https://launchpad.net/ubuntu/+source/relion/3.1.3-3build1/+build/25549284 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-s390x-001 5.4.0-137-generic #154-Ubuntu SMP Thu Jan 5 17:03:11 UTC 2023 s390x 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 13:08:28 ntpdate[1857]: adjust time server 10.211.37.1 offset 0.020100 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=lunar --arch=s390x PACKAGEBUILD-25549284 --image-type chroot /home/buildd/filecache-default/22b7ec405c1fe881d1e0795ebcfd3bff662be15c Creating target for build PACKAGEBUILD-25549284 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=lunar --arch=s390x PACKAGEBUILD-25549284 Starting target for build PACKAGEBUILD-25549284 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=lunar --arch=s390x PACKAGEBUILD-25549284 '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-25549284 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=lunar --arch=s390x PACKAGEBUILD-25549284 Updating target for build PACKAGEBUILD-25549284 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 s390x Packages [1314 kB] Get:6 http://ftpmaster.internal/ubuntu lunar/main Translation-en [508 kB] Get:7 http://ftpmaster.internal/ubuntu lunar/universe s390x Packages [14.3 MB] Get:8 http://ftpmaster.internal/ubuntu lunar/universe Translation-en [5893 kB] Get:9 http://ftpmaster.internal/ubuntu lunar-proposed/main s390x Packages [90.2 kB] Get:10 http://ftpmaster.internal/ubuntu lunar-proposed/main Translation-en [34.0 kB] Get:11 http://ftpmaster.internal/ubuntu lunar-proposed/universe s390x Packages [293 kB] Get:12 http://ftpmaster.internal/ubuntu lunar-proposed/universe Translation-en [136 kB] Fetched 23.1 MB in 4s (5542 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-s390x-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 liblzma5 libmpfr6 libncurses6 libncursesw6 libp11-kit0 libpcre2-8-0 libperl5.36 libreadline8 libselinux1 libsemanage-common libsemanage2 libsqlite3-0 libssl3 libstdc++-12-dev libstdc++6 libsystemd-shared libsystemd0 libtinfo6 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 88 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 82.5 MB of archives. After this operation, 3905 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu lunar/main s390x bash s390x 5.2.15-2ubuntu1 [786 kB] Get:2 http://ftpmaster.internal/ubuntu lunar/main s390x coreutils s390x 9.1-1ubuntu2 [1390 kB] Get:3 http://ftpmaster.internal/ubuntu lunar/main s390x diffutils s390x 1:3.8-3 [177 kB] Get:4 http://ftpmaster.internal/ubuntu lunar-proposed/main s390x libc-bin s390x 2.37-0ubuntu1 [599 kB] Get:5 http://ftpmaster.internal/ubuntu lunar/main s390x libcrypt-dev s390x 1:4.4.33-2 [114 kB] Get:6 http://ftpmaster.internal/ubuntu lunar-proposed/main s390x libc6-dev s390x 2.37-0ubuntu1 [1510 kB] Get:7 http://ftpmaster.internal/ubuntu lunar-proposed/main s390x libc-dev-bin s390x 2.37-0ubuntu1 [19.6 kB] Get:8 http://ftpmaster.internal/ubuntu lunar/main s390x libcrypt1 s390x 1:4.4.33-2 [82.2 kB] Get:9 http://ftpmaster.internal/ubuntu lunar-proposed/main s390x linux-libc-dev s390x 6.1.0-14.14 [1464 kB] Get:10 http://ftpmaster.internal/ubuntu lunar/main s390x libcc1-0 s390x 12.2.0-14ubuntu1 [45.5 kB] Get:11 http://ftpmaster.internal/ubuntu lunar/main s390x libctf0 s390x 2.40-2ubuntu1 [94.2 kB] Get:12 http://ftpmaster.internal/ubuntu lunar/main s390x libctf-nobfd0 s390x 2.40-2ubuntu1 [95.0 kB] Get:13 http://ftpmaster.internal/ubuntu lunar/main s390x binutils-s390x-linux-gnu s390x 2.40-2ubuntu1 [2061 kB] Get:14 http://ftpmaster.internal/ubuntu lunar/main s390x libbinutils s390x 2.40-2ubuntu1 [463 kB] Get:15 http://ftpmaster.internal/ubuntu lunar/main s390x binutils-common s390x 2.40-2ubuntu1 [226 kB] Get:16 http://ftpmaster.internal/ubuntu lunar/main s390x binutils s390x 2.40-2ubuntu1 [3060 B] Get:17 http://ftpmaster.internal/ubuntu lunar/main s390x gcc-12-base s390x 12.2.0-14ubuntu1 [19.3 kB] Get:18 http://ftpmaster.internal/ubuntu lunar/main s390x libgcc-s1 s390x 12.2.0-14ubuntu1 [28.4 kB] Get:19 http://ftpmaster.internal/ubuntu lunar/main s390x libgomp1 s390x 12.2.0-14ubuntu1 [122 kB] Get:20 http://ftpmaster.internal/ubuntu lunar/main s390x libitm1 s390x 12.2.0-14ubuntu1 [29.5 kB] Get:21 http://ftpmaster.internal/ubuntu lunar/main s390x libatomic1 s390x 12.2.0-14ubuntu1 [8942 B] Get:22 http://ftpmaster.internal/ubuntu lunar/main s390x libasan8 s390x 12.2.0-14ubuntu1 [2409 kB] Get:23 http://ftpmaster.internal/ubuntu lunar/main s390x libubsan1 s390x 12.2.0-14ubuntu1 [958 kB] Get:24 http://ftpmaster.internal/ubuntu lunar/main s390x g++-12 s390x 12.2.0-14ubuntu1 [9436 kB] Get:25 http://ftpmaster.internal/ubuntu lunar/main s390x libstdc++-12-dev s390x 12.2.0-14ubuntu1 [2192 kB] Get:26 http://ftpmaster.internal/ubuntu lunar/main s390x libgcc-12-dev s390x 12.2.0-14ubuntu1 [853 kB] Get:27 http://ftpmaster.internal/ubuntu lunar/main s390x gcc-12 s390x 12.2.0-14ubuntu1 [16.2 MB] Get:28 http://ftpmaster.internal/ubuntu lunar/main s390x cpp-12 s390x 12.2.0-14ubuntu1 [8165 kB] Get:29 http://ftpmaster.internal/ubuntu lunar/main s390x libstdc++6 s390x 12.2.0-14ubuntu1 [728 kB] Get:30 http://ftpmaster.internal/ubuntu lunar/main s390x zlib1g s390x 1:1.2.13.dfsg-1ubuntu4 [65.6 kB] Get:31 http://ftpmaster.internal/ubuntu lunar/main s390x libmpfr6 s390x 4.2.0-1 [278 kB] Get:32 http://ftpmaster.internal/ubuntu lunar/main s390x libzstd1 s390x 1.5.2+dfsg2-3 [261 kB] Get:33 http://ftpmaster.internal/ubuntu lunar-proposed/main s390x libc6 s390x 2.37-0ubuntu1 [2668 kB] Get:34 http://ftpmaster.internal/ubuntu lunar/main s390x liblzma5 s390x 5.4.1-0.0 [124 kB] Get:35 http://ftpmaster.internal/ubuntu lunar/main s390x libgcrypt20 s390x 1.10.1-3ubuntu1 [466 kB] Get:36 http://ftpmaster.internal/ubuntu lunar/main s390x libacl1 s390x 2.3.1-3 [16.5 kB] Get:37 http://ftpmaster.internal/ubuntu lunar/main s390x libaudit-common all 1:3.0.7-1.1 [5108 B] Get:38 http://ftpmaster.internal/ubuntu lunar/main s390x libaudit1 s390x 1:3.0.7-1.1 [45.5 kB] Get:39 http://ftpmaster.internal/ubuntu lunar-proposed/main s390x libcap2 s390x 1:2.66-3ubuntu1 [28.3 kB] Get:40 http://ftpmaster.internal/ubuntu lunar/main s390x libpcre2-8-0 s390x 10.42-1 [210 kB] Get:41 http://ftpmaster.internal/ubuntu lunar-proposed/main s390x libselinux1 s390x 3.4-1build3 [76.8 kB] Get:42 http://ftpmaster.internal/ubuntu lunar/main s390x libperl5.36 s390x 5.36.0-7 [4716 kB] Get:43 http://ftpmaster.internal/ubuntu lunar/main s390x perl s390x 5.36.0-7 [235 kB] Get:44 http://ftpmaster.internal/ubuntu lunar/main s390x perl-base s390x 5.36.0-7 [1713 kB] Get:45 http://ftpmaster.internal/ubuntu lunar/main s390x perl-modules-5.36 all 5.36.0-7 [2984 kB] Get:46 http://ftpmaster.internal/ubuntu lunar/main s390x libdb5.3 s390x 5.3.28+dfsg2-1 [707 kB] Get:47 http://ftpmaster.internal/ubuntu lunar/main s390x debconf all 1.5.82 [125 kB] Get:48 http://ftpmaster.internal/ubuntu lunar/main s390x libssl3 s390x 3.0.7-1ubuntu1 [1567 kB] Get:49 http://ftpmaster.internal/ubuntu lunar/main s390x systemd-sysv s390x 252.4-1ubuntu1 [11.4 kB] Get:50 http://ftpmaster.internal/ubuntu lunar/main s390x systemd s390x 252.4-1ubuntu1 [2857 kB] Get:51 http://ftpmaster.internal/ubuntu lunar/main s390x libsystemd-shared s390x 252.4-1ubuntu1 [1668 kB] Get:52 http://ftpmaster.internal/ubuntu lunar/main s390x libp11-kit0 s390x 0.24.1-2ubuntu1 [249 kB] Get:53 http://ftpmaster.internal/ubuntu lunar/main s390x libsystemd0 s390x 252.4-1ubuntu1 [317 kB] Get:54 http://ftpmaster.internal/ubuntu lunar/main s390x libudev1 s390x 252.4-1ubuntu1 [87.6 kB] Get:55 http://ftpmaster.internal/ubuntu lunar/main s390x libapt-pkg6.0 s390x 2.5.5 [867 kB] Get:56 http://ftpmaster.internal/ubuntu lunar/main s390x dpkg s390x 1.21.19ubuntu3 [1325 kB] Get:57 http://ftpmaster.internal/ubuntu lunar/main s390x grep s390x 3.8-5 [160 kB] Get:58 http://ftpmaster.internal/ubuntu lunar/main s390x ncurses-bin s390x 6.4-2 [186 kB] Get:59 http://ftpmaster.internal/ubuntu lunar/main s390x sed s390x 4.9-1 [193 kB] Get:60 http://ftpmaster.internal/ubuntu lunar/main s390x ncurses-base all 6.4-2 [21.3 kB] Get:61 http://ftpmaster.internal/ubuntu lunar/main s390x sysvinit-utils s390x 3.05-7ubuntu2 [27.4 kB] Get:62 http://ftpmaster.internal/ubuntu lunar/main s390x lsb-base all 11.5 [4296 B] Get:63 http://ftpmaster.internal/ubuntu lunar/main s390x adduser all 3.129ubuntu1 [59.0 kB] Get:64 http://ftpmaster.internal/ubuntu lunar/main s390x gpgv s390x 2.2.40-1ubuntu2 [134 kB] Get:65 http://ftpmaster.internal/ubuntu lunar/main s390x libgnutls30 s390x 3.7.8-4ubuntu1 [892 kB] Get:66 http://ftpmaster.internal/ubuntu lunar/main s390x apt s390x 2.5.5 [1351 kB] Get:67 http://ftpmaster.internal/ubuntu lunar/main s390x libattr1 s390x 1:2.5.1-4 [12.4 kB] Get:68 http://ftpmaster.internal/ubuntu lunar-proposed/main s390x libsemanage-common all 3.4-1build3 [9808 B] Get:69 http://ftpmaster.internal/ubuntu lunar-proposed/main s390x libsemanage2 s390x 3.4-1build3 [88.5 kB] Get:70 http://ftpmaster.internal/ubuntu lunar/main s390x libncurses6 s390x 6.4-2 [111 kB] Get:71 http://ftpmaster.internal/ubuntu lunar/main s390x libncursesw6 s390x 6.4-2 [143 kB] Get:72 http://ftpmaster.internal/ubuntu lunar/main s390x libtinfo6 s390x 6.4-2 [101 kB] Get:73 http://ftpmaster.internal/ubuntu lunar/main s390x sensible-utils all 0.0.17+nmu1 [19.3 kB] Get:74 http://ftpmaster.internal/ubuntu lunar/main s390x readline-common all 8.2-1.3 [55.7 kB] Get:75 http://ftpmaster.internal/ubuntu lunar/main s390x libreadline8 s390x 8.2-1.3 [151 kB] Get:76 http://ftpmaster.internal/ubuntu lunar/main s390x libsqlite3-0 s390x 3.40.1-1 [642 kB] Get:77 http://ftpmaster.internal/ubuntu lunar/main s390x openssl s390x 3.0.7-1ubuntu1 [1165 kB] Get:78 http://ftpmaster.internal/ubuntu lunar/main s390x tzdata all 2022g-2ubuntu1 [397 kB] Get:79 http://ftpmaster.internal/ubuntu lunar/main s390x xz-utils s390x 5.4.1-0.0 [239 kB] Get:80 http://ftpmaster.internal/ubuntu lunar/main s390x advancecomp s390x 2.5-1 [174 kB] Get:81 http://ftpmaster.internal/ubuntu lunar/main s390x dpkg-dev all 1.21.19ubuntu3 [1067 kB] Get:82 http://ftpmaster.internal/ubuntu lunar/main s390x libdpkg-perl all 1.21.19ubuntu3 [247 kB] Get:83 http://ftpmaster.internal/ubuntu lunar/main s390x libfakeroot s390x 1.30.1-1.1ubuntu1 [30.0 kB] Get:84 http://ftpmaster.internal/ubuntu lunar/main s390x fakeroot s390x 1.30.1-1.1ubuntu1 [59.7 kB] Get:85 http://ftpmaster.internal/ubuntu lunar/main s390x gpg s390x 2.2.40-1ubuntu2 [508 kB] Get:86 http://ftpmaster.internal/ubuntu lunar/main s390x gpgconf s390x 2.2.40-1ubuntu2 [94.8 kB] Get:87 http://ftpmaster.internal/ubuntu lunar/main s390x gpg-agent s390x 2.2.40-1ubuntu2 [213 kB] Get:88 http://ftpmaster.internal/ubuntu lunar/main s390x pkgbinarymangler all 151 [16.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 82.5 MB in 3s (24.0 MB/s) (Reading database ... 12875 files and directories currently installed.) Preparing to unpack .../bash_5.2.15-2ubuntu1_s390x.deb ... Unpacking bash (5.2.15-2ubuntu1) over (5.2-1ubuntu2) ... Setting up bash (5.2.15-2ubuntu1) ... update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode (Reading database ... 12875 files and directories currently installed.) Preparing to unpack .../coreutils_9.1-1ubuntu2_s390x.deb ... Unpacking coreutils (9.1-1ubuntu2) over (8.32-4.1ubuntu1) ... Setting up coreutils (9.1-1ubuntu2) ... (Reading database ... 12875 files and directories currently installed.) Preparing to unpack .../diffutils_1%3a3.8-3_s390x.deb ... Unpacking diffutils (1:3.8-3) over (1:3.8-1) ... Setting up diffutils (1:3.8-3) ... (Reading database ... 12875 files and directories currently installed.) Preparing to unpack .../libc-bin_2.37-0ubuntu1_s390x.deb ... Unpacking libc-bin (2.37-0ubuntu1) over (2.36-0ubuntu4) ... Setting up libc-bin (2.37-0ubuntu1) ... 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Setting up libgomp1:s390x (12.2.0-14ubuntu1) ... Setting up libfakeroot:s390x (1.30.1-1.1ubuntu1) ... Setting up tzdata (2022g-2ubuntu1) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Feb 4 13:08:49 UTC 2023. Universal Time is now: Sat Feb 4 13:08:49 UTC 2023. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up fakeroot (1.30.1-1.1ubuntu1) ... Setting up perl-modules-5.36 (5.36.0-7) ... Setting up libmpfr6:s390x (4.2.0-1) ... Setting up libncurses6:s390x (6.4-2) ... Setting up xz-utils (5.4.1-0.0) ... Setting up libatomic1:s390x (12.2.0-14ubuntu1) ... Setting up libsystemd-shared:s390x (252.4-1ubuntu1) ... Setting up libncursesw6:s390x (6.4-2) ... Setting up libubsan1:s390x (12.2.0-14ubuntu1) ... Setting up advancecomp (2.5-1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libcrypt-dev:s390x (1:4.4.33-2) ... Setting up libasan8:s390x (12.2.0-14ubuntu1) ... Setting up libbinutils:s390x (2.40-2ubuntu1) ... Setting up libc-dev-bin (2.37-0ubuntu1) ... Setting up openssl (3.0.7-1ubuntu1) ... Installing new version of config file /etc/ssl/openssl.cnf ... Setting up readline-common (8.2-1.3) ... Setting up libcc1-0:s390x (12.2.0-14ubuntu1) ... Setting up libperl5.36:s390x (5.36.0-7) ... Setting up libitm1:s390x (12.2.0-14ubuntu1) ... Setting up libctf0:s390x (2.40-2ubuntu1) ... Setting up cpp-12 (12.2.0-14ubuntu1) ... Setting up binutils-s390x-linux-gnu (2.40-2ubuntu1) ... Setting up pkgbinarymangler (151) ... Setting up libreadline8:s390x (8.2-1.3) ... Setting up systemd (252.4-1ubuntu1) ... Installing new version of config file /etc/systemd/logind.conf ... Installing new version of config file /etc/systemd/system.conf ... Installing new version of config file /etc/systemd/user.conf ... Initializing machine ID from random generator. Setting up binutils (2.40-2ubuntu1) ... Setting up perl (5.36.0-7) ... Setting up libgcc-12-dev:s390x (12.2.0-14ubuntu1) ... Setting up libdpkg-perl (1.21.19ubuntu3) ... Setting up gpgconf (2.2.40-1ubuntu2) ... Setting up libc6-dev:s390x (2.37-0ubuntu1) ... Setting up gpg (2.2.40-1ubuntu2) ... Setting up systemd-sysv (252.4-1ubuntu1) ... Setting up gpg-agent (2.2.40-1ubuntu2) ... Setting up libstdc++-12-dev:s390x (12.2.0-14ubuntu1) ... 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-25549284 s390x lunar-proposed -c chroot:build-PACKAGEBUILD-25549284 --arch=s390x --dist=lunar-proposed --nolog relion_3.1.3-3build1.dsc Initiating build PACKAGEBUILD-25549284 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-137-generic #154-Ubuntu SMP Thu Jan 5 17:03:11 UTC 2023 s390x sbuild (Debian sbuild) 0.79.0 (05 February 2020) on bos02-s390x-001.buildd +==============================================================================+ | relion 3.1.3-3build1 (s390x) Sat, 04 Feb 2023 13:08:50 +0000 | +==============================================================================+ Package: relion Version: 3.1.3-3build1 Source Version: 3.1.3-3build1 Distribution: lunar-proposed Machine Architecture: s390x Host Architecture: s390x Build Architecture: s390x Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-25549284/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/relion-Ivww1o/resolver-ROG0EB' 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-Ivww1o/relion-3.1.3' with '<>' I: NOTICE: Log filtering will replace 'build/relion-Ivww1o' 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 [486 B] Fetched 1848 B in 0s (0 B/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 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 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-multilib 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 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 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, 172 newly installed, 0 to remove and 0 not upgraded. Need to get 94.0 MB of archives. After this operation, 397 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 s390x sgml-base all 1.31 [11.4 kB] Get:3 http://ftpmaster.internal/ubuntu lunar/main s390x libbsd0 s390x 0.11.7-2 [45.2 kB] Get:4 http://ftpmaster.internal/ubuntu lunar/main s390x libelf1 s390x 0.188-2.1 [56.7 kB] Get:5 http://ftpmaster.internal/ubuntu lunar/main s390x libexpat1 s390x 2.5.0-1 [81.6 kB] Get:6 http://ftpmaster.internal/ubuntu lunar/main s390x libicu71 s390x 71.1-3ubuntu1 [10.5 MB] Get:7 http://ftpmaster.internal/ubuntu lunar/main s390x libxml2 s390x 2.9.14+dfsg-1.1 [717 kB] Get:8 http://ftpmaster.internal/ubuntu lunar/main s390x bsdextrautils s390x 2.38.1-4ubuntu1 [71.3 kB] Get:9 http://ftpmaster.internal/ubuntu lunar/main s390x libmagic-mgc s390x 1:5.44-3 [296 kB] Get:10 http://ftpmaster.internal/ubuntu lunar/main s390x libmagic1 s390x 1:5.44-3 [84.5 kB] Get:11 http://ftpmaster.internal/ubuntu lunar/main s390x file s390x 1:5.44-3 [21.7 kB] Get:12 http://ftpmaster.internal/ubuntu lunar/main s390x gettext-base s390x 0.21-11 [36.4 kB] Get:13 http://ftpmaster.internal/ubuntu lunar/main s390x libuchardet0 s390x 0.0.7-1build2 [76.4 kB] Get:14 http://ftpmaster.internal/ubuntu lunar/main s390x groff-base s390x 1.22.4-9 [914 kB] Get:15 http://ftpmaster.internal/ubuntu lunar/main s390x libcbor0.8 s390x 0.8.0-2ubuntu1 [23.9 kB] Get:16 http://ftpmaster.internal/ubuntu lunar/main s390x libdrm-common all 2.4.114-1 [5940 B] Get:17 http://ftpmaster.internal/ubuntu lunar/main s390x libdrm2 s390x 2.4.114-1 [38.2 kB] Get:18 http://ftpmaster.internal/ubuntu lunar/main s390x libedit2 s390x 3.1-20221030-2 [95.3 kB] Get:19 http://ftpmaster.internal/ubuntu lunar/main s390x libfido2-1 s390x 1.12.0-2 [78.6 kB] Get:20 http://ftpmaster.internal/ubuntu lunar/main s390x libnghttp2-14 s390x 1.51.0-1 [70.9 kB] Get:21 http://ftpmaster.internal/ubuntu lunar/main s390x libnuma1 s390x 2.0.16-1 [22.7 kB] Get:22 http://ftpmaster.internal/ubuntu lunar/main s390x libpipeline1 s390x 1.5.7-1 [23.4 kB] Get:23 http://ftpmaster.internal/ubuntu lunar/main s390x libpsl5 s390x 0.21.0-1.2build2 [58.5 kB] Get:24 http://ftpmaster.internal/ubuntu lunar/main s390x libuv1 s390x 1.44.2-1 [87.4 kB] Get:25 http://ftpmaster.internal/ubuntu lunar/main s390x libxau6 s390x 1:1.0.9-1build5 [7522 B] Get:26 http://ftpmaster.internal/ubuntu lunar/main s390x libxdmcp6 s390x 1:1.1.3-0ubuntu5 [10.8 kB] Get:27 http://ftpmaster.internal/ubuntu lunar/main s390x libxcb1 s390x 1.15-1 [48.3 kB] Get:28 http://ftpmaster.internal/ubuntu lunar/main s390x libx11-data all 2:1.8.3-3 [118 kB] Get:29 http://ftpmaster.internal/ubuntu lunar/main s390x libx11-6 s390x 2:1.8.3-3 [637 kB] Get:30 http://ftpmaster.internal/ubuntu lunar/main s390x libxext6 s390x 2:1.3.4-1build1 [30.5 kB] Get:31 http://ftpmaster.internal/ubuntu lunar/main s390x man-db s390x 2.11.2-1 [1216 kB] Get:32 http://ftpmaster.internal/ubuntu lunar/main s390x openssh-client s390x 1:9.0p1-1ubuntu8 [811 kB] Get:33 http://ftpmaster.internal/ubuntu lunar/main s390x m4 s390x 1.4.19-2 [243 kB] Get:34 http://ftpmaster.internal/ubuntu lunar/main s390x autoconf all 2.71-3 [339 kB] Get:35 http://ftpmaster.internal/ubuntu lunar/main s390x autotools-dev all 20220109.1 [44.9 kB] Get:36 http://ftpmaster.internal/ubuntu lunar/main s390x automake all 1:1.16.5-1.3 [558 kB] Get:37 http://ftpmaster.internal/ubuntu lunar/main s390x autopoint all 0.21-11 [420 kB] Get:38 http://ftpmaster.internal/ubuntu lunar-proposed/main s390x libarchive13 s390x 3.6.2-1ubuntu1 [372 kB] Get:39 http://ftpmaster.internal/ubuntu lunar/main s390x libbrotli1 s390x 1.0.9-2build7 [311 kB] Get:40 http://ftpmaster.internal/ubuntu lunar/main s390x libsasl2-modules-db s390x 2.1.28+dfsg-10 [20.1 kB] Get:41 http://ftpmaster.internal/ubuntu lunar/main s390x libsasl2-2 s390x 2.1.28+dfsg-10 [57.1 kB] Get:42 http://ftpmaster.internal/ubuntu lunar/main s390x libldap2 s390x 2.6.3+dfsg-1~exp1ubuntu1 [179 kB] Get:43 http://ftpmaster.internal/ubuntu lunar/main s390x librtmp1 s390x 2.4+20151223.gitfa8646d.1-2build4 [56.4 kB] Get:44 http://ftpmaster.internal/ubuntu lunar/main s390x libssh-4 s390x 0.10.4-2 [173 kB] Get:45 http://ftpmaster.internal/ubuntu lunar-proposed/main s390x libcurl4 s390x 7.87.0-2ubuntu1 [287 kB] Get:46 http://ftpmaster.internal/ubuntu lunar/main s390x libjsoncpp25 s390x 1.9.5-4 [74.8 kB] Get:47 http://ftpmaster.internal/ubuntu lunar/main s390x librhash0 s390x 1.4.3-3 [128 kB] Get:48 http://ftpmaster.internal/ubuntu lunar/main s390x cmake-data all 3.25.1-1 [2049 kB] Get:49 http://ftpmaster.internal/ubuntu lunar/main s390x cmake s390x 3.25.1-1 [4899 kB] Get:50 http://ftpmaster.internal/ubuntu lunar/main s390x libdebhelper-perl all 13.11.4ubuntu3 [66.1 kB] Get:51 http://ftpmaster.internal/ubuntu lunar/main s390x libtool all 2.4.7-5 [166 kB] Get:52 http://ftpmaster.internal/ubuntu lunar/main s390x dh-autoreconf all 20 [16.1 kB] Get:53 http://ftpmaster.internal/ubuntu lunar/main s390x libarchive-zip-perl all 1.68-1 [90.2 kB] Get:54 http://ftpmaster.internal/ubuntu lunar/main s390x libsub-override-perl all 0.09-4 [8706 B] Get:55 http://ftpmaster.internal/ubuntu lunar/main s390x libfile-stripnondeterminism-perl all 1.13.1-1 [18.1 kB] Get:56 http://ftpmaster.internal/ubuntu lunar/main s390x dh-strip-nondeterminism all 1.13.1-1 [5362 B] Get:57 http://ftpmaster.internal/ubuntu lunar/main s390x libdw1 s390x 0.188-2.1 [247 kB] Get:58 http://ftpmaster.internal/ubuntu lunar/main s390x debugedit s390x 1:5.0-5 [47.5 kB] Get:59 http://ftpmaster.internal/ubuntu lunar/main s390x dwz s390x 0.15-1 [108 kB] Get:60 http://ftpmaster.internal/ubuntu lunar/main s390x gettext s390x 0.21-11 [851 kB] Get:61 http://ftpmaster.internal/ubuntu lunar/main s390x intltool-debian all 0.35.0+20060710.6 [23.2 kB] Get:62 http://ftpmaster.internal/ubuntu lunar/main s390x po-debconf all 1.0.21+nmu1 [233 kB] Get:63 http://ftpmaster.internal/ubuntu lunar/main s390x debhelper all 13.11.4ubuntu3 [925 kB] Get:64 http://ftpmaster.internal/ubuntu lunar/main s390x libfreetype6 s390x 2.12.1+dfsg-4 [384 kB] Get:65 http://ftpmaster.internal/ubuntu lunar/main s390x fonts-dejavu-core all 2.37-2build2 [1137 kB] Get:66 http://ftpmaster.internal/ubuntu lunar/main s390x fontconfig-config s390x 2.14.1-3ubuntu1 [32.5 kB] Get:67 http://ftpmaster.internal/ubuntu lunar/main s390x libfontconfig1 s390x 2.14.1-3ubuntu1 [136 kB] Get:68 http://ftpmaster.internal/ubuntu lunar/main s390x libxfixes3 s390x 1:6.0.0-2 [10.6 kB] Get:69 http://ftpmaster.internal/ubuntu lunar/main s390x libxrender1 s390x 1:0.9.10-1.1 [19.4 kB] Get:70 http://ftpmaster.internal/ubuntu lunar/main s390x libxcursor1 s390x 1:1.2.1-1 [22.2 kB] Get:71 http://ftpmaster.internal/ubuntu lunar/main s390x libxft2 s390x 2.3.6-1 [44.3 kB] Get:72 http://ftpmaster.internal/ubuntu lunar/main s390x libxinerama1 s390x 2:1.1.4-3 [7110 B] Get:73 http://ftpmaster.internal/ubuntu lunar/universe s390x libfltk1.3 s390x 1.3.8-5 [604 kB] Get:74 http://ftpmaster.internal/ubuntu lunar/universe s390x libfltk-forms1.3 s390x 1.3.8-5 [13.7 kB] Get:75 http://ftpmaster.internal/ubuntu lunar/main s390x libjpeg-turbo8 s390x 2.1.2-0ubuntu1 [119 kB] Get:76 http://ftpmaster.internal/ubuntu lunar/main s390x libjpeg8 s390x 8c-2ubuntu10 [2264 B] Get:77 http://ftpmaster.internal/ubuntu lunar/universe s390x libfltk-images1.3 s390x 1.3.8-5 [27.8 kB] Get:78 http://ftpmaster.internal/ubuntu lunar/universe s390x fluid s390x 1.3.8-5 [208 kB] Get:79 http://ftpmaster.internal/ubuntu lunar/main s390x libgfortran5 s390x 12.2.0-14ubuntu1 [468 kB] Get:80 http://ftpmaster.internal/ubuntu lunar/main s390x libgfortran-12-dev s390x 12.2.0-14ubuntu1 [517 kB] Get:81 http://ftpmaster.internal/ubuntu lunar/main s390x gfortran-12 s390x 12.2.0-14ubuntu1 [8575 kB] Get:82 http://ftpmaster.internal/ubuntu lunar/main s390x libnl-3-200 s390x 3.7.0-0.2 [56.3 kB] Get:83 http://ftpmaster.internal/ubuntu lunar/main s390x libnl-route-3-200 s390x 3.7.0-0.2 [180 kB] Get:84 http://ftpmaster.internal/ubuntu lunar/main s390x libibverbs1 s390x 44.0-2 [64.3 kB] Get:85 http://ftpmaster.internal/ubuntu lunar/main s390x ibverbs-providers s390x 44.0-2 [350 kB] Get:86 http://ftpmaster.internal/ubuntu lunar/main s390x libpixman-1-0 s390x 0.42.2-1 [173 kB] Get:87 http://ftpmaster.internal/ubuntu lunar/main s390x libxcb-render0 s390x 1.15-1 [17.0 kB] Get:88 http://ftpmaster.internal/ubuntu lunar/main s390x libxcb-shm0 s390x 1.15-1 [5782 B] Get:89 http://ftpmaster.internal/ubuntu lunar/main s390x libcairo2 s390x 1.16.0-7 [493 kB] Get:90 http://ftpmaster.internal/ubuntu lunar/main s390x libdeflate0 s390x 1.14-1 [63.1 kB] Get:91 http://ftpmaster.internal/ubuntu lunar/main s390x libdeflate-dev s390x 1.14-1 [50.3 kB] Get:92 http://ftpmaster.internal/ubuntu lunar/main s390x libdrm-amdgpu1 s390x 2.4.114-1 [19.8 kB] Get:93 http://ftpmaster.internal/ubuntu lunar/main s390x libdrm-nouveau2 s390x 2.4.114-1 [17.1 kB] Get:94 http://ftpmaster.internal/ubuntu lunar/main s390x libdrm-radeon1 s390x 2.4.114-1 [21.3 kB] Get:95 http://ftpmaster.internal/ubuntu lunar/main s390x libevent-2.1-7a s390x 2.1.12-stable-5ubuntu1 [137 kB] Get:96 http://ftpmaster.internal/ubuntu lunar/main s390x libevent-core-2.1-7a s390x 2.1.12-stable-5ubuntu1 [88.2 kB] Get:97 http://ftpmaster.internal/ubuntu lunar/main s390x libevent-extra-2.1-7 s390x 2.1.12-stable-5ubuntu1 [61.0 kB] Get:98 http://ftpmaster.internal/ubuntu lunar/main s390x libevent-pthreads-2.1-7 s390x 2.1.12-stable-5ubuntu1 [7574 B] Get:99 http://ftpmaster.internal/ubuntu lunar/main s390x libevent-openssl-2.1-7 s390x 2.1.12-stable-5ubuntu1 [14.6 kB] Get:100 http://ftpmaster.internal/ubuntu lunar/main s390x libevent-dev s390x 2.1.12-stable-5ubuntu1 [268 kB] Get:101 http://ftpmaster.internal/ubuntu lunar/main s390x librdmacm1 s390x 44.0-2 [67.5 kB] Get:102 http://ftpmaster.internal/ubuntu lunar/universe s390x libfabric1 s390x 1.17.0-3 [513 kB] Get:103 http://ftpmaster.internal/ubuntu lunar/main s390x libfftw3-double3 s390x 3.3.8-2ubuntu8 [413 kB] Get:104 http://ftpmaster.internal/ubuntu lunar/main s390x libfftw3-long3 s390x 3.3.8-2ubuntu8 [437 kB] Get:105 http://ftpmaster.internal/ubuntu lunar/main s390x libfftw3-single3 s390x 3.3.8-2ubuntu8 [392 kB] Get:106 http://ftpmaster.internal/ubuntu lunar/main s390x libfftw3-bin s390x 3.3.8-2ubuntu8 [30.7 kB] Get:107 http://ftpmaster.internal/ubuntu lunar/main s390x libfftw3-dev s390x 3.3.8-2ubuntu8 [1098 kB] Get:108 http://ftpmaster.internal/ubuntu lunar/universe s390x libfltk-cairo1.3 s390x 1.3.8-5 [6594 B] Get:109 http://ftpmaster.internal/ubuntu lunar/main s390x libglvnd0 s390x 1.6.0-1 [110 kB] Get:110 http://ftpmaster.internal/ubuntu lunar/main s390x libglapi-mesa s390x 22.2.5-0ubuntu1 [64.6 kB] Get:111 http://ftpmaster.internal/ubuntu lunar/main s390x libx11-xcb1 s390x 2:1.8.3-3 [7750 B] Get:112 http://ftpmaster.internal/ubuntu lunar/main s390x libxcb-dri2-0 s390x 1.15-1 [7426 B] Get:113 http://ftpmaster.internal/ubuntu lunar/main s390x libxcb-dri3-0 s390x 1.15-1 [7270 B] Get:114 http://ftpmaster.internal/ubuntu lunar/main s390x libxcb-glx0 s390x 1.15-1 [25.8 kB] Get:115 http://ftpmaster.internal/ubuntu lunar/main s390x libxcb-present0 s390x 1.15-1 [5752 B] Get:116 http://ftpmaster.internal/ubuntu lunar/main s390x libxcb-sync1 s390x 1.15-1 [9392 B] Get:117 http://ftpmaster.internal/ubuntu lunar/main s390x libxcb-xfixes0 s390x 1.15-1 [10.5 kB] Get:118 http://ftpmaster.internal/ubuntu lunar/main s390x libxshmfence1 s390x 1.3-1build4 [5334 B] Get:119 http://ftpmaster.internal/ubuntu lunar/main s390x libxxf86vm1 s390x 1:1.1.4-1build3 [9900 B] Get:120 http://ftpmaster.internal/ubuntu lunar-proposed/main s390x libllvm15 s390x 1:15.0.7-1 [29.1 MB] Get:121 http://ftpmaster.internal/ubuntu lunar/main s390x libsensors-config all 1:3.6.0-7ubuntu1 [5274 B] Get:122 http://ftpmaster.internal/ubuntu lunar/main s390x libsensors5 s390x 1:3.6.0-7ubuntu1 [25.3 kB] Get:123 http://ftpmaster.internal/ubuntu lunar/main s390x libgl1-mesa-dri s390x 22.2.5-0ubuntu1 [5430 kB] Get:124 http://ftpmaster.internal/ubuntu lunar/main s390x libglx-mesa0 s390x 22.2.5-0ubuntu1 [166 kB] Get:125 http://ftpmaster.internal/ubuntu lunar/main s390x libglx0 s390x 1.6.0-1 [28.3 kB] Get:126 http://ftpmaster.internal/ubuntu lunar/main s390x libgl1 s390x 1.6.0-1 [137 kB] Get:127 http://ftpmaster.internal/ubuntu lunar/universe s390x libfltk-gl1.3 s390x 1.3.8-5 [41.7 kB] Get:128 http://ftpmaster.internal/ubuntu lunar/main s390x xorg-sgml-doctools all 1:1.11-1.1 [10.9 kB] Get:129 http://ftpmaster.internal/ubuntu lunar/main s390x x11proto-dev all 2022.1-1 [605 kB] Get:130 http://ftpmaster.internal/ubuntu lunar/main s390x libxau-dev s390x 1:1.0.9-1build5 [9702 B] Get:131 http://ftpmaster.internal/ubuntu lunar/main s390x libxdmcp-dev s390x 1:1.1.3-0ubuntu5 [26.5 kB] Get:132 http://ftpmaster.internal/ubuntu lunar/main s390x xtrans-dev all 1.4.0-1 [68.9 kB] Get:133 http://ftpmaster.internal/ubuntu lunar/main s390x libpthread-stubs0-dev s390x 0.4-1build2 [5508 B] Get:134 http://ftpmaster.internal/ubuntu lunar/main s390x libxcb1-dev s390x 1.15-1 [86.5 kB] Get:135 http://ftpmaster.internal/ubuntu lunar/main s390x libx11-dev s390x 2:1.8.3-3 [716 kB] Get:136 http://ftpmaster.internal/ubuntu lunar/universe s390x libfltk1.3-dev s390x 1.3.8-5 [887 kB] Get:137 http://ftpmaster.internal/ubuntu lunar/universe s390x libhwloc15 s390x 2.9.0-1 [148 kB] Get:138 http://ftpmaster.internal/ubuntu lunar/main s390x libjpeg-turbo8-dev s390x 2.1.2-0ubuntu1 [231 kB] Get:139 http://ftpmaster.internal/ubuntu lunar/main s390x libjpeg8-dev s390x 8c-2ubuntu10 [1478 B] Get:140 http://ftpmaster.internal/ubuntu lunar/main s390x libjpeg-dev s390x 8c-2ubuntu10 [1476 B] Get:141 http://ftpmaster.internal/ubuntu lunar/main s390x libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] Get:142 http://ftpmaster.internal/ubuntu lunar/universe s390x libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] Get:143 http://ftpmaster.internal/ubuntu lunar/main s390x libltdl7 s390x 2.4.7-5 [40.6 kB] Get:144 http://ftpmaster.internal/ubuntu lunar/main s390x libltdl-dev s390x 2.4.7-5 [169 kB] Get:145 http://ftpmaster.internal/ubuntu lunar/main s390x libnl-3-dev s390x 3.7.0-0.2 [99.9 kB] Get:146 http://ftpmaster.internal/ubuntu lunar/main s390x libnl-route-3-dev s390x 3.7.0-0.2 [207 kB] Get:147 http://ftpmaster.internal/ubuntu lunar/universe s390x libmunge2 s390x 0.5.15-2 [14.4 kB] Get:148 http://ftpmaster.internal/ubuntu lunar/main s390x libpciaccess0 s390x 0.17-2 [17.7 kB] Get:149 http://ftpmaster.internal/ubuntu lunar/main s390x libxnvctrl0 s390x 510.47.03-0ubuntu1 [11.7 kB] Get:150 http://ftpmaster.internal/ubuntu lunar/universe s390x ocl-icd-libopencl1 s390x 2.3.1-1 [39.0 kB] Get:151 http://ftpmaster.internal/ubuntu lunar/universe s390x libhwloc-plugins s390x 2.9.0-1 [15.6 kB] Get:152 http://ftpmaster.internal/ubuntu lunar/universe s390x libpmix2 s390x 4.2.2-1 [608 kB] Get:153 http://ftpmaster.internal/ubuntu lunar/universe s390x libopenmpi3 s390x 4.1.4-3ubuntu2 [2146 kB] Get:154 http://ftpmaster.internal/ubuntu lunar/main s390x libnuma-dev s390x 2.0.16-1 [36.5 kB] Get:155 http://ftpmaster.internal/ubuntu lunar/universe s390x libhwloc-dev s390x 2.9.0-1 [243 kB] Get:156 http://ftpmaster.internal/ubuntu lunar/main s390x zlib1g-dev s390x 1:1.2.13.dfsg-1ubuntu4 [896 kB] Get:157 http://ftpmaster.internal/ubuntu lunar/universe s390x libpmix-dev s390x 4.2.2-1 [917 kB] Get:158 http://ftpmaster.internal/ubuntu lunar/main s390x libjbig0 s390x 2.1-6ubuntu1 [29.7 kB] Get:159 http://ftpmaster.internal/ubuntu lunar/main s390x libjbig-dev s390x 2.1-6ubuntu1 [28.3 kB] Get:160 http://ftpmaster.internal/ubuntu lunar/main s390x liblzma-dev s390x 5.4.1-0.0 [176 kB] Get:161 http://ftpmaster.internal/ubuntu lunar/main s390x libzstd-dev s390x 1.5.2+dfsg2-3 [331 kB] Get:162 http://ftpmaster.internal/ubuntu lunar/main s390x libwebp7 s390x 1.2.4-0.1 [171 kB] Get:163 http://ftpmaster.internal/ubuntu lunar/main s390x libwebpmux3 s390x 1.2.4-0.1 [19.3 kB] Get:164 http://ftpmaster.internal/ubuntu lunar/main s390x libwebpdemux2 s390x 1.2.4-0.1 [9654 B] Get:165 http://ftpmaster.internal/ubuntu lunar/main s390x libwebp-dev s390x 1.2.4-0.1 [286 kB] Get:166 http://ftpmaster.internal/ubuntu lunar/main s390x libtiff6 s390x 4.5.0-4ubuntu1 [186 kB] Get:167 http://ftpmaster.internal/ubuntu lunar/main s390x libtiffxx6 s390x 4.5.0-4ubuntu1 [5734 B] Get:168 http://ftpmaster.internal/ubuntu lunar/main s390x libtiff-dev s390x 4.5.0-4ubuntu1 [327 kB] Get:169 http://ftpmaster.internal/ubuntu lunar/universe s390x openmpi-common all 4.1.4-3ubuntu2 [163 kB] Get:170 http://ftpmaster.internal/ubuntu lunar/universe s390x openmpi-bin s390x 4.1.4-3ubuntu2 [82.4 kB] Get:171 http://ftpmaster.internal/ubuntu lunar/main s390x libibverbs-dev s390x 44.0-2 [656 kB] Get:172 http://ftpmaster.internal/ubuntu lunar/universe s390x libopenmpi-dev s390x 4.1.4-3ubuntu2 [824 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 94.0 MB in 6s (14.5 MB/s) Selecting previously unselected package sgml-base. 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Setting up libglvnd0:s390x (1.6.0-1) ... Setting up libcbor0.8:s390x (0.8.0-2ubuntu1) ... Setting up libdebhelper-perl (13.11.4ubuntu3) ... Setting up libbrotli1:s390x (1.0.9-2build7) ... Setting up libsensors-config (1:3.6.0-7ubuntu1) ... Setting up libnghttp2-14:s390x (1.51.0-1) ... Setting up libmagic1:s390x (1:5.44-3) ... Setting up libdeflate0:s390x (1.14-1) ... Setting up libevent-openssl-2.1-7:s390x (2.1.12-stable-5ubuntu1) ... Setting up libfftw3-long3:s390x (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:s390x (0.4-1build2) ... Setting up libjbig0:s390x (2.1-6ubuntu1) ... Setting up libevent-2.1-7a:s390x (2.1.12-stable-5ubuntu1) ... Setting up libsasl2-modules-db:s390x (2.1.28+dfsg-10) ... Setting up xtrans-dev (1.4.0-1) ... Setting up autotools-dev (20220109.1) ... Setting up libuv1:s390x (1.44.2-1) ... Setting up libmunge2 (0.5.15-2) ... Setting up libfreetype6:s390x (2.12.1+dfsg-4) ... Setting up libx11-data (2:1.8.3-3) ... Setting up librtmp1:s390x (2.4+20151223.gitfa8646d.1-2build4) ... Setting up libhwloc15:s390x (2.9.0-1) ... Setting up autopoint (0.21-11) ... Setting up libjsoncpp25:s390x (1.9.5-4) ... Setting up fonts-dejavu-core (2.37-2build2) ... Setting up libsensors5:s390x (1:3.6.0-7ubuntu1) ... Setting up libjpeg-turbo8:s390x (2.1.2-0ubuntu1) ... Setting up libltdl7:s390x (2.4.7-5) ... Setting up libfftw3-double3:s390x (3.3.8-2ubuntu8) ... Setting up libglapi-mesa:s390x (22.2.5-0ubuntu1) ... Setting up libsasl2-2:s390x (2.1.28+dfsg-10) ... Setting up libssh-4:s390x (0.10.4-2) ... Setting up libgfortran5:s390x (12.2.0-14ubuntu1) ... Setting up autoconf (2.71-3) ... Setting up libwebp7:s390x (1.2.4-0.1) ... Setting up liblzma-dev:s390x (5.4.1-0.0) ... Setting up zlib1g-dev:s390x (1:1.2.13.dfsg-1ubuntu4) ... Setting up libnuma1:s390x (2.0.16-1) ... Setting up ocl-icd-libopencl1:s390x (2.3.1-1) ... Setting up libxshmfence1:s390x (1.3-1build4) ... Setting up librhash0:s390x (1.4.3-3) ... Setting up libuchardet0:s390x (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:s390x (1.12.0-2) ... Setting up libwebpmux3:s390x (1.2.4-0.1) ... Setting up libbsd0:s390x (0.11.7-2) ... Setting up libdeflate-dev:s390x (1.14-1) ... Setting up libdrm-common (2.4.114-1) ... Setting up libelf1:s390x (0.188-2.1) ... Setting up libxml2:s390x (2.9.14+dfsg-1.1) ... Setting up libldap2:s390x (2.6.3+dfsg-1~exp1ubuntu1) ... Setting up libevent-pthreads-2.1-7:s390x (2.1.12-stable-5ubuntu1) ... Setting up libjpeg8:s390x (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:s390x (0.188-2.1) ... Setting up libjpeg-turbo8-dev:s390x (2.1.2-0ubuntu1) ... Setting up libxdmcp6:s390x (1:1.1.3-0ubuntu5) ... Setting up libevent-extra-2.1-7:s390x (2.1.12-stable-5ubuntu1) ... Setting up libxcb1:s390x (1.15-1) ... Setting up gettext (0.21-11) ... Setting up libxcb-xfixes0:s390x (1.15-1) ... Setting up libxau-dev:s390x (1:1.0.9-1build5) ... Setting up libtool (2.4.7-5) ... Setting up libarchive13:s390x (3.6.2-1ubuntu1) ... Setting up libxcb-render0:s390x (1.15-1) ... Setting up libfftw3-bin (3.3.8-2ubuntu8) ... Setting up fontconfig-config (2.14.1-3ubuntu1) ... Setting up libxcb-glx0:s390x (1.15-1) ... Setting up libwebpdemux2:s390x (1.2.4-0.1) ... Setting up libedit2:s390x (3.1-20221030-2) ... Setting up libjbig-dev:s390x (2.1-6ubuntu1) ... Setting up libgfortran-12-dev:s390x (12.2.0-14ubuntu1) ... Setting up libxcb-shm0:s390x (1.15-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnuma-dev:s390x (2.0.16-1) ... Setting up libxcb-present0:s390x (1.15-1) ... Setting up dh-autoreconf (20) ... Setting up libltdl-dev:s390x (2.4.7-5) ... Setting up libxdmcp-dev:s390x (1:1.1.3-0ubuntu5) ... Setting up gfortran-12 (12.2.0-14ubuntu1) ... Setting up libwebp-dev:s390x (1.2.4-0.1) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libxcb-sync1:s390x (1.15-1) ... Setting up libevent-dev (2.1.12-stable-5ubuntu1) ... Setting up libxcb-dri2-0:s390x (1.15-1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libdrm2:s390x (2.4.114-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-9) ... Setting up libtiff6:s390x (4.5.0-4ubuntu1) ... Setting up libllvm15:s390x (1:15.0.7-1) ... Setting up libnl-3-200:s390x (3.7.0-0.2) ... Setting up debugedit (1:5.0-5) ... Setting up libcurl4:s390x (7.87.0-2ubuntu1) ... Setting up libx11-6:s390x (2:1.8.3-3) ... Setting up libhwloc-dev:s390x (2.9.0-1) ... Setting up libfontconfig1:s390x (2.14.1-3ubuntu1) ... Setting up libjpeg8-dev:s390x (8c-2ubuntu10) ... Setting up libtiffxx6:s390x (4.5.0-4ubuntu1) ... Setting up libfftw3-dev:s390x (3.3.8-2ubuntu8) ... Setting up libdrm-amdgpu1:s390x (2.4.114-1) ... Setting up libxcb-dri3-0:s390x (1.15-1) ... Setting up libx11-xcb1:s390x (2:1.8.3-3) ... Setting up libdrm-nouveau2:s390x (2.4.114-1) ... Setting up libxcb1-dev:s390x (1.15-1) ... Setting up libxrender1:s390x (1:0.9.10-1.1) ... Setting up libdrm-radeon1:s390x (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:s390x (22.2.5-0ubuntu1) ... Setting up libjpeg-dev:s390x (8c-2ubuntu10) ... Setting up libx11-dev:s390x (2:1.8.3-3) ... Setting up libxext6:s390x (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:s390x (1.16.0-7) ... Setting up libxxf86vm1:s390x (1:1.1.4-1build3) ... Setting up libnl-route-3-200:s390x (3.7.0-0.2) ... Setting up libxnvctrl0:s390x (510.47.03-0ubuntu1) ... Setting up libtiff-dev:s390x (4.5.0-4ubuntu1) ... Setting up libxfixes3:s390x (1:6.0.0-2) ... Setting up libxinerama1:s390x (2:1.1.4-3) ... Setting up libnl-3-dev:s390x (3.7.0-0.2) ... Setting up cmake (3.25.1-1) ... Setting up libibverbs1:s390x (44.0-2) ... Setting up libxft2:s390x (2.3.6-1) ... Setting up libglx-mesa0:s390x (22.2.5-0ubuntu1) ... Setting up libglx0:s390x (1.6.0-1) ... Setting up ibverbs-providers:s390x (44.0-2) ... Setting up libxcursor1:s390x (1:1.2.1-1) ... Setting up debhelper (13.11.4ubuntu3) ... Setting up libhwloc-plugins:s390x (2.9.0-1) ... Setting up libnl-route-3-dev:s390x (3.7.0-0.2) ... Setting up libgl1:s390x (1.6.0-1) ... Setting up librdmacm1:s390x (44.0-2) ... Setting up libpmix2:s390x (4.2.2-1) ... Setting up libfltk1.3:s390x (1.3.8-5) ... Setting up libfltk-gl1.3:s390x (1.3.8-5) ... Setting up libfltk-cairo1.3:s390x (1.3.8-5) ... Setting up libibverbs-dev:s390x (44.0-2) ... Setting up libfltk-images1.3:s390x (1.3.8-5) ... Setting up libfltk-forms1.3:s390x (1.3.8-5) ... Setting up libpmix-dev:s390x (4.2.2-1) ... Setting up libfltk1.3-dev:s390x (1.3.8-5) ... Setting up libfabric1:s390x (1.17.0-3) ... Setting up libopenmpi3:s390x (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:s390x (4.1.4-3ubuntu2) ... update-alternatives: using /usr/lib/s390x-linux-gnu/openmpi/include to provide /usr/include/s390x-linux-gnu/mpi (mpi-s390x-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 (s390x included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-137-generic #154-Ubuntu SMP Thu Jan 5 17:03:11 UTC 2023 s390x (s390x) 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 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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 relion_3.1.3-3build1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEETQvhLw5HdtiqzpaW5mx3Wuv+bH0FAmPeULUACgkQ5mx3Wuv+ 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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-25549284 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-25549284 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-25549284 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 s390x 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/s390x-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/lib/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") -- MPI_INCLUDE_PATH : /usr/lib/s390x-linux-gnu/openmpi/include;/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -- MPI_LIBRARIES : /usr/lib/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so;/usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so -- MPI_CXX_INCLUDE_PATH : /usr/lib/s390x-linux-gnu/openmpi/include;/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -- MPI_CXX_LIBRARIES : /usr/lib/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so;/usr/lib/s390x-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/s390x-linux-gnu/libX11.so -- Looking for XOpenDisplay in /usr/lib/s390x-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/s390x-linux-gnu/libX11.so;/usr/lib/s390x-linux-gnu/libm.so -- Found FFTW -- FFTW_PATH: /usr/include -- FFTW_INCLUDES: /usr/include -- FFTW_LIBRARIES: /usr/lib/s390x-linux-gnu/libfftw3f.so;/usr/lib/s390x-linux-gnu/libfftw3.so -- Looking for sincos -- Looking for sincos - found -- Looking for __sincos -- Looking for __sincos - not found -- Found TIFF: /usr/lib/s390x-linux-gnu/libtiff.so (found version "4.5.0") -- Found ZLIB: /usr/lib/s390x-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 [ 0%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/args.cpp.o [ 0%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/__/macros.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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/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/s390x-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/s390x-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 ()); | ~~~~~~~~~~~~~~~~~ [ 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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 [ 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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 [ 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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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_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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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_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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 [ 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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 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; | ^~ [ 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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 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; | ^~ [ 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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/__/projector.cpp.o [ 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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 [ 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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 [ 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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 [ 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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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_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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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 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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 [ 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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 [ 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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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_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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 [ 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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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_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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 [ 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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 [ 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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat 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-I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 CXX static library ../../lib/librelion_lib.a cd /<>/build/src/apps && /usr/bin/cmake -P CMakeFiles/relion_lib.dir/cmake_clean_target.cmake cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/relion_lib.dir/link.txt --verbose=1 /usr/bin/ar qc ../../lib/librelion_lib.a CMakeFiles/relion_lib.dir/__/__/macros.cpp.o CMakeFiles/relion_lib.dir/__/CPlot2D.cpp.o CMakeFiles/relion_lib.dir/__/args.cpp.o CMakeFiles/relion_lib.dir/__/assembly.cpp.o 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-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 [ 54%] Building CXX object src/apps/CMakeFiles/align_symmetry.dir/align_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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/relion_gui_lib.dir/__/displayer.cpp.o [ 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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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 -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/s390x-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 -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/s390x-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 [ 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 -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/s390x-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 ‘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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 ‘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' [ 56%] Built target align_symmetry /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 In function ‘free_Tvector’, inlined from ‘brent’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:594:25: 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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 /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 ‘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/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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 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 -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 57%] 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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 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 ‘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/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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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' [ 57%] Built target autopick /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' [ 57%] 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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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' [ 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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 [ 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 -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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_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 -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/s390x-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 ‘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 ‘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))); | ^ [ 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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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' [ 59%] Built target convert_star /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' [ 59%] 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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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' [ 59%] Built target convert_to_tiff /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' [ 59%] 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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 [ 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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 60%] 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 -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 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 -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/<>/build' [ 61%] Built target convert_to_tiff_mpi /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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 62%] 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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 [ 62%] 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 -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/s390x-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 ‘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 [ 62%] 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' [ 62%] Built target relion_gui_lib /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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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 ‘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 -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/s390x-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 ‘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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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 ‘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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 make[4]: Leaving directory '/<>/build' [ 63%] Built target ctf_toolbox /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' [ 63%] 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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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 -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gui_lib.a /usr/lib/s390x-linux-gnu/libfltk_images.so /usr/lib/s390x-linux-gnu/libfltk_forms.so /usr/lib/s390x-linux-gnu/libfltk.so -lX11 -lm -ltiff ../../lib/librelion_lib.a -lfftw3f -lfftw3 -ltiff [ 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 -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/<>/build' [ 65%] Built target ctf_refine_mpi /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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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))); | ^ [ 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 -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/s390x-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 [ 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 -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/s390x-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 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 ‘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 ‘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 ‘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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 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' [ 66%] Built target estimate_gain /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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 make[4]: Leaving directory '/<>/build' [ 66%] Built target demodulate /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' In file included from /<>/src/numerical_recipes.h:48, from /<>/src/funcs.h:59, from /<>/src/args.h:56, from /<>/src/apps/find_tiltpairs.cpp:20: In function ‘free_Tvector(int*&, int, int)void’, inlined from ‘gaussj(double*, int, double*, int)void’ at /<>/src/numerical_recipes.h:262:17: /<>/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ipiv’ with nonzero offset 4 [-Wfree-nonheap-object] 74 | free((char*)(v + nl)); | ~~~~^~~~~~~~~~~~~~~~~ /<>/src/numerical_recipes.h: In function ‘gaussj(double*, int, double*, int)void’: /<>/src/numerical_recipes.h:198:26: note: declared here 198 | int *indxc, *indxr, *ipiv; | ^~~~ In function ‘free_Tvector(int*&, int, int)void’, inlined from ‘gaussj(double*, int, double*, int)void’ at /<>/src/numerical_recipes.h:262:17: /<>/src/memory.h:74:13: warning: ‘free’ called on pointer ‘ipiv’ with nonzero offset 4 [-Wfree-nonheap-object] 74 | free((char*)(v + nl)); | ~~~~^~~~~~~~~~~~~~~~~ /<>/src/numerical_recipes.h: In function ‘gaussj(double*, int, double*, int)void’: /<>/src/numerical_recipes.h:198:26: note: declared here 198 | int *indxc, *indxr, *ipiv; | ^~~~ 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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 66%] 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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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 -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/<>/build' [ 67%] 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' [ 68%] 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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 [ 69%] 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 -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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 ‘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 [ 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 -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/s390x-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 -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/s390x-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 ‘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 ‘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 ‘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 ‘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' [ 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= 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' [ 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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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 ‘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: 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' [ 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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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 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 [ 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 -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/s390x-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' [ 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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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' [ 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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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 -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 71%] 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 -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 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 -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/s390x-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 ‘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 ‘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))); | ^ /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 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 ‘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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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 ‘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 [ 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 -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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' [ 73%] Built target image_handler /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' [ 73%] 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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 [ 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 -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gui_lib.a /usr/lib/s390x-linux-gnu/libfltk_images.so /usr/lib/s390x-linux-gnu/libfltk_forms.so /usr/lib/s390x-linux-gnu/libfltk.so -lX11 -lm -ltiff ../../lib/librelion_lib.a -lfftw3f -lfftw3 -ltiff 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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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_manualpick cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/manualpick.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gui_lib.a /usr/lib/s390x-linux-gnu/libfltk_images.so /usr/lib/s390x-linux-gnu/libfltk_forms.so /usr/lib/s390x-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 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: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' In function ‘free_Tvector’, inlined from ‘brent’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:594:25: [ 75%] Built target localsym /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 /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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 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 ‘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/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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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 ‘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 [ 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 -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/s390x-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 ‘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 manualpick /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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 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/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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 76%] 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 -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/s390x-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 ‘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' [ 76%] Built target localsym_mpi /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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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 [ 77%] Linking CXX executable ../../bin/relion_motion_refine cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/motion_refine.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/<>/build' [ 77%] Built target merge_particles /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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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 make[4]: Leaving directory '/<>/build' [ 77%] Built target relion /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= In function ‘free_Tvector’, inlined from ‘powell’ at /usr/src/relion-3.1.3-3build1/src/numerical_recipes.cpp:767:25: make[4]: Leaving directory '/<>/build' /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/bin/make -f src/apps/CMakeFiles/particle_FCC.dir/build.make src/apps/CMakeFiles/particle_FCC.dir/build /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]: Entering directory '/<>/build' [ 78%] 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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 [ 79%] Linking CXX executable ../../bin/relion_motion_refine_mpi cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/motion_refine_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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_mrc2vtk cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/mrc2vtk.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 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 -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/s390x-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 ‘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' [ 79%] Built target mrc2vtk /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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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 ‘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' [ 80%] Built target motion_refine /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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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' [ 80%] Built target particle_FCC /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 [ 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 -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 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/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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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 ‘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 ‘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 -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/s390x-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))); | ^ [ 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 -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/<>/build' [ 82%] Built target motion_refine_mpi /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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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 -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/s390x-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 ‘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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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 -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/s390x-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 ‘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 ‘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 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 ‘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' [ 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' [ 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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 [ 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 -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/<>/build' [ 84%] Built target particle_reposition /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' [ 84%] 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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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_subtract /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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 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 ‘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_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 -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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_postprocess cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/postprocess.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/s390x-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 ‘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 ‘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' [ 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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 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 -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/s390x-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: 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 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' [ 86%] Built target postprocess /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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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 ‘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' [ 86%] Built target pipeliner /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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 make[4]: Leaving directory '/<>/build' [ 86%] Built target plot_delocalisation /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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 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 -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 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 -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 /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 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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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 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 ‘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 ‘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 -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 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 -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/s390x-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' [ 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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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' [ 89%] 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' [ 89%] 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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 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 ‘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/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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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 -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 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 -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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 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 ‘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 ‘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 ‘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 -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/s390x-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 ‘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 project /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' [ 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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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 ‘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 [ 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 -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/s390x-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' [ 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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 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 ‘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/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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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' [ 92%] 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' [ 92%] 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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 92%] 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 -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 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 -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/s390x-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 ‘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 ‘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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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' [ 94%] Built target run_ctffind /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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 [ 95%] 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 -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/s390x-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 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 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/s390x-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 ‘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' [ 95%] Built target reposition /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' [ 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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 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/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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 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 -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/s390x-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 run_ctffind_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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 make[4]: Leaving directory '/<>/build' [ 96%] Built target refine_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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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 ‘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' [ 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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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_scheduler cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/scheduler.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/s390x-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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 /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 [ 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 -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/s390x-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 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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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 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/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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 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 -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/s390x-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 ‘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 ‘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 [ 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 -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/s390x-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))); | ^ make[4]: Leaving directory '/<>/build' [ 99%] Built target stack_create /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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-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/s390x-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [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 -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-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/s390x-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/s390x-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 make[4]: Leaving directory '/<>/build' [100%] Built target tiltpair_plot 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 ‘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 scheduler 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_image_handler -- Installing: /<>/debian/tmp/cli/usr/bin/relion_convert_to_tiff -- Installing: /<>/debian/tmp/cli/usr/bin/relion_ctf_refine_mpi -- Installing: /<>/debian/tmp/cli/usr/bin/relion_merge_particles -- Installing: /<>/debian/tmp/cli/usr/bin/relion_star_printtable -- Installing: /<>/debian/tmp/cli/usr/bin/relion_mask_create -- Installing: /<>/debian/tmp/cli/usr/bin/relion_tiltpair_plot -- Installing: /<>/debian/tmp/cli/usr/bin/relion_particle_select -- Installing: /<>/debian/tmp/cli/usr/bin/relion_manualpick -- Installing: /<>/debian/tmp/cli/usr/bin/relion_reconstruct_mpi -- Installing: /<>/debian/tmp/cli/usr/bin/relion_pipeliner -- Installing: /<>/debian/tmp/cli/usr/bin/relion_mrc2vtk -- Installing: /<>/debian/tmp/cli/usr/bin/relion_localsym_mpi -- Installing: /<>/debian/tmp/cli/usr/bin/relion_reconstruct -- Installing: /<>/debian/tmp/cli/usr/bin/relion_star_handler -- Installing: /<>/debian/tmp/cli/usr/bin/relion_ctf_mask_test -- Installing: /<>/debian/tmp/cli/usr/bin/relion_run_ctffind_mpi -- Installing: /<>/debian/tmp/cli/usr/bin/relion_flex_analyse -- Installing: /<>/debian/tmp/cli/usr/bin/relion_preprocess -- Installing: /<>/debian/tmp/cli/usr/bin/relion_motion_refine_mpi -- Installing: /<>/debian/tmp/cli/usr/bin/relion_particle_reposition -- Installing: /<>/debian/tmp/cli/usr/bin/relion_tomo_test -- Installing: /<>/debian/tmp/cli/usr/bin/relion_particle_FCC -- Installing: /<>/debian/tmp/cli/usr/bin/relion_qsub.csh -- Installing: /<>/debian/tmp/cli/usr/bin/relion_scheduler -- Installing: /<>/debian/tmp/cli/usr/bin/relion_ctf_refine -- Installing: /<>/debian/tmp/cli/usr/bin/relion_localsym -- Installing: /<>/debian/tmp/cli/usr/bin/relion_star_datablock_singlefiles -- Installing: /<>/debian/tmp/cli/usr/bin/relion_particle_symmetry_expand -- Installing: /<>/debian/tmp/cli/usr/bin/relion_helix_inimodel2d -- Installing: /<>/debian/tmp/cli/usr/bin/relion_star_plottable -- Installing: /<>/debian/tmp/cli/usr/bin/relion_run_ctffind -- Installing: /<>/debian/tmp/cli/usr/bin/relion_autopick_mpi -- 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_ctf_toolbox -- Installing: /<>/debian/tmp/cli/usr/bin/relion_star_loopheader -- Installing: /<>/debian/tmp/cli/usr/bin/relion_helix_toolbox -- Installing: /<>/debian/tmp/cli/usr/bin/relion_star_datablock_stack -- Installing: /<>/debian/tmp/cli/usr/bin/relion_reposition -- Installing: /<>/debian/tmp/cli/usr/bin/relion_plot_delocalisation -- Installing: /<>/debian/tmp/cli/usr/bin/relion_convert_star -- Installing: /<>/debian/tmp/cli/usr/bin/relion_external_reconstruct -- Installing: /<>/debian/tmp/cli/usr/bin/relion_convert_to_tiff_mpi -- Installing: /<>/debian/tmp/cli/usr/bin/relion_project -- Installing: /<>/debian/tmp/cli/usr/bin/relion_star_datablock_ctfdat -- Installing: /<>/debian/tmp/cli/usr/bin/relion_motion_refine -- Installing: /<>/debian/tmp/cli/usr/bin/relion_demodulate -- Installing: /<>/debian/tmp/cli/usr/bin/relion_estimate_gain -- Installing: /<>/debian/tmp/cli/usr/bin/relion_display -- Installing: /<>/debian/tmp/cli/usr/bin/relion_import -- Installing: /<>/debian/tmp/cli/usr/bin/relion_particle_subtract -- Installing: /<>/debian/tmp/cli/usr/bin/relion_run_motioncorr_mpi -- Installing: /<>/debian/tmp/cli/usr/bin/relion_autopick -- Installing: /<>/debian/tmp/cli/usr/bin/relion_flex_analyse_mpi -- Installing: /<>/debian/tmp/cli/usr/bin/relion_refine -- Installing: /<>/debian/tmp/cli/usr/bin/relion_prepare_subtomo -- Installing: /<>/debian/tmp/cli/usr/bin/relion_preprocess_mpi -- Installing: /<>/debian/tmp/cli/usr/bin/relion_refine_mpi -- Installing: /<>/debian/tmp/cli/usr/bin/relion_run_motioncorr -- Installing: /<>/debian/tmp/cli/usr/bin/relion_align_symmetry -- Installing: /<>/debian/tmp/cli/usr/bin/relion_postprocess_mpi -- Installing: /<>/debian/tmp/cli/usr/bin/relion_postprocess -- Installing: /<>/debian/tmp/cli/usr/bin/relion -- Installing: /<>/debian/tmp/cli/usr/bin/relion_find_tiltpairs -- 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-gui/usr/bin/relion_manualpick: Unknown DWARF DW_FORM_0x1f21 debugedit: debian/relion/usr/bin/relion_image_handler: Unknown DWARF DW_FORM_0x1f20 e4044ef6354a51d90a27d0f85e672d313659010d 74105dedb0cc238df8306e9915189263cfdeb6fd debugedit: debian/relion-gui/usr/bin/relion_display: Unknown DWARF DW_FORM_0x1f21 51361f5d9d134be18620043c64f58d449c6a1baa debugedit: debian/relion/usr/bin/relion_convert_to_tiff: Unknown DWARF DW_FORM_0x1f21 acfbd301e0cf76a8ee4bc2dfb7c3d0d8aaaa0cae debugedit: debian/relion/usr/bin/relion_ctf_refine_mpi: Unknown DWARF DW_FORM_0x1f21 debugedit: debian/relion-gui/usr/bin/relion: Unknown DWARF DW_FORM_0x1f21 416d2c4e8518bb9adb8c67c85aacd03cad5385fc 5e03d03c1a78901600916eaa7be72fb33704ddee debugedit: debian/relion/usr/bin/relion_merge_particles: Unknown DWARF DW_FORM_0x1f21 58b11fac592f09b2b1c85fb5262e33e438baa231 debugedit: debian/relion/usr/bin/relion_mask_create: Unknown DWARF DW_FORM_0x1f20 1e8788f92e91215020f9ce4b4c4de97010936479 debugedit: debian/relion/usr/bin/relion_tiltpair_plot: Unknown DWARF DW_FORM_0x1f21 691d91b19cd3a3bdba0eeda038c43a22db84e86f debugedit: debian/relion/usr/bin/relion_particle_select: Unknown DWARF DW_FORM_0x1f20 def464eda484e578752efb10f650c91b01ba4b4a debugedit: debian/relion/usr/bin/relion_reconstruct_mpi: Unknown DWARF DW_FORM_0x1f20 d99483e1fbcbdc1120d5322dd69e4d50d082ee6c debugedit: debian/relion/usr/bin/relion_pipeliner: Unknown DWARF DW_FORM_0x1f21 e588087ffe40e1c13275ca887387cdef35a23418 debugedit: debian/relion/usr/bin/relion_mrc2vtk: Unknown DWARF DW_FORM_0x1f20 69bb8c683bab4180bbb1a510f252379c99b832b3 debugedit: debian/relion/usr/bin/relion_localsym_mpi: Unknown DWARF DW_FORM_0x1f21 fc2f0fd97ca58f85e702fd4d206d6e1059e299da debugedit: debian/relion/usr/bin/relion_reconstruct: Unknown DWARF DW_FORM_0x1f21 1c80c271135654e0fe2aa2565d58e929239376eb debugedit: debian/relion/usr/bin/relion_star_handler: Unknown DWARF DW_FORM_0x1f21 bf3742c90b6395a741331052157410399c6625d5 debugedit: debian/relion/usr/bin/relion_ctf_mask_test: Unknown DWARF DW_FORM_0x1f20 54f0a0293b0c8939b8e01fb6fd1a097505bc1e3d debugedit: debian/relion/usr/bin/relion_run_ctffind_mpi: Unknown DWARF DW_FORM_0x1f20 5003ef81c307114af1ac9a74cc1dff3aaf43b412 debugedit: debian/relion/usr/bin/relion_flex_analyse: Unknown DWARF DW_FORM_0x1f21 2ba7e7bd52e3f8f0bb819dce728e4a70a315dfec debugedit: debian/relion/usr/bin/relion_preprocess: Unknown DWARF DW_FORM_0x1f21 6c2270e05017d0a4e0bba07c4b55eb0be9018812 debugedit: debian/relion/usr/bin/relion_motion_refine_mpi: Unknown DWARF DW_FORM_0x1f20 b8d2c815aeee5cd49f38c4d60f23fbc4bac99f11 debugedit: debian/relion/usr/bin/relion_particle_reposition: Unknown DWARF DW_FORM_0x1f21 aff187807dc139bf096b239f58b4dedccd4ebafe debugedit: debian/relion/usr/bin/relion_tomo_test: Unknown DWARF DW_FORM_0x1f21 185e6eaa3c2599d68bf73e06ccf987c5180d93bd debugedit: debian/relion/usr/bin/relion_particle_FCC: Unknown DWARF DW_FORM_0x1f20 5b45ab0547404e5e59a358fcef8cc1372490e3df debugedit: debian/relion/usr/bin/relion_scheduler: Unknown DWARF DW_FORM_0x1f21 55401363dc6b7ae3a3fdb7fac46a0bc355b01409 debugedit: debian/relion/usr/bin/relion_ctf_refine: Unknown DWARF DW_FORM_0x1f20 42b9f5000c18f34df6c7d797449c0219dbd7eb9b debugedit: debian/relion/usr/bin/relion_localsym: Unknown DWARF DW_FORM_0x1f21 774ccf63f444a6bfd523682713f76a0a3b46fb86 debugedit: debian/relion/usr/bin/relion_particle_symmetry_expand: Unknown DWARF DW_FORM_0x1f21 9d4ac8e012aeb137418d7e50916852ee2dd13732 debugedit: debian/relion/usr/bin/relion_helix_inimodel2d: Unknown DWARF DW_FORM_0x1f21 043a46a10184c0ef31c045fc6e5b7e338e5cdcc0 debugedit: debian/relion/usr/bin/relion_run_ctffind: Unknown DWARF DW_FORM_0x1f20 9ee953874638227c95ebddc0ea7d924f19ef65f0 debugedit: debian/relion/usr/bin/relion_autopick_mpi: Unknown DWARF DW_FORM_0x1f21 4d9bb4a4658f1e1e976ba5b603c8abec6423c774 debugedit: debian/relion/usr/bin/relion_stack_create: Unknown DWARF DW_FORM_0x1f21 1bae0d666c84fbc0c2ef0dee7812b9502c4c715b debugedit: debian/relion/usr/bin/relion_particle_subtract_mpi: Unknown DWARF DW_FORM_0x1f20 bfc3b8f3d282de53aa35e0c3df61e2543be6af5b debugedit: debian/relion/usr/bin/relion_ctf_toolbox: Unknown DWARF DW_FORM_0x1f20 e30272c4eba68e289fc7218c33bb2f0651510d5b debugedit: debian/relion/usr/bin/relion_helix_toolbox: Unknown DWARF DW_FORM_0x1f21 5f19b9c20742de2045ea1d8ee237f40cff8da05b debugedit: debian/relion/usr/bin/relion_reposition: Unknown DWARF DW_FORM_0x1f21 4ab585c40f840a3a2c6f54bea9b8c50770cff6d2 debugedit: debian/relion/usr/bin/relion_plot_delocalisation: Unknown DWARF DW_FORM_0x1f21 c279cb81f14d8e88b18df2d863ffee09fbaa5c56 debugedit: debian/relion/usr/bin/relion_convert_star: Unknown DWARF DW_FORM_0x1f21 c5b5d3a5ff998fca852b72878e1725a4b2be4408 debugedit: debian/relion/usr/bin/relion_external_reconstruct: Unknown DWARF DW_FORM_0x1f20 790089692c69108b461f0da6c23a0b27e80c3139 debugedit: debian/relion/usr/bin/relion_convert_to_tiff_mpi: Unknown DWARF DW_FORM_0x1f20 4ba37b36d6bbc81264ff79f8eb25bb80e8681852 debugedit: debian/relion/usr/bin/relion_project: Unknown DWARF DW_FORM_0x1f20 93d9f100884f014c1e5329efd7c6774703967e9b debugedit: debian/relion/usr/bin/relion_motion_refine: Unknown DWARF DW_FORM_0x1f20 8a7180157da917abb8b157a118113a79834442c4 debugedit: debian/relion/usr/bin/relion_demodulate: Unknown DWARF DW_FORM_0x1f20 5a10dc7da4f05438227fb800227a29611dc2c0ee debugedit: debian/relion/usr/bin/relion_estimate_gain: Unknown DWARF DW_FORM_0x1f21 8f5e814cf0770a7eadd6b3232d3320e30e873ea8 debugedit: debian/relion/usr/bin/relion_import: Unknown DWARF DW_FORM_0x1f21 eb1df0e8a185d77056548678b39fa7900d1acbd6 debugedit: debian/relion/usr/bin/relion_particle_subtract: Unknown DWARF DW_FORM_0x1f20 3411cc907e0190c547b9a85010d0cb172575da47 debugedit: debian/relion/usr/bin/relion_run_motioncorr_mpi: Unknown DWARF DW_FORM_0x1f21 4e227c0f4e64a2602ea0f691833099473ac3f3d9 debugedit: debian/relion/usr/bin/relion_autopick: Unknown DWARF DW_FORM_0x1f21 c9500bef9e4b6e350b02d22dc00deafcf8ff099a debugedit: debian/relion/usr/bin/relion_flex_analyse_mpi: Unknown DWARF DW_FORM_0x1f21 753f7cf1a5f42f07c39a26bed469c6ca5d2bf66d debugedit: debian/relion/usr/bin/relion_refine: Unknown DWARF DW_FORM_0x1f20 a7e06c017e14be75c4ccad2d5d0257bdb04a0eca debugedit: debian/relion/usr/bin/relion_prepare_subtomo: Unknown DWARF DW_FORM_0x1f20 8339fad4bbf0e6fcafeb15f31f18a736e83528c4 debugedit: debian/relion/usr/bin/relion_preprocess_mpi: Unknown DWARF DW_FORM_0x1f21 afcf888c68f0c27e645551a2497b407d8917d3f9 debugedit: debian/relion/usr/bin/relion_refine_mpi: Unknown DWARF DW_FORM_0x1f21 f1f6ca29aefda9abbeead0cab0c7a06d6ceca340 debugedit: debian/relion/usr/bin/relion_run_motioncorr: Unknown DWARF DW_FORM_0x1f21 6d8e3125046f83100d38c624da1b29401b190f95 debugedit: debian/relion/usr/bin/relion_align_symmetry: Unknown DWARF DW_FORM_0x1f20 979eea2d96443a88d448c7a760c1cad9197851c6 debugedit: debian/relion/usr/bin/relion_postprocess_mpi: Unknown DWARF DW_FORM_0x1f21 4b6d79f88bb5b5c89c579a66cf17d04429525f08 debugedit: debian/relion/usr/bin/relion_postprocess: Unknown DWARF DW_FORM_0x1f21 d16f4bf0fa8c0476e93daf5cc5e281d5af065f66 debugedit: debian/relion/usr/bin/relion_find_tiltpairs: Unknown DWARF DW_FORM_0x1f20 256fa92513bc7761b0d5dadb8b6533f7a16fc8f5 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 pkgstriptranslations: processing relion (in debian/relion); do_strip: , oemstrip: INFO: pkgstriptranslations version 151 pkgstriptranslations: processing relion-dbgsym (in debian/.debhelper/relion/dbgsym-root); do_strip: , oemstrip: pkgstriptranslations: processing relion-gui (in debian/relion-gui); 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: 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_s390x.deb'. pkgstripfiles: No PNG files. dpkg-deb: building package 'relion' in '../relion_3.1.3-3build1_s390x.deb'. pkgstripfiles: processing control file: debian/relion-gui/DEBIAN/control, package relion-gui, directory debian/relion-gui Searching for duplicated docs in dependency relion... symlinking changelog.Debian.gz in relion-gui to file in relion pkgstripfiles: Running PNG optimization (using 4 cpus) for package relion-gui ... pkgstripfiles: processing control file: debian/.debhelper/relion-gui/dbgsym-root/DEBIAN/control, package relion-gui-dbgsym, directory debian/.debhelper/relion-gui/dbgsym-root pkgstripfiles: No PNG files. dpkg-deb: building package 'relion-gui' in '../relion-gui_3.1.3-3build1_s390x.deb'. dpkg-deb: building package 'relion-gui-dbgsym' in 'debian/.debhelper/scratch-space/build-relion-gui/relion-gui-dbgsym_3.1.3-3build1_s390x.deb'. Renaming relion-gui-dbgsym_3.1.3-3build1_s390x.deb to relion-gui-dbgsym_3.1.3-3build1_s390x.ddeb Renaming relion-dbgsym_3.1.3-3build1_s390x.deb to relion-dbgsym_3.1.3-3build1_s390x.ddeb dpkg-genbuildinfo --build=any -O../relion_3.1.3-3build1_s390x.buildinfo dpkg-genchanges --build=any -mLaunchpad Build Daemon -O../relion_3.1.3-3build1_s390x.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 2023-02-04T13:32:10Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ relion_3.1.3-3build1_s390x.changes: ----------------------------------- Format: 1.8 Date: Sat, 04 Feb 2023 07:33:54 -0500 Source: relion Binary: relion relion-gui Built-For-Profiles: noudeb Architecture: s390x 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: 4d97ec4b32a18ce390bf4547de533c5acbc6fdf3 207778886 relion-dbgsym_3.1.3-3build1_s390x.ddeb 030e241abe6e1d8b13c2d29843ad6ce3c087c65f 14644654 relion-gui-dbgsym_3.1.3-3build1_s390x.ddeb 6da97a18c0ca524b0eabac93a9cfe4e7265f3c11 1205990 relion-gui_3.1.3-3build1_s390x.deb 29f6697ad2130c5e6f89ba70d05e895cb2addc59 10963 relion_3.1.3-3build1_s390x.buildinfo 915c58733c8e29fb9d8ad1c1ab63fa2109b8870a 12562040 relion_3.1.3-3build1_s390x.deb Checksums-Sha256: 653d6fc7b8834d7f92984c25ad171dee433223db974fe5c2219053d42a51331a 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/<>/relion_3.1.3-3build1_s390x.changes.new could not be renamed to /<>/relion_3.1.3-3build1_s390x.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: relion Binary: relion relion-dbgsym relion-gui relion-gui-dbgsym Architecture: s390x Version: 3.1.3-3build1 Checksums-Md5: ef8b20775c691795f5301c2fb61f2e6f 207778886 relion-dbgsym_3.1.3-3build1_s390x.ddeb 8fd6443b5fc2323ea097d72f54925999 14644654 relion-gui-dbgsym_3.1.3-3build1_s390x.ddeb cdf9993fdcf7371ae4e27c6013b6e2ee 1205990 relion-gui_3.1.3-3build1_s390x.deb eb6310135a0cbdd7ef935ccc7fbb578a 12562040 relion_3.1.3-3build1_s390x.deb Checksums-Sha1: 4d97ec4b32a18ce390bf4547de533c5acbc6fdf3 207778886 relion-dbgsym_3.1.3-3build1_s390x.ddeb 030e241abe6e1d8b13c2d29843ad6ce3c087c65f 14644654 relion-gui-dbgsym_3.1.3-3build1_s390x.ddeb 6da97a18c0ca524b0eabac93a9cfe4e7265f3c11 1205990 relion-gui_3.1.3-3build1_s390x.deb 915c58733c8e29fb9d8ad1c1ab63fa2109b8870a 12562040 relion_3.1.3-3build1_s390x.deb Checksums-Sha256: 653d6fc7b8834d7f92984c25ad171dee433223db974fe5c2219053d42a51331a 207778886 relion-dbgsym_3.1.3-3build1_s390x.ddeb edf5a796419125fb07005f0d09c039521513278387793733bb72068318e193f5 14644654 relion-gui-dbgsym_3.1.3-3build1_s390x.ddeb 554bcd75c166b7eacf8a5f2c7c7a68f2dbff9f485d7c742c2e21b41ede6ab470 1205990 relion-gui_3.1.3-3build1_s390x.deb 371ce388a1bf5e94ce47fc2db3d916b2345a52f2516a99b6848282d020df6740 12562040 relion_3.1.3-3build1_s390x.deb Build-Origin: Ubuntu Build-Architecture: s390x Build-Date: Sat, 04 Feb 2023 13:32:07 +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-s390x-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), libllvm15 (= 1:15.0.7-1), 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), 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), libubsan1 (= 12.2.0-14ubuntu1), libuchardet0 (= 0.0.7-1build2), 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_s390x.deb ---------------------------------- new Debian package, version 2.0. size 1205990 bytes: control archive=983 bytes. 1218 bytes, 23 lines control 308 bytes, 5 lines md5sums Package: relion-gui Source: relion Version: 3.1.3-3build1 Architecture: s390x Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 4828 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 2721472 2023-02-04 12:33 ./usr/bin/relion -rwxr-xr-x root/root 1178008 2023-02-04 12:33 ./usr/bin/relion_display -rwxr-xr-x root/root 1022360 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_s390x.deb ------------------------------ new Debian package, version 2.0. size 12562040 bytes: control archive=2657 bytes. 1233 bytes, 23 lines control 4218 bytes, 66 lines md5sums Package: relion Version: 3.1.3-3build1 Architecture: s390x Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 80088 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 862608 2023-02-04 12:33 ./usr/bin/relion_align_symmetry -rwxr-xr-x root/root 1796496 2023-02-04 12:33 ./usr/bin/relion_autopick -rwxr-xr-x root/root 1886608 2023-02-04 12:33 ./usr/bin/relion_autopick_mpi -rwxr-xr-x root/root 1325456 2023-02-04 12:33 ./usr/bin/relion_convert_star -rwxr-xr-x root/root 1087888 2023-02-04 12:33 ./usr/bin/relion_convert_to_tiff -rwxr-xr-x root/root 1153424 2023-02-04 12:33 ./usr/bin/relion_convert_to_tiff_mpi -rwxr-xr-x root/root 1468824 2023-02-04 12:33 ./usr/bin/relion_ctf_mask_test -rwxr-xr-x root/root 1878424 2023-02-04 12:33 ./usr/bin/relion_ctf_refine -rwxr-xr-x root/root 1968536 2023-02-04 12:33 ./usr/bin/relion_ctf_refine_mpi -rwxr-xr-x root/root 1005968 2023-02-04 12:33 ./usr/bin/relion_ctf_toolbox -rwxr-xr-x root/root 1382800 2023-02-04 12:33 ./usr/bin/relion_demodulate -rwxr-xr-x root/root 809360 2023-02-04 12:33 ./usr/bin/relion_estimate_gain -rwxr-xr-x root/root 952720 2023-02-04 12:33 ./usr/bin/relion_external_reconstruct -rwxr-xr-x root/root 579984 2023-02-04 12:33 ./usr/bin/relion_find_tiltpairs -rwxr-xr-x root/root 2029968 2023-02-04 12:33 ./usr/bin/relion_flex_analyse -rwxr-xr-x root/root 2029968 2023-02-04 12:33 ./usr/bin/relion_flex_analyse_mpi -rwxr-xr-x root/root 1034640 2023-02-04 12:33 ./usr/bin/relion_helix_inimodel2d -rwxr-xr-x root/root 1419664 2023-02-04 12:33 ./usr/bin/relion_helix_toolbox -rwxr-xr-x root/root 1137040 2023-02-04 12:33 ./usr/bin/relion_image_handler -rwxr-xr-x root/root 985488 2023-02-04 12:33 ./usr/bin/relion_import -rwxr-xr-x root/root 1726864 2023-02-04 12:33 ./usr/bin/relion_localsym -rwxr-xr-x root/root 1849744 2023-02-04 12:33 ./usr/bin/relion_localsym_mpi -rwxr-xr-x root/root 1366416 2023-02-04 12:33 ./usr/bin/relion_mask_create -rwxr-xr-x root/root 936336 2023-02-04 12:33 ./usr/bin/relion_merge_particles -rwxr-xr-x root/root 2230696 2023-02-04 12:33 ./usr/bin/relion_motion_refine -rwxr-xr-x root/root 2320808 2023-02-04 12:33 ./usr/bin/relion_motion_refine_mpi -rwxr-xr-x root/root 723336 2023-02-04 12:33 ./usr/bin/relion_mrc2vtk -rwxr-xr-x root/root 1603984 2023-02-04 12:33 ./usr/bin/relion_particle_FCC -rwxr-xr-x root/root 2578832 2023-02-04 12:33 ./usr/bin/relion_particle_reposition -rwxr-xr-x root/root 1382800 2023-02-04 12:33 ./usr/bin/relion_particle_select -rwxr-xr-x root/root 2599312 2023-02-04 12:33 ./usr/bin/relion_particle_subtract -rwxr-xr-x root/root 2673040 2023-02-04 12:33 ./usr/bin/relion_particle_subtract_mpi -rwxr-xr-x root/root 1030544 2023-02-04 12:33 ./usr/bin/relion_particle_symmetry_expand -rwxr-xr-x root/root 1407368 2023-02-04 12:33 ./usr/bin/relion_pipeliner -rwxr-xr-x root/root 1386896 2023-02-04 12:33 ./usr/bin/relion_plot_delocalisation -rwxr-xr-x root/root 919952 2023-02-04 12:33 ./usr/bin/relion_postprocess -rwxr-xr-x root/root 919952 2023-02-04 12:33 ./usr/bin/relion_postprocess_mpi -rwxr-xr-x root/root 838032 2023-02-04 12:33 ./usr/bin/relion_prepare_subtomo -rwxr-xr-x root/root 1419664 2023-02-04 12:33 ./usr/bin/relion_preprocess -rwxr-xr-x root/root 1509776 2023-02-04 12:33 ./usr/bin/relion_preprocess_mpi -rwxr-xr-x root/root 1919376 2023-02-04 12:33 ./usr/bin/relion_project -rwxr-xr-x root/root 1939856 2023-02-04 12:33 ./usr/bin/relion_reconstruct -rwxr-xr-x root/root 2013584 2023-02-04 12:33 ./usr/bin/relion_reconstruct_mpi -rwxr-xr-x root/root 2537872 2023-02-04 12:33 ./usr/bin/relion_refine -rwxr-xr-x root/root 2701712 2023-02-04 12:33 ./usr/bin/relion_refine_mpi -rwxr-xr-x root/root 1608080 2023-02-04 12:33 ./usr/bin/relion_reposition -rwxr-xr-x root/root 1055120 2023-02-04 12:33 ./usr/bin/relion_run_ctffind -rwxr-xr-x root/root 1145232 2023-02-04 12:33 ./usr/bin/relion_run_ctffind_mpi -rwxr-xr-x root/root 1321360 2023-02-04 12:33 ./usr/bin/relion_run_motioncorr -rwxr-xr-x root/root 1411472 2023-02-04 12:33 ./usr/bin/relion_run_motioncorr_mpi -rwxr-xr-x root/root 2066832 2023-02-04 12:33 ./usr/bin/relion_scheduler -rwxr-xr-x root/root 1014160 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 1063312 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 629136 2023-02-04 12:33 ./usr/bin/relion_tiltpair_plot -rwxr-xr-x root/root 1292688 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: s390x Build Type: any Build-Space: 3955536 Build-Time: 1383 Distribution: lunar-proposed Host Architecture: s390x Install-Time: 17 Job: relion_3.1.3-3build1.dsc Machine Architecture: s390x Package: relion Package-Time: 1400 Source-Version: 3.1.3-3build1 Space: 3955536 Status: successful Version: 3.1.3-3build1 -------------------------------------------------------------------------------- Finished at 2023-02-04T13:32:10Z Build needed 00:23:20, 3955536k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=lunar --arch=s390x PACKAGEBUILD-25549284 Scanning for processes to kill in build PACKAGEBUILD-25549284