/scheduler.cpp.o -MF CMakeFiles/relion_lib.dir/__/scheduler.cpp.o.d -o CMakeFiles/relion_lib.dir/__/scheduler.cpp.o -c /<>/src/scheduler.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/obs_model.h:24, from /<>/src/scheduler.h:26, from /<>/src/scheduler.cpp:20: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 20%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/strings.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/strings.cpp.o -MF CMakeFiles/relion_lib.dir/__/strings.cpp.o.d -o CMakeFiles/relion_lib.dir/__/strings.cpp.o -c /<>/src/strings.cpp [ 21%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/symmetries.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/symmetries.cpp.o -MF CMakeFiles/relion_lib.dir/__/symmetries.cpp.o.d -o CMakeFiles/relion_lib.dir/__/symmetries.cpp.o -c /<>/src/symmetries.cpp [ 21%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/tabfuncs.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/tabfuncs.cpp.o -MF CMakeFiles/relion_lib.dir/__/tabfuncs.cpp.o.d -o CMakeFiles/relion_lib.dir/__/tabfuncs.cpp.o -c /<>/src/tabfuncs.cpp [ 21%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/tiff_converter.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/tiff_converter.cpp.o -MF CMakeFiles/relion_lib.dir/__/tiff_converter.cpp.o.d -o CMakeFiles/relion_lib.dir/__/tiff_converter.cpp.o -c /<>/src/tiff_converter.cpp In file included from /<>/src/image.h:455, from /<>/src/tiff_converter.cpp:24: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/tiff_converter.cpp: In member function ‘void TIFFConverter::estimate(FileName)’: /<>/src/tiff_converter.cpp:141:101: warning: format ‘%d’ expects argument of type ‘int’, but argument 7 has type ‘long int’ [-Wformat=] 141 | printf(" %s Frame %03d #Changed %10d #Mismatch %10d, #Negative %10d, #Unreliable %10d / %10d\n", | ~~~^ | | | int | %10ld /<>/src/tiff_converter.cpp:141:108: warning: format ‘%d’ expects argument of type ‘int’, but argument 8 has type ‘long int’ [-Wformat=] 141 | printf(" %s Frame %03d #Changed %10d #Mismatch %10d, #Negative %10d, #Unreliable %10d / %10d\n", | ~~~^ | | | int | %10ld /<>/src/tiff_converter.cpp: In member function ‘int TIFFConverter::checkMRCtype(FileName)’: /<>/src/tiff_converter.cpp:309:14: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 309 | fread(headers, sizeof(int), 24, mrcin); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/tiff_converter.cpp: In member function ‘void TIFFConverter::initialise(int, int)’: /<>/src/tiff_converter.cpp:367:23: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | system(("mkdir -p " + fn_out.beforeLastOf("/")).c_str()); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/tiff_converter.cpp: In member function ‘void TIFFConverter::run()’: /<>/src/tiff_converter.cpp:530:31: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | system(("mkdir -p " + fn_tiff.beforeLastOf("/")).c_str()); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 22%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/time.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/time.cpp.o -MF CMakeFiles/relion_lib.dir/__/time.cpp.o.d -o CMakeFiles/relion_lib.dir/__/time.cpp.o -c /<>/src/time.cpp [ 22%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/transformations.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/transformations.cpp.o -MF CMakeFiles/relion_lib.dir/__/transformations.cpp.o.d -o CMakeFiles/relion_lib.dir/__/transformations.cpp.o -c /<>/src/transformations.cpp [ 23%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/Healpix_2.15a/cxxutils.cc.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/Healpix_2.15a/cxxutils.cc.o -MF CMakeFiles/relion_lib.dir/__/Healpix_2.15a/cxxutils.cc.o.d -o CMakeFiles/relion_lib.dir/__/Healpix_2.15a/cxxutils.cc.o -c /<>/src/Healpix_2.15a/cxxutils.cc [ 23%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/Healpix_2.15a/healpix_base.cc.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/Healpix_2.15a/healpix_base.cc.o -MF CMakeFiles/relion_lib.dir/__/Healpix_2.15a/healpix_base.cc.o.d -o CMakeFiles/relion_lib.dir/__/Healpix_2.15a/healpix_base.cc.o -c /<>/src/Healpix_2.15a/healpix_base.cc [ 23%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/Fourier_helper.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/Fourier_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/Fourier_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/Fourier_helper.cpp.o -c /<>/src/jaz/Fourier_helper.cpp [ 24%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/Gaussian_pyramid.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/Gaussian_pyramid.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/Gaussian_pyramid.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/Gaussian_pyramid.cpp.o -c /<>/src/jaz/Gaussian_pyramid.cpp [ 24%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/aberration_fit.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/aberration_fit.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/aberration_fit.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/aberration_fit.cpp.o -c /<>/src/jaz/aberration_fit.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/Fourier_helper.h:24, from /<>/src/jaz/Fourier_helper.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /<>/src/image.h:455, from /<>/src/jaz/aberration_fit.h:24, from /<>/src/jaz/aberration_fit.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 25%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/complex_io.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/complex_io.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/complex_io.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/complex_io.cpp.o -c /<>/src/jaz/complex_io.cpp [ 25%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/convolution_helper.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/convolution_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/convolution_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/convolution_helper.cpp.o -c /<>/src/jaz/convolution_helper.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/complex_io.h:24, from /<>/src/jaz/complex_io.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 25%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf_helper.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf_helper.cpp.o -c /<>/src/jaz/ctf_helper.cpp [ 26%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/damage_helper.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/damage_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/damage_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/damage_helper.cpp.o -c /<>/src/jaz/damage_helper.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/convolution_helper.h:24, from /<>/src/jaz/convolution_helper.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /<>/src/image.h:455, from /<>/src/jaz/obs_model.h:24, from /<>/src/ctf.h:50, from /<>/src/jaz/ctf_helper.h:24, from /<>/src/jaz/ctf_helper.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /<>/src/image.h:455, from /<>/src/jaz/obs_model.h:24, from /<>/src/ctf.h:50, from /<>/src/jaz/fsc_helper.h:24, from /<>/src/jaz/damage_helper.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 26%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/distribution_helper.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/distribution_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/distribution_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/distribution_helper.cpp.o -c /<>/src/jaz/distribution_helper.cpp [ 26%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/fftw_helper.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/fftw_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/fftw_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/fftw_helper.cpp.o -c /<>/src/jaz/fftw_helper.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/distribution_helper.h:25, from /<>/src/jaz/distribution_helper.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 27%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/fsc_helper.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/fsc_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/fsc_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/fsc_helper.cpp.o -c /<>/src/jaz/fsc_helper.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/obs_model.h:24, from /<>/src/ctf.h:50, from /<>/src/jaz/fsc_helper.h:24, from /<>/src/jaz/fsc_helper.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 27%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/image_log.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/image_log.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/image_log.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/image_log.cpp.o -c /<>/src/jaz/image_log.cpp [ 28%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/interpolation.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/interpolation.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/interpolation.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/interpolation.cpp.o -c /<>/src/jaz/interpolation.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/image_log.h:24, from /<>/src/jaz/image_log.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /<>/src/image.h:455, from /<>/src/jaz/interpolation.h:24, from /<>/src/jaz/interpolation.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 28%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/jaz_config.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/jaz_config.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/jaz_config.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/jaz_config.cpp.o -c /<>/src/jaz/jaz_config.cpp [ 28%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/legacy_obs_model.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/legacy_obs_model.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/legacy_obs_model.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/legacy_obs_model.cpp.o -c /<>/src/jaz/legacy_obs_model.cpp [ 29%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/local_motion_fit.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/local_motion_fit.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/local_motion_fit.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/local_motion_fit.cpp.o -c /<>/src/jaz/local_motion_fit.cpp [ 29%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/micrograph_handler.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/micrograph_handler.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/micrograph_handler.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/micrograph_handler.cpp.o -c /<>/src/jaz/micrograph_handler.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/legacy_obs_model.h:4, from /<>/src/jaz/legacy_obs_model.cpp:1: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /<>/src/image.h:455, from /<>/src/jaz/local_motion_fit.h:24, from /<>/src/jaz/local_motion_fit.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /<>/src/image.h:455, from /<>/src/jaz/micrograph_handler.h:31, from /<>/src/jaz/micrograph_handler.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 29%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/new_ft.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/new_ft.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/new_ft.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/new_ft.cpp.o -c /<>/src/jaz/new_ft.cpp [ 30%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/noise_helper.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/noise_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/noise_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/noise_helper.cpp.o -c /<>/src/jaz/noise_helper.cpp [ 30%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/obs_model.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/obs_model.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/obs_model.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/obs_model.cpp.o -c /<>/src/jaz/obs_model.cpp In file included from /<>/src/image.h:455, from /<>/src/projector.h:25, from /<>/src/jaz/noise_helper.h:25, from /<>/src/jaz/noise_helper.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /<>/src/image.h:455, from /<>/src/jaz/obs_model.h:24, from /<>/src/jaz/obs_model.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 31%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/parallel_ft.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/parallel_ft.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/parallel_ft.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/parallel_ft.cpp.o -c /<>/src/jaz/parallel_ft.cpp [ 31%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/reference_map.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/reference_map.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/reference_map.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/reference_map.cpp.o -c /<>/src/jaz/reference_map.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/reference_map.h:24, from /<>/src/jaz/reference_map.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 31%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/refinement_helper.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/refinement_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/refinement_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/refinement_helper.cpp.o -c /<>/src/jaz/refinement_helper.cpp [ 32%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/resampling_helper.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/resampling_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/resampling_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/resampling_helper.cpp.o -c /<>/src/jaz/resampling_helper.cpp [ 32%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/slice_helper.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/slice_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/slice_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/slice_helper.cpp.o -c /<>/src/jaz/slice_helper.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/obs_model.h:24, from /<>/src/ctf.h:50, from /<>/src/jaz/refinement_helper.h:24, from /<>/src/jaz/refinement_helper.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /<>/src/image.h:455, from /<>/src/jaz/slice_helper.h:24, from /<>/src/jaz/slice_helper.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 32%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/spectral_helper.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/spectral_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/spectral_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/spectral_helper.cpp.o -c /<>/src/jaz/spectral_helper.cpp [ 33%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/stack_helper.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/stack_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/stack_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/stack_helper.cpp.o -c /<>/src/jaz/stack_helper.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/spectral_helper.h:24, from /<>/src/jaz/spectral_helper.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /<>/src/image.h:455, from /<>/src/jaz/obs_model.h:24, from /<>/src/ctf.h:50, from /<>/src/jaz/stack_helper.h:24, from /<>/src/jaz/stack_helper.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 33%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/structure_tensor.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/structure_tensor.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/structure_tensor.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/structure_tensor.cpp.o -c /<>/src/jaz/structure_tensor.cpp [ 34%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/svd_helper.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/svd_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/svd_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/svd_helper.cpp.o -c /<>/src/jaz/svd_helper.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/img_proc/filter_helper.h:24, from /<>/src/jaz/structure_tensor.cpp:22: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 34%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/t_complex.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/t_complex.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/t_complex.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/t_complex.cpp.o -c /<>/src/jaz/t_complex.cpp [ 34%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/volume_converter.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/volume_converter.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/volume_converter.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/volume_converter.cpp.o -c /<>/src/jaz/volume_converter.cpp [ 35%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/volume_integration.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/volume_integration.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/volume_integration.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/volume_integration.cpp.o -c /<>/src/jaz/volume_integration.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/volume_converter.h:25, from /<>/src/jaz/volume_converter.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 35%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/vtk_helper.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/vtk_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/vtk_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/vtk_helper.cpp.o -c /<>/src/jaz/vtk_helper.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/volume_integration.h:26, from /<>/src/jaz/volume_integration.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 36%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/gradient_descent.cpp.o /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/gradient_descent.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/optimization/gradient_descent.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/optimization/gradient_descent.cpp.o -c /<>/src/jaz/optimization/gradient_descent.cpp /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /<>/src/image.h:455, from /<>/src/jaz/vtk_helper.h:24, from /<>/src/jaz/vtk_helper.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 36%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/lbfgs.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/lbfgs.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/optimization/lbfgs.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/optimization/lbfgs.cpp.o -c /<>/src/jaz/optimization/lbfgs.cpp [ 36%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/nelder_mead.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/nelder_mead.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/optimization/nelder_mead.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/optimization/nelder_mead.cpp.o -c /<>/src/jaz/optimization/nelder_mead.cpp [ 37%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/optimization.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/optimization.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/optimization/optimization.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/optimization/optimization.cpp.o -c /<>/src/jaz/optimization/optimization.cpp [ 37%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/aberration_estimator.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/aberration_estimator.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/aberration_estimator.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/aberration_estimator.cpp.o -c /<>/src/jaz/ctf/aberration_estimator.cpp [ 37%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/bfactor_refiner.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/bfactor_refiner.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/bfactor_refiner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/bfactor_refiner.cpp.o -c /<>/src/jaz/ctf/bfactor_refiner.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/ctf/aberration_estimator.h:4, from /<>/src/jaz/ctf/aberration_estimator.cpp:1: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 38%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner.cpp.o -c /<>/src/jaz/ctf/ctf_refiner.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/ctf/bfactor_refiner.h:4, from /<>/src/jaz/ctf/bfactor_refiner.cpp:1: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /<>/src/image.h:455, from /<>/src/jaz/obs_model.h:24, from /<>/src/jaz/ctf/ctf_refiner.h:24, from /<>/src/jaz/ctf/ctf_refiner.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 38%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner_mpi.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner_mpi.cpp.o -c /<>/src/jaz/ctf/ctf_refiner_mpi.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/obs_model.h:24, from /<>/src/jaz/ctf/ctf_refiner.h:24, from /<>/src/jaz/ctf/ctf_refiner_mpi.h:26, from /<>/src/jaz/ctf/ctf_refiner_mpi.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 39%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_estimator.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_estimator.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_estimator.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_estimator.cpp.o -c /<>/src/jaz/ctf/defocus_estimator.cpp [ 39%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_helper.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_helper.cpp.o -c /<>/src/jaz/ctf/defocus_helper.cpp [ 39%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/delocalisation_helper.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/delocalisation_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/delocalisation_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/delocalisation_helper.cpp.o -c /<>/src/jaz/ctf/delocalisation_helper.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/ctf/defocus_estimator.h:24, from /<>/src/jaz/ctf/defocus_estimator.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /<>/src/image.h:455, from /<>/src/jaz/obs_model.h:24, from /<>/src/ctf.h:50, from /<>/src/jaz/ctf/defocus_helper.h:24, from /<>/src/jaz/ctf/defocus_helper.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /<>/src/image.h:455, from /<>/src/jaz/obs_model.h:24, from /<>/src/ctf.h:50, from /<>/src/jaz/ctf/delocalisation_helper.h:4, from /<>/src/jaz/ctf/delocalisation_helper.cpp:1: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 40%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/equation2x2.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/equation2x2.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/equation2x2.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/equation2x2.cpp.o -c /<>/src/jaz/ctf/equation2x2.cpp [ 40%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_estimator.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_estimator.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_estimator.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_estimator.cpp.o -c /<>/src/jaz/ctf/magnification_estimator.cpp [ 40%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_helper.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_helper.cpp.o -c /<>/src/jaz/ctf/magnification_helper.cpp [ 41%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/modular_ctf_optimisation.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/modular_ctf_optimisation.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/modular_ctf_optimisation.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/modular_ctf_optimisation.cpp.o -c /<>/src/jaz/ctf/modular_ctf_optimisation.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/ctf/magnification_estimator.h:28, from /<>/src/jaz/ctf/magnification_estimator.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /<>/src/image.h:455, from /<>/src/jaz/obs_model.h:24, from /<>/src/ctf.h:50, from /<>/src/jaz/ctf/magnification_helper.h:24, from /<>/src/jaz/ctf/magnification_helper.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /<>/src/image.h:455, from /<>/src/jaz/ctf/modular_ctf_optimisation.h:5, from /<>/src/jaz/ctf/modular_ctf_optimisation.cpp:1: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 41%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_estimator.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_estimator.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_estimator.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_estimator.cpp.o -c /<>/src/jaz/ctf/tilt_estimator.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/ctf/tilt_estimator.h:24, from /<>/src/jaz/ctf/tilt_estimator.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 42%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_helper.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_helper.cpp.o -c /<>/src/jaz/ctf/tilt_helper.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/obs_model.h:24, from /<>/src/ctf.h:50, from /<>/src/jaz/ctf/tilt_helper.h:24, from /<>/src/jaz/ctf/tilt_helper.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 42%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/alignment_set.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/alignment_set.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/alignment_set.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/alignment_set.cpp.o -c /<>/src/jaz/motion/alignment_set.cpp [ 42%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/frame_recombiner.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/frame_recombiner.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/frame_recombiner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/frame_recombiner.cpp.o -c /<>/src/jaz/motion/frame_recombiner.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/motion/frame_recombiner.h:24, from /<>/src/jaz/motion/frame_recombiner.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 43%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/gp_motion_fit.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/gp_motion_fit.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/gp_motion_fit.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/gp_motion_fit.cpp.o -c /<>/src/jaz/motion/gp_motion_fit.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/motion/gp_motion_fit.h:24, from /<>/src/jaz/motion/gp_motion_fit.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 43%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_estimator.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_estimator.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/motion_estimator.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_estimator.cpp.o -c /<>/src/jaz/motion/motion_estimator.cpp [ 43%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_helper.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/motion_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_helper.cpp.o -c /<>/src/jaz/motion/motion_helper.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/motion/motion_estimator.h:24, from /<>/src/jaz/motion/motion_estimator.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 44%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_param_estimator.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_param_estimator.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/motion_param_estimator.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_param_estimator.cpp.o -c /<>/src/jaz/motion/motion_param_estimator.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/obs_model.h:24, from /<>/src/ctf.h:50, from /<>/src/jaz/motion/motion_helper.h:24, from /<>/src/jaz/motion/motion_helper.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /<>/src/image.h:455, from /<>/src/jaz/motion/alignment_set.h:24, from /<>/src/jaz/motion/motion_param_estimator.h:24, from /<>/src/jaz/motion/motion_param_estimator.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 44%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner.cpp.o -c /<>/src/jaz/motion/motion_refiner.cpp [ 45%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner_mpi.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner_mpi.cpp.o -c /<>/src/jaz/motion/motion_refiner_mpi.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/obs_model.h:24, from /<>/src/ctf.h:50, from /<>/src/jaz/motion/motion_refiner.h:25, from /<>/src/jaz/motion/motion_refiner.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /<>/src/image.h:455, from /<>/src/jaz/obs_model.h:24, from /<>/src/ctf.h:50, from /<>/src/jaz/motion/motion_refiner.h:25, from /<>/src/jaz/motion/motion_refiner_mpi.h:27, from /<>/src/jaz/motion/motion_refiner_mpi.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 45%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/three_hyperparameter_fit.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/three_hyperparameter_fit.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/three_hyperparameter_fit.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/three_hyperparameter_fit.cpp.o -c /<>/src/jaz/motion/three_hyperparameter_fit.cpp [ 45%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/two_hyperparameter_fit.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/two_hyperparameter_fit.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/two_hyperparameter_fit.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/two_hyperparameter_fit.cpp.o -c /<>/src/jaz/motion/two_hyperparameter_fit.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/motion/alignment_set.h:24, from /<>/src/jaz/motion/motion_param_estimator.h:24, from /<>/src/jaz/motion/three_hyperparameter_fit.cpp:22: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /<>/src/image.h:455, from /<>/src/jaz/motion/alignment_set.h:24, from /<>/src/jaz/motion/motion_param_estimator.h:24, from /<>/src/jaz/motion/two_hyperparameter_fit.cpp:22: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 46%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/math/Zernike.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/math/Zernike.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/math/Zernike.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/math/Zernike.cpp.o -c /<>/src/jaz/math/Zernike.cpp [ 46%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/color_helper.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/color_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/img_proc/color_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/img_proc/color_helper.cpp.o -c /<>/src/jaz/img_proc/color_helper.cpp [ 46%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/filter_helper.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/filter_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/img_proc/filter_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/img_proc/filter_helper.cpp.o -c /<>/src/jaz/img_proc/filter_helper.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/img_proc/color_helper.h:5, from /<>/src/jaz/img_proc/color_helper.cpp:1: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 47%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/image_op.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/image_op.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/img_proc/image_op.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/img_proc/image_op.cpp.o -c /<>/src/jaz/img_proc/image_op.cpp [ 47%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/backprojection_helper.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/backprojection_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/tomo/backprojection_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/tomo/backprojection_helper.cpp.o -c /<>/src/jaz/tomo/backprojection_helper.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/img_proc/filter_helper.h:24, from /<>/src/jaz/img_proc/filter_helper.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 48%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/imod_helper.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/imod_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/tomo/imod_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/tomo/imod_helper.cpp.o -c /<>/src/jaz/tomo/imod_helper.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/tomo/backprojection_helper.h:24, from /<>/src/jaz/tomo/backprojection_helper.cpp:23: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 48%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/projection_helper.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/projection_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/tomo/projection_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/tomo/projection_helper.cpp.o -c /<>/src/jaz/tomo/projection_helper.cpp [ 48%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/tomo_stack.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/tomo_stack.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/tomo/tomo_stack.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/tomo/tomo_stack.cpp.o -c /<>/src/jaz/tomo/tomo_stack.cpp [ 49%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/io/star_converter.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/io/star_converter.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/io/star_converter.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/io/star_converter.cpp.o -c /<>/src/jaz/io/star_converter.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/tomo/tomo_stack.h:25, from /<>/src/jaz/tomo/tomo_stack.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /<>/src/image.h:455, from /<>/src/jaz/io/star_converter.h:5, from /<>/src/jaz/io/star_converter.cpp:1: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 49%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyev2.c.o cd /<>/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyev2.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyev2.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyev2.c.o -c /<>/src/jaz/d3x3/dsyev2.c [ 50%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevc3.c.o cd /<>/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevc3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevc3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevc3.c.o -c /<>/src/jaz/d3x3/dsyevc3.c [ 50%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevd3.c.o cd /<>/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevd3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevd3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevd3.c.o -c /<>/src/jaz/d3x3/dsyevd3.c [ 50%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevh3.c.o cd /<>/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevh3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevh3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevh3.c.o -c /<>/src/jaz/d3x3/dsyevh3.c [ 51%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevj3.c.o cd /<>/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevj3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevj3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevj3.c.o -c /<>/src/jaz/d3x3/dsyevj3.c [ 51%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevq3.c.o cd /<>/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevq3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevq3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevq3.c.o -c /<>/src/jaz/d3x3/dsyevq3.c [ 51%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevv3.c.o cd /<>/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevv3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevv3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevv3.c.o -c /<>/src/jaz/d3x3/dsyevv3.c [ 52%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsytrd3.c.o cd /<>/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsytrd3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsytrd3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsytrd3.c.o -c /<>/src/jaz/d3x3/dsytrd3.c [ 52%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/slvsec3.c.o cd /<>/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/slvsec3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/slvsec3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/slvsec3.c.o -c /<>/src/jaz/d3x3/slvsec3.c [ 53%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/lbfgs/lbfgs.c.o cd /<>/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/lbfgs/lbfgs.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/lbfgs/lbfgs.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/lbfgs/lbfgs.c.o -c /<>/src/jaz/lbfgs/lbfgs.c [ 53%] Linking 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CMakeFiles/relion_lib.dir/__/jaz/tomo/backprojection_helper.cpp.o CMakeFiles/relion_lib.dir/__/jaz/tomo/imod_helper.cpp.o CMakeFiles/relion_lib.dir/__/jaz/tomo/projection_helper.cpp.o CMakeFiles/relion_lib.dir/__/jaz/tomo/tomo_stack.cpp.o CMakeFiles/relion_lib.dir/__/jaz/io/star_converter.cpp.o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyev2.c.o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevc3.c.o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevd3.c.o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevh3.c.o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevj3.c.o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevq3.c.o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevv3.c.o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsytrd3.c.o CMakeFiles/relion_lib.dir/__/jaz/d3x3/slvsec3.c.o CMakeFiles/relion_lib.dir/__/jaz/lbfgs/lbfgs.c.o /usr/bin/ranlib ../../lib/librelion_lib.a make[4]: Leaving directory '/<>/build' [ 53%] Built target relion_lib /usr/bin/make -f src/apps/CMakeFiles/relion_gui_lib.dir/build.make src/apps/CMakeFiles/relion_gui_lib.dir/depend /usr/bin/make -f src/apps/CMakeFiles/align_symmetry.dir/build.make src/apps/CMakeFiles/align_symmetry.dir/depend /usr/bin/make -f src/apps/CMakeFiles/autopick.dir/build.make src/apps/CMakeFiles/autopick.dir/depend /usr/bin/make -f src/apps/CMakeFiles/autopick_mpi.dir/build.make src/apps/CMakeFiles/autopick_mpi.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/relion_gui_lib.dir/DependInfo.cmake --color= make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/autopick.dir/DependInfo.cmake --color= make[4]: Entering directory '/<>/build' make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/align_symmetry.dir/DependInfo.cmake --color= cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/autopick_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/relion_gui_lib.dir/build.make src/apps/CMakeFiles/relion_gui_lib.dir/build make[4]: Leaving directory '/<>/build' make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/align_symmetry.dir/build.make src/apps/CMakeFiles/align_symmetry.dir/build /usr/bin/make -f src/apps/CMakeFiles/autopick.dir/build.make src/apps/CMakeFiles/autopick.dir/build /usr/bin/make -f src/apps/CMakeFiles/autopick_mpi.dir/build.make src/apps/CMakeFiles/autopick_mpi.dir/build make[4]: Entering directory '/<>/build' make[4]: Entering directory '/<>/build' make[4]: Entering directory '/<>/build' make[4]: Entering directory '/<>/build' [ 54%] Building CXX object src/apps/CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o [ 54%] Building CXX object src/apps/CMakeFiles/autopick.dir/autopick.cpp.o [ 54%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o -MF CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o.d -o CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o -c /<>/src/displayer.cpp cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/autopick.dir/autopick.cpp.o -MF CMakeFiles/autopick.dir/autopick.cpp.o.d -o CMakeFiles/autopick.dir/autopick.cpp.o -c /<>/src/apps/autopick.cpp cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o -MF CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o.d -o CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o -c /<>/src/apps/align_symmetry.cpp [ 54%] Building CXX object src/apps/CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o -MF CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o.d -o CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o -c /<>/src/apps/autopick_mpi.cpp In file included from /<>/src/image.h:455, from /<>/src/autopicker.h:10, from /<>/src/apps/autopick.cpp:20: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /<>/src/image.h:455, from /<>/src/projector.h:25, from /<>/src/apps/align_symmetry.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /<>/src/image.h:455, from /<>/src/displayer.h:40, from /<>/src/displayer.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /<>/src/image.h:455, from /<>/src/autopicker.h:10, from /<>/src/autopicker_mpi.h:12, from /<>/src/apps/autopick_mpi.cpp:20: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 54%] Linking CXX executable ../../bin/relion_autopick cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/autopick.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/autopick.dir/autopick.cpp.o -o ../../bin/relion_autopick ../../lib/librelion_lib.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 55%] Linking CXX executable ../../bin/relion_autopick_mpi cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/autopick_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o -o ../../bin/relion_autopick_mpi ../../lib/librelion_lib.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In member function ‘deallocate’, inlined from ‘deallocate’ at /usr/include/c++/12/bits/alloc_traits.h:496:23, inlined from ‘_M_deallocate’ at /usr/include/c++/12/bits/stl_vector.h:387:19, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:366:15, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:733:7, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1963:1: /usr/include/c++/12/bits/new_allocator.h:158:33: warning: ‘operator delete’ called on pointer ‘_831’ with nonzero offset [1, 9223372036854775807] [-Wfree-nonheap-object] 158 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In member function ‘allocate’, inlined from ‘allocate’ at /usr/include/c++/12/bits/alloc_traits.h:464:28, inlined from ‘_M_allocate’ at /usr/include/c++/12/bits/stl_vector.h:378:33, inlined from ‘_M_create_storage’ at /usr/include/c++/12/bits/stl_vector.h:395:44, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:332:26, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:566:47, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1876:52: /usr/include/c++/12/bits/new_allocator.h:137:55: note: returned from ‘operator new’ 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /usr/src/relion-3.1.3-3build1/src/strings.cpp: In function ‘integerToString.constprop’: /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-2, -1] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-3, -2] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-4, -3] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-5, -4] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp: In function ‘integerToString.constprop’: /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-2, -1] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-3, -2] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-4, -3] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-5, -4] into destination object ‘aux’ of size 15 [ 55%] Linking CXX executable ../../bin/relion_align_symmetry cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/align_symmetry.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o -o ../../bin/relion_align_symmetry ../../lib/librelion_lib.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In member function ‘deallocate’, inlined from ‘deallocate’ at /usr/include/c++/12/bits/alloc_traits.h:496:23, inlined from ‘_M_deallocate’ at /usr/include/c++/12/bits/stl_vector.h:387:19, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:366:15, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:733:7, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1963:1: /usr/include/c++/12/bits/new_allocator.h:158:33: warning: ‘operator delete’ called on pointer ‘_831’ with nonzero offset [1, 9223372036854775807] [-Wfree-nonheap-object] 158 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In member function ‘allocate’, inlined from ‘allocate’ at /usr/include/c++/12/bits/alloc_traits.h:464:28, inlined from ‘_M_allocate’ at /usr/include/c++/12/bits/stl_vector.h:378:33, inlined from ‘_M_create_storage’ at /usr/include/c++/12/bits/stl_vector.h:395:44, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:332:26, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:566:47, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1876:52: /usr/include/c++/12/bits/new_allocator.h:137:55: note: returned from ‘operator new’ 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function ‘deallocate’, inlined from ‘deallocate’ at /usr/include/c++/12/bits/alloc_traits.h:496:23, inlined from ‘_M_deallocate’ at /usr/include/c++/12/bits/stl_vector.h:387:19, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:366:15, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:733:7, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1963:1: /usr/include/c++/12/bits/new_allocator.h:158:33: warning: ‘operator delete’ called on pointer ‘_831’ with nonzero offset [1, 9223372036854775807] [-Wfree-nonheap-object] 158 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In member function ‘allocate’, inlined from ‘allocate’ at /usr/include/c++/12/bits/alloc_traits.h:464:28, inlined from ‘_M_allocate’ at /usr/include/c++/12/bits/stl_vector.h:378:33, inlined from ‘_M_create_storage’ at /usr/include/c++/12/bits/stl_vector.h:395:44, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:332:26, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:566:47, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1876:52: /usr/include/c++/12/bits/new_allocator.h:137:55: note: returned from ‘operator new’ 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In function ‘free_Tvector’, inlined from ‘brent’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:594:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘brent’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:579:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:767:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:24: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:768:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:18: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:769:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:13: note: declared here [ 56%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o -MF CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o.d -o CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o -c /<>/src/gui_entries.cpp [ 56%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o -MF CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o.d -o CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o -c /<>/src/gui_jobwindow.cpp In function ‘free_Tvector’, inlined from ‘brent’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:594:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘brent’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:579:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:767:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:24: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:768:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:18: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:769:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:13: note: declared here In function ‘free_Tvector’, inlined from ‘brent’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:594:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘brent’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:579:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:767:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:24: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:768:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:18: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:769:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:13: note: declared here [ 56%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o -MF CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o.d -o CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o -c /<>/src/gui_mainwindow.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/obs_model.h:24, from /<>/src/scheduler.h:26, from /<>/src/gui_mainwindow.h:28, from /<>/src/gui_mainwindow.cpp:22: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/<>/build' [ 56%] Built target autopick /usr/bin/make -f src/apps/CMakeFiles/convert_star.dir/build.make src/apps/CMakeFiles/convert_star.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/convert_star.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/convert_star.dir/build.make src/apps/CMakeFiles/convert_star.dir/build make[4]: Entering directory '/<>/build' [ 56%] Building CXX object src/apps/CMakeFiles/convert_star.dir/convert_star.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/convert_star.dir/convert_star.cpp.o -MF CMakeFiles/convert_star.dir/convert_star.cpp.o.d -o CMakeFiles/convert_star.dir/convert_star.cpp.o -c /<>/src/apps/convert_star.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/io/star_converter.h:5, from /<>/src/apps/convert_star.cpp:24: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/<>/build' [ 56%] Built target align_symmetry /usr/bin/make -f src/apps/CMakeFiles/convert_to_tiff.dir/build.make src/apps/CMakeFiles/convert_to_tiff.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/convert_to_tiff.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/convert_to_tiff.dir/build.make src/apps/CMakeFiles/convert_to_tiff.dir/build make[4]: Entering directory '/<>/build' [ 56%] Building CXX object src/apps/CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o -MF CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o.d -o CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o -c /<>/src/apps/convert_to_tiff.cpp [ 57%] Linking CXX executable ../../bin/relion_convert_star cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/convert_star.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/convert_star.dir/convert_star.cpp.o -o ../../bin/relion_convert_star ../../lib/librelion_lib.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/<>/build' [ 57%] Built target autopick_mpi /usr/bin/make -f src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build.make src/apps/CMakeFiles/convert_to_tiff_mpi.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/convert_to_tiff_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build.make src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build make[4]: Entering directory '/<>/build' [ 58%] Building CXX object src/apps/CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o -MF CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o.d -o CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o -c /<>/src/apps/convert_to_tiff_mpi.cpp In file included from /<>/src/image.h:455, from /<>/src/tiff_converter.h:24, from /<>/src/apps/convert_to_tiff.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /<>/src/image.h:455, from /<>/src/tiff_converter.h:24, from /<>/src/apps/convert_to_tiff_mpi.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 58%] Linking CXX executable ../../bin/relion_convert_to_tiff cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/convert_to_tiff.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o -o ../../bin/relion_convert_to_tiff ../../lib/librelion_lib.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 58%] Linking CXX executable ../../bin/relion_convert_to_tiff_mpi cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/convert_to_tiff_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o -o ../../bin/relion_convert_to_tiff_mpi ../../lib/librelion_lib.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In member function ‘deallocate’, inlined from ‘deallocate’ at /usr/include/c++/12/bits/alloc_traits.h:496:23, inlined from ‘_M_deallocate’ at /usr/include/c++/12/bits/stl_vector.h:387:19, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:366:15, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:733:7, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1963:1: /usr/include/c++/12/bits/new_allocator.h:158:33: warning: ‘operator delete’ called on pointer ‘_831’ with nonzero offset [1, 9223372036854775807] [-Wfree-nonheap-object] 158 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In member function ‘allocate’, inlined from ‘allocate’ at /usr/include/c++/12/bits/alloc_traits.h:464:28, inlined from ‘_M_allocate’ at /usr/include/c++/12/bits/stl_vector.h:378:33, inlined from ‘_M_create_storage’ at /usr/include/c++/12/bits/stl_vector.h:395:44, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:332:26, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:566:47, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1876:52: /usr/include/c++/12/bits/new_allocator.h:137:55: note: returned from ‘operator new’ 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In function ‘free_Tvector’, inlined from ‘brent’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:594:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘brent’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:579:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:767:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:24: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:768:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:18: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:769:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:13: note: declared here In function ‘free_Tvector’, inlined from ‘brent’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:594:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘brent’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:579:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:767:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:24: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:768:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:18: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:769:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:13: note: declared here In function ‘free_Tvector’, inlined from ‘brent’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:594:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘brent’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:579:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:767:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:24: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:768:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:18: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:769:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:13: note: declared here [ 59%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/manualpicker.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/manualpicker.cpp.o -MF CMakeFiles/relion_gui_lib.dir/__/manualpicker.cpp.o.d -o CMakeFiles/relion_gui_lib.dir/__/manualpicker.cpp.o -c /<>/src/manualpicker.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/obs_model.h:24, from /<>/src/manualpicker.h:43, from /<>/src/manualpicker.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In member function ‘deallocate’, inlined from ‘deallocate’ at /usr/include/c++/12/bits/alloc_traits.h:496:23, inlined from ‘_M_deallocate’ at /usr/include/c++/12/bits/stl_vector.h:387:19, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:366:15, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:733:7, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1963:1: /usr/include/c++/12/bits/new_allocator.h:158:33: warning: ‘operator delete’ called on pointer ‘_831’ with nonzero offset [1, 9223372036854775807] [-Wfree-nonheap-object] 158 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In member function ‘allocate’, inlined from ‘allocate’ at /usr/include/c++/12/bits/alloc_traits.h:464:28, inlined from ‘_M_allocate’ at /usr/include/c++/12/bits/stl_vector.h:378:33, inlined from ‘_M_create_storage’ at /usr/include/c++/12/bits/stl_vector.h:395:44, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:332:26, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:566:47, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1876:52: /usr/include/c++/12/bits/new_allocator.h:137:55: note: returned from ‘operator new’ 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ [ 59%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/cxxutils.cc.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/cxxutils.cc.o -MF CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/cxxutils.cc.o.d -o CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/cxxutils.cc.o -c /<>/src/Healpix_2.15a/cxxutils.cc [ 60%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o -MF CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o.d -o CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o -c /<>/src/Healpix_2.15a/healpix_base.cc [ 60%] Linking CXX static library ../../lib/librelion_gui_lib.a cd /<>/build/src/apps && /usr/bin/cmake -P CMakeFiles/relion_gui_lib.dir/cmake_clean_target.cmake cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/relion_gui_lib.dir/link.txt --verbose=1 /usr/bin/ar qc ../../lib/librelion_gui_lib.a CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o CMakeFiles/relion_gui_lib.dir/__/manualpicker.cpp.o CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/cxxutils.cc.o CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o /usr/bin/ranlib ../../lib/librelion_gui_lib.a make[4]: Leaving directory '/<>/build' [ 60%] Built target relion_gui_lib /usr/bin/make -f src/apps/CMakeFiles/ctf_mask_test.dir/build.make src/apps/CMakeFiles/ctf_mask_test.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/ctf_mask_test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/ctf_mask_test.dir/build.make src/apps/CMakeFiles/ctf_mask_test.dir/build make[4]: Entering directory '/<>/build' [ 60%] Building CXX object src/apps/CMakeFiles/ctf_mask_test.dir/ctf_mask_test.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/ctf_mask_test.dir/ctf_mask_test.cpp.o -MF CMakeFiles/ctf_mask_test.dir/ctf_mask_test.cpp.o.d -o CMakeFiles/ctf_mask_test.dir/ctf_mask_test.cpp.o -c /<>/src/apps/ctf_mask_test.cpp In file included from /<>/src/image.h:455, from /<>/src/apps/ctf_mask_test.cpp:7: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/<>/build' [ 60%] Built target convert_star /usr/bin/make -f src/apps/CMakeFiles/ctf_refine.dir/build.make src/apps/CMakeFiles/ctf_refine.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/ctf_refine.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/ctf_refine.dir/build.make src/apps/CMakeFiles/ctf_refine.dir/build make[4]: Entering directory '/<>/build' [ 60%] Building CXX object src/apps/CMakeFiles/ctf_refine.dir/ctf_refine.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/ctf_refine.dir/ctf_refine.cpp.o -MF CMakeFiles/ctf_refine.dir/ctf_refine.cpp.o.d -o CMakeFiles/ctf_refine.dir/ctf_refine.cpp.o -c /<>/src/apps/ctf_refine.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/obs_model.h:24, from /<>/src/jaz/ctf/ctf_refiner.h:24, from /<>/src/apps/ctf_refine.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 61%] Linking CXX executable ../../bin/relion_ctf_mask_test cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/ctf_mask_test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ctf_mask_test.dir/ctf_mask_test.cpp.o -o ../../bin/relion_ctf_mask_test ../../lib/librelion_lib.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/<>/build' [ 61%] Built target convert_to_tiff /usr/bin/make -f src/apps/CMakeFiles/ctf_refine_mpi.dir/build.make src/apps/CMakeFiles/ctf_refine_mpi.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/ctf_refine_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/ctf_refine_mpi.dir/build.make src/apps/CMakeFiles/ctf_refine_mpi.dir/build make[4]: Entering directory '/<>/build' [ 61%] Building CXX object src/apps/CMakeFiles/ctf_refine_mpi.dir/ctf_refine_mpi.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/ctf_refine_mpi.dir/ctf_refine_mpi.cpp.o -MF CMakeFiles/ctf_refine_mpi.dir/ctf_refine_mpi.cpp.o.d -o CMakeFiles/ctf_refine_mpi.dir/ctf_refine_mpi.cpp.o -c /<>/src/apps/ctf_refine_mpi.cpp [ 62%] Linking CXX executable ../../bin/relion_ctf_refine cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/ctf_refine.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ctf_refine.dir/ctf_refine.cpp.o -o ../../bin/relion_ctf_refine ../../lib/librelion_lib.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /<>/src/image.h:455, from /<>/src/jaz/obs_model.h:24, from /<>/src/jaz/ctf/ctf_refiner.h:24, from /<>/src/jaz/ctf/ctf_refiner_mpi.h:26, from /<>/src/apps/ctf_refine_mpi.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/<>/build' [ 62%] Built target convert_to_tiff_mpi /usr/bin/make -f src/apps/CMakeFiles/ctf_toolbox.dir/build.make src/apps/CMakeFiles/ctf_toolbox.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/ctf_toolbox.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/ctf_toolbox.dir/build.make src/apps/CMakeFiles/ctf_toolbox.dir/build make[4]: Entering directory '/<>/build' [ 63%] Building CXX object src/apps/CMakeFiles/ctf_toolbox.dir/ctf_toolbox.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/ctf_toolbox.dir/ctf_toolbox.cpp.o -MF CMakeFiles/ctf_toolbox.dir/ctf_toolbox.cpp.o.d -o CMakeFiles/ctf_toolbox.dir/ctf_toolbox.cpp.o -c /<>/src/apps/ctf_toolbox.cpp In file included from /<>/src/image.h:455, from /<>/src/apps/ctf_toolbox.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In function ‘free_Tvector’, inlined from ‘brent’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:594:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘brent’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:579:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here [ 63%] Linking CXX executable ../../bin/relion_ctf_refine_mpi cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/ctf_refine_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ctf_refine_mpi.dir/ctf_refine_mpi.cpp.o -o ../../bin/relion_ctf_refine_mpi ../../lib/librelion_lib.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:767:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:24: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:768:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:18: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:769:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:13: note: declared here [ 63%] Linking CXX executable ../../bin/relion_ctf_toolbox cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/ctf_toolbox.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ctf_toolbox.dir/ctf_toolbox.cpp.o -o ../../bin/relion_ctf_toolbox ../../lib/librelion_lib.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In function ‘free_Tvector’, inlined from ‘brent’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:594:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘brent’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:579:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:767:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:24: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:768:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:18: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:769:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:13: note: declared here In member function ‘deallocate’, inlined from ‘deallocate’ at /usr/include/c++/12/bits/alloc_traits.h:496:23, inlined from ‘_M_deallocate’ at /usr/include/c++/12/bits/stl_vector.h:387:19, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:366:15, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:733:7, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1963:1: /usr/include/c++/12/bits/new_allocator.h:158:33: warning: ‘operator delete’ called on pointer ‘_831’ with nonzero offset [1, 9223372036854775807] [-Wfree-nonheap-object] 158 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In member function ‘allocate’, inlined from ‘allocate’ at /usr/include/c++/12/bits/alloc_traits.h:464:28, inlined from ‘_M_allocate’ at /usr/include/c++/12/bits/stl_vector.h:378:33, inlined from ‘_M_create_storage’ at /usr/include/c++/12/bits/stl_vector.h:395:44, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:332:26, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:566:47, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1876:52: /usr/include/c++/12/bits/new_allocator.h:137:55: note: returned from ‘operator new’ 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In function ‘free_Tvector’, inlined from ‘brent’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:594:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘brent’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:579:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:767:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:24: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:768:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:18: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:769:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:13: note: declared here make[4]: Leaving directory '/<>/build' [ 63%] Built target ctf_mask_test /usr/bin/make -f src/apps/CMakeFiles/demodulate.dir/build.make src/apps/CMakeFiles/demodulate.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/demodulate.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/demodulate.dir/build.make src/apps/CMakeFiles/demodulate.dir/build make[4]: Entering directory '/<>/build' [ 63%] Building CXX object src/apps/CMakeFiles/demodulate.dir/demodulate.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/demodulate.dir/demodulate.cpp.o -MF CMakeFiles/demodulate.dir/demodulate.cpp.o.d -o CMakeFiles/demodulate.dir/demodulate.cpp.o -c /<>/src/apps/demodulate.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/vtk_helper.h:24, from /<>/src/apps/demodulate.cpp:1: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In function ‘free_Tvector’, inlined from ‘brent’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:594:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘brent’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:579:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:767:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:24: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:768:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:18: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:769:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:13: note: declared here make[4]: Leaving directory '/<>/build' [ 63%] Built target ctf_refine /usr/bin/make -f src/apps/CMakeFiles/display.dir/build.make src/apps/CMakeFiles/display.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/display.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/display.dir/build.make src/apps/CMakeFiles/display.dir/build make[4]: Entering directory '/<>/build' [ 63%] Building CXX object src/apps/CMakeFiles/display.dir/display.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/display.dir/display.cpp.o -MF CMakeFiles/display.dir/display.cpp.o.d -o CMakeFiles/display.dir/display.cpp.o -c /<>/src/apps/display.cpp In file included from /<>/src/image.h:455, from /<>/src/apps/display.cpp:25: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 64%] Linking CXX executable ../../bin/relion_display cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/display.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/display.dir/display.cpp.o -o ../../bin/relion_display ../../lib/librelion_lib.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gui_lib.a /usr/lib/powerpc64le-linux-gnu/libfltk_images.so /usr/lib/powerpc64le-linux-gnu/libfltk_forms.so /usr/lib/powerpc64le-linux-gnu/libfltk.so -lX11 -lm -ltiff ../../lib/librelion_lib.a -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/<>/build' [ 64%] Built target ctf_refine_mpi /usr/bin/make -f src/apps/CMakeFiles/estimate_gain.dir/build.make src/apps/CMakeFiles/estimate_gain.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/estimate_gain.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/estimate_gain.dir/build.make src/apps/CMakeFiles/estimate_gain.dir/build make[4]: Entering directory '/<>/build' [ 64%] Building CXX object src/apps/CMakeFiles/estimate_gain.dir/estimate_gain.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/estimate_gain.dir/estimate_gain.cpp.o -MF CMakeFiles/estimate_gain.dir/estimate_gain.cpp.o.d -o CMakeFiles/estimate_gain.dir/estimate_gain.cpp.o -c /<>/src/apps/estimate_gain.cpp [ 65%] Linking CXX executable ../../bin/relion_demodulate cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/demodulate.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/demodulate.dir/demodulate.cpp.o -o ../../bin/relion_demodulate ../../lib/librelion_lib.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /<>/src/image.h:455, from /<>/src/apps/estimate_gain.cpp:27: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/<>/build' [ 65%] Built target ctf_toolbox /usr/bin/make -f src/apps/CMakeFiles/external_reconstruct.dir/build.make src/apps/CMakeFiles/external_reconstruct.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/external_reconstruct.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/external_reconstruct.dir/build.make src/apps/CMakeFiles/external_reconstruct.dir/build make[4]: Entering directory '/<>/build' [ 66%] Building CXX object src/apps/CMakeFiles/external_reconstruct.dir/external_reconstruct.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/external_reconstruct.dir/external_reconstruct.cpp.o -MF CMakeFiles/external_reconstruct.dir/external_reconstruct.cpp.o.d -o CMakeFiles/external_reconstruct.dir/external_reconstruct.cpp.o -c /<>/src/apps/external_reconstruct.cpp In file included from /<>/src/image.h:455, from /<>/src/apps/external_reconstruct.cpp:24: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In member function ‘deallocate’, inlined from ‘deallocate’ at /usr/include/c++/12/bits/alloc_traits.h:496:23, inlined from ‘_M_deallocate’ at /usr/include/c++/12/bits/stl_vector.h:387:19, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:366:15, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:733:7, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1963:1: /usr/include/c++/12/bits/new_allocator.h:158:33: warning: ‘operator delete’ called on pointer ‘_831’ with nonzero offset [1, 9223372036854775807] [-Wfree-nonheap-object] 158 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In member function ‘allocate’, inlined from ‘allocate’ at /usr/include/c++/12/bits/alloc_traits.h:464:28, inlined from ‘_M_allocate’ at /usr/include/c++/12/bits/stl_vector.h:378:33, inlined from ‘_M_create_storage’ at /usr/include/c++/12/bits/stl_vector.h:395:44, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:332:26, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:566:47, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1876:52: /usr/include/c++/12/bits/new_allocator.h:137:55: note: returned from ‘operator new’ 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In function ‘free_Tvector’, inlined from ‘brent’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:594:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘brent’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:579:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:767:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:24: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:768:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:18: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:769:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:13: note: declared here [ 66%] Linking CXX executable ../../bin/relion_estimate_gain cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/estimate_gain.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/estimate_gain.dir/estimate_gain.cpp.o -o ../../bin/relion_estimate_gain ../../lib/librelion_lib.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In member function ‘deallocate’, inlined from ‘deallocate’ at /usr/include/c++/12/bits/alloc_traits.h:496:23, inlined from ‘_M_deallocate’ at /usr/include/c++/12/bits/stl_vector.h:387:19, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:366:15, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:733:7, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1963:1: /usr/include/c++/12/bits/new_allocator.h:158:33: warning: ‘operator delete’ called on pointer ‘_831’ with nonzero offset [1, 9223372036854775807] [-Wfree-nonheap-object] 158 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In member function ‘allocate’, inlined from ‘allocate’ at /usr/include/c++/12/bits/alloc_traits.h:464:28, inlined from ‘_M_allocate’ at /usr/include/c++/12/bits/stl_vector.h:378:33, inlined from ‘_M_create_storage’ at /usr/include/c++/12/bits/stl_vector.h:395:44, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:332:26, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:566:47, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1876:52: /usr/include/c++/12/bits/new_allocator.h:137:55: note: returned from ‘operator new’ 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ [ 66%] Linking CXX executable ../../bin/relion_external_reconstruct cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/external_reconstruct.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/external_reconstruct.dir/external_reconstruct.cpp.o -o ../../bin/relion_external_reconstruct ../../lib/librelion_lib.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In member function ‘deallocate’, inlined from ‘deallocate’ at /usr/include/c++/12/bits/alloc_traits.h:496:23, inlined from ‘_M_deallocate’ at /usr/include/c++/12/bits/stl_vector.h:387:19, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:366:15, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:733:7, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1963:1: /usr/include/c++/12/bits/new_allocator.h:158:33: warning: ‘operator delete’ called on pointer ‘_831’ with nonzero offset [1, 9223372036854775807] [-Wfree-nonheap-object] 158 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In member function ‘allocate’, inlined from ‘allocate’ at /usr/include/c++/12/bits/alloc_traits.h:464:28, inlined from ‘_M_allocate’ at /usr/include/c++/12/bits/stl_vector.h:378:33, inlined from ‘_M_create_storage’ at /usr/include/c++/12/bits/stl_vector.h:395:44, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:332:26, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:566:47, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1876:52: /usr/include/c++/12/bits/new_allocator.h:137:55: note: returned from ‘operator new’ 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function ‘deallocate’, inlined from ‘deallocate’ at /usr/include/c++/12/bits/alloc_traits.h:496:23, inlined from ‘_M_deallocate’ at /usr/include/c++/12/bits/stl_vector.h:387:19, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:366:15, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:733:7, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1963:1: /usr/include/c++/12/bits/new_allocator.h:158:33: warning: ‘operator delete’ called on pointer ‘_831’ with nonzero offset [1, 9223372036854775807] [-Wfree-nonheap-object] 158 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In member function ‘allocate’, inlined from ‘allocate’ at /usr/include/c++/12/bits/alloc_traits.h:464:28, inlined from ‘_M_allocate’ at /usr/include/c++/12/bits/stl_vector.h:378:33, inlined from ‘_M_create_storage’ at /usr/include/c++/12/bits/stl_vector.h:395:44, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:332:26, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:566:47, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1876:52: /usr/include/c++/12/bits/new_allocator.h:137:55: note: returned from ‘operator new’ 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In function ‘free_Tvector’, inlined from ‘brent’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:594:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘brent’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:579:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:767:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:24: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:768:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:18: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:769:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:13: note: declared here In function ‘free_Tvector’, inlined from ‘brent’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:594:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘brent’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:579:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:767:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:24: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:768:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:18: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:769:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:13: note: declared here In function ‘free_Tvector’, inlined from ‘brent’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:594:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘brent’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:579:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:767:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:24: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:768:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:18: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:769:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:13: note: declared here make[4]: Leaving directory '/<>/build' [ 66%] Built target display /usr/bin/make -f src/apps/CMakeFiles/find_tiltpairs.dir/build.make src/apps/CMakeFiles/find_tiltpairs.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/find_tiltpairs.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/find_tiltpairs.dir/build.make src/apps/CMakeFiles/find_tiltpairs.dir/build make[4]: Entering directory '/<>/build' [ 66%] Building CXX object src/apps/CMakeFiles/find_tiltpairs.dir/find_tiltpairs.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/find_tiltpairs.dir/find_tiltpairs.cpp.o -MF CMakeFiles/find_tiltpairs.dir/find_tiltpairs.cpp.o.d -o CMakeFiles/find_tiltpairs.dir/find_tiltpairs.cpp.o -c /<>/src/apps/find_tiltpairs.cpp make[4]: Leaving directory '/<>/build' [ 66%] Built target demodulate /usr/bin/make -f src/apps/CMakeFiles/flex_analyse.dir/build.make src/apps/CMakeFiles/flex_analyse.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/flex_analyse.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/flex_analyse.dir/build.make src/apps/CMakeFiles/flex_analyse.dir/build make[4]: Entering directory '/<>/build' [ 66%] Building CXX object src/apps/CMakeFiles/flex_analyse.dir/flex_analyse.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/flex_analyse.dir/flex_analyse.cpp.o -MF CMakeFiles/flex_analyse.dir/flex_analyse.cpp.o.d -o CMakeFiles/flex_analyse.dir/flex_analyse.cpp.o -c /<>/src/apps/flex_analyse.cpp In file included from /<>/src/image.h:455, from /<>/src/exp_model.h:24, from /<>/src/apps/../flex_analyser.h:24, from /<>/src/apps/flex_analyse.cpp:22: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 67%] Linking CXX executable ../../bin/relion_find_tiltpairs cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/find_tiltpairs.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/find_tiltpairs.dir/find_tiltpairs.cpp.o -o ../../bin/relion_find_tiltpairs ../../lib/librelion_lib.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 68%] Linking CXX executable ../../bin/relion_flex_analyse cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/flex_analyse.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/flex_analyse.dir/flex_analyse.cpp.o -o ../../bin/relion_flex_analyse ../../lib/librelion_lib.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In function ‘free_Tvector’, inlined from ‘gaussj’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.h:262:17, inlined from ‘solve’ at /usr/src/relion-3.1.3-3build1/src/matrix2d.h:1345:11, inlined from ‘optimiseTransformationMatrixContinuous’ at /usr/src/relion-3.1.3-3build1/src/apps/find_tiltpairs.cpp:377:8, inlined from ‘run’ at /usr/src/relion-3.1.3-3build1/src/apps/find_tiltpairs.cpp:425:42, inlined from ‘main’ at /usr/src/relion-3.1.3-3build1/src/apps/find_tiltpairs.cpp:480:10: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ipiv’ with nonzero offset 4 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.h: In function ‘main’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.h:198:26: note: declared here In function ‘free_Tvector’, inlined from ‘gaussj’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.h:263:17, inlined from ‘solve’ at /usr/src/relion-3.1.3-3build1/src/matrix2d.h:1345:11, inlined from ‘optimiseTransformationMatrixContinuous’ at /usr/src/relion-3.1.3-3build1/src/apps/find_tiltpairs.cpp:377:8, inlined from ‘run’ at /usr/src/relion-3.1.3-3build1/src/apps/find_tiltpairs.cpp:425:42, inlined from ‘main’ at /usr/src/relion-3.1.3-3build1/src/apps/find_tiltpairs.cpp:480:10: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘indxr’ with nonzero offset 4 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.h: In function ‘main’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.h:198:18: note: declared here In function ‘free_Tvector’, inlined from ‘gaussj’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.h:264:17, inlined from ‘solve’ at /usr/src/relion-3.1.3-3build1/src/matrix2d.h:1345:11, inlined from ‘optimiseTransformationMatrixContinuous’ at /usr/src/relion-3.1.3-3build1/src/apps/find_tiltpairs.cpp:377:8, inlined from ‘run’ at /usr/src/relion-3.1.3-3build1/src/apps/find_tiltpairs.cpp:425:42, inlined from ‘main’ at /usr/src/relion-3.1.3-3build1/src/apps/find_tiltpairs.cpp:480:10: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘indxc’ with nonzero offset 4 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.h: In function ‘main’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.h:198:10: note: declared here make[4]: Leaving directory '/<>/build' [ 68%] Built target estimate_gain /usr/bin/make -f src/apps/CMakeFiles/flex_analyse_mpi.dir/build.make src/apps/CMakeFiles/flex_analyse_mpi.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/flex_analyse_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/flex_analyse_mpi.dir/build.make src/apps/CMakeFiles/flex_analyse_mpi.dir/build make[4]: Entering directory '/<>/build' [ 68%] Building CXX object src/apps/CMakeFiles/flex_analyse_mpi.dir/flex_analyse_mpi.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/flex_analyse_mpi.dir/flex_analyse_mpi.cpp.o -MF CMakeFiles/flex_analyse_mpi.dir/flex_analyse_mpi.cpp.o.d -o CMakeFiles/flex_analyse_mpi.dir/flex_analyse_mpi.cpp.o -c /<>/src/apps/flex_analyse_mpi.cpp In file included from /<>/src/image.h:455, from /<>/src/exp_model.h:24, from /<>/src/apps/../flex_analyser.h:24, from /<>/src/apps/flex_analyse_mpi.cpp:22: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/<>/build' [ 68%] Built target external_reconstruct /usr/bin/make -f src/apps/CMakeFiles/helix_inimodel2d.dir/build.make src/apps/CMakeFiles/helix_inimodel2d.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/helix_inimodel2d.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/helix_inimodel2d.dir/build.make src/apps/CMakeFiles/helix_inimodel2d.dir/build make[4]: Entering directory '/<>/build' [ 69%] Building CXX object src/apps/CMakeFiles/helix_inimodel2d.dir/helix_inimodel2d.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/helix_inimodel2d.dir/helix_inimodel2d.cpp.o -MF CMakeFiles/helix_inimodel2d.dir/helix_inimodel2d.cpp.o.d -o CMakeFiles/helix_inimodel2d.dir/helix_inimodel2d.cpp.o -c /<>/src/apps/helix_inimodel2d.cpp In function ‘free_Tvector’, inlined from ‘brent’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:594:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘brent’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:579:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:767:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:24: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:768:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:18: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:769:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:13: note: declared here In file included from /<>/src/image.h:455, from /<>/src/apps/../helix_inimodel2d.h:29, from /<>/src/apps/helix_inimodel2d.cpp:22: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 69%] Linking CXX executable ../../bin/relion_helix_inimodel2d cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/helix_inimodel2d.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/helix_inimodel2d.dir/helix_inimodel2d.cpp.o -o ../../bin/relion_helix_inimodel2d ../../lib/librelion_lib.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 69%] Linking CXX executable ../../bin/relion_flex_analyse_mpi cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/flex_analyse_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/flex_analyse_mpi.dir/flex_analyse_mpi.cpp.o -o ../../bin/relion_flex_analyse_mpi ../../lib/librelion_lib.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In function ‘integerToString’, inlined from ‘writeOut’ at /usr/src/relion-3.1.3-3build1/src/helix_inimodel2d.cpp:1110:53: /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp: In member function ‘writeOut’: /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-2, -1] into destination object ‘aux’ of size 15 In function ‘integerToString’, inlined from ‘writeOut’ at /usr/src/relion-3.1.3-3build1/src/helix_inimodel2d.cpp:1110:53: /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp: In member function ‘writeOut’: /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-3, -2] into destination object ‘aux’ of size 15 In function ‘integerToString’, inlined from ‘writeOut’ at /usr/src/relion-3.1.3-3build1/src/helix_inimodel2d.cpp:1110:53: /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp: In member function ‘writeOut’: /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-4, -3] into destination object ‘aux’ of size 15 In function ‘integerToString’, inlined from ‘writeOut’ at /usr/src/relion-3.1.3-3build1/src/helix_inimodel2d.cpp:1110:53: /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp: In member function ‘writeOut’: /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-5, -4] into destination object ‘aux’ of size 15 In function ‘integerToString’, inlined from ‘writeOut’ at /usr/src/relion-3.1.3-3build1/src/helix_inimodel2d.cpp:1110:53: /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp: In member function ‘writeOut’: /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-6, -5] into destination object ‘aux’ of size 15 In function ‘integerToString’, inlined from ‘writeOut’ at /usr/src/relion-3.1.3-3build1/src/helix_inimodel2d.cpp:1110:53: /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp: In member function ‘writeOut’: /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-7, -6] into destination object ‘aux’ of size 15 In function ‘integerToString’, inlined from ‘writeOut’ at /usr/src/relion-3.1.3-3build1/src/helix_inimodel2d.cpp:1110:53: /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp: In member function ‘writeOut’: /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-8, -7] into destination object ‘aux’ of size 15 In member function ‘deallocate’, inlined from ‘deallocate’ at /usr/include/c++/12/bits/alloc_traits.h:496:23, inlined from ‘_M_deallocate’ at /usr/include/c++/12/bits/stl_vector.h:387:19, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:366:15, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:733:7, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1963:1: /usr/include/c++/12/bits/new_allocator.h:158:33: warning: ‘operator delete’ called on pointer ‘_831’ with nonzero offset [1, 9223372036854775807] [-Wfree-nonheap-object] 158 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In member function ‘allocate’, inlined from ‘allocate’ at /usr/include/c++/12/bits/alloc_traits.h:464:28, inlined from ‘_M_allocate’ at /usr/include/c++/12/bits/stl_vector.h:378:33, inlined from ‘_M_create_storage’ at /usr/include/c++/12/bits/stl_vector.h:395:44, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:332:26, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:566:47, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1876:52: /usr/include/c++/12/bits/new_allocator.h:137:55: note: returned from ‘operator new’ 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In function ‘free_Tvector’, inlined from ‘brent’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:594:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘brent’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:579:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:767:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:24: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:768:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:18: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:769:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:13: note: declared here /usr/src/relion-3.1.3-3build1/src/strings.cpp: In function ‘integerToString.constprop’: /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-2, -1] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-3, -2] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-4, -3] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-5, -4] into destination object ‘aux’ of size 15 In function ‘free_Tvector’, inlined from ‘brent’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:594:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘brent’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:579:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:767:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:24: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:768:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:18: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:769:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:13: note: declared here In function ‘free_Tvector’, inlined from ‘brent’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:594:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘brent’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:579:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:767:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:24: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:768:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:18: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:769:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:13: note: declared here /usr/src/relion-3.1.3-3build1/src/strings.cpp: In function ‘integerToString.constprop’: /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-2, -1] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-3, -2] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-4, -3] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-5, -4] into destination object ‘aux’ of size 15 make[4]: Leaving directory '/<>/build' [ 69%] Built target find_tiltpairs /usr/bin/make -f src/apps/CMakeFiles/helix_toolbox.dir/build.make src/apps/CMakeFiles/helix_toolbox.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/helix_toolbox.dir/DependInfo.cmake --color= In function ‘integerToString’, inlined from ‘outputSelectedParticles’ at /usr/src/relion-3.1.3-3build1/src/flex_analyser.cpp:695:47: make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/helix_toolbox.dir/build.make src/apps/CMakeFiles/helix_toolbox.dir/build /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp: In member function ‘outputSelectedParticles’: /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-2, -1] into destination object ‘aux’ of size 15 In function ‘integerToString’, inlined from ‘outputSelectedParticles’ at /usr/src/relion-3.1.3-3build1/src/flex_analyser.cpp:695:47: /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp: In member function ‘outputSelectedParticles’: /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-3, -2] into destination object ‘aux’ of size 15 In function ‘integerToString’, inlined from ‘outputSelectedParticles’ at /usr/src/relion-3.1.3-3build1/src/flex_analyser.cpp:695:47: /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp: In member function ‘outputSelectedParticles’: /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-4, -3] into destination object ‘aux’ of size 15 In function ‘integerToString’, inlined from ‘outputSelectedParticles’ at /usr/src/relion-3.1.3-3build1/src/flex_analyser.cpp:695:47: /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp: In member function ‘outputSelectedParticles’: /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-5, -4] into destination object ‘aux’ of size 15 In function ‘integerToString’, inlined from ‘outputSelectedParticles’ at /usr/src/relion-3.1.3-3build1/src/flex_analyser.cpp:695:47: /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp: In member function ‘outputSelectedParticles’: /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-6, -5] into destination object ‘aux’ of size 15 In function ‘integerToString’, inlined from ‘outputSelectedParticles’ at /usr/src/relion-3.1.3-3build1/src/flex_analyser.cpp:695:47: /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp: In member function ‘outputSelectedParticles’: /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-7, -6] into destination object ‘aux’ of size 15 In function ‘integerToString’, inlined from ‘outputSelectedParticles’ at /usr/src/relion-3.1.3-3build1/src/flex_analyser.cpp:695:47: /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp: In member function ‘outputSelectedParticles’: /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-8, -7] into destination object ‘aux’ of size 15 make[4]: Entering directory '/<>/build' [ 70%] Building CXX object src/apps/CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o -MF CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o.d -o CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o -c /<>/src/apps/helix_toolbox.cpp In file included from /<>/src/image.h:455, from /<>/src/helix.h:30, from /<>/src/apps/helix_toolbox.cpp:22: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In function ‘integerToString’, inlined from ‘outputSelectedParticles’ at /usr/src/relion-3.1.3-3build1/src/flex_analyser.cpp:695:47: /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp: In member function ‘outputSelectedParticles’: /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-2, -1] into destination object ‘aux’ of size 15 In function ‘integerToString’, inlined from ‘outputSelectedParticles’ at /usr/src/relion-3.1.3-3build1/src/flex_analyser.cpp:695:47: /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp: In member function ‘outputSelectedParticles’: /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-3, -2] into destination object ‘aux’ of size 15 In function ‘integerToString’, inlined from ‘outputSelectedParticles’ at /usr/src/relion-3.1.3-3build1/src/flex_analyser.cpp:695:47: /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp: In member function ‘outputSelectedParticles’: /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-4, -3] into destination object ‘aux’ of size 15 In function ‘integerToString’, inlined from ‘outputSelectedParticles’ at /usr/src/relion-3.1.3-3build1/src/flex_analyser.cpp:695:47: /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp: In member function ‘outputSelectedParticles’: /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-5, -4] into destination object ‘aux’ of size 15 In function ‘integerToString’, inlined from ‘outputSelectedParticles’ at /usr/src/relion-3.1.3-3build1/src/flex_analyser.cpp:695:47: /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp: In member function ‘outputSelectedParticles’: /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-6, -5] into destination object ‘aux’ of size 15 In function ‘integerToString’, inlined from ‘outputSelectedParticles’ at /usr/src/relion-3.1.3-3build1/src/flex_analyser.cpp:695:47: /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp: In member function ‘outputSelectedParticles’: /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-7, -6] into destination object ‘aux’ of size 15 In function ‘integerToString’, inlined from ‘outputSelectedParticles’ at /usr/src/relion-3.1.3-3build1/src/flex_analyser.cpp:695:47: /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp: In member function ‘outputSelectedParticles’: /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-8, -7] into destination object ‘aux’ of size 15 make[4]: Leaving directory '/<>/build' [ 70%] Built target helix_inimodel2d /usr/bin/make -f src/apps/CMakeFiles/image_handler.dir/build.make src/apps/CMakeFiles/image_handler.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/image_handler.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/image_handler.dir/build.make src/apps/CMakeFiles/image_handler.dir/build make[4]: Entering directory '/<>/build' [ 70%] Building CXX object src/apps/CMakeFiles/image_handler.dir/image_handler.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/image_handler.dir/image_handler.cpp.o -MF CMakeFiles/image_handler.dir/image_handler.cpp.o.d -o CMakeFiles/image_handler.dir/image_handler.cpp.o -c /<>/src/apps/image_handler.cpp make[4]: Leaving directory '/<>/build' [ 70%] Built target flex_analyse /usr/bin/make -f src/apps/CMakeFiles/import.dir/build.make src/apps/CMakeFiles/import.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/import.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/import.dir/build.make src/apps/CMakeFiles/import.dir/build make[4]: Entering directory '/<>/build' [ 70%] Building CXX object src/apps/CMakeFiles/import.dir/import.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/import.dir/import.cpp.o -MF CMakeFiles/import.dir/import.cpp.o.d -o CMakeFiles/import.dir/import.cpp.o -c /<>/src/apps/import.cpp In file included from /<>/src/image.h:455, from /<>/src/apps/image_handler.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /<>/src/image.h:455, from /<>/src/jaz/obs_model.h:24, from /<>/src/apps/import.cpp:22: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 70%] Linking CXX executable ../../bin/relion_helix_toolbox cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/helix_toolbox.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o -o ../../bin/relion_helix_toolbox ../../lib/librelion_lib.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 70%] Linking CXX executable ../../bin/relion_import cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/import.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/import.dir/import.cpp.o -o ../../bin/relion_import ../../lib/librelion_lib.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/<>/build' [ 70%] Built target flex_analyse_mpi /usr/bin/make -f src/apps/CMakeFiles/localsym.dir/build.make src/apps/CMakeFiles/localsym.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/localsym.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/localsym.dir/build.make src/apps/CMakeFiles/localsym.dir/build make[4]: Entering directory '/<>/build' [ 71%] Building CXX object src/apps/CMakeFiles/localsym.dir/localsym.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/localsym.dir/localsym.cpp.o -MF CMakeFiles/localsym.dir/localsym.cpp.o.d -o CMakeFiles/localsym.dir/localsym.cpp.o -c /<>/src/apps/localsym.cpp In file included from /<>/src/image.h:455, from /<>/src/local_symmetry.h:30, from /<>/src/apps/localsym.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 71%] Linking CXX executable ../../bin/relion_localsym cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/localsym.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/localsym.dir/localsym.cpp.o -o ../../bin/relion_localsym ../../lib/librelion_lib.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In member function ‘deallocate’, inlined from ‘deallocate’ at /usr/include/c++/12/bits/alloc_traits.h:496:23, inlined from ‘_M_deallocate’ at /usr/include/c++/12/bits/stl_vector.h:387:19, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:366:15, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:733:7, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1963:1: /usr/include/c++/12/bits/new_allocator.h:158:33: warning: ‘operator delete’ called on pointer ‘_831’ with nonzero offset [1, 9223372036854775807] [-Wfree-nonheap-object] 158 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In member function ‘allocate’, inlined from ‘allocate’ at /usr/include/c++/12/bits/alloc_traits.h:464:28, inlined from ‘_M_allocate’ at /usr/include/c++/12/bits/stl_vector.h:378:33, inlined from ‘_M_create_storage’ at /usr/include/c++/12/bits/stl_vector.h:395:44, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:332:26, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:566:47, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1876:52: /usr/include/c++/12/bits/new_allocator.h:137:55: note: returned from ‘operator new’ 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In function ‘free_Tvector’, inlined from ‘brent’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:594:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘brent’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:579:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:767:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:24: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:768:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:18: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:769:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:13: note: declared here In member function ‘deallocate’, inlined from ‘deallocate’ at /usr/include/c++/12/bits/alloc_traits.h:496:23, inlined from ‘_M_deallocate’ at /usr/include/c++/12/bits/stl_vector.h:387:19, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:366:15, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:733:7, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1963:1: /usr/include/c++/12/bits/new_allocator.h:158:33: warning: ‘operator delete’ called on pointer ‘_831’ with nonzero offset [1, 9223372036854775807] [-Wfree-nonheap-object] 158 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In member function ‘allocate’, inlined from ‘allocate’ at /usr/include/c++/12/bits/alloc_traits.h:464:28, inlined from ‘_M_allocate’ at /usr/include/c++/12/bits/stl_vector.h:378:33, inlined from ‘_M_create_storage’ at /usr/include/c++/12/bits/stl_vector.h:395:44, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:332:26, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:566:47, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1876:52: /usr/include/c++/12/bits/new_allocator.h:137:55: note: returned from ‘operator new’ 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function ‘deallocate’, inlined from ‘deallocate’ at /usr/include/c++/12/bits/alloc_traits.h:496:23, inlined from ‘_M_deallocate’ at /usr/include/c++/12/bits/stl_vector.h:387:19, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:366:15, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:733:7, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1963:1: /usr/include/c++/12/bits/new_allocator.h:158:33: warning: ‘operator delete’ called on pointer ‘_831’ with nonzero offset [1, 9223372036854775807] [-Wfree-nonheap-object] 158 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In member function ‘allocate’, inlined from ‘allocate’ at /usr/include/c++/12/bits/alloc_traits.h:464:28, inlined from ‘_M_allocate’ at /usr/include/c++/12/bits/stl_vector.h:378:33, inlined from ‘_M_create_storage’ at /usr/include/c++/12/bits/stl_vector.h:395:44, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:332:26, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:566:47, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1876:52: /usr/include/c++/12/bits/new_allocator.h:137:55: note: returned from ‘operator new’ 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In function ‘free_Tvector’, inlined from ‘brent’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:594:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘brent’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:579:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:767:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:24: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:768:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:18: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:769:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:13: note: declared here In function ‘free_Tvector’, inlined from ‘brent’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:594:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘brent’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:579:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:767:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:24: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:768:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:18: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:769:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:13: note: declared here [ 72%] Linking CXX executable ../../bin/relion_image_handler cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/image_handler.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/image_handler.dir/image_handler.cpp.o -o ../../bin/relion_image_handler ../../lib/librelion_lib.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff /usr/src/relion-3.1.3-3build1/src/strings.cpp: In function ‘integerToString.constprop’: /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-2, -1] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-3, -2] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-4, -3] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-5, -4] into destination object ‘aux’ of size 15 In member function ‘deallocate’, inlined from ‘deallocate’ at /usr/include/c++/12/bits/alloc_traits.h:496:23, inlined from ‘_M_deallocate’ at /usr/include/c++/12/bits/stl_vector.h:387:19, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:366:15, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:733:7, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1963:1: /usr/include/c++/12/bits/new_allocator.h:158:33: warning: ‘operator delete’ called on pointer ‘_831’ with nonzero offset [1, 9223372036854775807] [-Wfree-nonheap-object] 158 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In member function ‘allocate’, inlined from ‘allocate’ at /usr/include/c++/12/bits/alloc_traits.h:464:28, inlined from ‘_M_allocate’ at /usr/include/c++/12/bits/stl_vector.h:378:33, inlined from ‘_M_create_storage’ at /usr/include/c++/12/bits/stl_vector.h:395:44, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:332:26, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:566:47, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1876:52: /usr/include/c++/12/bits/new_allocator.h:137:55: note: returned from ‘operator new’ 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /usr/src/relion-3.1.3-3build1/src/strings.cpp: In function ‘integerToString.constprop’: /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-2, -1] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-3, -2] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-4, -3] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-5, -4] into destination object ‘aux’ of size 15 In function ‘free_Tvector’, inlined from ‘brent’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:594:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘brent’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:579:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:767:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:24: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:768:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:18: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:769:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:13: note: declared here make[4]: Leaving directory '/<>/build' [ 72%] Built target helix_toolbox /usr/bin/make -f src/apps/CMakeFiles/localsym_mpi.dir/build.make src/apps/CMakeFiles/localsym_mpi.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/localsym_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/localsym_mpi.dir/build.make src/apps/CMakeFiles/localsym_mpi.dir/build make[4]: Entering directory '/<>/build' [ 73%] Building CXX object src/apps/CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o -MF CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o.d -o CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o -c /<>/src/apps/localsym_mpi.cpp make[4]: Leaving directory '/<>/build' [ 73%] Built target import /usr/bin/make -f src/apps/CMakeFiles/relion.dir/build.make src/apps/CMakeFiles/relion.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/relion.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/relion.dir/build.make src/apps/CMakeFiles/relion.dir/build make[4]: Entering directory '/<>/build' [ 73%] Building CXX object src/apps/CMakeFiles/relion.dir/maingui.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion.dir/maingui.cpp.o -MF CMakeFiles/relion.dir/maingui.cpp.o.d -o CMakeFiles/relion.dir/maingui.cpp.o -c /<>/src/apps/maingui.cpp In file included from /<>/src/image.h:455, from /<>/src/local_symmetry.h:30, from /<>/src/local_symmetry_mpi.h:5, from /<>/src/apps/localsym_mpi.cpp:1: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /<>/src/image.h:455, from /<>/src/jaz/obs_model.h:24, from /<>/src/scheduler.h:26, from /<>/src/gui_mainwindow.h:28, from /<>/src/apps/maingui.cpp:23: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 73%] Linking CXX executable ../../bin/relion_localsym_mpi cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/localsym_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o -o ../../bin/relion_localsym_mpi ../../lib/librelion_lib.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 74%] Linking CXX executable ../../bin/relion cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/relion.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/relion.dir/maingui.cpp.o -o ../../bin/relion ../../lib/librelion_lib.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gui_lib.a /usr/lib/powerpc64le-linux-gnu/libfltk_images.so /usr/lib/powerpc64le-linux-gnu/libfltk_forms.so /usr/lib/powerpc64le-linux-gnu/libfltk.so -lX11 -lm -ltiff ../../lib/librelion_lib.a -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/<>/build' [ 74%] Built target localsym /usr/bin/make -f src/apps/CMakeFiles/manualpick.dir/build.make src/apps/CMakeFiles/manualpick.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/manualpick.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/manualpick.dir/build.make src/apps/CMakeFiles/manualpick.dir/build make[4]: Entering directory '/<>/build' [ 74%] Building CXX object src/apps/CMakeFiles/manualpick.dir/manualpick.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/manualpick.dir/manualpick.cpp.o -MF CMakeFiles/manualpick.dir/manualpick.cpp.o.d -o CMakeFiles/manualpick.dir/manualpick.cpp.o -c /<>/src/apps/manualpick.cpp In file included from /<>/src/image.h:455, from /<>/src/apps/manualpick.cpp:25: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In member function ‘deallocate’, inlined from ‘deallocate’ at /usr/include/c++/12/bits/alloc_traits.h:496:23, inlined from ‘_M_deallocate’ at /usr/include/c++/12/bits/stl_vector.h:387:19, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:366:15, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:733:7, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1963:1: /usr/include/c++/12/bits/new_allocator.h:158:33: warning: ‘operator delete’ called on pointer ‘_831’ with nonzero offset [1, 9223372036854775807] [-Wfree-nonheap-object] 158 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In member function ‘allocate’, inlined from ‘allocate’ at /usr/include/c++/12/bits/alloc_traits.h:464:28, inlined from ‘_M_allocate’ at /usr/include/c++/12/bits/stl_vector.h:378:33, inlined from ‘_M_create_storage’ at /usr/include/c++/12/bits/stl_vector.h:395:44, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:332:26, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:566:47, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1876:52: /usr/include/c++/12/bits/new_allocator.h:137:55: note: returned from ‘operator new’ 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /usr/src/relion-3.1.3-3build1/src/strings.cpp: In function ‘integerToString.constprop’: /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-2, -1] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-3, -2] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-4, -3] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-5, -4] into destination object ‘aux’ of size 15 [ 75%] Linking CXX executable ../../bin/relion_manualpick cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/manualpick.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/manualpick.dir/manualpick.cpp.o -o ../../bin/relion_manualpick ../../lib/librelion_lib.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gui_lib.a /usr/lib/powerpc64le-linux-gnu/libfltk_images.so /usr/lib/powerpc64le-linux-gnu/libfltk_forms.so /usr/lib/powerpc64le-linux-gnu/libfltk.so -lX11 -lm -ltiff ../../lib/librelion_lib.a -lfftw3f -lfftw3 -ltiff /usr/src/relion-3.1.3-3build1/src/strings.cpp: In function ‘integerToString.constprop’: /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-2, -1] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-3, -2] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-4, -3] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-5, -4] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-6, -5] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-7, -6] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-8, -7] into destination object ‘aux’ of size 15 In function ‘free_Tvector’, inlined from ‘brent’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:594:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘brent’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:579:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:767:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:24: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:768:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:18: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:769:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:13: note: declared here make[4]: Leaving directory '/<>/build' [ 75%] Built target image_handler /usr/bin/make -f src/apps/CMakeFiles/mask_create.dir/build.make src/apps/CMakeFiles/mask_create.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/mask_create.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/mask_create.dir/build.make src/apps/CMakeFiles/mask_create.dir/build make[4]: Entering directory '/<>/build' [ 75%] Building CXX object src/apps/CMakeFiles/mask_create.dir/mask_create.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/mask_create.dir/mask_create.cpp.o -MF CMakeFiles/mask_create.dir/mask_create.cpp.o.d -o CMakeFiles/mask_create.dir/mask_create.cpp.o -c /<>/src/apps/mask_create.cpp In file included from /<>/src/image.h:455, from /<>/src/apps/mask_create.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In member function ‘deallocate’, inlined from ‘deallocate’ at /usr/include/c++/12/bits/alloc_traits.h:496:23, inlined from ‘_M_deallocate’ at /usr/include/c++/12/bits/stl_vector.h:387:19, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:366:15, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:733:7, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1963:1: /usr/include/c++/12/bits/new_allocator.h:158:33: warning: ‘operator delete’ called on pointer ‘_831’ with nonzero offset [1, 9223372036854775807] [-Wfree-nonheap-object] 158 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In member function ‘allocate’, inlined from ‘allocate’ at /usr/include/c++/12/bits/alloc_traits.h:464:28, inlined from ‘_M_allocate’ at /usr/include/c++/12/bits/stl_vector.h:378:33, inlined from ‘_M_create_storage’ at /usr/include/c++/12/bits/stl_vector.h:395:44, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:332:26, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:566:47, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1876:52: /usr/include/c++/12/bits/new_allocator.h:137:55: note: returned from ‘operator new’ 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ [ 75%] Linking CXX executable ../../bin/relion_mask_create cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/mask_create.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/mask_create.dir/mask_create.cpp.o -o ../../bin/relion_mask_create ../../lib/librelion_lib.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In function ‘free_Tvector’, inlined from ‘brent’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:594:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘brent’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:579:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:767:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:24: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:768:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:18: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:769:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:13: note: declared here In function ‘free_Tvector’, inlined from ‘brent’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:594:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘brent’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:579:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:767:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:24: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:768:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:18: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:769:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:13: note: declared here In function ‘free_Tvector’, inlined from ‘brent’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:594:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘brent’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:579:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:767:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:24: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:768:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:18: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:769:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:13: note: declared here In member function ‘deallocate’, inlined from ‘deallocate’ at /usr/include/c++/12/bits/alloc_traits.h:496:23, inlined from ‘_M_deallocate’ at /usr/include/c++/12/bits/stl_vector.h:387:19, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:366:15, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:733:7, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1963:1: /usr/include/c++/12/bits/new_allocator.h:158:33: warning: ‘operator delete’ called on pointer ‘_831’ with nonzero offset [1, 9223372036854775807] [-Wfree-nonheap-object] 158 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In member function ‘allocate’, inlined from ‘allocate’ at /usr/include/c++/12/bits/alloc_traits.h:464:28, inlined from ‘_M_allocate’ at /usr/include/c++/12/bits/stl_vector.h:378:33, inlined from ‘_M_create_storage’ at /usr/include/c++/12/bits/stl_vector.h:395:44, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:332:26, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:566:47, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1876:52: /usr/include/c++/12/bits/new_allocator.h:137:55: note: returned from ‘operator new’ 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /usr/src/relion-3.1.3-3build1/src/strings.cpp: In function ‘integerToString.constprop’: /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-2, -1] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-3, -2] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-4, -3] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-5, -4] into destination object ‘aux’ of size 15 make[4]: Leaving directory '/<>/build' [ 75%] Built target localsym_mpi /usr/bin/make -f src/apps/CMakeFiles/merge_particles.dir/build.make src/apps/CMakeFiles/merge_particles.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/merge_particles.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/merge_particles.dir/build.make src/apps/CMakeFiles/merge_particles.dir/build make[4]: Entering directory '/<>/build' [ 76%] Building CXX object src/apps/CMakeFiles/merge_particles.dir/merge_particles.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/merge_particles.dir/merge_particles.cpp.o -MF CMakeFiles/merge_particles.dir/merge_particles.cpp.o.d -o CMakeFiles/merge_particles.dir/merge_particles.cpp.o -c /<>/src/apps/merge_particles.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/io/star_converter.h:5, from /<>/src/apps/merge_particles.cpp:2: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/<>/build' [ 76%] Built target manualpick /usr/bin/make -f src/apps/CMakeFiles/motion_refine.dir/build.make src/apps/CMakeFiles/motion_refine.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/motion_refine.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/motion_refine.dir/build.make src/apps/CMakeFiles/motion_refine.dir/build make[4]: Entering directory '/<>/build' [ 77%] Building CXX object src/apps/CMakeFiles/motion_refine.dir/motion_refine.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/motion_refine.dir/motion_refine.cpp.o -MF CMakeFiles/motion_refine.dir/motion_refine.cpp.o.d -o CMakeFiles/motion_refine.dir/motion_refine.cpp.o -c /<>/src/apps/motion_refine.cpp [ 77%] Linking CXX executable ../../bin/relion_merge_particles cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/merge_particles.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/merge_particles.dir/merge_particles.cpp.o -o ../../bin/relion_merge_particles ../../lib/librelion_lib.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /<>/src/image.h:455, from /<>/src/jaz/obs_model.h:24, from /<>/src/ctf.h:50, from /<>/src/jaz/motion/motion_refiner.h:25, from /<>/src/apps/motion_refine.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In function ‘free_Tvector’, inlined from ‘brent’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:594:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘brent’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:579:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here [ 77%] Linking CXX executable ../../bin/relion_motion_refine In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:767:25: cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/motion_refine.dir/link.txt --verbose=1 /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:24: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:768:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:18: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:769:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:13: note: declared here /usr/bin/mpicxx -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/motion_refine.dir/motion_refine.cpp.o -o ../../bin/relion_motion_refine ../../lib/librelion_lib.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/<>/build' [ 77%] Built target relion /usr/bin/make -f src/apps/CMakeFiles/motion_refine_mpi.dir/build.make src/apps/CMakeFiles/motion_refine_mpi.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/motion_refine_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/motion_refine_mpi.dir/build.make src/apps/CMakeFiles/motion_refine_mpi.dir/build make[4]: Entering directory '/<>/build' [ 77%] Building CXX object src/apps/CMakeFiles/motion_refine_mpi.dir/motion_refine_mpi.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/motion_refine_mpi.dir/motion_refine_mpi.cpp.o -MF CMakeFiles/motion_refine_mpi.dir/motion_refine_mpi.cpp.o.d -o CMakeFiles/motion_refine_mpi.dir/motion_refine_mpi.cpp.o -c /<>/src/apps/motion_refine_mpi.cpp In member function ‘deallocate’, inlined from ‘deallocate’ at /usr/include/c++/12/bits/alloc_traits.h:496:23, inlined from ‘_M_deallocate’ at /usr/include/c++/12/bits/stl_vector.h:387:19, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:366:15, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:733:7, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1963:1: /usr/include/c++/12/bits/new_allocator.h:158:33: warning: ‘operator delete’ called on pointer ‘_831’ with nonzero offset [1, 9223372036854775807] [-Wfree-nonheap-object] 158 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In member function ‘allocate’, inlined from ‘allocate’ at /usr/include/c++/12/bits/alloc_traits.h:464:28, inlined from ‘_M_allocate’ at /usr/include/c++/12/bits/stl_vector.h:378:33, inlined from ‘_M_create_storage’ at /usr/include/c++/12/bits/stl_vector.h:395:44, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:332:26, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:566:47, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1876:52: /usr/include/c++/12/bits/new_allocator.h:137:55: note: returned from ‘operator new’ 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In file included from /<>/src/image.h:455, from /<>/src/jaz/obs_model.h:24, from /<>/src/ctf.h:50, from /<>/src/jaz/motion/motion_refiner.h:25, from /<>/src/jaz/motion/motion_refiner_mpi.h:27, from /<>/src/apps/motion_refine_mpi.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/<>/build' [ 77%] Built target mask_create /usr/bin/make -f src/apps/CMakeFiles/mrc2vtk.dir/build.make src/apps/CMakeFiles/mrc2vtk.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/mrc2vtk.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/mrc2vtk.dir/build.make src/apps/CMakeFiles/mrc2vtk.dir/build make[4]: Entering directory '/<>/build' [ 77%] Building CXX object src/apps/CMakeFiles/mrc2vtk.dir/mrc2vtk.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/mrc2vtk.dir/mrc2vtk.cpp.o -MF CMakeFiles/mrc2vtk.dir/mrc2vtk.cpp.o.d -o CMakeFiles/mrc2vtk.dir/mrc2vtk.cpp.o -c /<>/src/apps/mrc2vtk.cpp In file included from /<>/src/image.h:455, from /<>/src/apps/mrc2vtk.cpp:1: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In function ‘free_Tvector’, inlined from ‘brent’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:594:25: [ 78%] Linking CXX executable ../../bin/relion_motion_refine_mpi /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘brent’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:579:13: note: declared here cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/motion_refine_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/motion_refine_mpi.dir/motion_refine_mpi.cpp.o -o ../../bin/relion_motion_refine_mpi ../../lib/librelion_lib.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:767:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:24: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:768:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:18: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:769:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:13: note: declared here [ 78%] Linking CXX executable ../../bin/relion_mrc2vtk cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/mrc2vtk.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/mrc2vtk.dir/mrc2vtk.cpp.o -o ../../bin/relion_mrc2vtk ../../lib/librelion_lib.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In member function ‘deallocate’, inlined from ‘deallocate’ at /usr/include/c++/12/bits/alloc_traits.h:496:23, inlined from ‘_M_deallocate’ at /usr/include/c++/12/bits/stl_vector.h:387:19, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:366:15, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:733:7, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1963:1: /usr/include/c++/12/bits/new_allocator.h:158:33: warning: ‘operator delete’ called on pointer ‘_831’ with nonzero offset [1, 9223372036854775807] [-Wfree-nonheap-object] 158 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In member function ‘allocate’, inlined from ‘allocate’ at /usr/include/c++/12/bits/alloc_traits.h:464:28, inlined from ‘_M_allocate’ at /usr/include/c++/12/bits/stl_vector.h:378:33, inlined from ‘_M_create_storage’ at /usr/include/c++/12/bits/stl_vector.h:395:44, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:332:26, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:566:47, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1876:52: /usr/include/c++/12/bits/new_allocator.h:137:55: note: returned from ‘operator new’ 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In function ‘free_Tvector’, inlined from ‘brent’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:594:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘brent’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:579:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:767:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:24: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:768:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:18: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:769:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:13: note: declared here make[4]: Leaving directory '/<>/build' [ 78%] Built target merge_particles /usr/bin/make -f src/apps/CMakeFiles/particle_FCC.dir/build.make src/apps/CMakeFiles/particle_FCC.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/particle_FCC.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/particle_FCC.dir/build.make src/apps/CMakeFiles/particle_FCC.dir/build make[4]: Entering directory '/<>/build' [ 79%] Building CXX object src/apps/CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o -MF CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o.d -o CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o -c /<>/src/apps/particle_FCC.cpp In file included from /<>/src/image.h:455, from /<>/src/apps/particle_FCC.cpp:7: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 79%] Linking CXX executable ../../bin/relion_particle_FCC cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_FCC.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o -o ../../bin/relion_particle_FCC ../../lib/librelion_lib.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/<>/build' [ 79%] Built target motion_refine /usr/bin/make -f src/apps/CMakeFiles/particle_reposition.dir/build.make src/apps/CMakeFiles/particle_reposition.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/particle_reposition.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/particle_reposition.dir/build.make src/apps/CMakeFiles/particle_reposition.dir/build make[4]: Entering directory '/<>/build' [ 80%] Building CXX object src/apps/CMakeFiles/particle_reposition.dir/particle_reposition.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/particle_reposition.dir/particle_reposition.cpp.o -MF CMakeFiles/particle_reposition.dir/particle_reposition.cpp.o.d -o CMakeFiles/particle_reposition.dir/particle_reposition.cpp.o -c /<>/src/apps/particle_reposition.cpp make[4]: Leaving directory '/<>/build' [ 80%] Built target mrc2vtk /usr/bin/make -f src/apps/CMakeFiles/particle_select.dir/build.make src/apps/CMakeFiles/particle_select.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/particle_select.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/particle_select.dir/build.make src/apps/CMakeFiles/particle_select.dir/build make[4]: Entering directory '/<>/build' [ 80%] Building CXX object src/apps/CMakeFiles/particle_select.dir/particle_select.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/particle_select.dir/particle_select.cpp.o -MF CMakeFiles/particle_select.dir/particle_select.cpp.o.d -o CMakeFiles/particle_select.dir/particle_select.cpp.o -c /<>/src/apps/particle_select.cpp In file included from /<>/src/image.h:455, from /<>/src/projector.h:25, from /<>/src/ml_model.h:23, from /<>/src/ml_optimiser.h:35, from /<>/src/apps/particle_reposition.cpp:22: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /<>/src/image.h:455, from /<>/src/jaz/obs_model.h:24, from /<>/src/ctf.h:50, from /<>/src/jaz/stack_helper.h:24, from /<>/src/apps/particle_select.cpp:1: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In function ‘free_Tvector’, inlined from ‘brent’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:594:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘brent’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:579:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:767:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:24: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:768:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:18: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:769:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:13: note: declared here [ 81%] Linking CXX executable ../../bin/relion_particle_select cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_select.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/particle_select.dir/particle_select.cpp.o -o ../../bin/relion_particle_select ../../lib/librelion_lib.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In function ‘free_Tvector’, inlined from ‘brent’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:594:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘brent’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:579:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:767:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:24: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:768:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:18: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:769:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:13: note: declared here make[4]: Leaving directory '/<>/build' [ 81%] Built target motion_refine_mpi /usr/bin/make -f src/apps/CMakeFiles/particle_subtract.dir/build.make src/apps/CMakeFiles/particle_subtract.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/particle_subtract.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/particle_subtract.dir/build.make src/apps/CMakeFiles/particle_subtract.dir/build make[4]: Entering directory '/<>/build' [ 81%] Building CXX object src/apps/CMakeFiles/particle_subtract.dir/particle_subtract.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/particle_subtract.dir/particle_subtract.cpp.o -MF CMakeFiles/particle_subtract.dir/particle_subtract.cpp.o.d -o CMakeFiles/particle_subtract.dir/particle_subtract.cpp.o -c /<>/src/apps/particle_subtract.cpp In member function ‘deallocate’, inlined from ‘deallocate’ at /usr/include/c++/12/bits/alloc_traits.h:496:23, inlined from ‘_M_deallocate’ at /usr/include/c++/12/bits/stl_vector.h:387:19, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:366:15, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:733:7, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1963:1: /usr/include/c++/12/bits/new_allocator.h:158:33: warning: ‘operator delete’ called on pointer ‘_831’ with nonzero offset [1, 9223372036854775807] [-Wfree-nonheap-object] 158 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In member function ‘allocate’, inlined from ‘allocate’ at /usr/include/c++/12/bits/alloc_traits.h:464:28, inlined from ‘_M_allocate’ at /usr/include/c++/12/bits/stl_vector.h:378:33, inlined from ‘_M_create_storage’ at /usr/include/c++/12/bits/stl_vector.h:395:44, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:332:26, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:566:47, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1876:52: /usr/include/c++/12/bits/new_allocator.h:137:55: note: returned from ‘operator new’ 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In file included from /<>/src/image.h:455, from /<>/src/projector.h:25, from /<>/src/ml_model.h:23, from /<>/src/ml_optimiser.h:35, from /<>/src/apps/../particle_subtractor.h:24, from /<>/src/apps/particle_subtract.cpp:22: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In function ‘free_Tvector’, inlined from ‘brent’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:594:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘brent’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:579:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:767:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:24: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:768:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:18: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:769:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:13: note: declared here [ 81%] Linking CXX executable ../../bin/relion_particle_reposition cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_reposition.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/particle_reposition.dir/particle_reposition.cpp.o -o ../../bin/relion_particle_reposition ../../lib/librelion_lib.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 82%] Linking CXX executable ../../bin/relion_particle_subtract cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_subtract.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/particle_subtract.dir/particle_subtract.cpp.o -o ../../bin/relion_particle_subtract ../../lib/librelion_lib.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/<>/build' [ 82%] Built target particle_FCC /usr/bin/make -f src/apps/CMakeFiles/particle_subtract_mpi.dir/build.make src/apps/CMakeFiles/particle_subtract_mpi.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/particle_subtract_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/particle_subtract_mpi.dir/build.make src/apps/CMakeFiles/particle_subtract_mpi.dir/build make[4]: Entering directory '/<>/build' [ 82%] Building CXX object src/apps/CMakeFiles/particle_subtract_mpi.dir/particle_subtract_mpi.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/particle_subtract_mpi.dir/particle_subtract_mpi.cpp.o -MF CMakeFiles/particle_subtract_mpi.dir/particle_subtract_mpi.cpp.o.d -o CMakeFiles/particle_subtract_mpi.dir/particle_subtract_mpi.cpp.o -c /<>/src/apps/particle_subtract_mpi.cpp In file included from /<>/src/image.h:455, from /<>/src/projector.h:25, from /<>/src/ml_model.h:23, from /<>/src/ml_optimiser.h:35, from /<>/src/apps/../particle_subtractor.h:24, from /<>/src/apps/particle_subtract_mpi.cpp:22: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 82%] Linking CXX executable ../../bin/relion_particle_subtract_mpi cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_subtract_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/particle_subtract_mpi.dir/particle_subtract_mpi.cpp.o -o ../../bin/relion_particle_subtract_mpi ../../lib/librelion_lib.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In function ‘free_Tvector’, inlined from ‘brent’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:594:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘brent’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:579:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:767:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:24: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:768:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:18: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:769:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:13: note: declared here /usr/src/relion-3.1.3-3build1/src/strings.cpp: In function ‘integerToString.constprop’: /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-2, -1] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-3, -2] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-4, -3] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-5, -4] into destination object ‘aux’ of size 15 make[4]: Leaving directory '/<>/build' [ 82%] Built target particle_select /usr/bin/make -f src/apps/CMakeFiles/particle_symmetry_expand.dir/build.make src/apps/CMakeFiles/particle_symmetry_expand.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/particle_symmetry_expand.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/particle_symmetry_expand.dir/build.make src/apps/CMakeFiles/particle_symmetry_expand.dir/build make[4]: Entering directory '/<>/build' [ 83%] Building CXX object src/apps/CMakeFiles/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o -MF CMakeFiles/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o.d -o CMakeFiles/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o -c /<>/src/apps/particle_symmetry_expand.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/obs_model.h:24, from /<>/src/apps/particle_symmetry_expand.cpp:26: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 83%] Linking CXX executable ../../bin/relion_particle_symmetry_expand cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_symmetry_expand.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o -o ../../bin/relion_particle_symmetry_expand ../../lib/librelion_lib.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In function ‘free_Tvector’, inlined from ‘brent’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:594:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘brent’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:579:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:767:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:24: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:768:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:18: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:769:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:13: note: declared here In function ‘free_Tvector’, inlined from ‘brent’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:594:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘brent’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:579:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:767:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:24: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:768:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:18: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:769:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:13: note: declared here In member function ‘deallocate’, inlined from ‘deallocate’ at /usr/include/c++/12/bits/alloc_traits.h:496:23, inlined from ‘_M_deallocate’ at /usr/include/c++/12/bits/stl_vector.h:387:19, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:366:15, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:733:7, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1963:1: /usr/include/c++/12/bits/new_allocator.h:158:33: warning: ‘operator delete’ called on pointer ‘_831’ with nonzero offset [1, 9223372036854775807] [-Wfree-nonheap-object] 158 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In member function ‘allocate’, inlined from ‘allocate’ at /usr/include/c++/12/bits/alloc_traits.h:464:28, inlined from ‘_M_allocate’ at /usr/include/c++/12/bits/stl_vector.h:378:33, inlined from ‘_M_create_storage’ at /usr/include/c++/12/bits/stl_vector.h:395:44, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:332:26, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:566:47, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1876:52: /usr/include/c++/12/bits/new_allocator.h:137:55: note: returned from ‘operator new’ 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /usr/src/relion-3.1.3-3build1/src/strings.cpp: In function ‘integerToString.constprop’: /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-2, -1] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-3, -2] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-4, -3] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-5, -4] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp: In function ‘integerToString.constprop’: /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-2, -1] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-3, -2] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-4, -3] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-5, -4] into destination object ‘aux’ of size 15 In function ‘free_Tvector’, inlined from ‘brent’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:594:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘brent’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:579:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:767:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:24: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:768:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:18: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:769:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:13: note: declared here make[4]: Leaving directory '/<>/build' [ 83%] Built target particle_reposition /usr/bin/make -f src/apps/CMakeFiles/pipeliner.dir/build.make src/apps/CMakeFiles/pipeliner.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/pipeliner.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/pipeliner.dir/build.make src/apps/CMakeFiles/pipeliner.dir/build make[4]: Entering directory '/<>/build' [ 83%] Building CXX object src/apps/CMakeFiles/pipeliner.dir/pipeliner.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/pipeliner.dir/pipeliner.cpp.o -MF CMakeFiles/pipeliner.dir/pipeliner.cpp.o.d -o CMakeFiles/pipeliner.dir/pipeliner.cpp.o -c /<>/src/apps/pipeliner.cpp make[4]: Leaving directory '/<>/build' [ 83%] Built target particle_subtract /usr/bin/make -f src/apps/CMakeFiles/plot_delocalisation.dir/build.make src/apps/CMakeFiles/plot_delocalisation.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/plot_delocalisation.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/plot_delocalisation.dir/build.make src/apps/CMakeFiles/plot_delocalisation.dir/build make[4]: Entering directory '/<>/build' [ 83%] Building CXX object src/apps/CMakeFiles/plot_delocalisation.dir/plot_delocalisation.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/plot_delocalisation.dir/plot_delocalisation.cpp.o -MF CMakeFiles/plot_delocalisation.dir/plot_delocalisation.cpp.o.d -o CMakeFiles/plot_delocalisation.dir/plot_delocalisation.cpp.o -c /<>/src/apps/plot_delocalisation.cpp [ 84%] Linking CXX executable ../../bin/relion_pipeliner cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/pipeliner.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/pipeliner.dir/pipeliner.cpp.o -o ../../bin/relion_pipeliner ../../lib/librelion_lib.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /<>/src/image.h:455, from /<>/src/apps/plot_delocalisation.cpp:7: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/<>/build' [ 84%] Built target particle_symmetry_expand /usr/bin/make -f src/apps/CMakeFiles/postprocess.dir/build.make src/apps/CMakeFiles/postprocess.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/postprocess.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/postprocess.dir/build.make src/apps/CMakeFiles/postprocess.dir/build make[4]: Entering directory '/<>/build' [ 84%] Building CXX object src/apps/CMakeFiles/postprocess.dir/postprocess.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/postprocess.dir/postprocess.cpp.o -MF CMakeFiles/postprocess.dir/postprocess.cpp.o.d -o CMakeFiles/postprocess.dir/postprocess.cpp.o -c /<>/src/apps/postprocess.cpp In file included from /<>/src/image.h:455, from /<>/src/postprocessing.h:24, from /<>/src/apps/postprocess.cpp:20: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 85%] Linking CXX executable ../../bin/relion_plot_delocalisation cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/plot_delocalisation.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/plot_delocalisation.dir/plot_delocalisation.cpp.o -o ../../bin/relion_plot_delocalisation ../../lib/librelion_lib.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In function ‘free_Tvector’, inlined from ‘brent’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:594:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘brent’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:579:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:767:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:24: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:768:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:18: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:769:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:13: note: declared here [ 85%] Linking CXX executable ../../bin/relion_postprocess cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/postprocess.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/postprocess.dir/postprocess.cpp.o -o ../../bin/relion_postprocess ../../lib/librelion_lib.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff /usr/src/relion-3.1.3-3build1/src/strings.cpp: In function ‘integerToString.constprop’: /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-2, -1] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-3, -2] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-4, -3] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-5, -4] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-6, -5] into destination object ‘aux’ of size 15 In function ‘free_Tvector’, inlined from ‘brent’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:594:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘brent’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:579:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:767:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:24: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:768:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:18: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:769:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:13: note: declared here In member function ‘deallocate’, inlined from ‘deallocate’ at /usr/include/c++/12/bits/alloc_traits.h:496:23, inlined from ‘_M_deallocate’ at /usr/include/c++/12/bits/stl_vector.h:387:19, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:366:15, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:733:7, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1963:1: /usr/include/c++/12/bits/new_allocator.h:158:33: warning: ‘operator delete’ called on pointer ‘_831’ with nonzero offset [1, 9223372036854775807] [-Wfree-nonheap-object] 158 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In member function ‘allocate’, inlined from ‘allocate’ at /usr/include/c++/12/bits/alloc_traits.h:464:28, inlined from ‘_M_allocate’ at /usr/include/c++/12/bits/stl_vector.h:378:33, inlined from ‘_M_create_storage’ at /usr/include/c++/12/bits/stl_vector.h:395:44, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:332:26, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:566:47, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1876:52: /usr/include/c++/12/bits/new_allocator.h:137:55: note: returned from ‘operator new’ 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ make[4]: Leaving directory '/<>/build' [ 85%] Built target particle_subtract_mpi /usr/bin/make -f src/apps/CMakeFiles/postprocess_mpi.dir/build.make src/apps/CMakeFiles/postprocess_mpi.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/postprocess_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/postprocess_mpi.dir/build.make src/apps/CMakeFiles/postprocess_mpi.dir/build make[4]: Entering directory '/<>/build' [ 86%] Building CXX object src/apps/CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o -MF CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o.d -o CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o -c /<>/src/apps/postprocess_mpi.cpp In file included from /<>/src/image.h:455, from /<>/src/postprocessing.h:24, from /<>/src/apps/postprocess_mpi.cpp:20: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In function ‘free_Tvector’, inlined from ‘brent’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:594:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘brent’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:579:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:767:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:24: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:768:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:18: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:769:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:13: note: declared here [ 86%] Linking CXX executable ../../bin/relion_postprocess_mpi cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/postprocess_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o -o ../../bin/relion_postprocess_mpi ../../lib/librelion_lib.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff /usr/src/relion-3.1.3-3build1/src/strings.cpp: In function ‘integerToString.constprop’: /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-2, -1] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-3, -2] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-4, -3] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-5, -4] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-6, -5] into destination object ‘aux’ of size 15 In function ‘free_Tvector’, inlined from ‘brent’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:594:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘brent’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:579:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In member function ‘deallocate’, inlined from ‘deallocate’ at /usr/include/c++/12/bits/alloc_traits.h:496:23, inlined from ‘_M_deallocate’ at /usr/include/c++/12/bits/stl_vector.h:387:19, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:366:15, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:733:7, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1963:1: /usr/include/c++/12/bits/new_allocator.h:158:33: warning: ‘operator delete’ called on pointer ‘_831’ with nonzero offset [1, 9223372036854775807] [-Wfree-nonheap-object] 158 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In member function ‘allocate’, inlined from ‘allocate’ at /usr/include/c++/12/bits/alloc_traits.h:464:28, inlined from ‘_M_allocate’ at /usr/include/c++/12/bits/stl_vector.h:378:33, inlined from ‘_M_create_storage’ at /usr/include/c++/12/bits/stl_vector.h:395:44, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:332:26, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:566:47, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1876:52: /usr/include/c++/12/bits/new_allocator.h:137:55: note: returned from ‘operator new’ 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:767:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:24: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:768:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:18: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:769:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:13: note: declared here /usr/src/relion-3.1.3-3build1/src/strings.cpp: In function ‘integerToString.constprop’: /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-2, -1] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-3, -2] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-4, -3] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-5, -4] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-6, -5] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-7, -6] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-8, -7] into destination object ‘aux’ of size 15 make[4]: Leaving directory '/<>/build' [ 86%] Built target pipeliner /usr/bin/make -f src/apps/CMakeFiles/prepare_subtomo.dir/build.make src/apps/CMakeFiles/prepare_subtomo.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/prepare_subtomo.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/prepare_subtomo.dir/build.make src/apps/CMakeFiles/prepare_subtomo.dir/build make[4]: Entering directory '/<>/build' [ 86%] Building CXX object src/apps/CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o -MF CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o.d -o CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o -c /<>/src/apps/prepare_subtomo.cpp In file included from /<>/src/image.h:455, from /<>/src/helix.h:30, from /<>/src/apps/prepare_subtomo.cpp:22: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/<>/build' [ 86%] Built target plot_delocalisation /usr/bin/make -f src/apps/CMakeFiles/preprocess.dir/build.make src/apps/CMakeFiles/preprocess.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/preprocess.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/preprocess.dir/build.make src/apps/CMakeFiles/preprocess.dir/build make[4]: Entering directory '/<>/build' [ 86%] Building CXX object src/apps/CMakeFiles/preprocess.dir/preprocess.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/preprocess.dir/preprocess.cpp.o -MF CMakeFiles/preprocess.dir/preprocess.cpp.o.d -o CMakeFiles/preprocess.dir/preprocess.cpp.o -c /<>/src/apps/preprocess.cpp In file included from /<>/src/image.h:455, from /<>/src/preprocessing.h:29, from /<>/src/apps/preprocess.cpp:20: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/<>/build' [ 86%] Built target postprocess /usr/bin/make -f src/apps/CMakeFiles/preprocess_mpi.dir/build.make src/apps/CMakeFiles/preprocess_mpi.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/preprocess_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/preprocess_mpi.dir/build.make src/apps/CMakeFiles/preprocess_mpi.dir/build make[4]: Entering directory '/<>/build' [ 86%] Building CXX object src/apps/CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o -MF CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o.d -o CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o -c /<>/src/apps/preprocess_mpi.cpp [ 87%] Linking CXX executable ../../bin/relion_preprocess cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/preprocess.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/preprocess.dir/preprocess.cpp.o -o ../../bin/relion_preprocess ../../lib/librelion_lib.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /<>/src/image.h:455, from /<>/src/preprocessing.h:29, from /<>/src/preprocessing_mpi.h:24, from /<>/src/apps/preprocess_mpi.cpp:20: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /usr/src/relion-3.1.3-3build1/src/strings.cpp: In function ‘integerToString.constprop’: /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-2, -1] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-3, -2] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-4, -3] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-5, -4] into destination object ‘aux’ of size 15 [ 87%] Linking CXX executable ../../bin/relion_preprocess_mpi cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/preprocess_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o -o ../../bin/relion_preprocess_mpi ../../lib/librelion_lib.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In member function ‘deallocate’, inlined from ‘deallocate’ at /usr/include/c++/12/bits/alloc_traits.h:496:23, inlined from ‘_M_deallocate’ at /usr/include/c++/12/bits/stl_vector.h:387:19, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:366:15, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:733:7, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1963:1: /usr/include/c++/12/bits/new_allocator.h:158:33: warning: ‘operator delete’ called on pointer ‘_831’ with nonzero offset [1, 9223372036854775807] [-Wfree-nonheap-object] 158 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In member function ‘allocate’, inlined from ‘allocate’ at /usr/include/c++/12/bits/alloc_traits.h:464:28, inlined from ‘_M_allocate’ at /usr/include/c++/12/bits/stl_vector.h:378:33, inlined from ‘_M_create_storage’ at /usr/include/c++/12/bits/stl_vector.h:395:44, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:332:26, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:566:47, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1876:52: /usr/include/c++/12/bits/new_allocator.h:137:55: note: returned from ‘operator new’ 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function ‘deallocate’, inlined from ‘deallocate’ at /usr/include/c++/12/bits/alloc_traits.h:496:23, inlined from ‘_M_deallocate’ at /usr/include/c++/12/bits/stl_vector.h:387:19, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:366:15, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:733:7, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1963:1: /usr/include/c++/12/bits/new_allocator.h:158:33: warning: ‘operator delete’ called on pointer ‘_831’ with nonzero offset [1, 9223372036854775807] [-Wfree-nonheap-object] 158 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In member function ‘allocate’, inlined from ‘allocate’ at /usr/include/c++/12/bits/alloc_traits.h:464:28, inlined from ‘_M_allocate’ at /usr/include/c++/12/bits/stl_vector.h:378:33, inlined from ‘_M_create_storage’ at /usr/include/c++/12/bits/stl_vector.h:395:44, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:332:26, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:566:47, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1876:52: /usr/include/c++/12/bits/new_allocator.h:137:55: note: returned from ‘operator new’ 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /usr/src/relion-3.1.3-3build1/src/strings.cpp: In function ‘integerToString.constprop’: /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-2, -1] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-3, -2] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-4, -3] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-5, -4] into destination object ‘aux’ of size 15 make[4]: Leaving directory '/<>/build' [ 87%] Built target postprocess_mpi /usr/bin/make -f src/apps/CMakeFiles/project.dir/build.make src/apps/CMakeFiles/project.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/project.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/project.dir/build.make src/apps/CMakeFiles/project.dir/build make[4]: Entering directory '/<>/build' [ 88%] Building CXX object src/apps/CMakeFiles/project.dir/project.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/project.dir/project.cpp.o -MF CMakeFiles/project.dir/project.cpp.o.d -o CMakeFiles/project.dir/project.cpp.o -c /<>/src/apps/project.cpp In file included from /<>/src/image.h:455, from /<>/src/projector.h:25, from /<>/src/apps/project.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In function ‘free_Tvector’, inlined from ‘brent’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:594:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘brent’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:579:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:767:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:24: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:768:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:18: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:769:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:13: note: declared here [ 89%] Linking CXX executable ../../bin/relion_prepare_subtomo cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/prepare_subtomo.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o -o ../../bin/relion_prepare_subtomo ../../lib/librelion_lib.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In member function ‘deallocate’, inlined from ‘deallocate’ at /usr/include/c++/12/bits/alloc_traits.h:496:23, inlined from ‘_M_deallocate’ at /usr/include/c++/12/bits/stl_vector.h:387:19, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:366:15, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:733:7, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1963:1: /usr/include/c++/12/bits/new_allocator.h:158:33: warning: ‘operator delete’ called on pointer ‘_831’ with nonzero offset [1, 9223372036854775807] [-Wfree-nonheap-object] 158 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In member function ‘allocate’, inlined from ‘allocate’ at /usr/include/c++/12/bits/alloc_traits.h:464:28, inlined from ‘_M_allocate’ at /usr/include/c++/12/bits/stl_vector.h:378:33, inlined from ‘_M_create_storage’ at /usr/include/c++/12/bits/stl_vector.h:395:44, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:332:26, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:566:47, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1876:52: /usr/include/c++/12/bits/new_allocator.h:137:55: note: returned from ‘operator new’ 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In function ‘free_Tvector’, inlined from ‘brent’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:594:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘brent’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:579:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:767:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:24: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:768:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:18: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:769:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:13: note: declared here [ 89%] Linking CXX executable ../../bin/relion_project cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/project.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/project.dir/project.cpp.o -o ../../bin/relion_project ../../lib/librelion_lib.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In function ‘free_Tvector’, inlined from ‘brent’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:594:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘brent’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:579:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:767:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:24: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:768:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:18: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:769:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:13: note: declared here make[4]: Leaving directory '/<>/build' [ 89%] Built target preprocess /usr/bin/make -f src/apps/CMakeFiles/reconstruct.dir/build.make src/apps/CMakeFiles/reconstruct.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/reconstruct.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/reconstruct.dir/build.make src/apps/CMakeFiles/reconstruct.dir/build make[4]: Entering directory '/<>/build' [ 89%] Building CXX object src/apps/CMakeFiles/reconstruct.dir/reconstruct.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/reconstruct.dir/reconstruct.cpp.o -MF CMakeFiles/reconstruct.dir/reconstruct.cpp.o.d -o CMakeFiles/reconstruct.dir/reconstruct.cpp.o -c /<>/src/apps/reconstruct.cpp In file included from /<>/src/image.h:455, from /<>/src/projector.h:25, from /<>/src/backprojector.h:33, from /<>/src/reconstructor.h:23, from /<>/src/apps/reconstruct.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 90%] Linking CXX executable ../../bin/relion_reconstruct cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/reconstruct.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/reconstruct.dir/reconstruct.cpp.o -o ../../bin/relion_reconstruct ../../lib/librelion_lib.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/<>/build' [ 90%] Built target preprocess_mpi /usr/bin/make -f src/apps/CMakeFiles/reconstruct_mpi.dir/build.make src/apps/CMakeFiles/reconstruct_mpi.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/reconstruct_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/reconstruct_mpi.dir/build.make src/apps/CMakeFiles/reconstruct_mpi.dir/build make[4]: Entering directory '/<>/build' [ 90%] Building CXX object src/apps/CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o -MF CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o.d -o CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o -c /<>/src/apps/reconstruct_mpi.cpp In file included from /<>/src/image.h:455, from /<>/src/projector.h:25, from /<>/src/backprojector.h:33, from /<>/src/reconstructor.h:23, from /<>/src/reconstructor_mpi.h:25, from /<>/src/apps/reconstruct_mpi.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /usr/src/relion-3.1.3-3build1/src/strings.cpp: In function ‘integerToString.constprop’: /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-2, -1] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-3, -2] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-4, -3] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-5, -4] into destination object ‘aux’ of size 15 [ 91%] Linking CXX executable ../../bin/relion_reconstruct_mpi cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/reconstruct_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o -o ../../bin/relion_reconstruct_mpi ../../lib/librelion_lib.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In function ‘free_Tvector’, inlined from ‘brent’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:594:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘brent’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:579:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:767:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:24: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:768:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:18: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:769:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:13: note: declared here make[4]: Leaving directory '/<>/build' [ 91%] Built target prepare_subtomo /usr/bin/make -f src/apps/CMakeFiles/refine.dir/build.make src/apps/CMakeFiles/refine.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/refine.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/refine.dir/build.make src/apps/CMakeFiles/refine.dir/build make[4]: Entering directory '/<>/build' [ 91%] Building CXX object src/apps/CMakeFiles/refine.dir/refine.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/refine.dir/refine.cpp.o -MF CMakeFiles/refine.dir/refine.cpp.o.d -o CMakeFiles/refine.dir/refine.cpp.o -c /<>/src/apps/refine.cpp In file included from /<>/src/image.h:455, from /<>/src/projector.h:25, from /<>/src/ml_model.h:23, from /<>/src/ml_optimiser.h:35, from /<>/src/apps/refine.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In function ‘free_Tvector’, inlined from ‘brent’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:594:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘brent’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:579:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:767:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:24: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:768:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:18: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:769:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:13: note: declared here [ 91%] Linking CXX executable ../../bin/relion_refine cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/refine.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/refine.dir/refine.cpp.o -o ../../bin/relion_refine ../../lib/librelion_lib.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/<>/build' [ 91%] Built target project /usr/bin/make -f src/apps/CMakeFiles/refine_mpi.dir/build.make src/apps/CMakeFiles/refine_mpi.dir/depend In function ‘free_Tvector’, inlined from ‘brent’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:594:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘brent’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:579:13: note: declared here make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/refine_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/refine_mpi.dir/build.make src/apps/CMakeFiles/refine_mpi.dir/build make[4]: Entering directory '/<>/build' [ 92%] Building CXX object src/apps/CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o -MF CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o.d -o CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o -c /<>/src/apps/refine_mpi.cpp In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:767:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:24: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:768:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:18: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:769:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:13: note: declared here In file included from /<>/src/image.h:455, from /<>/src/projector.h:25, from /<>/src/ml_model.h:23, from /<>/src/ml_optimiser.h:35, from /<>/src/ml_optimiser_mpi.h:24, from /<>/src/apps/refine_mpi.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In function ‘free_Tvector’, inlined from ‘brent’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:594:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘brent’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:579:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:767:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:24: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:768:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:18: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:769:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:13: note: declared here [ 92%] Linking CXX executable ../../bin/relion_refine_mpi cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/refine_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o -o ../../bin/relion_refine_mpi ../../lib/librelion_lib.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff /usr/src/relion-3.1.3-3build1/src/strings.cpp: In function ‘integerToString.constprop’: /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-2, -1] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-3, -2] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-4, -3] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-5, -4] into destination object ‘aux’ of size 15 In function ‘free_Tvector’, inlined from ‘brent’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:594:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘brent’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:579:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:767:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:24: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:768:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:18: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:769:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:13: note: declared here make[4]: Leaving directory '/<>/build' [ 92%] Built target reconstruct /usr/bin/make -f src/apps/CMakeFiles/reposition.dir/build.make src/apps/CMakeFiles/reposition.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/reposition.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/reposition.dir/build.make src/apps/CMakeFiles/reposition.dir/build make[4]: Entering directory '/<>/build' [ 92%] Building CXX object src/apps/CMakeFiles/reposition.dir/reposition.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/reposition.dir/reposition.cpp.o -MF CMakeFiles/reposition.dir/reposition.cpp.o.d -o CMakeFiles/reposition.dir/reposition.cpp.o -c /<>/src/apps/reposition.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/obs_model.h:24, from /<>/src/apps/reposition.cpp:1: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /usr/src/relion-3.1.3-3build1/src/strings.cpp: In function ‘integerToString.constprop’: /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-2, -1] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-3, -2] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-4, -3] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-5, -4] into destination object ‘aux’ of size 15 [ 93%] Linking CXX executable ../../bin/relion_reposition cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/reposition.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/reposition.dir/reposition.cpp.o -o ../../bin/relion_reposition ../../lib/librelion_lib.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/<>/build' [ 93%] Built target reconstruct_mpi /usr/bin/make -f src/apps/CMakeFiles/run_ctffind.dir/build.make src/apps/CMakeFiles/run_ctffind.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/run_ctffind.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/run_ctffind.dir/build.make src/apps/CMakeFiles/run_ctffind.dir/build make[4]: Entering directory '/<>/build' [ 93%] Building CXX object src/apps/CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o -MF CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o.d -o CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o -c /<>/src/apps/run_ctffind.cpp In file included from /<>/src/image.h:455, from /<>/src/ctffind_runner.h:31, from /<>/src/apps/run_ctffind.cpp:20: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 93%] Linking CXX executable ../../bin/relion_run_ctffind cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/run_ctffind.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o -o ../../bin/relion_run_ctffind ../../lib/librelion_lib.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In function ‘free_Tvector’, inlined from ‘brent’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:594:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘brent’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:579:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:767:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:24: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:768:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:18: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:769:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:13: note: declared here /usr/src/relion-3.1.3-3build1/src/strings.cpp: In function ‘integerToString.constprop’: /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-2, -1] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-3, -2] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-4, -3] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-5, -4] into destination object ‘aux’ of size 15 In member function ‘deallocate’, inlined from ‘deallocate’ at /usr/include/c++/12/bits/alloc_traits.h:496:23, inlined from ‘_M_deallocate’ at /usr/include/c++/12/bits/stl_vector.h:387:19, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:366:15, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:733:7, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1963:1: /usr/include/c++/12/bits/new_allocator.h:158:33: warning: ‘operator delete’ called on pointer ‘_831’ with nonzero offset [1, 9223372036854775807] [-Wfree-nonheap-object] 158 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In member function ‘allocate’, inlined from ‘allocate’ at /usr/include/c++/12/bits/alloc_traits.h:464:28, inlined from ‘_M_allocate’ at /usr/include/c++/12/bits/stl_vector.h:378:33, inlined from ‘_M_create_storage’ at /usr/include/c++/12/bits/stl_vector.h:395:44, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:332:26, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:566:47, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1876:52: /usr/include/c++/12/bits/new_allocator.h:137:55: note: returned from ‘operator new’ 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In function ‘free_Tvector’, inlined from ‘brent’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:594:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘brent’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:579:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:767:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:24: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:768:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:18: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:769:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:13: note: declared here make[4]: Leaving directory '/<>/build' [ 93%] Built target refine /usr/bin/make -f src/apps/CMakeFiles/run_ctffind_mpi.dir/build.make src/apps/CMakeFiles/run_ctffind_mpi.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/run_ctffind_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/run_ctffind_mpi.dir/build.make src/apps/CMakeFiles/run_ctffind_mpi.dir/build make[4]: Entering directory '/<>/build' [ 94%] Building CXX object src/apps/CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o -MF CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o.d -o CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o -c /<>/src/apps/run_ctffind_mpi.cpp In file included from /<>/src/image.h:455, from /<>/src/ctffind_runner.h:31, from /<>/src/ctffind_runner_mpi.h:25, from /<>/src/apps/run_ctffind_mpi.cpp:20: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 94%] Linking CXX executable ../../bin/relion_run_ctffind_mpi cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/run_ctffind_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o -o ../../bin/relion_run_ctffind_mpi ../../lib/librelion_lib.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff /usr/src/relion-3.1.3-3build1/src/strings.cpp: In function ‘integerToString.constprop’: /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-2, -1] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-3, -2] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-4, -3] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-5, -4] into destination object ‘aux’ of size 15 make[4]: Leaving directory '/<>/build' [ 94%] Built target reposition /usr/bin/make -f src/apps/CMakeFiles/run_motioncorr.dir/build.make src/apps/CMakeFiles/run_motioncorr.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/run_motioncorr.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/run_motioncorr.dir/build.make src/apps/CMakeFiles/run_motioncorr.dir/build make[4]: Entering directory '/<>/build' [ 95%] Building CXX object src/apps/CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o -MF CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o.d -o CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o -c /<>/src/apps/run_motioncorr.cpp In file included from /<>/src/image.h:455, from /<>/src/motioncorr_runner.h:32, from /<>/src/apps/run_motioncorr.cpp:20: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/<>/build' [ 95%] Built target run_ctffind /usr/bin/make -f src/apps/CMakeFiles/run_motioncorr_mpi.dir/build.make src/apps/CMakeFiles/run_motioncorr_mpi.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/run_motioncorr_mpi.dir/DependInfo.cmake --color= [ 95%] Linking CXX executable ../../bin/relion_run_motioncorr cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/run_motioncorr.dir/link.txt --verbose=1 make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/run_motioncorr_mpi.dir/build.make src/apps/CMakeFiles/run_motioncorr_mpi.dir/build /usr/bin/mpicxx -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o -o ../../bin/relion_run_motioncorr ../../lib/librelion_lib.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Entering directory '/<>/build' [ 95%] Building CXX object src/apps/CMakeFiles/run_motioncorr_mpi.dir/run_motioncorr_mpi.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/run_motioncorr_mpi.dir/run_motioncorr_mpi.cpp.o -MF CMakeFiles/run_motioncorr_mpi.dir/run_motioncorr_mpi.cpp.o.d -o CMakeFiles/run_motioncorr_mpi.dir/run_motioncorr_mpi.cpp.o -c /<>/src/apps/run_motioncorr_mpi.cpp In member function ‘deallocate’, inlined from ‘deallocate’ at /usr/include/c++/12/bits/alloc_traits.h:496:23, inlined from ‘_M_deallocate’ at /usr/include/c++/12/bits/stl_vector.h:387:19, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:366:15, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:733:7, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1963:1: /usr/include/c++/12/bits/new_allocator.h:158:33: warning: ‘operator delete’ called on pointer ‘_831’ with nonzero offset [1, 9223372036854775807] [-Wfree-nonheap-object] 158 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In member function ‘allocate’, inlined from ‘allocate’ at /usr/include/c++/12/bits/alloc_traits.h:464:28, inlined from ‘_M_allocate’ at /usr/include/c++/12/bits/stl_vector.h:378:33, inlined from ‘_M_create_storage’ at /usr/include/c++/12/bits/stl_vector.h:395:44, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:332:26, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:566:47, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1876:52: /usr/include/c++/12/bits/new_allocator.h:137:55: note: returned from ‘operator new’ 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In function ‘free_Tvector’, inlined from ‘brent’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:594:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘brent’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:579:13: note: declared here In file included from /<>/src/image.h:455, from /<>/src/motioncorr_runner.h:32, from /<>/src/motioncorr_runner_mpi.h:25, from /<>/src/apps/run_motioncorr_mpi.cpp:20: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:767:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:24: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:768:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:18: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:769:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:13: note: declared here In function ‘free_Tvector’, inlined from ‘brent’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:594:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘brent’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:579:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:767:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:24: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:768:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:18: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:769:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:13: note: declared here [ 96%] Linking CXX executable ../../bin/relion_run_motioncorr_mpi cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/run_motioncorr_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/run_motioncorr_mpi.dir/run_motioncorr_mpi.cpp.o -o ../../bin/relion_run_motioncorr_mpi ../../lib/librelion_lib.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In member function ‘deallocate’, inlined from ‘deallocate’ at /usr/include/c++/12/bits/alloc_traits.h:496:23, inlined from ‘_M_deallocate’ at /usr/include/c++/12/bits/stl_vector.h:387:19, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:366:15, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:733:7, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1963:1: /usr/include/c++/12/bits/new_allocator.h:158:33: warning: ‘operator delete’ called on pointer ‘_831’ with nonzero offset [1, 9223372036854775807] [-Wfree-nonheap-object] 158 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In member function ‘allocate’, inlined from ‘allocate’ at /usr/include/c++/12/bits/alloc_traits.h:464:28, inlined from ‘_M_allocate’ at /usr/include/c++/12/bits/stl_vector.h:378:33, inlined from ‘_M_create_storage’ at /usr/include/c++/12/bits/stl_vector.h:395:44, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:332:26, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:566:47, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1876:52: /usr/include/c++/12/bits/new_allocator.h:137:55: note: returned from ‘operator new’ 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ make[4]: Leaving directory '/<>/build' [ 96%] Built target refine_mpi /usr/bin/make -f src/apps/CMakeFiles/scheduler.dir/build.make src/apps/CMakeFiles/scheduler.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/scheduler.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/scheduler.dir/build.make src/apps/CMakeFiles/scheduler.dir/build make[4]: Entering directory '/<>/build' [ 96%] Building CXX object src/apps/CMakeFiles/scheduler.dir/scheduler.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/scheduler.dir/scheduler.cpp.o -MF CMakeFiles/scheduler.dir/scheduler.cpp.o.d -o CMakeFiles/scheduler.dir/scheduler.cpp.o -c /<>/src/apps/scheduler.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/obs_model.h:24, from /<>/src/scheduler.h:26, from /<>/src/apps/scheduler.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In member function ‘deallocate’, inlined from ‘deallocate’ at /usr/include/c++/12/bits/alloc_traits.h:496:23, inlined from ‘_M_deallocate’ at /usr/include/c++/12/bits/stl_vector.h:387:19, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:366:15, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:733:7, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1963:1: /usr/include/c++/12/bits/new_allocator.h:158:33: warning: ‘operator delete’ called on pointer ‘_831’ with nonzero offset [1, 9223372036854775807] [-Wfree-nonheap-object] 158 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In member function ‘allocate’, inlined from ‘allocate’ at /usr/include/c++/12/bits/alloc_traits.h:464:28, inlined from ‘_M_allocate’ at /usr/include/c++/12/bits/stl_vector.h:378:33, inlined from ‘_M_create_storage’ at /usr/include/c++/12/bits/stl_vector.h:395:44, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:332:26, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:566:47, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1876:52: /usr/include/c++/12/bits/new_allocator.h:137:55: note: returned from ‘operator new’ 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ [ 96%] Linking CXX executable ../../bin/relion_scheduler cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/scheduler.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/scheduler.dir/scheduler.cpp.o -o ../../bin/relion_scheduler ../../lib/librelion_lib.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff /usr/src/relion-3.1.3-3build1/src/strings.cpp: In function ‘integerToString.constprop’: /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-2, -1] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-3, -2] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-4, -3] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-5, -4] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-6, -5] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-7, -6] into destination object ‘aux’ of size 15 /usr/src/relion-3.1.3-3build1/src/strings.cpp:388:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] /usr/src/relion-3.1.3-3build1/src/strings.cpp:361:7: note: at offset [-8, -7] into destination object ‘aux’ of size 15 In function ‘free_Tvector’, inlined from ‘brent’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:594:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘brent’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:579:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:767:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:24: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:768:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:18: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:769:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:13: note: declared here In function ‘free_Tvector’, inlined from ‘brent’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:594:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘brent’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:579:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:767:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:24: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:768:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:18: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:769:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:13: note: declared here make[4]: Leaving directory '/<>/build' [ 96%] Built target run_ctffind_mpi /usr/bin/make -f src/apps/CMakeFiles/stack_create.dir/build.make src/apps/CMakeFiles/stack_create.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/stack_create.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/stack_create.dir/build.make src/apps/CMakeFiles/stack_create.dir/build make[4]: Entering directory '/<>/build' [ 97%] Building CXX object src/apps/CMakeFiles/stack_create.dir/stack_create.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/stack_create.dir/stack_create.cpp.o -MF CMakeFiles/stack_create.dir/stack_create.cpp.o.d -o CMakeFiles/stack_create.dir/stack_create.cpp.o -c /<>/src/apps/stack_create.cpp In file included from /<>/src/image.h:455, from /<>/src/apps/stack_create.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/<>/build' [ 97%] Built target run_motioncorr /usr/bin/make -f src/apps/CMakeFiles/star_handler.dir/build.make src/apps/CMakeFiles/star_handler.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/star_handler.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/star_handler.dir/build.make src/apps/CMakeFiles/star_handler.dir/build make[4]: Entering directory '/<>/build' [ 98%] Building CXX object src/apps/CMakeFiles/star_handler.dir/star_handler.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/star_handler.dir/star_handler.cpp.o -MF CMakeFiles/star_handler.dir/star_handler.cpp.o.d -o CMakeFiles/star_handler.dir/star_handler.cpp.o -c /<>/src/apps/star_handler.cpp [ 98%] Linking CXX executable ../../bin/relion_stack_create cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/stack_create.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/stack_create.dir/stack_create.cpp.o -o ../../bin/relion_stack_create ../../lib/librelion_lib.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /<>/src/image.h:455, from /<>/src/apps/star_handler.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/<>/build' [ 98%] Built target run_motioncorr_mpi /usr/bin/make -f src/apps/CMakeFiles/tiltpair_plot.dir/build.make src/apps/CMakeFiles/tiltpair_plot.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/tiltpair_plot.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/tiltpair_plot.dir/build.make src/apps/CMakeFiles/tiltpair_plot.dir/build make[4]: Entering directory '/<>/build' [ 98%] Building CXX object src/apps/CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o -MF CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o.d -o CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o -c /<>/src/apps/tiltpair_plot.cpp In file included from /<>/src/image.h:455, from /<>/src/apps/tiltpair_plot.cpp:25: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In member function ‘deallocate’, inlined from ‘deallocate’ at /usr/include/c++/12/bits/alloc_traits.h:496:23, inlined from ‘_M_deallocate’ at /usr/include/c++/12/bits/stl_vector.h:387:19, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:366:15, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:733:7, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1963:1: /usr/include/c++/12/bits/new_allocator.h:158:33: warning: ‘operator delete’ called on pointer ‘_831’ with nonzero offset [1, 9223372036854775807] [-Wfree-nonheap-object] 158 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In member function ‘allocate’, inlined from ‘allocate’ at /usr/include/c++/12/bits/alloc_traits.h:464:28, inlined from ‘_M_allocate’ at /usr/include/c++/12/bits/stl_vector.h:378:33, inlined from ‘_M_create_storage’ at /usr/include/c++/12/bits/stl_vector.h:395:44, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:332:26, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:566:47, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1876:52: /usr/include/c++/12/bits/new_allocator.h:137:55: note: returned from ‘operator new’ 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ [ 99%] Linking CXX executable ../../bin/relion_tiltpair_plot cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiltpair_plot.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o -o ../../bin/relion_tiltpair_plot ../../lib/librelion_lib.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In function ‘free_Tvector’, inlined from ‘brent’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:594:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘brent’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:579:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:767:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:24: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:768:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:18: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:769:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:13: note: declared here In function ‘free_Tvector’, inlined from ‘brent’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:594:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘brent’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:579:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:767:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:24: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:768:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:18: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:769:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:13: note: declared here In member function ‘deallocate’, inlined from ‘deallocate’ at /usr/include/c++/12/bits/alloc_traits.h:496:23, inlined from ‘_M_deallocate’ at /usr/include/c++/12/bits/stl_vector.h:387:19, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:366:15, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:733:7, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1963:1: /usr/include/c++/12/bits/new_allocator.h:158:33: warning: ‘operator delete’ called on pointer ‘_831’ with nonzero offset [1, 9223372036854775807] [-Wfree-nonheap-object] 158 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In member function ‘allocate’, inlined from ‘allocate’ at /usr/include/c++/12/bits/alloc_traits.h:464:28, inlined from ‘_M_allocate’ at /usr/include/c++/12/bits/stl_vector.h:378:33, inlined from ‘_M_create_storage’ at /usr/include/c++/12/bits/stl_vector.h:395:44, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:332:26, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:566:47, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1876:52: /usr/include/c++/12/bits/new_allocator.h:137:55: note: returned from ‘operator new’ 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ [ 99%] Linking CXX executable ../../bin/relion_star_handler cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/star_handler.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/star_handler.dir/star_handler.cpp.o -o ../../bin/relion_star_handler ../../lib/librelion_lib.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/<>/build' [ 99%] Built target scheduler /usr/bin/make -f src/apps/CMakeFiles/tomo_test.dir/build.make src/apps/CMakeFiles/tomo_test.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/tomo_test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/tomo_test.dir/build.make src/apps/CMakeFiles/tomo_test.dir/build make[4]: Entering directory '/<>/build' [ 99%] Building CXX object src/apps/CMakeFiles/tomo_test.dir/tomo_test.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/tomo_test.dir/tomo_test.cpp.o -MF CMakeFiles/tomo_test.dir/tomo_test.cpp.o.d -o CMakeFiles/tomo_test.dir/tomo_test.cpp.o -c /<>/src/apps/tomo_test.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/tomo/tomo_stack.h:25, from /<>/src/apps/tomo_test.cpp:2: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/powerpc64le-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/powerpc64le-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In member function ‘deallocate’, inlined from ‘deallocate’ at /usr/include/c++/12/bits/alloc_traits.h:496:23, inlined from ‘_M_deallocate’ at /usr/include/c++/12/bits/stl_vector.h:387:19, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:366:15, inlined from ‘__dt_base ’ at /usr/include/c++/12/bits/stl_vector.h:733:7, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1963:1: /usr/include/c++/12/bits/new_allocator.h:158:33: warning: ‘operator delete’ called on pointer ‘_831’ with nonzero offset [1, 9223372036854775807] [-Wfree-nonheap-object] 158 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In member function ‘allocate’, inlined from ‘allocate’ at /usr/include/c++/12/bits/alloc_traits.h:464:28, inlined from ‘_M_allocate’ at /usr/include/c++/12/bits/stl_vector.h:378:33, inlined from ‘_M_create_storage’ at /usr/include/c++/12/bits/stl_vector.h:395:44, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:332:26, inlined from ‘__ct ’ at /usr/include/c++/12/bits/stl_vector.h:566:47, inlined from ‘removeDuplicatedParticles’ at /usr/src/relion-3.1.3-3build1/src/metadata_table.cpp:1876:52: /usr/include/c++/12/bits/new_allocator.h:137:55: note: returned from ‘operator new’ 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ [100%] Linking CXX executable ../../bin/relion_tomo_test cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/tomo_test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/tomo_test.dir/tomo_test.cpp.o -o ../../bin/relion_tomo_test ../../lib/librelion_lib.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In function ‘free_Tvector’, inlined from ‘brent’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:594:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘brent’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:579:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:767:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:24: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:768:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:18: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:769:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:13: note: declared here In function ‘free_Tvector’, inlined from ‘brent’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:594:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘brent’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:579:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘linmin’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:691:17: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xicom’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘linmin’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:673:13: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:767:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:24: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:768:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:18: note: declared here In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:769:25: /usr/src/relion-3.1.3-3build1/src/memory.h:74:13: warning: ‘free’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object] /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp: In function ‘powell’: /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:703:13: note: declared here make[4]: Leaving directory '/<>/build' [100%] Built target stack_create make[4]: Leaving directory '/<>/build' [100%] Built target tiltpair_plot make[4]: Leaving directory '/<>/build' [100%] Built target star_handler make[4]: Leaving directory '/<>/build' [100%] Built target tomo_test make[3]: Leaving directory '/<>/build' /usr/bin/cmake -E cmake_progress_start /<>/build/CMakeFiles 0 make[2]: Leaving directory '/<>/build' make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_prep -a debian/rules override_dh_auto_install make[1]: Entering directory '/<>' /usr/bin/make -C build install DESTDIR=/<>/debian/tmp/cli make[2]: Entering directory '/<>/build' /usr/bin/cmake -S/<> -B/<>/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/build/CMakeFiles /<>/build//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/<>/build' /usr/bin/make -f CMakeFiles/copy_scripts.dir/build.make CMakeFiles/copy_scripts.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<> /<>/build /<>/build /<>/build/CMakeFiles/copy_scripts.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f CMakeFiles/copy_scripts.dir/build.make CMakeFiles/copy_scripts.dir/build make[4]: Entering directory '/<>/build' /usr/bin/cmake -E copy /<>/scripts/star_printtable /<>/build/bin/relion_star_printtable /usr/bin/cmake -E copy /<>/scripts/star_plottable /<>/build/bin/relion_star_plottable /usr/bin/cmake -E copy /<>/scripts/star_loopheader /<>/build/bin/relion_star_loopheader /usr/bin/cmake -E copy /<>/scripts/star_datablock_stack /<>/build/bin/relion_star_datablock_stack /usr/bin/cmake -E copy /<>/scripts/star_datablock_singlefiles /<>/build/bin/relion_star_datablock_singlefiles /usr/bin/cmake -E copy /<>/scripts/star_datablock_ctfdat /<>/build/bin/relion_star_datablock_ctfdat /usr/bin/cmake -E copy /<>/scripts/qsub.csh /<>/build/bin/relion_qsub.csh make[4]: Leaving directory '/<>/build' [ 0%] Built target copy_scripts /usr/bin/make -f src/apps/CMakeFiles/relion_lib.dir/build.make src/apps/CMakeFiles/relion_lib.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/relion_lib.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/relion_lib.dir/build.make src/apps/CMakeFiles/relion_lib.dir/build make[4]: Entering directory '/<>/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/relion_lib.dir/build'. make[4]: Leaving directory '/<>/build' [ 53%] Built target relion_lib /usr/bin/make -f src/apps/CMakeFiles/relion_gui_lib.dir/build.make src/apps/CMakeFiles/relion_gui_lib.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/relion_gui_lib.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/relion_gui_lib.dir/build.make src/apps/CMakeFiles/relion_gui_lib.dir/build make[4]: Entering directory '/<>/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/relion_gui_lib.dir/build'. make[4]: Leaving directory '/<>/build' [ 56%] Built target relion_gui_lib /usr/bin/make -f src/apps/CMakeFiles/align_symmetry.dir/build.make src/apps/CMakeFiles/align_symmetry.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/align_symmetry.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/align_symmetry.dir/build.make src/apps/CMakeFiles/align_symmetry.dir/build make[4]: Entering directory '/<>/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/align_symmetry.dir/build'. make[4]: Leaving directory '/<>/build' [ 56%] Built target align_symmetry /usr/bin/make -f src/apps/CMakeFiles/autopick.dir/build.make src/apps/CMakeFiles/autopick.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/autopick.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/autopick.dir/build.make src/apps/CMakeFiles/autopick.dir/build make[4]: Entering directory '/<>/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/autopick.dir/build'. make[4]: Leaving directory '/<>/build' [ 57%] Built target autopick /usr/bin/make -f src/apps/CMakeFiles/autopick_mpi.dir/build.make src/apps/CMakeFiles/autopick_mpi.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/autopick_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/autopick_mpi.dir/build.make src/apps/CMakeFiles/autopick_mpi.dir/build make[4]: Entering directory '/<>/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/autopick_mpi.dir/build'. make[4]: Leaving directory '/<>/build' [ 58%] Built target autopick_mpi /usr/bin/make -f src/apps/CMakeFiles/convert_star.dir/build.make src/apps/CMakeFiles/convert_star.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/convert_star.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/convert_star.dir/build.make src/apps/CMakeFiles/convert_star.dir/build make[4]: Entering directory '/<>/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/convert_star.dir/build'. make[4]: Leaving directory '/<>/build' [ 59%] Built target convert_star /usr/bin/make -f src/apps/CMakeFiles/convert_to_tiff.dir/build.make src/apps/CMakeFiles/convert_to_tiff.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/convert_to_tiff.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/convert_to_tiff.dir/build.make src/apps/CMakeFiles/convert_to_tiff.dir/build make[4]: Entering directory '/<>/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/convert_to_tiff.dir/build'. make[4]: Leaving directory '/<>/build' [ 59%] Built target convert_to_tiff /usr/bin/make -f src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build.make src/apps/CMakeFiles/convert_to_tiff_mpi.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/convert_to_tiff_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build.make src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build make[4]: Entering directory '/<>/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build'. make[4]: Leaving directory '/<>/build' [ 60%] Built target convert_to_tiff_mpi /usr/bin/make -f src/apps/CMakeFiles/ctf_mask_test.dir/build.make src/apps/CMakeFiles/ctf_mask_test.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/ctf_mask_test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/ctf_mask_test.dir/build.make src/apps/CMakeFiles/ctf_mask_test.dir/build make[4]: Entering directory '/<>/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/ctf_mask_test.dir/build'. make[4]: Leaving directory '/<>/build' [ 61%] Built target ctf_mask_test /usr/bin/make -f src/apps/CMakeFiles/ctf_refine.dir/build.make src/apps/CMakeFiles/ctf_refine.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/ctf_refine.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/ctf_refine.dir/build.make src/apps/CMakeFiles/ctf_refine.dir/build make[4]: Entering directory '/<>/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/ctf_refine.dir/build'. make[4]: Leaving directory '/<>/build' [ 62%] Built target ctf_refine /usr/bin/make -f src/apps/CMakeFiles/ctf_refine_mpi.dir/build.make src/apps/CMakeFiles/ctf_refine_mpi.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/ctf_refine_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/ctf_refine_mpi.dir/build.make src/apps/CMakeFiles/ctf_refine_mpi.dir/build make[4]: Entering directory '/<>/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/ctf_refine_mpi.dir/build'. make[4]: Leaving directory '/<>/build' [ 62%] Built target ctf_refine_mpi /usr/bin/make -f src/apps/CMakeFiles/ctf_toolbox.dir/build.make src/apps/CMakeFiles/ctf_toolbox.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/ctf_toolbox.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/ctf_toolbox.dir/build.make src/apps/CMakeFiles/ctf_toolbox.dir/build make[4]: Entering directory '/<>/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/ctf_toolbox.dir/build'. make[4]: Leaving directory '/<>/build' [ 63%] Built target ctf_toolbox /usr/bin/make -f src/apps/CMakeFiles/demodulate.dir/build.make src/apps/CMakeFiles/demodulate.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/demodulate.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/demodulate.dir/build.make src/apps/CMakeFiles/demodulate.dir/build make[4]: Entering directory '/<>/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/demodulate.dir/build'. make[4]: Leaving directory '/<>/build' [ 64%] Built target demodulate /usr/bin/make -f src/apps/CMakeFiles/display.dir/build.make src/apps/CMakeFiles/display.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/display.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/display.dir/build.make src/apps/CMakeFiles/display.dir/build make[4]: Entering directory '/<>/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/display.dir/build'. make[4]: Leaving directory '/<>/build' [ 65%] Built target display /usr/bin/make -f src/apps/CMakeFiles/estimate_gain.dir/build.make src/apps/CMakeFiles/estimate_gain.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/estimate_gain.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/estimate_gain.dir/build.make src/apps/CMakeFiles/estimate_gain.dir/build make[4]: Entering directory '/<>/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/estimate_gain.dir/build'. make[4]: Leaving directory '/<>/build' [ 65%] Built target estimate_gain /usr/bin/make -f src/apps/CMakeFiles/external_reconstruct.dir/build.make src/apps/CMakeFiles/external_reconstruct.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/external_reconstruct.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/external_reconstruct.dir/build.make src/apps/CMakeFiles/external_reconstruct.dir/build make[4]: Entering directory '/<>/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/external_reconstruct.dir/build'. make[4]: Leaving directory '/<>/build' [ 66%] Built target external_reconstruct /usr/bin/make -f src/apps/CMakeFiles/find_tiltpairs.dir/build.make src/apps/CMakeFiles/find_tiltpairs.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/find_tiltpairs.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/find_tiltpairs.dir/build.make src/apps/CMakeFiles/find_tiltpairs.dir/build make[4]: Entering directory '/<>/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/find_tiltpairs.dir/build'. make[4]: Leaving directory '/<>/build' [ 67%] Built target find_tiltpairs /usr/bin/make -f src/apps/CMakeFiles/flex_analyse.dir/build.make src/apps/CMakeFiles/flex_analyse.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/flex_analyse.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/flex_analyse.dir/build.make src/apps/CMakeFiles/flex_analyse.dir/build make[4]: Entering directory '/<>/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/flex_analyse.dir/build'. make[4]: Leaving directory '/<>/build' [ 68%] Built target flex_analyse /usr/bin/make -f src/apps/CMakeFiles/flex_analyse_mpi.dir/build.make src/apps/CMakeFiles/flex_analyse_mpi.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/flex_analyse_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/flex_analyse_mpi.dir/build.make src/apps/CMakeFiles/flex_analyse_mpi.dir/build make[4]: Entering directory '/<>/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/flex_analyse_mpi.dir/build'. make[4]: Leaving directory '/<>/build' [ 68%] Built target flex_analyse_mpi /usr/bin/make -f src/apps/CMakeFiles/helix_inimodel2d.dir/build.make src/apps/CMakeFiles/helix_inimodel2d.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/helix_inimodel2d.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/helix_inimodel2d.dir/build.make src/apps/CMakeFiles/helix_inimodel2d.dir/build make[4]: Entering directory '/<>/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/helix_inimodel2d.dir/build'. make[4]: Leaving directory '/<>/build' [ 69%] Built target helix_inimodel2d /usr/bin/make -f src/apps/CMakeFiles/helix_toolbox.dir/build.make src/apps/CMakeFiles/helix_toolbox.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/helix_toolbox.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/helix_toolbox.dir/build.make src/apps/CMakeFiles/helix_toolbox.dir/build make[4]: Entering directory '/<>/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/helix_toolbox.dir/build'. make[4]: Leaving directory '/<>/build' [ 70%] Built target helix_toolbox /usr/bin/make -f src/apps/CMakeFiles/image_handler.dir/build.make src/apps/CMakeFiles/image_handler.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/image_handler.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/image_handler.dir/build.make src/apps/CMakeFiles/image_handler.dir/build make[4]: Entering directory '/<>/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/image_handler.dir/build'. make[4]: Leaving directory '/<>/build' [ 71%] Built target image_handler /usr/bin/make -f src/apps/CMakeFiles/import.dir/build.make src/apps/CMakeFiles/import.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/import.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/import.dir/build.make src/apps/CMakeFiles/import.dir/build make[4]: Entering directory '/<>/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/import.dir/build'. make[4]: Leaving directory '/<>/build' [ 71%] Built target import /usr/bin/make -f src/apps/CMakeFiles/localsym.dir/build.make src/apps/CMakeFiles/localsym.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/localsym.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/localsym.dir/build.make src/apps/CMakeFiles/localsym.dir/build make[4]: Entering directory '/<>/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/localsym.dir/build'. make[4]: Leaving directory '/<>/build' [ 72%] Built target localsym /usr/bin/make -f src/apps/CMakeFiles/localsym_mpi.dir/build.make src/apps/CMakeFiles/localsym_mpi.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/localsym_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/localsym_mpi.dir/build.make src/apps/CMakeFiles/localsym_mpi.dir/build make[4]: Entering directory '/<>/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/localsym_mpi.dir/build'. make[4]: Leaving directory '/<>/build' [ 73%] Built target localsym_mpi /usr/bin/make -f src/apps/CMakeFiles/relion.dir/build.make src/apps/CMakeFiles/relion.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/relion.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/relion.dir/build.make src/apps/CMakeFiles/relion.dir/build make[4]: Entering directory '/<>/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/relion.dir/build'. make[4]: Leaving directory '/<>/build' [ 74%] Built target relion /usr/bin/make -f src/apps/CMakeFiles/manualpick.dir/build.make src/apps/CMakeFiles/manualpick.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/manualpick.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/manualpick.dir/build.make src/apps/CMakeFiles/manualpick.dir/build make[4]: Entering directory '/<>/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/manualpick.dir/build'. make[4]: Leaving directory '/<>/build' [ 75%] Built target manualpick /usr/bin/make -f src/apps/CMakeFiles/mask_create.dir/build.make src/apps/CMakeFiles/mask_create.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/mask_create.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/mask_create.dir/build.make src/apps/CMakeFiles/mask_create.dir/build make[4]: Entering directory '/<>/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/mask_create.dir/build'. make[4]: Leaving directory '/<>/build' [ 75%] Built target mask_create /usr/bin/make -f src/apps/CMakeFiles/merge_particles.dir/build.make src/apps/CMakeFiles/merge_particles.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/merge_particles.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/merge_particles.dir/build.make src/apps/CMakeFiles/merge_particles.dir/build make[4]: Entering directory '/<>/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/merge_particles.dir/build'. make[4]: Leaving directory '/<>/build' [ 76%] Built target merge_particles /usr/bin/make -f src/apps/CMakeFiles/motion_refine.dir/build.make src/apps/CMakeFiles/motion_refine.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/motion_refine.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/motion_refine.dir/build.make src/apps/CMakeFiles/motion_refine.dir/build make[4]: Entering directory '/<>/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/motion_refine.dir/build'. make[4]: Leaving directory '/<>/build' [ 77%] Built target motion_refine /usr/bin/make -f src/apps/CMakeFiles/motion_refine_mpi.dir/build.make src/apps/CMakeFiles/motion_refine_mpi.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/motion_refine_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/motion_refine_mpi.dir/build.make src/apps/CMakeFiles/motion_refine_mpi.dir/build make[4]: Entering directory '/<>/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/motion_refine_mpi.dir/build'. make[4]: Leaving directory '/<>/build' [ 78%] Built target motion_refine_mpi /usr/bin/make -f src/apps/CMakeFiles/mrc2vtk.dir/build.make src/apps/CMakeFiles/mrc2vtk.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/mrc2vtk.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/mrc2vtk.dir/build.make src/apps/CMakeFiles/mrc2vtk.dir/build make[4]: Entering directory '/<>/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/mrc2vtk.dir/build'. make[4]: Leaving directory '/<>/build' [ 78%] Built target mrc2vtk /usr/bin/make -f src/apps/CMakeFiles/particle_FCC.dir/build.make src/apps/CMakeFiles/particle_FCC.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/particle_FCC.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/particle_FCC.dir/build.make src/apps/CMakeFiles/particle_FCC.dir/build make[4]: Entering directory '/<>/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/particle_FCC.dir/build'. make[4]: Leaving directory '/<>/build' [ 79%] Built target particle_FCC /usr/bin/make -f src/apps/CMakeFiles/particle_reposition.dir/build.make src/apps/CMakeFiles/particle_reposition.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/particle_reposition.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/particle_reposition.dir/build.make src/apps/CMakeFiles/particle_reposition.dir/build make[4]: Entering directory '/<>/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/particle_reposition.dir/build'. make[4]: Leaving directory '/<>/build' [ 80%] Built target particle_reposition /usr/bin/make -f src/apps/CMakeFiles/particle_select.dir/build.make src/apps/CMakeFiles/particle_select.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/particle_select.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/particle_select.dir/build.make src/apps/CMakeFiles/particle_select.dir/build make[4]: Entering directory '/<>/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/particle_select.dir/build'. make[4]: Leaving directory '/<>/build' [ 81%] Built target particle_select /usr/bin/make -f src/apps/CMakeFiles/particle_subtract.dir/build.make src/apps/CMakeFiles/particle_subtract.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/particle_subtract.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/particle_subtract.dir/build.make src/apps/CMakeFiles/particle_subtract.dir/build make[4]: Entering directory '/<>/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/particle_subtract.dir/build'. make[4]: Leaving directory '/<>/build' [ 82%] Built target particle_subtract /usr/bin/make -f src/apps/CMakeFiles/particle_subtract_mpi.dir/build.make src/apps/CMakeFiles/particle_subtract_mpi.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/particle_subtract_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/particle_subtract_mpi.dir/build.make src/apps/CMakeFiles/particle_subtract_mpi.dir/build make[4]: Entering directory '/<>/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/particle_subtract_mpi.dir/build'. make[4]: Leaving directory '/<>/build' [ 82%] Built target particle_subtract_mpi /usr/bin/make -f src/apps/CMakeFiles/particle_symmetry_expand.dir/build.make src/apps/CMakeFiles/particle_symmetry_expand.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/particle_symmetry_expand.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/particle_symmetry_expand.dir/build.make src/apps/CMakeFiles/particle_symmetry_expand.dir/build make[4]: Entering directory '/<>/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/particle_symmetry_expand.dir/build'. make[4]: Leaving directory '/<>/build' [ 83%] Built target particle_symmetry_expand /usr/bin/make -f src/apps/CMakeFiles/pipeliner.dir/build.make src/apps/CMakeFiles/pipeliner.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/pipeliner.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/pipeliner.dir/build.make src/apps/CMakeFiles/pipeliner.dir/build make[4]: Entering directory '/<>/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/pipeliner.dir/build'. make[4]: Leaving directory '/<>/build' [ 84%] Built target pipeliner /usr/bin/make -f src/apps/CMakeFiles/plot_delocalisation.dir/build.make src/apps/CMakeFiles/plot_delocalisation.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/plot_delocalisation.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/plot_delocalisation.dir/build.make src/apps/CMakeFiles/plot_delocalisation.dir/build make[4]: Entering directory '/<>/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/plot_delocalisation.dir/build'. make[4]: Leaving directory '/<>/build' [ 85%] Built target plot_delocalisation /usr/bin/make -f src/apps/CMakeFiles/postprocess.dir/build.make src/apps/CMakeFiles/postprocess.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/postprocess.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/postprocess.dir/build.make src/apps/CMakeFiles/postprocess.dir/build make[4]: Entering directory '/<>/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/postprocess.dir/build'. make[4]: Leaving directory '/<>/build' [ 85%] Built target postprocess /usr/bin/make -f src/apps/CMakeFiles/postprocess_mpi.dir/build.make src/apps/CMakeFiles/postprocess_mpi.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/postprocess_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/postprocess_mpi.dir/build.make src/apps/CMakeFiles/postprocess_mpi.dir/build make[4]: Entering directory '/<>/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/postprocess_mpi.dir/build'. make[4]: Leaving directory '/<>/build' [ 86%] Built target postprocess_mpi /usr/bin/make -f src/apps/CMakeFiles/prepare_subtomo.dir/build.make src/apps/CMakeFiles/prepare_subtomo.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/prepare_subtomo.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/prepare_subtomo.dir/build.make src/apps/CMakeFiles/prepare_subtomo.dir/build make[4]: Entering directory '/<>/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/prepare_subtomo.dir/build'. make[4]: Leaving directory '/<>/build' [ 87%] Built target prepare_subtomo /usr/bin/make -f src/apps/CMakeFiles/preprocess.dir/build.make src/apps/CMakeFiles/preprocess.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/preprocess.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/preprocess.dir/build.make src/apps/CMakeFiles/preprocess.dir/build make[4]: Entering directory '/<>/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/preprocess.dir/build'. make[4]: Leaving directory '/<>/build' [ 88%] Built target preprocess /usr/bin/make -f src/apps/CMakeFiles/preprocess_mpi.dir/build.make src/apps/CMakeFiles/preprocess_mpi.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/preprocess_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/preprocess_mpi.dir/build.make src/apps/CMakeFiles/preprocess_mpi.dir/build make[4]: Entering directory '/<>/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/preprocess_mpi.dir/build'. make[4]: Leaving directory '/<>/build' [ 88%] Built target preprocess_mpi /usr/bin/make -f src/apps/CMakeFiles/project.dir/build.make src/apps/CMakeFiles/project.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/project.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/project.dir/build.make src/apps/CMakeFiles/project.dir/build make[4]: Entering directory '/<>/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/project.dir/build'. make[4]: Leaving directory '/<>/build' [ 89%] Built target project /usr/bin/make -f src/apps/CMakeFiles/reconstruct.dir/build.make src/apps/CMakeFiles/reconstruct.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/reconstruct.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/reconstruct.dir/build.make src/apps/CMakeFiles/reconstruct.dir/build make[4]: Entering directory '/<>/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/reconstruct.dir/build'. make[4]: Leaving directory '/<>/build' [ 90%] Built target reconstruct /usr/bin/make -f src/apps/CMakeFiles/reconstruct_mpi.dir/build.make src/apps/CMakeFiles/reconstruct_mpi.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/reconstruct_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/reconstruct_mpi.dir/build.make src/apps/CMakeFiles/reconstruct_mpi.dir/build make[4]: Entering directory '/<>/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/reconstruct_mpi.dir/build'. make[4]: Leaving directory '/<>/build' [ 91%] Built target reconstruct_mpi /usr/bin/make -f src/apps/CMakeFiles/refine.dir/build.make src/apps/CMakeFiles/refine.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/refine.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/refine.dir/build.make src/apps/CMakeFiles/refine.dir/build make[4]: Entering directory '/<>/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/refine.dir/build'. make[4]: Leaving directory '/<>/build' [ 91%] Built target refine /usr/bin/make -f src/apps/CMakeFiles/refine_mpi.dir/build.make src/apps/CMakeFiles/refine_mpi.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/refine_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/refine_mpi.dir/build.make src/apps/CMakeFiles/refine_mpi.dir/build make[4]: Entering directory '/<>/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/refine_mpi.dir/build'. make[4]: Leaving directory '/<>/build' [ 92%] Built target refine_mpi /usr/bin/make -f src/apps/CMakeFiles/reposition.dir/build.make src/apps/CMakeFiles/reposition.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/reposition.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/reposition.dir/build.make src/apps/CMakeFiles/reposition.dir/build make[4]: Entering directory '/<>/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/reposition.dir/build'. make[4]: Leaving directory '/<>/build' [ 93%] Built target reposition /usr/bin/make -f src/apps/CMakeFiles/run_ctffind.dir/build.make src/apps/CMakeFiles/run_ctffind.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/run_ctffind.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/run_ctffind.dir/build.make src/apps/CMakeFiles/run_ctffind.dir/build make[4]: Entering directory '/<>/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/run_ctffind.dir/build'. make[4]: Leaving directory '/<>/build' [ 93%] Built target run_ctffind /usr/bin/make -f src/apps/CMakeFiles/run_ctffind_mpi.dir/build.make src/apps/CMakeFiles/run_ctffind_mpi.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/run_ctffind_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/run_ctffind_mpi.dir/build.make src/apps/CMakeFiles/run_ctffind_mpi.dir/build make[4]: Entering directory '/<>/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/run_ctffind_mpi.dir/build'. make[4]: Leaving directory '/<>/build' [ 94%] Built target run_ctffind_mpi /usr/bin/make -f src/apps/CMakeFiles/run_motioncorr.dir/build.make src/apps/CMakeFiles/run_motioncorr.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/run_motioncorr.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/run_motioncorr.dir/build.make src/apps/CMakeFiles/run_motioncorr.dir/build make[4]: Entering directory '/<>/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/run_motioncorr.dir/build'. make[4]: Leaving directory '/<>/build' [ 95%] Built target run_motioncorr /usr/bin/make -f src/apps/CMakeFiles/run_motioncorr_mpi.dir/build.make src/apps/CMakeFiles/run_motioncorr_mpi.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/run_motioncorr_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/run_motioncorr_mpi.dir/build.make src/apps/CMakeFiles/run_motioncorr_mpi.dir/build make[4]: Entering directory '/<>/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/run_motioncorr_mpi.dir/build'. make[4]: Leaving directory '/<>/build' [ 96%] Built target run_motioncorr_mpi /usr/bin/make -f src/apps/CMakeFiles/scheduler.dir/build.make src/apps/CMakeFiles/scheduler.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/scheduler.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/scheduler.dir/build.make src/apps/CMakeFiles/scheduler.dir/build make[4]: Entering directory '/<>/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/scheduler.dir/build'. make[4]: Leaving directory '/<>/build' [ 96%] Built target scheduler /usr/bin/make -f src/apps/CMakeFiles/stack_create.dir/build.make src/apps/CMakeFiles/stack_create.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/stack_create.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/stack_create.dir/build.make src/apps/CMakeFiles/stack_create.dir/build make[4]: Entering directory '/<>/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/stack_create.dir/build'. make[4]: Leaving directory '/<>/build' [ 97%] Built target stack_create /usr/bin/make -f src/apps/CMakeFiles/star_handler.dir/build.make src/apps/CMakeFiles/star_handler.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/star_handler.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/star_handler.dir/build.make src/apps/CMakeFiles/star_handler.dir/build make[4]: Entering directory '/<>/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/star_handler.dir/build'. make[4]: Leaving directory '/<>/build' [ 98%] Built target star_handler /usr/bin/make -f src/apps/CMakeFiles/tiltpair_plot.dir/build.make src/apps/CMakeFiles/tiltpair_plot.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/tiltpair_plot.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/tiltpair_plot.dir/build.make src/apps/CMakeFiles/tiltpair_plot.dir/build make[4]: Entering directory '/<>/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/tiltpair_plot.dir/build'. make[4]: Leaving directory '/<>/build' [ 99%] Built target tiltpair_plot /usr/bin/make -f src/apps/CMakeFiles/tomo_test.dir/build.make src/apps/CMakeFiles/tomo_test.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/tomo_test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/tomo_test.dir/build.make src/apps/CMakeFiles/tomo_test.dir/build make[4]: Entering directory '/<>/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/tomo_test.dir/build'. make[4]: Leaving directory '/<>/build' [100%] Built target tomo_test make[3]: Leaving directory '/<>/build' /usr/bin/cmake -E cmake_progress_start /<>/build/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/<>/build' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/<>/build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /<>/debian/tmp/cli/usr/bin -- Installing: /<>/debian/tmp/cli/usr/bin/relion_particle_reposition -- Installing: /<>/debian/tmp/cli/usr/bin/relion -- Installing: /<>/debian/tmp/cli/usr/bin/relion_scheduler -- Installing: /<>/debian/tmp/cli/usr/bin/relion_star_printtable -- Installing: /<>/debian/tmp/cli/usr/bin/relion_pipeliner -- Installing: /<>/debian/tmp/cli/usr/bin/relion_preprocess -- Installing: /<>/debian/tmp/cli/usr/bin/relion_estimate_gain -- Installing: /<>/debian/tmp/cli/usr/bin/relion_merge_particles -- Installing: /<>/debian/tmp/cli/usr/bin/relion_prepare_subtomo -- Installing: /<>/debian/tmp/cli/usr/bin/relion_refine -- Installing: /<>/debian/tmp/cli/usr/bin/relion_star_datablock_singlefiles -- Installing: /<>/debian/tmp/cli/usr/bin/relion_autopick_mpi -- Installing: /<>/debian/tmp/cli/usr/bin/relion_run_ctffind_mpi -- Installing: /<>/debian/tmp/cli/usr/bin/relion_convert_to_tiff -- Installing: /<>/debian/tmp/cli/usr/bin/relion_star_loopheader -- Installing: /<>/debian/tmp/cli/usr/bin/relion_ctf_refine -- Installing: /<>/debian/tmp/cli/usr/bin/relion_star_datablock_stack -- Installing: /<>/debian/tmp/cli/usr/bin/relion_find_tiltpairs -- Installing: /<>/debian/tmp/cli/usr/bin/relion_project -- Installing: /<>/debian/tmp/cli/usr/bin/relion_autopick -- Installing: /<>/debian/tmp/cli/usr/bin/relion_reposition -- Installing: /<>/debian/tmp/cli/usr/bin/relion_display -- Installing: /<>/debian/tmp/cli/usr/bin/relion_flex_analyse -- Installing: /<>/debian/tmp/cli/usr/bin/relion_helix_toolbox -- Installing: /<>/debian/tmp/cli/usr/bin/relion_reconstruct_mpi -- Installing: /<>/debian/tmp/cli/usr/bin/relion_convert_star -- Installing: /<>/debian/tmp/cli/usr/bin/relion_image_handler -- Installing: /<>/debian/tmp/cli/usr/bin/relion_preprocess_mpi -- Installing: /<>/debian/tmp/cli/usr/bin/relion_run_ctffind -- Installing: /<>/debian/tmp/cli/usr/bin/relion_particle_symmetry_expand -- Installing: /<>/debian/tmp/cli/usr/bin/relion_external_reconstruct -- Installing: /<>/debian/tmp/cli/usr/bin/relion_qsub.csh -- Installing: /<>/debian/tmp/cli/usr/bin/relion_reconstruct -- Installing: /<>/debian/tmp/cli/usr/bin/relion_star_datablock_ctfdat -- Installing: /<>/debian/tmp/cli/usr/bin/relion_demodulate -- Installing: /<>/debian/tmp/cli/usr/bin/relion_convert_to_tiff_mpi -- Installing: /<>/debian/tmp/cli/usr/bin/relion_plot_delocalisation -- Installing: /<>/debian/tmp/cli/usr/bin/relion_refine_mpi -- Installing: /<>/debian/tmp/cli/usr/bin/relion_run_motioncorr_mpi -- Installing: /<>/debian/tmp/cli/usr/bin/relion_ctf_toolbox -- Installing: /<>/debian/tmp/cli/usr/bin/relion_star_plottable -- Installing: /<>/debian/tmp/cli/usr/bin/relion_import -- Installing: /<>/debian/tmp/cli/usr/bin/relion_manualpick -- Installing: /<>/debian/tmp/cli/usr/bin/relion_stack_create -- Installing: /<>/debian/tmp/cli/usr/bin/relion_particle_subtract_mpi -- Installing: /<>/debian/tmp/cli/usr/bin/relion_align_symmetry -- Installing: /<>/debian/tmp/cli/usr/bin/relion_ctf_refine_mpi -- Installing: /<>/debian/tmp/cli/usr/bin/relion_tomo_test -- Installing: /<>/debian/tmp/cli/usr/bin/relion_localsym_mpi -- Installing: /<>/debian/tmp/cli/usr/bin/relion_run_motioncorr -- Installing: /<>/debian/tmp/cli/usr/bin/relion_star_handler -- Installing: /<>/debian/tmp/cli/usr/bin/relion_mrc2vtk -- Installing: /<>/debian/tmp/cli/usr/bin/relion_postprocess -- Installing: /<>/debian/tmp/cli/usr/bin/relion_particle_select -- Installing: /<>/debian/tmp/cli/usr/bin/relion_postprocess_mpi -- Installing: /<>/debian/tmp/cli/usr/bin/relion_particle_subtract -- Installing: /<>/debian/tmp/cli/usr/bin/relion_ctf_mask_test -- Installing: /<>/debian/tmp/cli/usr/bin/relion_mask_create -- Installing: /<>/debian/tmp/cli/usr/bin/relion_helix_inimodel2d -- Installing: /<>/debian/tmp/cli/usr/bin/relion_motion_refine -- Installing: /<>/debian/tmp/cli/usr/bin/relion_particle_FCC -- Installing: /<>/debian/tmp/cli/usr/bin/relion_localsym -- Installing: /<>/debian/tmp/cli/usr/bin/relion_motion_refine_mpi -- Installing: /<>/debian/tmp/cli/usr/bin/relion_tiltpair_plot -- Installing: /<>/debian/tmp/cli/usr/bin/relion_flex_analyse_mpi -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_align_symmetry -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_autopick -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_autopick_mpi -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_convert_star -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_convert_to_tiff -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_convert_to_tiff_mpi -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_ctf_mask_test -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_ctf_refine -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_ctf_refine_mpi -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_ctf_toolbox -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_demodulate -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_display -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_estimate_gain -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_external_reconstruct -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_find_tiltpairs -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_flex_analyse -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_flex_analyse_mpi -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_helix_inimodel2d -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_helix_toolbox -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_image_handler -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_import -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_localsym -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_localsym_mpi -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_manualpick -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_mask_create -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_merge_particles -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_motion_refine -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_motion_refine_mpi -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_mrc2vtk -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_particle_FCC -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_particle_reposition -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_particle_select -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_particle_subtract -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_particle_subtract_mpi -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_particle_symmetry_expand -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_pipeliner -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_plot_delocalisation -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_postprocess -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_postprocess_mpi -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_prepare_subtomo -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_preprocess -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_preprocess_mpi -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_project -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_reconstruct -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_reconstruct_mpi -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_refine -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_refine_mpi -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_reposition -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_run_ctffind -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_run_ctffind_mpi -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_run_motioncorr -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_run_motioncorr_mpi -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_scheduler -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_stack_create -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_star_handler -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_tiltpair_plot -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_tomo_test make[2]: Leaving directory '/<>/build' mkdir -p /<>/debian/tmp/gui/usr/bin rm /<>/debian/tmp/cli/usr/bin/*.csh # Useless ... set -e; for prog in relion relion_display relion_manualpick; do \ mv /<>/debian/tmp/cli/usr/bin/$prog \ /<>/debian/tmp/gui/usr/bin; done make[1]: Leaving directory '/<>' dh_install -a dh_installdocs -a dh_installchangelogs -a dh_lintian -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a dh_strip -a debugedit: debian/relion/usr/bin/relion_particle_reposition: Unknown DWARF DW_FORM_0x1f20 debugedit: debian/relion-gui/usr/bin/relion: Unknown DWARF DW_FORM_0x1f21 d0233328177c427d4ad0dbda49703192da999c14 f7b2630e2b769597c49790b393dfce213d700535 debugedit: debian/relion/usr/bin/relion_scheduler: Unknown DWARF DW_FORM_0x1f20 cd7a3b49f7fb8b26d3dc3ef2d808d471b94d1dc3 debugedit: debian/relion-gui/usr/bin/relion_display: Unknown DWARF DW_FORM_0x1f21 fc6a32b14e35410887858af0b9dfdb9ffe35b7fc debugedit: debian/relion-gui/usr/bin/relion_manualpick: Unknown DWARF DW_FORM_0x1f21 16eaa13405df0f393d32dde7eeb421873071fb29 debugedit: debian/relion/usr/bin/relion_pipeliner: Unknown DWARF DW_FORM_0x1f20 5ed98cd6dc9b9c222d763bd6a453f9aae5dc3853 debugedit: debian/relion/usr/bin/relion_preprocess: Unknown DWARF DW_FORM_0x1f20 a799c68adb3a1da621dd0696aaf7d505f6dd3423 debugedit: debian/relion/usr/bin/relion_estimate_gain: Unknown DWARF DW_FORM_0x1f20 e1add65b9938ccb4cdf6fbe3287add68fa963561 debugedit: debian/relion/usr/bin/relion_merge_particles: Unknown DWARF DW_FORM_0x1f20 b0853e957854b0b83888472871e000abfa3a7299 debugedit: debian/relion/usr/bin/relion_prepare_subtomo: Unknown DWARF DW_FORM_0x1f20 577e4aa60519a10b5da4568ad97bf06ea8821dc0 debugedit: debian/relion/usr/bin/relion_refine: Unknown DWARF DW_FORM_0x1f20 497dcef1b09ec8d833ef9e4561d4c07cbf5f715b debugedit: debian/relion/usr/bin/relion_autopick_mpi: Unknown DWARF DW_FORM_0x1f21 d169f2828ff17731fc250c6eb19896d7c412d741 debugedit: debian/relion/usr/bin/relion_run_ctffind_mpi: Unknown DWARF DW_FORM_0x1f20 0e7af0a8e39ee4f35b07aeced053d3606c1d7ddf debugedit: debian/relion/usr/bin/relion_convert_to_tiff: Unknown DWARF DW_FORM_0x1f20 c3fea49d9f2f156ed77f0e12beecad92f006c9b6 debugedit: debian/relion/usr/bin/relion_ctf_refine: Unknown DWARF DW_FORM_0x1f20 105d34d21e2e3036c44bf3e38e34c59d3b643912 debugedit: debian/relion/usr/bin/relion_find_tiltpairs: Unknown DWARF DW_FORM_0x1f20 b9ba79a7d3e761e597dc347610bdd805b8f77217 debugedit: debian/relion/usr/bin/relion_project: Unknown DWARF DW_FORM_0x1f20 67210b47ef1924879c57951f9ecb7ce0b02c8f37 debugedit: debian/relion/usr/bin/relion_autopick: Unknown DWARF DW_FORM_0x1f20 f73447c370f9d7795467e51f6c4427ce479d114c debugedit: debian/relion/usr/bin/relion_reposition: Unknown DWARF DW_FORM_0x1f20 c6aba2ab572a476bee46ed22c32743eb6bf00447 debugedit: debian/relion/usr/bin/relion_flex_analyse: Unknown DWARF DW_FORM_0x1f20 d327e25a72886a3722316ef7de940de21eddb4d6 debugedit: debian/relion/usr/bin/relion_helix_toolbox: Unknown DWARF DW_FORM_0x1f20 bc0fb8b48cde6a05d8b8bc0f468752e688c83c9f debugedit: debian/relion/usr/bin/relion_reconstruct_mpi: Unknown DWARF DW_FORM_0x1f20 c6410ce7cb3b418dc554b29685930a3772cce3b9 debugedit: debian/relion/usr/bin/relion_convert_star: Unknown DWARF DW_FORM_0x1f20 e2b0f5c32de562c09fd314aab5be4faa661bceaa debugedit: debian/relion/usr/bin/relion_image_handler: Unknown DWARF DW_FORM_0x1f20 d5cedbefcbe8fcde78395ef34b6466e51ce1cfc4 debugedit: debian/relion/usr/bin/relion_preprocess_mpi: Unknown DWARF DW_FORM_0x1f20 0280a628733777b4bdffbc11b9a65a8f4c8a3390 debugedit: debian/relion/usr/bin/relion_run_ctffind: Unknown DWARF DW_FORM_0x1f20 df250804d70967d8f02b57245125b4c7b74e76de debugedit: debian/relion/usr/bin/relion_particle_symmetry_expand: Unknown DWARF DW_FORM_0x1f20 06a7677572014b16f4d0b371d04f6ce6d47d55e1 debugedit: debian/relion/usr/bin/relion_external_reconstruct: Unknown DWARF DW_FORM_0x1f20 a9d9188faf0289a568266f3dcf0f8284055ddbb7 debugedit: debian/relion/usr/bin/relion_reconstruct: Unknown DWARF DW_FORM_0x1f20 1bf19a7c3e32bce8c176d0b99754f57b46bddeae debugedit: debian/relion/usr/bin/relion_demodulate: Unknown DWARF DW_FORM_0x1f20 be40f5459224360236539c251bdf7235910d2d5c debugedit: debian/relion/usr/bin/relion_convert_to_tiff_mpi: Unknown DWARF DW_FORM_0x1f21 10a2edb68e0d45bc76db94ffbfbfb2edd419afa3 debugedit: debian/relion/usr/bin/relion_plot_delocalisation: Unknown DWARF DW_FORM_0x1f20 89bf281f1fe44f5574b4f9374b4ea9c12f28017d debugedit: debian/relion/usr/bin/relion_refine_mpi: Unknown DWARF DW_FORM_0x1f20 5c48bb6f09dfd1b8a2a0f69cf3810fec1650e867 debugedit: debian/relion/usr/bin/relion_run_motioncorr_mpi: Unknown DWARF DW_FORM_0x1f20 eb1f6fc5628547b1cc267640081f30e8b65fdf4b debugedit: debian/relion/usr/bin/relion_ctf_toolbox: Unknown DWARF DW_FORM_0x1f20 0232bb807785a24283331bce2c58919d68c141bb debugedit: debian/relion/usr/bin/relion_import: Unknown DWARF DW_FORM_0x1f20 edce94506a3e653d29ad90d987cb0dea35a22098 debugedit: debian/relion/usr/bin/relion_stack_create: Unknown DWARF DW_FORM_0x1f20 66c5177fc7e4fe0df6bf32e8898e037c012f1db8 debugedit: debian/relion/usr/bin/relion_particle_subtract_mpi: Unknown DWARF DW_FORM_0x1f20 df0fd8edbdaafe735c64491e32482cb2b2722205 debugedit: debian/relion/usr/bin/relion_align_symmetry: Unknown DWARF DW_FORM_0x1f20 eb9a3a71128024a29623c32c7037c1d438924a25 debugedit: debian/relion/usr/bin/relion_ctf_refine_mpi: Unknown DWARF DW_FORM_0x1f20 03d904d2a0549e0ba7d57e5264209c95769064a6 debugedit: debian/relion/usr/bin/relion_tomo_test: Unknown DWARF DW_FORM_0x1f20 18f8065028a4651dde4f116d08eeaba0ef7d9fb6 debugedit: debian/relion/usr/bin/relion_localsym_mpi: Unknown DWARF DW_FORM_0x1f20 8a2e6b1c91926468caf7c51f4567bc8bd489ce1b debugedit: debian/relion/usr/bin/relion_run_motioncorr: Unknown DWARF DW_FORM_0x1f20 65aeda829ffc5e9e4ffac6529c19f6a8d54a7716 debugedit: debian/relion/usr/bin/relion_star_handler: Unknown DWARF DW_FORM_0x1f20 b956bb59c836f6d4757a8d48a4a96c2e66054e08 debugedit: debian/relion/usr/bin/relion_mrc2vtk: Unknown DWARF DW_FORM_0x1f20 f75a2d215093af4f149ecd064eab88b5f95f52f4 debugedit: debian/relion/usr/bin/relion_postprocess: Unknown DWARF DW_FORM_0x1f20 0d6d466e29eae086e8330445d9e2c56439030898 debugedit: debian/relion/usr/bin/relion_particle_select: Unknown DWARF DW_FORM_0x1f20 90c94faf82622e691990ad10f63cb5ea92ebaae0 debugedit: debian/relion/usr/bin/relion_postprocess_mpi: Unknown DWARF DW_FORM_0x1f20 0746e52ae808b2147a597c091875bfbefef2691b debugedit: debian/relion/usr/bin/relion_particle_subtract: Unknown DWARF DW_FORM_0x1f20 8b127a596bcea0a47671341cb212c8f9f38b74fd debugedit: debian/relion/usr/bin/relion_ctf_mask_test: Unknown DWARF DW_FORM_0x1f20 9f89a2420fe5818a6dbb3093f81036a642a59883 debugedit: debian/relion/usr/bin/relion_mask_create: Unknown DWARF DW_FORM_0x1f20 93131fc14a81f5e6654549afa521437648d39166 debugedit: debian/relion/usr/bin/relion_helix_inimodel2d: Unknown DWARF DW_FORM_0x1f20 a1ba1fcf84c1562ab6bf4dca1224280aa2bc69e1 debugedit: debian/relion/usr/bin/relion_motion_refine: Unknown DWARF DW_FORM_0x1f20 f153ad7781ce2aa0b6bcb785157e1a0440d0f992 debugedit: debian/relion/usr/bin/relion_particle_FCC: Unknown DWARF DW_FORM_0x1f20 8bdb1ecc28a21ab3132576ea54fbbc5b07d4b69a debugedit: debian/relion/usr/bin/relion_localsym: Unknown DWARF DW_FORM_0x1f20 6567cdf8a408bc40ec5d034387249464802c253a debugedit: debian/relion/usr/bin/relion_motion_refine_mpi: Unknown DWARF DW_FORM_0x1f20 633ce535172451e2edc056c997bf62bb023f4b14 debugedit: debian/relion/usr/bin/relion_tiltpair_plot: Unknown DWARF DW_FORM_0x1f20 aa3a1fd7ac7bb8d0aae9d8e95ba624a337ba21fa debugedit: debian/relion/usr/bin/relion_flex_analyse_mpi: Unknown DWARF DW_FORM_0x1f20 ec2fde326a9af50a4b91adf4c2432c450fc4e930 dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a INFO: pkgstriptranslations version 151 INFO: pkgstriptranslations version 151 INFO: pkgstriptranslations version 151 INFO: pkgstriptranslations version 151 pkgstriptranslations: processing relion (in debian/relion); do_strip: , oemstrip: pkgstriptranslations: processing relion-gui (in debian/relion-gui); do_strip: , oemstrip: pkgstriptranslations: processing relion-dbgsym (in debian/.debhelper/relion/dbgsym-root); do_strip: , oemstrip: pkgstriptranslations: processing relion-gui-dbgsym (in debian/.debhelper/relion-gui/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/relion/DEBIAN/control, package relion, directory debian/relion pkgstripfiles: Running PNG optimization (using 4 cpus) for package relion ... pkgstripfiles: No PNG files. dpkg-deb: building package 'relion' in '../relion_3.1.3-3build1_ppc64el.deb'. pkgstripfiles: processing control file: debian/relion-gui/DEBIAN/control, package relion-gui, directory debian/relion-gui pkgstripfiles: processing control file: debian/.debhelper/relion/dbgsym-root/DEBIAN/control, package relion-dbgsym, directory debian/.debhelper/relion/dbgsym-root dpkg-deb: building package 'relion-dbgsym' in 'debian/.debhelper/scratch-space/build-relion/relion-dbgsym_3.1.3-3build1_ppc64el.deb'. Searching for duplicated docs in dependency relion... pkgstripfiles: processing control file: debian/.debhelper/relion-gui/dbgsym-root/DEBIAN/control, package relion-gui-dbgsym, directory debian/.debhelper/relion-gui/dbgsym-root dpkg-deb: building package 'relion-gui-dbgsym' in 'debian/.debhelper/scratch-space/build-relion-gui/relion-gui-dbgsym_3.1.3-3build1_ppc64el.deb'. symlinking changelog.Debian.gz in relion-gui to file in relion pkgstripfiles: Running PNG optimization (using 4 cpus) for package relion-gui ... pkgstripfiles: No PNG files. dpkg-deb: building package 'relion-gui' in '../relion-gui_3.1.3-3build1_ppc64el.deb'. Renaming relion-gui-dbgsym_3.1.3-3build1_ppc64el.deb to relion-gui-dbgsym_3.1.3-3build1_ppc64el.ddeb Renaming relion-dbgsym_3.1.3-3build1_ppc64el.deb to relion-dbgsym_3.1.3-3build1_ppc64el.ddeb dpkg-genbuildinfo --build=any -O../relion_3.1.3-3build1_ppc64el.buildinfo dpkg-genchanges --build=any -mLaunchpad Build Daemon -O../relion_3.1.3-3build1_ppc64el.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2023-02-04T13:24:25Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ relion_3.1.3-3build1_ppc64el.changes: ------------------------------------- Format: 1.8 Date: Sat, 04 Feb 2023 07:33:54 -0500 Source: relion Binary: relion relion-gui Built-For-Profiles: noudeb Architecture: ppc64el Version: 3.1.3-3build1 Distribution: lunar-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Jeremy Bicha Description: relion - toolkit for 3D reconstructions in cryo-electron microscopy relion-gui - toolkit for 3D reconstructions in cryo-electron microscopy (gui a Changes: relion (3.1.3-3build1) lunar; urgency=medium . * Rebuild against latest tiff Checksums-Sha1: c93371429d18642fd9d37584f1a30bed7612f99f 208198808 relion-dbgsym_3.1.3-3build1_ppc64el.ddeb 5273d276023155b995f51e6917247ed9415b238b 14680360 relion-gui-dbgsym_3.1.3-3build1_ppc64el.ddeb 5158df5f940d48fb205216303fc6cd7056f43482 1296946 relion-gui_3.1.3-3build1_ppc64el.deb 8795034337a6f49edf4365e32e7e312f36fc2103 11189 relion_3.1.3-3build1_ppc64el.buildinfo 6921f6cd613fb1417546f70cd7c512b35c4a0b3b 13508884 relion_3.1.3-3build1_ppc64el.deb Checksums-Sha256: 9be9a915089d888f9299fa1d1aa4fc6d984895b375bc9d4d3cd5321650901bde 208198808 relion-dbgsym_3.1.3-3build1_ppc64el.ddeb be4ec444491da0c412c992f280c85ba9cee664b235587d3c27fb09a0cddd2f16 14680360 relion-gui-dbgsym_3.1.3-3build1_ppc64el.ddeb 0148ff422fce7ad53400a2d0e060e2a9e22e6a69a6d7982e9dc282ca6a48f719 1296946 relion-gui_3.1.3-3build1_ppc64el.deb 009a4be6ed0e14553d651ebd6c0f08e35394556155c97c057b79f3f28edb1c7a 11189 relion_3.1.3-3build1_ppc64el.buildinfo f3f2ae809f78cf67c572505113990af75c2d52e4838d9ba0993e4beed1da94c1 13508884 relion_3.1.3-3build1_ppc64el.deb Files: 8c90eeb95a1db0cfc14a25eed43e9c23 208198808 debug optional relion-dbgsym_3.1.3-3build1_ppc64el.ddeb 3923dfc537a51b651ee22c54eb8cc905 14680360 debug optional relion-gui-dbgsym_3.1.3-3build1_ppc64el.ddeb 1f4f735b9e62e231331647f84457f592 1296946 science optional relion-gui_3.1.3-3build1_ppc64el.deb 80ca757088937e464fac82751ea8f81e 11189 science optional relion_3.1.3-3build1_ppc64el.buildinfo 7a1d53fa4fd68349bf45b310895157ef 13508884 science optional relion_3.1.3-3build1_ppc64el.deb /<>/relion_3.1.3-3build1_ppc64el.changes.new could not be renamed to /<>/relion_3.1.3-3build1_ppc64el.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: relion Binary: relion relion-dbgsym relion-gui relion-gui-dbgsym Architecture: ppc64el Version: 3.1.3-3build1 Checksums-Md5: 8c90eeb95a1db0cfc14a25eed43e9c23 208198808 relion-dbgsym_3.1.3-3build1_ppc64el.ddeb 3923dfc537a51b651ee22c54eb8cc905 14680360 relion-gui-dbgsym_3.1.3-3build1_ppc64el.ddeb 1f4f735b9e62e231331647f84457f592 1296946 relion-gui_3.1.3-3build1_ppc64el.deb 7a1d53fa4fd68349bf45b310895157ef 13508884 relion_3.1.3-3build1_ppc64el.deb Checksums-Sha1: c93371429d18642fd9d37584f1a30bed7612f99f 208198808 relion-dbgsym_3.1.3-3build1_ppc64el.ddeb 5273d276023155b995f51e6917247ed9415b238b 14680360 relion-gui-dbgsym_3.1.3-3build1_ppc64el.ddeb 5158df5f940d48fb205216303fc6cd7056f43482 1296946 relion-gui_3.1.3-3build1_ppc64el.deb 6921f6cd613fb1417546f70cd7c512b35c4a0b3b 13508884 relion_3.1.3-3build1_ppc64el.deb Checksums-Sha256: 9be9a915089d888f9299fa1d1aa4fc6d984895b375bc9d4d3cd5321650901bde 208198808 relion-dbgsym_3.1.3-3build1_ppc64el.ddeb be4ec444491da0c412c992f280c85ba9cee664b235587d3c27fb09a0cddd2f16 14680360 relion-gui-dbgsym_3.1.3-3build1_ppc64el.ddeb 0148ff422fce7ad53400a2d0e060e2a9e22e6a69a6d7982e9dc282ca6a48f719 1296946 relion-gui_3.1.3-3build1_ppc64el.deb f3f2ae809f78cf67c572505113990af75c2d52e4838d9ba0993e4beed1da94c1 13508884 relion_3.1.3-3build1_ppc64el.deb Build-Origin: Ubuntu Build-Architecture: ppc64el Build-Date: Sat, 04 Feb 2023 13:24:22 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: adduser (= 3.129ubuntu1), autoconf (= 2.71-3), automake (= 1:1.16.5-1.3), autopoint (= 0.21-11), autotools-dev (= 20220109.1), base-files (= 12.3ubuntu1), base-passwd (= 3.6.1), bash (= 5.2.15-2ubuntu1), binutils (= 2.40-2ubuntu1), binutils-common (= 2.40-2ubuntu1), binutils-powerpc64le-linux-gnu (= 2.40-2ubuntu1), bsdextrautils (= 2.38.1-4ubuntu1), bsdutils (= 1:2.38.1-4ubuntu1), build-essential (= 12.9ubuntu3), bzip2 (= 1.0.8-5build1), cmake (= 3.25.1-1), cmake-data (= 3.25.1-1), coreutils (= 9.1-1ubuntu2), cpp (= 4:12.2.0-1ubuntu1), cpp-12 (= 12.2.0-14ubuntu1), dash (= 0.5.11+git20210903+057cd650a4ed-9ubuntu1), debconf (= 1.5.82), debhelper (= 13.11.4ubuntu3), debianutils (= 5.7-0.4), debugedit (= 1:5.0-5), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.13.1-1), diffutils (= 1:3.8-3), dpkg (= 1.21.19ubuntu3), dpkg-dev (= 1.21.19ubuntu3), dwz (= 0.15-1), file (= 1:5.44-3), findutils (= 4.9.0-3ubuntu1), fluid (= 1.3.8-5), fontconfig-config (= 2.14.1-3ubuntu1), fonts-dejavu-core (= 2.37-2build2), g++ (= 4:12.2.0-1ubuntu1), g++-12 (= 12.2.0-14ubuntu1), gcc (= 4:12.2.0-1ubuntu1), gcc-12 (= 12.2.0-14ubuntu1), gcc-12-base (= 12.2.0-14ubuntu1), gettext (= 0.21-11), gettext-base (= 0.21-11), gfortran-12 (= 12.2.0-14ubuntu1), grep (= 3.8-5), groff-base (= 1.22.4-9), gzip (= 1.12-1ubuntu1), hostname (= 3.23ubuntu2), ibverbs-providers (= 44.0-2), init-system-helpers (= 1.65.2), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.1-3), libarchive-zip-perl (= 1.68-1), libarchive13 (= 3.6.2-1ubuntu1), libasan8 (= 12.2.0-14ubuntu1), libatomic1 (= 12.2.0-14ubuntu1), libattr1 (= 1:2.5.1-4), libaudit-common (= 1:3.0.7-1.1), libaudit1 (= 1:3.0.7-1.1), libbinutils (= 2.40-2ubuntu1), libblkid1 (= 2.38.1-4ubuntu1), libbrotli1 (= 1.0.9-2build7), libbsd0 (= 0.11.7-2), libbz2-1.0 (= 1.0.8-5build1), libc-bin (= 2.37-0ubuntu1), libc-dev-bin (= 2.37-0ubuntu1), libc6 (= 2.37-0ubuntu1), libc6-dev (= 2.37-0ubuntu1), libcairo2 (= 1.16.0-7), libcap-ng0 (= 0.8.3-1build1), libcap2 (= 1:2.66-3ubuntu1), libcbor0.8 (= 0.8.0-2ubuntu1), libcc1-0 (= 12.2.0-14ubuntu1), libcom-err2 (= 1.46.6~rc1-1ubuntu1), libcrypt-dev (= 1:4.4.33-2), libcrypt1 (= 1:4.4.33-2), libctf-nobfd0 (= 2.40-2ubuntu1), libctf0 (= 2.40-2ubuntu1), libcurl4 (= 7.87.0-2ubuntu1), libdb5.3 (= 5.3.28+dfsg2-1), libdebconfclient0 (= 0.264ubuntu1), libdebhelper-perl (= 13.11.4ubuntu3), libdeflate-dev (= 1.14-1), libdeflate0 (= 1.14-1), libdpkg-perl (= 1.21.19ubuntu3), libdrm-amdgpu1 (= 2.4.114-1), libdrm-common (= 2.4.114-1), libdrm-nouveau2 (= 2.4.114-1), libdrm-radeon1 (= 2.4.114-1), libdrm2 (= 2.4.114-1), libdw1 (= 0.188-2.1), libedit2 (= 3.1-20221030-2), libelf1 (= 0.188-2.1), libevent-2.1-7a (= 2.1.12-stable-5ubuntu1), libevent-core-2.1-7a (= 2.1.12-stable-5ubuntu1), libevent-dev (= 2.1.12-stable-5ubuntu1), libevent-extra-2.1-7 (= 2.1.12-stable-5ubuntu1), libevent-openssl-2.1-7 (= 2.1.12-stable-5ubuntu1), libevent-pthreads-2.1-7 (= 2.1.12-stable-5ubuntu1), libexpat1 (= 2.5.0-1), libfabric1 (= 1.17.0-3), libffi8 (= 3.4.4-1), libfftw3-bin (= 3.3.8-2ubuntu8), libfftw3-dev (= 3.3.8-2ubuntu8), libfftw3-double3 (= 3.3.8-2ubuntu8), libfftw3-long3 (= 3.3.8-2ubuntu8), libfftw3-single3 (= 3.3.8-2ubuntu8), libfido2-1 (= 1.12.0-2), libfile-stripnondeterminism-perl (= 1.13.1-1), libfltk-cairo1.3 (= 1.3.8-5), libfltk-forms1.3 (= 1.3.8-5), libfltk-gl1.3 (= 1.3.8-5), libfltk-images1.3 (= 1.3.8-5), libfltk1.3 (= 1.3.8-5), libfltk1.3-dev (= 1.3.8-5), libfontconfig1 (= 2.14.1-3ubuntu1), libfreetype6 (= 2.12.1+dfsg-4), libgcc-12-dev (= 12.2.0-14ubuntu1), libgcc-s1 (= 12.2.0-14ubuntu1), libgcrypt20 (= 1.10.1-3ubuntu1), libgdbm-compat4 (= 1.23-3), libgdbm6 (= 1.23-3), libgfortran-12-dev (= 12.2.0-14ubuntu1), libgfortran5 (= 12.2.0-14ubuntu1), libgl1 (= 1.6.0-1), libgl1-mesa-dri (= 22.2.5-0ubuntu1), libglapi-mesa (= 22.2.5-0ubuntu1), libglvnd0 (= 1.6.0-1), libglx-mesa0 (= 22.2.5-0ubuntu1), libglx0 (= 1.6.0-1), libgmp10 (= 2:6.2.1+dfsg1-1.1ubuntu1), libgnutls30 (= 3.7.8-4ubuntu1), libgomp1 (= 12.2.0-14ubuntu1), libgpg-error0 (= 1.46-1), libgssapi-krb5-2 (= 1.20.1-1build1), libhogweed6 (= 3.8.1-2), libhwloc-dev (= 2.9.0-1), libhwloc-plugins (= 2.9.0-1), libhwloc15 (= 2.9.0-1), libibverbs-dev (= 44.0-2), libibverbs1 (= 44.0-2), libicu71 (= 71.1-3ubuntu1), libidn2-0 (= 2.3.3-1build1), libisl23 (= 0.25-1), libitm1 (= 12.2.0-14ubuntu1), libjansson4 (= 2.14-2), libjbig-dev (= 2.1-6ubuntu1), libjbig0 (= 2.1-6ubuntu1), libjpeg-dev (= 8c-2ubuntu10), libjpeg-turbo8 (= 2.1.2-0ubuntu1), libjpeg-turbo8-dev (= 2.1.2-0ubuntu1), libjpeg8 (= 8c-2ubuntu10), libjpeg8-dev (= 8c-2ubuntu10), libjs-jquery (= 3.6.1+dfsg+~3.5.14-1), libjs-jquery-ui (= 1.13.2+dfsg-1), libjsoncpp25 (= 1.9.5-4), libk5crypto3 (= 1.20.1-1build1), libkeyutils1 (= 1.6.3-2), libkrb5-3 (= 1.20.1-1build1), libkrb5support0 (= 1.20.1-1build1), libldap2 (= 2.6.3+dfsg-1~exp1ubuntu1), liblerc-dev (= 4.0.0+ds-2ubuntu2), liblerc4 (= 4.0.0+ds-2ubuntu2), libllvm15 (= 1:15.0.7-1), liblsan0 (= 12.2.0-14ubuntu1), libltdl-dev (= 2.4.7-5), libltdl7 (= 2.4.7-5), liblz4-1 (= 1.9.4-1), liblzma-dev (= 5.4.1-0.0), liblzma5 (= 5.4.1-0.0), libmagic-mgc (= 1:5.44-3), libmagic1 (= 1:5.44-3), libmd0 (= 1.0.4-2), libmount1 (= 2.38.1-4ubuntu1), libmpc3 (= 1.3.1-1), libmpfr6 (= 4.2.0-1), libmunge2 (= 0.5.15-2), libncurses6 (= 6.4-2), libncursesw6 (= 6.4-2), libnettle8 (= 3.8.1-2), libnghttp2-14 (= 1.51.0-1), libnl-3-200 (= 3.7.0-0.2), libnl-3-dev (= 3.7.0-0.2), libnl-route-3-200 (= 3.7.0-0.2), libnl-route-3-dev (= 3.7.0-0.2), libnsl-dev (= 1.3.0-2build2), libnsl2 (= 1.3.0-2build2), libnuma-dev (= 2.0.16-1), libnuma1 (= 2.0.16-1), libopenmpi-dev (= 4.1.4-3ubuntu2), libopenmpi3 (= 4.1.4-3ubuntu2), libp11-kit0 (= 0.24.1-2ubuntu1), libpam-modules (= 1.5.2-5ubuntu1), libpam-modules-bin (= 1.5.2-5ubuntu1), libpam-runtime (= 1.5.2-5ubuntu1), libpam0g (= 1.5.2-5ubuntu1), libpciaccess0 (= 0.17-2), libpcre2-8-0 (= 10.42-1), libperl5.36 (= 5.36.0-7), libpipeline1 (= 1.5.7-1), libpixman-1-0 (= 0.42.2-1), libpmix-dev (= 4.2.2-1), libpmix2 (= 4.2.2-1), libpng16-16 (= 1.6.39-2), libprocps8 (= 2:3.3.17-7ubuntu1), libpsl5 (= 0.21.0-1.2build2), libpthread-stubs0-dev (= 0.4-1build2), libquadmath0 (= 12.2.0-14ubuntu1), librdmacm1 (= 44.0-2), librhash0 (= 1.4.3-3), librtmp1 (= 2.4+20151223.gitfa8646d.1-2build4), libsasl2-2 (= 2.1.28+dfsg-10), libsasl2-modules-db (= 2.1.28+dfsg-10), libseccomp2 (= 2.5.4-1ubuntu2), libselinux1 (= 3.4-1build3), libsemanage-common (= 3.4-1build3), libsemanage2 (= 3.4-1build3), libsensors-config (= 1:3.6.0-7ubuntu1), libsensors5 (= 1:3.6.0-7ubuntu1), libsepol2 (= 3.4-2), libsmartcols1 (= 2.38.1-4ubuntu1), libssh-4 (= 0.10.4-2), libssl3 (= 3.0.7-1ubuntu1), libstdc++-12-dev (= 12.2.0-14ubuntu1), libstdc++6 (= 12.2.0-14ubuntu1), libsub-override-perl (= 0.09-4), libsystemd0 (= 252.4-1ubuntu1), libtasn1-6 (= 4.19.0-2), libtiff-dev (= 4.5.0-4ubuntu1), libtiff6 (= 4.5.0-4ubuntu1), libtiffxx6 (= 4.5.0-4ubuntu1), libtinfo6 (= 6.4-2), libtirpc-common (= 1.3.3+ds-1), libtirpc-dev (= 1.3.3+ds-1), libtirpc3 (= 1.3.3+ds-1), libtool (= 2.4.7-5), libtsan2 (= 12.2.0-14ubuntu1), libubsan1 (= 12.2.0-14ubuntu1), libuchardet0 (= 0.0.7-1build2), libucx0 (= 1.13.1-1), libudev1 (= 252.4-1ubuntu1), libunistring2 (= 1.0-2), libuuid1 (= 2.38.1-4ubuntu1), libuv1 (= 1.44.2-1), libwebp-dev (= 1.2.4-0.1), libwebp7 (= 1.2.4-0.1), libwebpdemux2 (= 1.2.4-0.1), libwebpmux3 (= 1.2.4-0.1), libx11-6 (= 2:1.8.3-3), libx11-data (= 2:1.8.3-3), libx11-dev (= 2:1.8.3-3), libx11-xcb1 (= 2:1.8.3-3), libxau-dev (= 1:1.0.9-1build5), libxau6 (= 1:1.0.9-1build5), libxcb-dri2-0 (= 1.15-1), libxcb-dri3-0 (= 1.15-1), libxcb-glx0 (= 1.15-1), libxcb-present0 (= 1.15-1), libxcb-render0 (= 1.15-1), libxcb-shm0 (= 1.15-1), libxcb-sync1 (= 1.15-1), libxcb-xfixes0 (= 1.15-1), libxcb1 (= 1.15-1), libxcb1-dev (= 1.15-1), libxcursor1 (= 1:1.2.1-1), libxdmcp-dev (= 1:1.1.3-0ubuntu5), libxdmcp6 (= 1:1.1.3-0ubuntu5), libxext6 (= 2:1.3.4-1build1), libxfixes3 (= 1:6.0.0-2), libxft2 (= 2.3.6-1), libxinerama1 (= 2:1.1.4-3), libxml2 (= 2.9.14+dfsg-1.1), libxnvctrl0 (= 510.47.03-0ubuntu1), libxrender1 (= 1:0.9.10-1.1), libxshmfence1 (= 1.3-1build4), libxxf86vm1 (= 1:1.1.4-1build3), libzstd-dev (= 1.5.2+dfsg2-3), libzstd1 (= 1.5.2+dfsg2-3), linux-libc-dev (= 6.1.0-14.14), login (= 1:4.13+dfsg1-1ubuntu1), lsb-base (= 11.5), lto-disabled-list (= 37), m4 (= 1.4.19-2), make (= 4.3-4.1build1), man-db (= 2.11.2-1), mawk (= 1.3.4.20200120-3.1), ncurses-base (= 6.4-2), ncurses-bin (= 6.4-2), ocl-icd-libopencl1 (= 2.3.1-1), openmpi-bin (= 4.1.4-3ubuntu2), openmpi-common (= 4.1.4-3ubuntu2), openssh-client (= 1:9.0p1-1ubuntu8), passwd (= 1:4.13+dfsg1-1ubuntu1), patch (= 2.7.6-7build2), perl (= 5.36.0-7), perl-base (= 5.36.0-7), perl-modules-5.36 (= 5.36.0-7), po-debconf (= 1.0.21+nmu1), procps (= 2:3.3.17-7ubuntu1), rpcsvc-proto (= 1.4.2-0ubuntu6), sed (= 4.9-1), sensible-utils (= 0.0.17+nmu1), sgml-base (= 1.31), sysvinit-utils (= 3.05-7ubuntu2), tar (= 1.34+dfsg-1.1), usrmerge (= 33ubuntu1), util-linux (= 2.38.1-4ubuntu1), util-linux-extra (= 2.38.1-4ubuntu1), x11proto-dev (= 2022.1-1), xorg-sgml-doctools (= 1:1.11-1.1), xtrans-dev (= 1.4.0-1), xz-utils (= 5.4.1-0.0), zlib1g (= 1:1.2.13.dfsg-1ubuntu4), zlib1g-dev (= 1:1.2.13.dfsg-1ubuntu4) Environment: DEB_BUILD_OPTIONS="parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1675514034" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ relion-gui_3.1.3-3build1_ppc64el.deb ------------------------------------ new Debian package, version 2.0. size 1296946 bytes: control archive=989 bytes. 1220 bytes, 23 lines control 308 bytes, 5 lines md5sums Package: relion-gui Source: relion Version: 3.1.3-3build1 Architecture: ppc64el Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 5348 Depends: relion (= 3.1.3-3build1), libc6 (>= 2.34), libfftw3-double3 (>= 3.3.5), libfltk1.3 (>= 1.3.4), libgcc-s1 (>= 3.3.1), libgomp1 (>= 4.9), libstdc++6 (>= 11), libtiff6 (>= 4.0.3) Conflicts: relion-cuda-gui Breaks: relion-bin, relion-bin+gui, relion-bin+mpi, relion-bin+mpi+gui Replaces: relion-bin, relion-bin+gui, relion-bin+mpi, relion-bin+mpi+gui Section: science Priority: optional Homepage: https://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page Description: toolkit for 3D reconstructions in cryo-electron microscopy (gui apps) RELION (for REgularised LIkelihood OptimisatioN) is a stand-alone computer program for Maximum A Posteriori refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy. . RELION provides a GUI, several command-line tools in parallel (MPI) and serial versions, optionally with CUDA/GPU support. . relion-gui provides the graphical user interface without CUDA/GPU support. drwxr-xr-x root/root 0 2023-02-04 12:33 ./ drwxr-xr-x root/root 0 2023-02-04 12:33 ./usr/ drwxr-xr-x root/root 0 2023-02-04 12:33 ./usr/bin/ -rwxr-xr-x root/root 2959152 2023-02-04 12:33 ./usr/bin/relion -rwxr-xr-x root/root 1313288 2023-02-04 12:33 ./usr/bin/relion_display -rwxr-xr-x root/root 1182216 2023-02-04 12:33 ./usr/bin/relion_manualpick drwxr-xr-x root/root 0 2023-02-04 12:33 ./usr/share/ drwxr-xr-x root/root 0 2023-02-04 12:33 ./usr/share/doc/ drwxr-xr-x root/root 0 2023-02-04 12:33 ./usr/share/doc/relion-gui/ lrwxrwxrwx root/root 0 2023-02-04 12:33 ./usr/share/doc/relion-gui/changelog.Debian.gz -> ../relion/changelog.Debian.gz -rw-r--r-- root/root 7408 2022-12-06 10:56 ./usr/share/doc/relion-gui/copyright drwxr-xr-x root/root 0 2023-02-04 12:33 ./usr/share/lintian/ drwxr-xr-x root/root 0 2023-02-04 12:33 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 15 2022-12-06 10:56 ./usr/share/lintian/overrides/relion-gui relion_3.1.3-3build1_ppc64el.deb -------------------------------- new Debian package, version 2.0. size 13508884 bytes: control archive=2651 bytes. 1235 bytes, 23 lines control 4218 bytes, 66 lines md5sums Package: relion Version: 3.1.3-3build1 Architecture: ppc64el Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 89864 Depends: openmpi-gcc | openmpi-bin, libc6 (>= 2.34), libfftw3-double3 (>= 3.3.5), libfftw3-single3 (>= 3.3.5), libgcc-s1 (>= 3.3.1), libgomp1 (>= 4.9), libopenmpi3 (>= 4.1.4), libstdc++6 (>= 11), libtiff6 (>= 4.0.3) Conflicts: relion-cuda Breaks: relion-bin, relion-bin+gui, relion-bin+mpi, relion-bin+mpi+gui Replaces: relion-bin, relion-bin+gui, relion-bin+mpi, relion-bin+mpi+gui Section: science Priority: optional Homepage: https://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page Description: toolkit for 3D reconstructions in cryo-electron microscopy RELION (for REgularised LIkelihood OptimisatioN) is a stand-alone computer program for Maximum A Posteriori refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy. . RELION provides a GUI, several command-line tools in parallel (MPI) and serial versions, optionally with CUDA/GPU support. . relion provides the serial and parallel (MPI) command-line tools without CUDA/GPU support. drwxr-xr-x root/root 0 2023-02-04 12:33 ./ drwxr-xr-x root/root 0 2023-02-04 12:33 ./usr/ drwxr-xr-x root/root 0 2023-02-04 12:33 ./usr/bin/ -rwxr-xr-x root/root 985608 2023-02-04 12:33 ./usr/bin/relion_align_symmetry -rwxr-xr-x root/root 2034184 2023-02-04 12:33 ./usr/bin/relion_autopick -rwxr-xr-x root/root 2099720 2023-02-04 12:33 ./usr/bin/relion_autopick_mpi -rwxr-xr-x root/root 1509896 2023-02-04 12:33 ./usr/bin/relion_convert_star -rwxr-xr-x root/root 1247752 2023-02-04 12:33 ./usr/bin/relion_convert_to_tiff -rwxr-xr-x root/root 1313288 2023-02-04 12:33 ./usr/bin/relion_convert_to_tiff_mpi -rwxr-xr-x root/root 1640968 2023-02-04 12:33 ./usr/bin/relion_ctf_mask_test -rwxr-xr-x root/root 2099720 2023-02-04 12:33 ./usr/bin/relion_ctf_refine -rwxr-xr-x root/root 2165256 2023-02-04 12:33 ./usr/bin/relion_ctf_refine_mpi -rwxr-xr-x root/root 1116680 2023-02-04 12:33 ./usr/bin/relion_ctf_toolbox -rwxr-xr-x root/root 1509896 2023-02-04 12:33 ./usr/bin/relion_demodulate -rwxr-xr-x root/root 920072 2023-02-04 12:33 ./usr/bin/relion_estimate_gain -rwxr-xr-x root/root 1051144 2023-02-04 12:33 ./usr/bin/relion_external_reconstruct -rwxr-xr-x root/root 657928 2023-02-04 12:33 ./usr/bin/relion_find_tiltpairs -rwxr-xr-x root/root 2296328 2023-02-04 12:33 ./usr/bin/relion_flex_analyse -rwxr-xr-x root/root 2296328 2023-02-04 12:33 ./usr/bin/relion_flex_analyse_mpi -rwxr-xr-x root/root 1182216 2023-02-04 12:33 ./usr/bin/relion_helix_inimodel2d -rwxr-xr-x root/root 1575432 2023-02-04 12:33 ./usr/bin/relion_helix_toolbox -rwxr-xr-x root/root 1313288 2023-02-04 12:33 ./usr/bin/relion_image_handler -rwxr-xr-x root/root 1116672 2023-02-04 12:33 ./usr/bin/relion_import -rwxr-xr-x root/root 1968648 2023-02-04 12:33 ./usr/bin/relion_localsym -rwxr-xr-x root/root 2099720 2023-02-04 12:33 ./usr/bin/relion_localsym_mpi -rwxr-xr-x root/root 1575432 2023-02-04 12:33 ./usr/bin/relion_mask_create -rwxr-xr-x root/root 1051144 2023-02-04 12:33 ./usr/bin/relion_merge_particles -rwxr-xr-x root/root 2492952 2023-02-04 12:33 ./usr/bin/relion_motion_refine -rwxr-xr-x root/root 2558488 2023-02-04 12:33 ./usr/bin/relion_motion_refine_mpi -rwxr-xr-x root/root 854528 2023-02-04 12:33 ./usr/bin/relion_mrc2vtk -rwxr-xr-x root/root 1772040 2023-02-04 12:33 ./usr/bin/relion_particle_FCC -rwxr-xr-x root/root 2820616 2023-02-04 12:33 ./usr/bin/relion_particle_reposition -rwxr-xr-x root/root 1509888 2023-02-04 12:33 ./usr/bin/relion_particle_select -rwxr-xr-x root/root 2886152 2023-02-04 12:33 ./usr/bin/relion_particle_subtract -rwxr-xr-x root/root 2951688 2023-02-04 12:33 ./usr/bin/relion_particle_subtract_mpi -rwxr-xr-x root/root 1182216 2023-02-04 12:33 ./usr/bin/relion_particle_symmetry_expand -rwxr-xr-x root/root 1575416 2023-02-04 12:33 ./usr/bin/relion_pipeliner -rwxr-xr-x root/root 1575432 2023-02-04 12:33 ./usr/bin/relion_plot_delocalisation -rwxr-xr-x root/root 1051144 2023-02-04 12:33 ./usr/bin/relion_postprocess -rwxr-xr-x root/root 1051144 2023-02-04 12:33 ./usr/bin/relion_postprocess_mpi -rwxr-xr-x root/root 985608 2023-02-04 12:33 ./usr/bin/relion_prepare_subtomo -rwxr-xr-x root/root 1575432 2023-02-04 12:33 ./usr/bin/relion_preprocess -rwxr-xr-x root/root 1706504 2023-02-04 12:33 ./usr/bin/relion_preprocess_mpi -rwxr-xr-x root/root 2165256 2023-02-04 12:33 ./usr/bin/relion_project -rwxr-xr-x root/root 2165256 2023-02-04 12:33 ./usr/bin/relion_reconstruct -rwxr-xr-x root/root 2230792 2023-02-04 12:33 ./usr/bin/relion_reconstruct_mpi -rwxr-xr-x root/root 2820616 2023-02-04 12:33 ./usr/bin/relion_refine -rwxr-xr-x root/root 2951688 2023-02-04 12:33 ./usr/bin/relion_refine_mpi -rwxr-xr-x root/root 1772032 2023-02-04 12:33 ./usr/bin/relion_reposition -rwxr-xr-x root/root 1182216 2023-02-04 12:33 ./usr/bin/relion_run_ctffind -rwxr-xr-x root/root 1313288 2023-02-04 12:33 ./usr/bin/relion_run_ctffind_mpi -rwxr-xr-x root/root 1509896 2023-02-04 12:33 ./usr/bin/relion_run_motioncorr -rwxr-xr-x root/root 1575432 2023-02-04 12:33 ./usr/bin/relion_run_motioncorr_mpi -rwxr-xr-x root/root 2296320 2023-02-04 12:33 ./usr/bin/relion_scheduler -rwxr-xr-x root/root 1182216 2023-02-04 12:33 ./usr/bin/relion_stack_create -rwxr-xr-x root/root 1055 2023-02-04 12:33 ./usr/bin/relion_star_datablock_ctfdat -rwxr-xr-x root/root 714 2023-02-04 12:33 ./usr/bin/relion_star_datablock_singlefiles -rwxr-xr-x root/root 767 2023-02-04 12:33 ./usr/bin/relion_star_datablock_stack -rwxr-xr-x root/root 1247752 2023-02-04 12:33 ./usr/bin/relion_star_handler -rwxr-xr-x root/root 675 2023-02-04 12:33 ./usr/bin/relion_star_loopheader -rwxr-xr-x root/root 1217 2023-02-04 12:33 ./usr/bin/relion_star_plottable -rwxr-xr-x root/root 2263 2023-02-04 12:33 ./usr/bin/relion_star_printtable -rwxr-xr-x root/root 723464 2023-02-04 12:33 ./usr/bin/relion_tiltpair_plot -rwxr-xr-x root/root 1444360 2023-02-04 12:33 ./usr/bin/relion_tomo_test drwxr-xr-x root/root 0 2023-02-04 12:33 ./usr/share/ drwxr-xr-x root/root 0 2023-02-04 12:33 ./usr/share/doc/ drwxr-xr-x root/root 0 2023-02-04 12:33 ./usr/share/doc/relion/ -rw-r--r-- root/root 1433 2021-08-31 10:17 ./usr/share/doc/relion/AUTHORS -rw-r--r-- root/root 2810 2021-08-31 10:17 ./usr/share/doc/relion/README.md.gz -rw-r--r-- root/root 1162 2023-02-04 12:33 ./usr/share/doc/relion/changelog.Debian.gz -rw-r--r-- root/root 7408 2022-12-06 10:56 ./usr/share/doc/relion/copyright drwxr-xr-x root/root 0 2023-02-04 12:33 ./usr/share/lintian/ drwxr-xr-x root/root 0 2023-02-04 12:33 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 15 2022-12-06 10:56 ./usr/share/lintian/overrides/relion +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: ppc64el Build Type: any Build-Space: 4019320 Build-Time: 1465 Distribution: lunar-proposed Host Architecture: ppc64el Install-Time: 22 Job: relion_3.1.3-3build1.dsc Machine Architecture: ppc64el Package: relion Package-Time: 1487 Source-Version: 3.1.3-3build1 Space: 4019320 Status: successful Version: 3.1.3-3build1 -------------------------------------------------------------------------------- Finished at 2023-02-04T13:24:25Z Build needed 00:24:47, 4019320k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=lunar --arch=ppc64el PACKAGEBUILD-25549282 Scanning for processes to kill in build PACKAGEBUILD-25549282