https://launchpad.net/ubuntu/+source/relion/3.1.3-3build1/+build/25549283 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux riscv64-qemu-lgw01-004 5.13.0-1019-generic #21~20.04.1-Ubuntu SMP Thu Mar 24 22:36:01 UTC 2022 riscv64 Buildd toolchain package versions: launchpad-buildd_229~619~ubuntu20.04.1 python3-lpbuildd_229~619~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git_1:2.25.1-1ubuntu3.2 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1. Syncing the system clock with the buildd NTP service... 4 Feb 12:59:09 ntpdate[759467]: adjust time server 10.211.37.1 offset -0.000589 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=lunar --arch=riscv64 PACKAGEBUILD-25549283 --image-type chroot /home/buildd/filecache-default/859743d4aa431be74cb50b11ddbd51d0d1ab094f Creating target for build PACKAGEBUILD-25549283 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=lunar --arch=riscv64 PACKAGEBUILD-25549283 Starting target for build PACKAGEBUILD-25549283 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=lunar --arch=riscv64 PACKAGEBUILD-25549283 '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-25549283 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=lunar --arch=riscv64 PACKAGEBUILD-25549283 Updating target for build PACKAGEBUILD-25549283 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 riscv64 Packages [1311 kB] Get:6 http://ftpmaster.internal/ubuntu lunar/main Translation-en [508 kB] Get:7 http://ftpmaster.internal/ubuntu lunar/universe riscv64 Packages [14.2 MB] Get:8 http://ftpmaster.internal/ubuntu lunar/universe Translation-en [5893 kB] Get:9 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 Packages [86.5 kB] Get:10 http://ftpmaster.internal/ubuntu lunar-proposed/main Translation-en [34.0 kB] Get:11 http://ftpmaster.internal/ubuntu lunar-proposed/universe riscv64 Packages [280 kB] Get:12 http://ftpmaster.internal/ubuntu lunar-proposed/universe Translation-en [136 kB] Fetched 23.0 MB in 31s (742 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-riscv64-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 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 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 86 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 85.4 MB of archives. After this operation, 4442 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu lunar/main riscv64 bash riscv64 5.2.15-2ubuntu1 [672 kB] Get:2 http://ftpmaster.internal/ubuntu lunar/main riscv64 coreutils riscv64 9.1-1ubuntu2 [1309 kB] Get:3 http://ftpmaster.internal/ubuntu lunar/main riscv64 diffutils riscv64 1:3.8-3 [167 kB] Get:4 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libc-bin riscv64 2.37-0ubuntu1 [550 kB] Get:5 http://ftpmaster.internal/ubuntu lunar/main riscv64 libcrypt-dev riscv64 1:4.4.33-2 [234 kB] Get:6 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libc6-dev riscv64 2.37-0ubuntu1 [3134 kB] Get:7 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libc-dev-bin riscv64 2.37-0ubuntu1 [18.8 kB] Get:8 http://ftpmaster.internal/ubuntu lunar/main riscv64 libcrypt1 riscv64 1:4.4.33-2 [93.4 kB] Get:9 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 linux-libc-dev riscv64 6.1.0-14.14 [1408 kB] Get:10 http://ftpmaster.internal/ubuntu lunar/main riscv64 libcc1-0 riscv64 12.2.0-14ubuntu1 [42.9 kB] Get:11 http://ftpmaster.internal/ubuntu lunar/main riscv64 libctf0 riscv64 2.40-2ubuntu1 [87.4 kB] Get:12 http://ftpmaster.internal/ubuntu lunar/main riscv64 libctf-nobfd0 riscv64 2.40-2ubuntu1 [88.9 kB] Get:13 http://ftpmaster.internal/ubuntu lunar/main riscv64 binutils-riscv64-linux-gnu riscv64 2.40-2ubuntu1 [820 kB] Get:14 http://ftpmaster.internal/ubuntu lunar/main riscv64 libbinutils riscv64 2.40-2ubuntu1 [459 kB] Get:15 http://ftpmaster.internal/ubuntu lunar/main riscv64 binutils-common riscv64 2.40-2ubuntu1 [218 kB] Get:16 http://ftpmaster.internal/ubuntu lunar/main riscv64 binutils riscv64 2.40-2ubuntu1 [2980 B] Get:17 http://ftpmaster.internal/ubuntu lunar/main riscv64 gcc-12-base riscv64 12.2.0-14ubuntu1 [19.3 kB] Get:18 http://ftpmaster.internal/ubuntu lunar/main riscv64 libgcc-s1 riscv64 12.2.0-14ubuntu1 [44.1 kB] Get:19 http://ftpmaster.internal/ubuntu lunar/main riscv64 libgomp1 riscv64 12.2.0-14ubuntu1 [111 kB] Get:20 http://ftpmaster.internal/ubuntu lunar/main riscv64 libatomic1 riscv64 12.2.0-14ubuntu1 [7878 B] Get:21 http://ftpmaster.internal/ubuntu lunar/main riscv64 libasan8 riscv64 12.2.0-14ubuntu1 [2309 kB] Get:22 http://ftpmaster.internal/ubuntu lunar/main riscv64 g++-12 riscv64 12.2.0-14ubuntu1 [9557 kB] Get:23 http://ftpmaster.internal/ubuntu lunar/main riscv64 libstdc++-12-dev riscv64 12.2.0-14ubuntu1 [4964 kB] Get:24 http://ftpmaster.internal/ubuntu lunar/main riscv64 libgcc-12-dev riscv64 12.2.0-14ubuntu1 [2633 kB] Get:25 http://ftpmaster.internal/ubuntu lunar/main riscv64 gcc-12 riscv64 12.2.0-14ubuntu1 [16.3 MB] Get:26 http://ftpmaster.internal/ubuntu lunar/main riscv64 cpp-12 riscv64 12.2.0-14ubuntu1 [8287 kB] Get:27 http://ftpmaster.internal/ubuntu lunar/main riscv64 libstdc++6 riscv64 12.2.0-14ubuntu1 [674 kB] Get:28 http://ftpmaster.internal/ubuntu lunar/main riscv64 zlib1g riscv64 1:1.2.13.dfsg-1ubuntu4 [54.0 kB] Get:29 http://ftpmaster.internal/ubuntu lunar/main riscv64 libmpfr6 riscv64 4.2.0-1 [260 kB] Get:30 http://ftpmaster.internal/ubuntu lunar/main riscv64 libzstd1 riscv64 1.5.2+dfsg2-3 [299 kB] Get:31 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libc6 riscv64 2.37-0ubuntu1 [2593 kB] Get:32 http://ftpmaster.internal/ubuntu lunar/main riscv64 liblzma5 riscv64 5.4.1-0.0 [115 kB] Get:33 http://ftpmaster.internal/ubuntu lunar/main riscv64 libgcrypt20 riscv64 1.10.1-3ubuntu1 [503 kB] Get:34 http://ftpmaster.internal/ubuntu lunar/main riscv64 libacl1 riscv64 2.3.1-3 [15.7 kB] Get:35 http://ftpmaster.internal/ubuntu lunar/main riscv64 libaudit-common all 1:3.0.7-1.1 [5108 B] Get:36 http://ftpmaster.internal/ubuntu lunar/main riscv64 libaudit1 riscv64 1:3.0.7-1.1 [43.4 kB] Get:37 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libcap2 riscv64 1:2.66-3ubuntu1 [25.2 kB] Get:38 http://ftpmaster.internal/ubuntu lunar/main riscv64 libpcre2-8-0 riscv64 10.42-1 [142 kB] Get:39 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libselinux1 riscv64 3.4-1build3 [71.3 kB] Get:40 http://ftpmaster.internal/ubuntu lunar/main riscv64 libperl5.36 riscv64 5.36.0-7 [4197 kB] Get:41 http://ftpmaster.internal/ubuntu lunar/main riscv64 perl riscv64 5.36.0-7 [235 kB] Get:42 http://ftpmaster.internal/ubuntu lunar/main riscv64 perl-base riscv64 5.36.0-7 [1649 kB] Get:43 http://ftpmaster.internal/ubuntu lunar/main riscv64 perl-modules-5.36 all 5.36.0-7 [2984 kB] Get:44 http://ftpmaster.internal/ubuntu lunar/main riscv64 libdb5.3 riscv64 5.3.28+dfsg2-1 [691 kB] Get:45 http://ftpmaster.internal/ubuntu lunar/main riscv64 debconf all 1.5.82 [125 kB] Get:46 http://ftpmaster.internal/ubuntu lunar/main riscv64 libssl3 riscv64 3.0.7-1ubuntu1 [1438 kB] Get:47 http://ftpmaster.internal/ubuntu lunar/main riscv64 systemd-sysv riscv64 252.4-1ubuntu1 [11.4 kB] Get:48 http://ftpmaster.internal/ubuntu lunar/main riscv64 systemd riscv64 252.4-1ubuntu1 [2814 kB] Get:49 http://ftpmaster.internal/ubuntu lunar/main riscv64 libsystemd-shared riscv64 252.4-1ubuntu1 [1567 kB] Get:50 http://ftpmaster.internal/ubuntu lunar/main riscv64 libp11-kit0 riscv64 0.24.1-2ubuntu1 [196 kB] Get:51 http://ftpmaster.internal/ubuntu lunar/main riscv64 libsystemd0 riscv64 252.4-1ubuntu1 [299 kB] Get:52 http://ftpmaster.internal/ubuntu lunar/main riscv64 libudev1 riscv64 252.4-1ubuntu1 [82.1 kB] Get:53 http://ftpmaster.internal/ubuntu lunar/main riscv64 libapt-pkg6.0 riscv64 2.5.5 [919 kB] Get:54 http://ftpmaster.internal/ubuntu lunar/main riscv64 dpkg riscv64 1.21.19ubuntu3 [1289 kB] Get:55 http://ftpmaster.internal/ubuntu lunar/main riscv64 grep riscv64 3.8-5 [155 kB] Get:56 http://ftpmaster.internal/ubuntu lunar/main riscv64 ncurses-bin riscv64 6.4-2 [177 kB] Get:57 http://ftpmaster.internal/ubuntu lunar/main riscv64 sed riscv64 4.9-1 [191 kB] Get:58 http://ftpmaster.internal/ubuntu lunar/main riscv64 ncurses-base all 6.4-2 [21.3 kB] Get:59 http://ftpmaster.internal/ubuntu lunar/main riscv64 sysvinit-utils riscv64 3.05-7ubuntu2 [27.3 kB] Get:60 http://ftpmaster.internal/ubuntu lunar/main riscv64 lsb-base all 11.5 [4296 B] Get:61 http://ftpmaster.internal/ubuntu lunar/main riscv64 adduser all 3.129ubuntu1 [59.0 kB] Get:62 http://ftpmaster.internal/ubuntu lunar/main riscv64 gpgv riscv64 2.2.40-1ubuntu2 [202 kB] Get:63 http://ftpmaster.internal/ubuntu lunar/main riscv64 libgnutls30 riscv64 3.7.8-4ubuntu1 [897 kB] Get:64 http://ftpmaster.internal/ubuntu lunar/main riscv64 apt riscv64 2.5.5 [1338 kB] Get:65 http://ftpmaster.internal/ubuntu lunar/main riscv64 libattr1 riscv64 1:2.5.1-4 [11.4 kB] Get:66 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libsemanage-common all 3.4-1build3 [9808 B] Get:67 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libsemanage2 riscv64 3.4-1build3 [83.5 kB] Get:68 http://ftpmaster.internal/ubuntu lunar/main riscv64 libncurses6 riscv64 6.4-2 [93.3 kB] Get:69 http://ftpmaster.internal/ubuntu lunar/main riscv64 libncursesw6 riscv64 6.4-2 [126 kB] Get:70 http://ftpmaster.internal/ubuntu lunar/main riscv64 libtinfo6 riscv64 6.4-2 [90.6 kB] Get:71 http://ftpmaster.internal/ubuntu lunar/main riscv64 sensible-utils all 0.0.17+nmu1 [19.3 kB] Get:72 http://ftpmaster.internal/ubuntu lunar/main riscv64 readline-common all 8.2-1.3 [55.7 kB] Get:73 http://ftpmaster.internal/ubuntu lunar/main riscv64 libreadline8 riscv64 8.2-1.3 [131 kB] Get:74 http://ftpmaster.internal/ubuntu lunar/main riscv64 libsqlite3-0 riscv64 3.40.1-1 [583 kB] Get:75 http://ftpmaster.internal/ubuntu lunar/main riscv64 openssl riscv64 3.0.7-1ubuntu1 [1141 kB] Get:76 http://ftpmaster.internal/ubuntu lunar/main riscv64 tzdata all 2022g-2ubuntu1 [397 kB] Get:77 http://ftpmaster.internal/ubuntu lunar/main riscv64 xz-utils riscv64 5.4.1-0.0 [235 kB] Get:78 http://ftpmaster.internal/ubuntu lunar/main riscv64 advancecomp riscv64 2.5-1 [216 kB] Get:79 http://ftpmaster.internal/ubuntu lunar/main riscv64 dpkg-dev all 1.21.19ubuntu3 [1067 kB] Get:80 http://ftpmaster.internal/ubuntu lunar/main riscv64 libdpkg-perl all 1.21.19ubuntu3 [247 kB] Get:81 http://ftpmaster.internal/ubuntu lunar/main riscv64 libfakeroot riscv64 1.30.1-1.1ubuntu1 [26.5 kB] Get:82 http://ftpmaster.internal/ubuntu lunar/main riscv64 fakeroot riscv64 1.30.1-1.1ubuntu1 [68.0 kB] Get:83 http://ftpmaster.internal/ubuntu lunar/main riscv64 gpg riscv64 2.2.40-1ubuntu2 [491 kB] Get:84 http://ftpmaster.internal/ubuntu lunar/main riscv64 gpgconf riscv64 2.2.40-1ubuntu2 [119 kB] Get:85 http://ftpmaster.internal/ubuntu lunar/main riscv64 gpg-agent riscv64 2.2.40-1ubuntu2 [239 kB] Get:86 http://ftpmaster.internal/ubuntu lunar/main riscv64 pkgbinarymangler all 151 [16.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 85.4 MB in 17s (5135 kB/s) (Reading database ... 13011 files and directories currently installed.) Preparing to unpack .../bash_5.2.15-2ubuntu1_riscv64.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 ... 13011 files and directories currently installed.) Preparing to unpack .../coreutils_9.1-1ubuntu2_riscv64.deb ... Unpacking coreutils (9.1-1ubuntu2) over (8.32-4.1ubuntu1) ... Setting up coreutils (9.1-1ubuntu2) ... (Reading database ... 13011 files and directories currently installed.) Preparing to unpack .../diffutils_1%3a3.8-3_riscv64.deb ... Unpacking diffutils (1:3.8-3) over (1:3.8-1) ... Setting up diffutils (1:3.8-3) ... (Reading database ... 13011 files and directories currently installed.) Preparing to unpack .../libc-bin_2.37-0ubuntu1_riscv64.deb ... Unpacking libc-bin (2.37-0ubuntu1) over (2.36-0ubuntu4) ... Setting up libc-bin (2.37-0ubuntu1) ... 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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:riscv64 (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-25549283 riscv64 lunar-proposed -c chroot:build-PACKAGEBUILD-25549283 --arch=riscv64 --dist=lunar-proposed --nolog relion_3.1.3-3build1.dsc Initiating build PACKAGEBUILD-25549283 with 8 jobs across 8 processor cores. Kernel reported to sbuild: 5.13.0-1019-generic #21~20.04.1-Ubuntu SMP Thu Mar 24 22:36:01 UTC 2022 riscv64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on riscv64-qemu-lgw01-004.buildd +==============================================================================+ | relion 3.1.3-3build1 (riscv64) Sat, 04 Feb 2023 13:06:45 +0000 | +==============================================================================+ Package: relion Version: 3.1.3-3build1 Source Version: 3.1.3-3build1 Distribution: lunar-proposed Machine Architecture: riscv64 Host Architecture: riscv64 Build Architecture: riscv64 Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-25549283/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/relion-jgZXCW/resolver-239DtE' 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-jgZXCW/relion-3.1.3' with '<>' I: NOTICE: Log filtering will replace 'build/relion-jgZXCW' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: cmake, debhelper-compat (= 13), libfftw3-dev, libfltk1.3-dev, libopenmpi-dev, libtiff-dev, fluid, build-essential, fakeroot Filtered Build-Depends: cmake, debhelper-compat (= 13), libfftw3-dev, libfltk1.3-dev, libopenmpi-dev, libtiff-dev, fluid, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [405 B] Get:5 copy:/<>/apt_archive ./ Packages [487 B] Fetched 1849 B in 1s (2524 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 liblerc-dev liblerc4 libllvm15 libltdl-dev libltdl7 liblzma-dev libmagic-mgc libmagic1 libmunge2 libnghttp2-14 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi3 libpciaccess0 libpipeline1 libpixman-1-0 libpmix-dev libpmix2 libpsl5 libpthread-stubs0-dev librdmacm1 librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libssh-4 libsub-override-perl libtiff-dev libtiff6 libtiffxx6 libtool libuchardet0 libuv1 libwebp-dev libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libx11-dev libx11-xcb1 libxau-dev libxau6 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcb1 libxcb1-dev libxcursor1 libxdmcp-dev libxdmcp6 libxext6 libxfixes3 libxft2 libxinerama1 libxml2 libxnvctrl0 libxrender1 libxshmfence1 libxxf86vm1 libzstd-dev m4 man-db ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client po-debconf sgml-base x11proto-dev xorg-sgml-doctools xtrans-dev zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc cmake-doc cmake-format elpa-cmake-mode ninja-build dh-make gettext-doc libasprintf-dev libgettextpo-dev gfortran-12-doc libcoarrays-dev groff lrzip libfftw3-doc fltk1.3-doc libcairo2-dev libpng-dev libxext-dev libxft-dev libxinerama-dev libjs-jquery-ui-docs libtool-doc liblzma-doc openmpi-doc pciutils lm-sensors gcj-jdk libx11-doc libxcb-doc m4-doc apparmor less www-browser opencl-icd gfortran | fortran-compiler keychain libpam-ssh monkeysphere ssh-askpass libmail-box-perl sgml-base-doc Recommended packages: fltk1.3-doc curl | wget | lynx libarchive-cpio-perl libgl-dev libglu1-mesa-dev | libglu-dev libgl1-amber-dri javascript-common libldap-common libcoarrays-openmpi-dev publicsuffix libsasl2-modules xauth libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils cmake cmake-data debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file fluid fontconfig-config fonts-dejavu-core gettext gettext-base gfortran-12 groff-base ibverbs-providers intltool-debian libarchive-zip-perl libarchive13 libbrotli1 libbsd0 libcairo2 libcbor0.8 libcurl4 libdebhelper-perl libdeflate-dev libdeflate0 libdrm-amdgpu1 libdrm-common libdrm-nouveau2 libdrm-radeon1 libdrm2 libdw1 libedit2 libelf1 libevent-2.1-7a libevent-core-2.1-7a libevent-dev libevent-extra-2.1-7 libevent-openssl-2.1-7 libevent-pthreads-2.1-7 libexpat1 libfabric1 libfftw3-bin libfftw3-dev libfftw3-double3 libfftw3-long3 libfftw3-single3 libfido2-1 libfile-stripnondeterminism-perl libfltk-cairo1.3 libfltk-forms1.3 libfltk-gl1.3 libfltk-images1.3 libfltk1.3 libfltk1.3-dev libfontconfig1 libfreetype6 libgfortran-12-dev libgfortran5 libgl1 libgl1-mesa-dri libglapi-mesa libglvnd0 libglx-mesa0 libglx0 libhwloc-dev libhwloc-plugins libhwloc15 libibverbs-dev libibverbs1 libicu71 libjbig-dev libjbig0 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev libjs-jquery libjs-jquery-ui libjsoncpp25 libldap2 liblerc-dev liblerc4 libllvm15 libltdl-dev libltdl7 liblzma-dev libmagic-mgc libmagic1 libmunge2 libnghttp2-14 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi3 libpciaccess0 libpipeline1 libpixman-1-0 libpmix-dev libpmix2 libpsl5 libpthread-stubs0-dev librdmacm1 librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libssh-4 libsub-override-perl libtiff-dev libtiff6 libtiffxx6 libtool libuchardet0 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, 174 newly installed, 0 to remove and 0 not upgraded. Need to get 97.7 MB of archives. After this operation, 425 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 riscv64 sgml-base all 1.31 [11.4 kB] Get:3 http://ftpmaster.internal/ubuntu lunar/main riscv64 libbsd0 riscv64 0.11.7-2 [40.3 kB] Get:4 http://ftpmaster.internal/ubuntu lunar/main riscv64 libelf1 riscv64 0.188-2.1 [49.1 kB] Get:5 http://ftpmaster.internal/ubuntu lunar/main riscv64 libexpat1 riscv64 2.5.0-1 [77.1 kB] Get:6 http://ftpmaster.internal/ubuntu lunar/main riscv64 libicu71 riscv64 71.1-3ubuntu1 [10.5 MB] Get:7 http://ftpmaster.internal/ubuntu lunar/main riscv64 libxml2 riscv64 2.9.14+dfsg-1.1 [598 kB] Get:8 http://ftpmaster.internal/ubuntu lunar/main riscv64 bsdextrautils riscv64 2.38.1-4ubuntu1 [81.6 kB] Get:9 http://ftpmaster.internal/ubuntu lunar/main riscv64 libmagic-mgc riscv64 1:5.44-3 [293 kB] Get:10 http://ftpmaster.internal/ubuntu lunar/main riscv64 libmagic1 riscv64 1:5.44-3 [85.1 kB] Get:11 http://ftpmaster.internal/ubuntu lunar/main riscv64 file riscv64 1:5.44-3 [21.0 kB] Get:12 http://ftpmaster.internal/ubuntu lunar/main riscv64 gettext-base riscv64 0.21-11 [37.3 kB] Get:13 http://ftpmaster.internal/ubuntu lunar/main riscv64 libuchardet0 riscv64 0.0.7-1build2 [78.9 kB] Get:14 http://ftpmaster.internal/ubuntu lunar/main riscv64 groff-base riscv64 1.22.4-9 [906 kB] Get:15 http://ftpmaster.internal/ubuntu lunar/main riscv64 libcbor0.8 riscv64 0.8.0-2ubuntu1 [20.7 kB] Get:16 http://ftpmaster.internal/ubuntu lunar/main riscv64 libdrm-common all 2.4.114-1 [5940 B] Get:17 http://ftpmaster.internal/ubuntu lunar/main riscv64 libdrm2 riscv64 2.4.114-1 [35.8 kB] Get:18 http://ftpmaster.internal/ubuntu lunar/main riscv64 libedit2 riscv64 3.1-20221030-2 [82.0 kB] Get:19 http://ftpmaster.internal/ubuntu lunar/main riscv64 libfido2-1 riscv64 1.12.0-2 [72.9 kB] Get:20 http://ftpmaster.internal/ubuntu lunar/main riscv64 libnghttp2-14 riscv64 1.51.0-1 [69.2 kB] Get:21 http://ftpmaster.internal/ubuntu lunar/main riscv64 libnuma1 riscv64 2.0.16-1 [19.9 kB] Get:22 http://ftpmaster.internal/ubuntu lunar/main riscv64 libpipeline1 riscv64 1.5.7-1 [26.8 kB] Get:23 http://ftpmaster.internal/ubuntu lunar/main riscv64 libpsl5 riscv64 0.21.0-1.2build2 [57.3 kB] Get:24 http://ftpmaster.internal/ubuntu lunar/main riscv64 libuv1 riscv64 1.44.2-1 [77.1 kB] Get:25 http://ftpmaster.internal/ubuntu lunar/main riscv64 libxau6 riscv64 1:1.0.9-1build5 [6836 B] Get:26 http://ftpmaster.internal/ubuntu lunar/main riscv64 libxdmcp6 riscv64 1:1.1.3-0ubuntu5 [10.3 kB] Get:27 http://ftpmaster.internal/ubuntu lunar/main riscv64 libxcb1 riscv64 1.15-1 [42.1 kB] Get:28 http://ftpmaster.internal/ubuntu lunar/main riscv64 libx11-data all 2:1.8.3-3 [118 kB] Get:29 http://ftpmaster.internal/ubuntu lunar/main riscv64 libx11-6 riscv64 2:1.8.3-3 [605 kB] Get:30 http://ftpmaster.internal/ubuntu lunar/main riscv64 libxext6 riscv64 2:1.3.4-1build1 [27.8 kB] Get:31 http://ftpmaster.internal/ubuntu lunar/main riscv64 man-db riscv64 2.11.2-1 [1177 kB] Get:32 http://ftpmaster.internal/ubuntu lunar/main riscv64 openssh-client riscv64 1:9.0p1-1ubuntu8 [784 kB] Get:33 http://ftpmaster.internal/ubuntu lunar/main riscv64 m4 riscv64 1.4.19-2 [242 kB] Get:34 http://ftpmaster.internal/ubuntu lunar/main riscv64 autoconf all 2.71-3 [339 kB] Get:35 http://ftpmaster.internal/ubuntu lunar/main riscv64 autotools-dev all 20220109.1 [44.9 kB] Get:36 http://ftpmaster.internal/ubuntu lunar/main riscv64 automake all 1:1.16.5-1.3 [558 kB] Get:37 http://ftpmaster.internal/ubuntu lunar/main riscv64 autopoint all 0.21-11 [420 kB] Get:38 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libarchive13 riscv64 3.6.2-1ubuntu1 [342 kB] Get:39 http://ftpmaster.internal/ubuntu lunar/main riscv64 libbrotli1 riscv64 1.0.9-2build7 [324 kB] Get:40 http://ftpmaster.internal/ubuntu lunar/main riscv64 libsasl2-modules-db riscv64 2.1.28+dfsg-10 [18.9 kB] Get:41 http://ftpmaster.internal/ubuntu lunar/main riscv64 libsasl2-2 riscv64 2.1.28+dfsg-10 [55.1 kB] Get:42 http://ftpmaster.internal/ubuntu lunar/main riscv64 libldap2 riscv64 2.6.3+dfsg-1~exp1ubuntu1 [163 kB] Get:43 http://ftpmaster.internal/ubuntu lunar/main riscv64 librtmp1 riscv64 2.4+20151223.gitfa8646d.1-2build4 [54.6 kB] Get:44 http://ftpmaster.internal/ubuntu lunar/main riscv64 libssh-4 riscv64 0.10.4-2 [162 kB] Get:45 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libcurl4 riscv64 7.87.0-2ubuntu1 [259 kB] Get:46 http://ftpmaster.internal/ubuntu lunar/main riscv64 libjsoncpp25 riscv64 1.9.5-4 [78.8 kB] Get:47 http://ftpmaster.internal/ubuntu lunar/main riscv64 librhash0 riscv64 1.4.3-3 [139 kB] Get:48 http://ftpmaster.internal/ubuntu lunar/main riscv64 cmake-data all 3.25.1-1 [2049 kB] Get:49 http://ftpmaster.internal/ubuntu lunar/main riscv64 cmake riscv64 3.25.1-1 [5865 kB] Get:50 http://ftpmaster.internal/ubuntu lunar/main riscv64 libdebhelper-perl all 13.11.4ubuntu3 [66.1 kB] Get:51 http://ftpmaster.internal/ubuntu lunar/main riscv64 libtool all 2.4.7-5 [166 kB] Get:52 http://ftpmaster.internal/ubuntu lunar/main riscv64 dh-autoreconf all 20 [16.1 kB] Get:53 http://ftpmaster.internal/ubuntu lunar/main riscv64 libarchive-zip-perl all 1.68-1 [90.2 kB] Get:54 http://ftpmaster.internal/ubuntu lunar/main riscv64 libsub-override-perl all 0.09-4 [8706 B] Get:55 http://ftpmaster.internal/ubuntu lunar/main riscv64 libfile-stripnondeterminism-perl all 1.13.1-1 [18.1 kB] Get:56 http://ftpmaster.internal/ubuntu lunar/main riscv64 dh-strip-nondeterminism all 1.13.1-1 [5362 B] Get:57 http://ftpmaster.internal/ubuntu lunar/main riscv64 libdw1 riscv64 0.188-2.1 [229 kB] Get:58 http://ftpmaster.internal/ubuntu lunar/main riscv64 debugedit riscv64 1:5.0-5 [48.8 kB] Get:59 http://ftpmaster.internal/ubuntu lunar/main riscv64 dwz riscv64 0.15-1 [115 kB] Get:60 http://ftpmaster.internal/ubuntu lunar/main riscv64 gettext riscv64 0.21-11 [811 kB] Get:61 http://ftpmaster.internal/ubuntu lunar/main riscv64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] Get:62 http://ftpmaster.internal/ubuntu lunar/main riscv64 po-debconf all 1.0.21+nmu1 [233 kB] Get:63 http://ftpmaster.internal/ubuntu lunar/main riscv64 debhelper all 13.11.4ubuntu3 [925 kB] Get:64 http://ftpmaster.internal/ubuntu lunar/main riscv64 libfreetype6 riscv64 2.12.1+dfsg-4 [361 kB] Get:65 http://ftpmaster.internal/ubuntu lunar/main riscv64 fonts-dejavu-core all 2.37-2build2 [1137 kB] Get:66 http://ftpmaster.internal/ubuntu lunar/main riscv64 fontconfig-config riscv64 2.14.1-3ubuntu1 [32.5 kB] Get:67 http://ftpmaster.internal/ubuntu lunar/main riscv64 libfontconfig1 riscv64 2.14.1-3ubuntu1 [119 kB] Get:68 http://ftpmaster.internal/ubuntu lunar/main riscv64 libxfixes3 riscv64 1:6.0.0-2 [9620 B] Get:69 http://ftpmaster.internal/ubuntu lunar/main riscv64 libxrender1 riscv64 1:0.9.10-1.1 [17.5 kB] Get:70 http://ftpmaster.internal/ubuntu lunar/main riscv64 libxcursor1 riscv64 1:1.2.1-1 [18.9 kB] Get:71 http://ftpmaster.internal/ubuntu lunar/main riscv64 libxft2 riscv64 2.3.6-1 [39.0 kB] Get:72 http://ftpmaster.internal/ubuntu lunar/main riscv64 libxinerama1 riscv64 2:1.1.4-3 [6616 B] Get:73 http://ftpmaster.internal/ubuntu lunar/universe riscv64 libfltk1.3 riscv64 1.3.8-5 [587 kB] Get:74 http://ftpmaster.internal/ubuntu lunar/universe riscv64 libfltk-forms1.3 riscv64 1.3.8-5 [13.3 kB] Get:75 http://ftpmaster.internal/ubuntu lunar/main riscv64 libjpeg-turbo8 riscv64 2.1.2-0ubuntu1 [113 kB] Get:76 http://ftpmaster.internal/ubuntu lunar/main riscv64 libjpeg8 riscv64 8c-2ubuntu10 [2270 B] Get:77 http://ftpmaster.internal/ubuntu lunar/universe riscv64 libfltk-images1.3 riscv64 1.3.8-5 [26.9 kB] Get:78 http://ftpmaster.internal/ubuntu lunar/universe riscv64 fluid riscv64 1.3.8-5 [204 kB] Get:79 http://ftpmaster.internal/ubuntu lunar/main riscv64 libgfortran5 riscv64 12.2.0-14ubuntu1 [386 kB] Get:80 http://ftpmaster.internal/ubuntu lunar/main riscv64 libgfortran-12-dev riscv64 12.2.0-14ubuntu1 [1141 kB] Get:81 http://ftpmaster.internal/ubuntu lunar/main riscv64 gfortran-12 riscv64 12.2.0-14ubuntu1 [8731 kB] Get:82 http://ftpmaster.internal/ubuntu lunar/main riscv64 libnl-3-200 riscv64 3.7.0-0.2 [49.5 kB] Get:83 http://ftpmaster.internal/ubuntu lunar/main riscv64 libnl-route-3-200 riscv64 3.7.0-0.2 [165 kB] Get:84 http://ftpmaster.internal/ubuntu lunar/main riscv64 libibverbs1 riscv64 44.0-2 [56.8 kB] Get:85 http://ftpmaster.internal/ubuntu lunar/main riscv64 ibverbs-providers riscv64 44.0-2 [333 kB] Get:86 http://ftpmaster.internal/ubuntu lunar/main riscv64 libpixman-1-0 riscv64 0.42.2-1 [165 kB] Get:87 http://ftpmaster.internal/ubuntu lunar/main riscv64 libxcb-render0 riscv64 1.15-1 [13.8 kB] Get:88 http://ftpmaster.internal/ubuntu lunar/main riscv64 libxcb-shm0 riscv64 1.15-1 [5326 B] Get:89 http://ftpmaster.internal/ubuntu lunar/main riscv64 libcairo2 riscv64 1.16.0-7 [463 kB] Get:90 http://ftpmaster.internal/ubuntu lunar/main riscv64 libdeflate0 riscv64 1.14-1 [52.8 kB] Get:91 http://ftpmaster.internal/ubuntu lunar/main riscv64 libdeflate-dev riscv64 1.14-1 [110 kB] Get:92 http://ftpmaster.internal/ubuntu lunar/main riscv64 libdrm-amdgpu1 riscv64 2.4.114-1 [17.3 kB] Get:93 http://ftpmaster.internal/ubuntu lunar/main riscv64 libdrm-nouveau2 riscv64 2.4.114-1 [15.6 kB] Get:94 http://ftpmaster.internal/ubuntu lunar/main riscv64 libdrm-radeon1 riscv64 2.4.114-1 [20.0 kB] Get:95 http://ftpmaster.internal/ubuntu lunar/main riscv64 libevent-2.1-7a riscv64 2.1.12-stable-5ubuntu1 [122 kB] Get:96 http://ftpmaster.internal/ubuntu lunar/main riscv64 libevent-core-2.1-7a riscv64 2.1.12-stable-5ubuntu1 [77.7 kB] Get:97 http://ftpmaster.internal/ubuntu lunar/main riscv64 libevent-extra-2.1-7 riscv64 2.1.12-stable-5ubuntu1 [55.0 kB] Get:98 http://ftpmaster.internal/ubuntu lunar/main riscv64 libevent-pthreads-2.1-7 riscv64 2.1.12-stable-5ubuntu1 [7182 B] Get:99 http://ftpmaster.internal/ubuntu lunar/main riscv64 libevent-openssl-2.1-7 riscv64 2.1.12-stable-5ubuntu1 [13.0 kB] Get:100 http://ftpmaster.internal/ubuntu lunar/main riscv64 libevent-dev riscv64 2.1.12-stable-5ubuntu1 [500 kB] Get:101 http://ftpmaster.internal/ubuntu lunar/main riscv64 librdmacm1 riscv64 44.0-2 [64.3 kB] Get:102 http://ftpmaster.internal/ubuntu lunar/universe riscv64 libfabric1 riscv64 1.17.0-3 [481 kB] Get:103 http://ftpmaster.internal/ubuntu lunar/main riscv64 libfftw3-double3 riscv64 3.3.8-2ubuntu8 [359 kB] Get:104 http://ftpmaster.internal/ubuntu lunar/main riscv64 libfftw3-long3 riscv64 3.3.8-2ubuntu8 [757 kB] Get:105 http://ftpmaster.internal/ubuntu lunar/main riscv64 libfftw3-single3 riscv64 3.3.8-2ubuntu8 [361 kB] Get:106 http://ftpmaster.internal/ubuntu lunar/main riscv64 libfftw3-bin riscv64 3.3.8-2ubuntu8 [28.3 kB] Get:107 http://ftpmaster.internal/ubuntu lunar/main riscv64 libfftw3-dev riscv64 3.3.8-2ubuntu8 [1503 kB] Get:108 http://ftpmaster.internal/ubuntu lunar/universe riscv64 libfltk-cairo1.3 riscv64 1.3.8-5 [6506 B] Get:109 http://ftpmaster.internal/ubuntu lunar/main riscv64 libglvnd0 riscv64 1.6.0-1 [69.5 kB] Get:110 http://ftpmaster.internal/ubuntu lunar/main riscv64 libglapi-mesa riscv64 22.2.5-0ubuntu1 [46.4 kB] Get:111 http://ftpmaster.internal/ubuntu lunar/main riscv64 libx11-xcb1 riscv64 2:1.8.3-3 [7502 B] Get:112 http://ftpmaster.internal/ubuntu lunar/main riscv64 libxcb-dri2-0 riscv64 1.15-1 [6400 B] Get:113 http://ftpmaster.internal/ubuntu lunar/main riscv64 libxcb-dri3-0 riscv64 1.15-1 [6270 B] Get:114 http://ftpmaster.internal/ubuntu lunar/main riscv64 libxcb-glx0 riscv64 1.15-1 [20.5 kB] Get:115 http://ftpmaster.internal/ubuntu lunar/main riscv64 libxcb-present0 riscv64 1.15-1 [5224 B] Get:116 http://ftpmaster.internal/ubuntu lunar/main riscv64 libxcb-sync1 riscv64 1.15-1 [8022 B] Get:117 http://ftpmaster.internal/ubuntu lunar/main riscv64 libxcb-xfixes0 riscv64 1.15-1 [8928 B] Get:118 http://ftpmaster.internal/ubuntu lunar/main riscv64 libxshmfence1 riscv64 1.3-1build4 [4976 B] Get:119 http://ftpmaster.internal/ubuntu lunar/main riscv64 libxxf86vm1 riscv64 1:1.1.4-1build3 [9744 B] Get:120 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libllvm15 riscv64 1:15.0.7-1 [23.1 MB] Get:121 http://ftpmaster.internal/ubuntu lunar/main riscv64 libsensors-config all 1:3.6.0-7ubuntu1 [5274 B] Get:122 http://ftpmaster.internal/ubuntu lunar/main riscv64 libsensors5 riscv64 1:3.6.0-7ubuntu1 [24.4 kB] Get:123 http://ftpmaster.internal/ubuntu lunar/main riscv64 libgl1-mesa-dri riscv64 22.2.5-0ubuntu1 [5222 kB] Get:124 http://ftpmaster.internal/ubuntu lunar/main riscv64 libglx-mesa0 riscv64 22.2.5-0ubuntu1 [148 kB] Get:125 http://ftpmaster.internal/ubuntu lunar/main riscv64 libglx0 riscv64 1.6.0-1 [25.9 kB] Get:126 http://ftpmaster.internal/ubuntu lunar/main riscv64 libgl1 riscv64 1.6.0-1 [118 kB] Get:127 http://ftpmaster.internal/ubuntu lunar/universe riscv64 libfltk-gl1.3 riscv64 1.3.8-5 [39.5 kB] Get:128 http://ftpmaster.internal/ubuntu lunar/main riscv64 xorg-sgml-doctools all 1:1.11-1.1 [10.9 kB] Get:129 http://ftpmaster.internal/ubuntu lunar/main riscv64 x11proto-dev all 2022.1-1 [605 kB] Get:130 http://ftpmaster.internal/ubuntu lunar/main riscv64 libxau-dev riscv64 1:1.0.9-1build5 [12.9 kB] Get:131 http://ftpmaster.internal/ubuntu lunar/main riscv64 libxdmcp-dev riscv64 1:1.1.3-0ubuntu5 [36.1 kB] Get:132 http://ftpmaster.internal/ubuntu lunar/main riscv64 xtrans-dev all 1.4.0-1 [68.9 kB] Get:133 http://ftpmaster.internal/ubuntu lunar/main riscv64 libpthread-stubs0-dev riscv64 0.4-1build2 [5500 B] Get:134 http://ftpmaster.internal/ubuntu lunar/main riscv64 libxcb1-dev riscv64 1.15-1 [151 kB] Get:135 http://ftpmaster.internal/ubuntu lunar/main riscv64 libx11-dev riscv64 2:1.8.3-3 [1248 kB] Get:136 http://ftpmaster.internal/ubuntu lunar/universe riscv64 libfltk1.3-dev riscv64 1.3.8-5 [1707 kB] Get:137 http://ftpmaster.internal/ubuntu lunar/universe riscv64 libhwloc15 riscv64 2.9.0-1 [138 kB] Get:138 http://ftpmaster.internal/ubuntu lunar/main riscv64 libjpeg-turbo8-dev riscv64 2.1.2-0ubuntu1 [435 kB] Get:139 http://ftpmaster.internal/ubuntu lunar/main riscv64 libjpeg8-dev riscv64 8c-2ubuntu10 [1476 B] Get:140 http://ftpmaster.internal/ubuntu lunar/main riscv64 libjpeg-dev riscv64 8c-2ubuntu10 [1476 B] Get:141 http://ftpmaster.internal/ubuntu lunar/main riscv64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] Get:142 http://ftpmaster.internal/ubuntu lunar/universe riscv64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] Get:143 http://ftpmaster.internal/ubuntu lunar/main riscv64 liblerc4 riscv64 4.0.0+ds-2ubuntu2 [172 kB] Get:144 http://ftpmaster.internal/ubuntu lunar/main riscv64 liblerc-dev riscv64 4.0.0+ds-2ubuntu2 [829 kB] Get:145 http://ftpmaster.internal/ubuntu lunar/main riscv64 libltdl7 riscv64 2.4.7-5 [37.2 kB] Get:146 http://ftpmaster.internal/ubuntu lunar/main riscv64 libltdl-dev riscv64 2.4.7-5 [190 kB] Get:147 http://ftpmaster.internal/ubuntu lunar/main riscv64 libnl-3-dev riscv64 3.7.0-0.2 [183 kB] Get:148 http://ftpmaster.internal/ubuntu lunar/main riscv64 libnl-route-3-dev riscv64 3.7.0-0.2 [542 kB] Get:149 http://ftpmaster.internal/ubuntu lunar/universe riscv64 libmunge2 riscv64 0.5.15-2 [17.9 kB] Get:150 http://ftpmaster.internal/ubuntu lunar/main riscv64 libpciaccess0 riscv64 0.17-2 [16.1 kB] Get:151 http://ftpmaster.internal/ubuntu lunar/main riscv64 libxnvctrl0 riscv64 510.47.03-0ubuntu1 [10.9 kB] Get:152 http://ftpmaster.internal/ubuntu lunar/universe riscv64 ocl-icd-libopencl1 riscv64 2.3.1-1 [33.5 kB] Get:153 http://ftpmaster.internal/ubuntu lunar/universe riscv64 libhwloc-plugins riscv64 2.9.0-1 [13.7 kB] Get:154 http://ftpmaster.internal/ubuntu lunar/universe riscv64 libpmix2 riscv64 4.2.2-1 [602 kB] Get:155 http://ftpmaster.internal/ubuntu lunar/universe riscv64 libopenmpi3 riscv64 4.1.4-3ubuntu2 [1994 kB] Get:156 http://ftpmaster.internal/ubuntu lunar/main riscv64 libnuma-dev riscv64 2.0.16-1 [66.4 kB] Get:157 http://ftpmaster.internal/ubuntu lunar/universe riscv64 libhwloc-dev riscv64 2.9.0-1 [526 kB] Get:158 http://ftpmaster.internal/ubuntu lunar/main riscv64 zlib1g-dev riscv64 1:1.2.13.dfsg-1ubuntu4 [957 kB] Get:159 http://ftpmaster.internal/ubuntu lunar/universe riscv64 libpmix-dev riscv64 4.2.2-1 [2658 kB] Get:160 http://ftpmaster.internal/ubuntu lunar/main riscv64 libjbig0 riscv64 2.1-6ubuntu1 [27.8 kB] Get:161 http://ftpmaster.internal/ubuntu lunar/main riscv64 libjbig-dev riscv64 2.1-6ubuntu1 [49.3 kB] Get:162 http://ftpmaster.internal/ubuntu lunar/main riscv64 liblzma-dev riscv64 5.4.1-0.0 [315 kB] Get:163 http://ftpmaster.internal/ubuntu lunar/main riscv64 libzstd-dev riscv64 1.5.2+dfsg2-3 [1581 kB] Get:164 http://ftpmaster.internal/ubuntu lunar/main riscv64 libwebp7 riscv64 1.2.4-0.1 [166 kB] Get:165 http://ftpmaster.internal/ubuntu lunar/main riscv64 libwebpmux3 riscv64 1.2.4-0.1 [18.4 kB] Get:166 http://ftpmaster.internal/ubuntu lunar/main riscv64 libwebpdemux2 riscv64 1.2.4-0.1 [9040 B] Get:167 http://ftpmaster.internal/ubuntu lunar/main riscv64 libwebp-dev riscv64 1.2.4-0.1 [667 kB] Get:168 http://ftpmaster.internal/ubuntu lunar/main riscv64 libtiff6 riscv64 4.5.0-4ubuntu1 [173 kB] Get:169 http://ftpmaster.internal/ubuntu lunar/main riscv64 libtiffxx6 riscv64 4.5.0-4ubuntu1 [5642 B] Get:170 http://ftpmaster.internal/ubuntu lunar/main riscv64 libtiff-dev riscv64 4.5.0-4ubuntu1 [632 kB] Get:171 http://ftpmaster.internal/ubuntu lunar/universe riscv64 openmpi-common all 4.1.4-3ubuntu2 [163 kB] Get:172 http://ftpmaster.internal/ubuntu lunar/universe riscv64 openmpi-bin riscv64 4.1.4-3ubuntu2 [81.7 kB] Get:173 http://ftpmaster.internal/ubuntu lunar/main riscv64 libibverbs-dev riscv64 44.0-2 [1618 kB] Get:174 http://ftpmaster.internal/ubuntu lunar/universe riscv64 libopenmpi-dev riscv64 4.1.4-3ubuntu2 [824 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 97.7 MB in 18s (5513 kB/s) Selecting previously unselected package sgml-base. (Reading database ... 15051 files and directories currently installed.) Preparing to unpack .../000-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package libbsd0:riscv64. Preparing to unpack .../001-libbsd0_0.11.7-2_riscv64.deb ... Unpacking libbsd0:riscv64 (0.11.7-2) ... Selecting previously unselected package libelf1:riscv64. Preparing to unpack .../002-libelf1_0.188-2.1_riscv64.deb ... Unpacking libelf1:riscv64 (0.188-2.1) ... Selecting previously unselected package libexpat1:riscv64. Preparing to unpack .../003-libexpat1_2.5.0-1_riscv64.deb ... Unpacking libexpat1:riscv64 (2.5.0-1) ... Selecting previously unselected package libicu71:riscv64. Preparing to unpack .../004-libicu71_71.1-3ubuntu1_riscv64.deb ... Unpacking libicu71:riscv64 (71.1-3ubuntu1) ... Selecting previously unselected package libxml2:riscv64. Preparing to unpack .../005-libxml2_2.9.14+dfsg-1.1_riscv64.deb ... Unpacking libxml2:riscv64 (2.9.14+dfsg-1.1) ... 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Setting up libedit2:riscv64 (3.1-20221030-2) ... Setting up libjbig-dev:riscv64 (2.1-6ubuntu1) ... Setting up libgfortran-12-dev:riscv64 (12.2.0-14ubuntu1) ... Setting up libxcb-shm0:riscv64 (1.15-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnuma-dev:riscv64 (2.0.16-1) ... Setting up libxcb-present0:riscv64 (1.15-1) ... Setting up dh-autoreconf (20) ... Setting up libltdl-dev:riscv64 (2.4.7-5) ... Setting up libxdmcp-dev:riscv64 (1:1.1.3-0ubuntu5) ... Setting up gfortran-12 (12.2.0-14ubuntu1) ... Setting up libwebp-dev:riscv64 (1.2.4-0.1) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libxcb-sync1:riscv64 (1.15-1) ... Setting up libevent-dev (2.1.12-stable-5ubuntu1) ... Setting up libxcb-dri2-0:riscv64 (1.15-1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libdrm2:riscv64 (2.4.114-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-9) ... Setting up libtiff6:riscv64 (4.5.0-4ubuntu1) ... Setting up libllvm15:riscv64 (1:15.0.7-1) ... Setting up libnl-3-200:riscv64 (3.7.0-0.2) ... Setting up debugedit (1:5.0-5) ... Setting up libcurl4:riscv64 (7.87.0-2ubuntu1) ... Setting up libx11-6:riscv64 (2:1.8.3-3) ... Setting up libhwloc-dev:riscv64 (2.9.0-1) ... Setting up libfontconfig1:riscv64 (2.14.1-3ubuntu1) ... Setting up libjpeg8-dev:riscv64 (8c-2ubuntu10) ... Setting up libtiffxx6:riscv64 (4.5.0-4ubuntu1) ... Setting up libfftw3-dev:riscv64 (3.3.8-2ubuntu8) ... Setting up libdrm-amdgpu1:riscv64 (2.4.114-1) ... Setting up libxcb-dri3-0:riscv64 (1.15-1) ... Setting up libx11-xcb1:riscv64 (2:1.8.3-3) ... Setting up libdrm-nouveau2:riscv64 (2.4.114-1) ... Setting up libxcb1-dev:riscv64 (1.15-1) ... Setting up libxrender1:riscv64 (1:0.9.10-1.1) ... Setting up libdrm-radeon1:riscv64 (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:riscv64 (22.2.5-0ubuntu1) ... Setting up libjpeg-dev:riscv64 (8c-2ubuntu10) ... Setting up libx11-dev:riscv64 (2:1.8.3-3) ... Setting up libxext6:riscv64 (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:riscv64 (1.16.0-7) ... Setting up libxxf86vm1:riscv64 (1:1.1.4-1build3) ... Setting up libnl-route-3-200:riscv64 (3.7.0-0.2) ... Setting up libxnvctrl0:riscv64 (510.47.03-0ubuntu1) ... Setting up libtiff-dev:riscv64 (4.5.0-4ubuntu1) ... Setting up libxfixes3:riscv64 (1:6.0.0-2) ... Setting up libxinerama1:riscv64 (2:1.1.4-3) ... Setting up libnl-3-dev:riscv64 (3.7.0-0.2) ... Setting up cmake (3.25.1-1) ... Setting up libibverbs1:riscv64 (44.0-2) ... Setting up libxft2:riscv64 (2.3.6-1) ... Setting up libglx-mesa0:riscv64 (22.2.5-0ubuntu1) ... Setting up libglx0:riscv64 (1.6.0-1) ... Setting up ibverbs-providers:riscv64 (44.0-2) ... Setting up libxcursor1:riscv64 (1:1.2.1-1) ... Setting up debhelper (13.11.4ubuntu3) ... Setting up libhwloc-plugins:riscv64 (2.9.0-1) ... Setting up libnl-route-3-dev:riscv64 (3.7.0-0.2) ... Setting up libgl1:riscv64 (1.6.0-1) ... Setting up librdmacm1:riscv64 (44.0-2) ... Setting up libpmix2:riscv64 (4.2.2-1) ... Setting up libfltk1.3:riscv64 (1.3.8-5) ... Setting up libfltk-gl1.3:riscv64 (1.3.8-5) ... Setting up libfltk-cairo1.3:riscv64 (1.3.8-5) ... Setting up libibverbs-dev:riscv64 (44.0-2) ... Setting up libfltk-images1.3:riscv64 (1.3.8-5) ... Setting up libfltk-forms1.3:riscv64 (1.3.8-5) ... Setting up libpmix-dev:riscv64 (4.2.2-1) ... Setting up libfltk1.3-dev:riscv64 (1.3.8-5) ... Setting up libfabric1:riscv64 (1.17.0-3) ... Setting up libopenmpi3:riscv64 (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:riscv64 (4.1.4-3ubuntu2) ... update-alternatives: using /usr/lib/riscv64-linux-gnu/openmpi/include to provide /usr/include/riscv64-linux-gnu/mpi (mpi-riscv64-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 (riscv64 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.13.0-1019-generic #21~20.04.1-Ubuntu SMP Thu Mar 24 22:36:01 UTC 2022 riscv64 (riscv64) Toolchain package versions: binutils_2.40-2ubuntu1 dpkg-dev_1.21.19ubuntu3 g++-12_12.2.0-14ubuntu1 gcc-12_12.2.0-14ubuntu1 libc6-dev_2.37-0ubuntu1 libstdc++-12-dev_12.2.0-14ubuntu1 libstdc++6_12.2.0-14ubuntu1 linux-libc-dev_6.1.0-14.14 Package versions: adduser_3.129ubuntu1 advancecomp_2.5-1 apt_2.5.5 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-11 autotools-dev_20220109.1 base-files_12.3ubuntu1 base-passwd_3.6.1 bash_5.2.15-2ubuntu1 binutils_2.40-2ubuntu1 binutils-common_2.40-2ubuntu1 binutils-riscv64-linux-gnu_2.40-2ubuntu1 bsdextrautils_2.38.1-4ubuntu1 bsdutils_1:2.38.1-4ubuntu1 build-essential_12.9ubuntu3 bzip2_1.0.8-5build1 ca-certificates_20211016ubuntu1 cmake_3.25.1-1 cmake-data_3.25.1-1 coreutils_9.1-1ubuntu2 cpp_4:12.2.0-1ubuntu1 cpp-12_12.2.0-14ubuntu1 dash_0.5.11+git20210903+057cd650a4ed-9ubuntu1 debconf_1.5.82 debhelper_13.11.4ubuntu3 debianutils_5.7-0.4 debugedit_1:5.0-5 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.8-3 dpkg_1.21.19ubuntu3 dpkg-dev_1.21.19ubuntu3 dwz_0.15-1 e2fsprogs_1.46.6~rc1-1ubuntu1 fakeroot_1.30.1-1.1ubuntu1 file_1:5.44-3 findutils_4.9.0-3ubuntu1 fluid_1.3.8-5 fontconfig-config_2.14.1-3ubuntu1 fonts-dejavu-core_2.37-2build2 g++_4:12.2.0-1ubuntu1 g++-12_12.2.0-14ubuntu1 gcc_4:12.2.0-1ubuntu1 gcc-12_12.2.0-14ubuntu1 gcc-12-base_12.2.0-14ubuntu1 gettext_0.21-11 gettext-base_0.21-11 gfortran-12_12.2.0-14ubuntu1 gpg_2.2.40-1ubuntu2 gpg-agent_2.2.40-1ubuntu2 gpgconf_2.2.40-1ubuntu2 gpgv_2.2.40-1ubuntu2 grep_3.8-5 groff-base_1.22.4-9 gzip_1.12-1ubuntu1 hostname_3.23ubuntu2 ibverbs-providers_44.0-2 init_1.65.2 init-system-helpers_1.65.2 intltool-debian_0.35.0+20060710.6 libacl1_2.3.1-3 libapparmor1_3.0.8-1ubuntu1 libapt-pkg6.0_2.5.5 libarchive-zip-perl_1.68-1 libarchive13_3.6.2-1ubuntu1 libargon2-1_0~20171227-0.3 libasan8_12.2.0-14ubuntu1 libassuan0_2.5.5-5 libatomic1_12.2.0-14ubuntu1 libattr1_1:2.5.1-4 libaudit-common_1:3.0.7-1.1 libaudit1_1:3.0.7-1.1 libbinutils_2.40-2ubuntu1 libblkid1_2.38.1-4ubuntu1 libbrotli1_1.0.9-2build7 libbsd0_0.11.7-2 libbz2-1.0_1.0.8-5build1 libc-bin_2.37-0ubuntu1 libc-dev-bin_2.37-0ubuntu1 libc6_2.37-0ubuntu1 libc6-dev_2.37-0ubuntu1 libcairo2_1.16.0-7 libcap-ng0_0.8.3-1build1 libcap2_1:2.66-3ubuntu1 libcbor0.8_0.8.0-2ubuntu1 libcc1-0_12.2.0-14ubuntu1 libcom-err2_1.46.6~rc1-1ubuntu1 libcrypt-dev_1:4.4.33-2 libcrypt1_1:4.4.33-2 libcryptsetup12_2:2.5.0-6ubuntu3 libctf-nobfd0_2.40-2ubuntu1 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libfile-stripnondeterminism-perl_1.13.1-1 libfltk-cairo1.3_1.3.8-5 libfltk-forms1.3_1.3.8-5 libfltk-gl1.3_1.3.8-5 libfltk-images1.3_1.3.8-5 libfltk1.3_1.3.8-5 libfltk1.3-dev_1.3.8-5 libfontconfig1_2.14.1-3ubuntu1 libfreetype6_2.12.1+dfsg-4 libgcc-12-dev_12.2.0-14ubuntu1 libgcc-s1_12.2.0-14ubuntu1 libgcrypt20_1.10.1-3ubuntu1 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libgfortran-12-dev_12.2.0-14ubuntu1 libgfortran5_12.2.0-14ubuntu1 libgl1_1.6.0-1 libgl1-mesa-dri_22.2.5-0ubuntu1 libglapi-mesa_22.2.5-0ubuntu1 libglvnd0_1.6.0-1 libglx-mesa0_22.2.5-0ubuntu1 libglx0_1.6.0-1 libgmp10_2:6.2.1+dfsg1-1.1ubuntu1 libgnutls30_3.7.8-4ubuntu1 libgomp1_12.2.0-14ubuntu1 libgpg-error0_1.46-1 libgssapi-krb5-2_1.20.1-1build1 libhogweed6_3.8.1-2 libhwloc-dev_2.9.0-1 libhwloc-plugins_2.9.0-1 libhwloc15_2.9.0-1 libibverbs-dev_44.0-2 libibverbs1_44.0-2 libicu71_71.1-3ubuntu1 libidn2-0_2.3.3-1build1 libip4tc2_1.8.7-1ubuntu7 libisl23_0.25-1 libjansson4_2.14-2 libjbig-dev_2.1-6ubuntu1 libjbig0_2.1-6ubuntu1 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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=8 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-25549283 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-25549283 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-25549283 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 riscv64 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/riscv64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi_cxx.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") -- MPI_INCLUDE_PATH : /usr/lib/riscv64-linux-gnu/openmpi/include;/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -- MPI_LIBRARIES : /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi_cxx.so;/usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi.so -- MPI_CXX_INCLUDE_PATH : /usr/lib/riscv64-linux-gnu/openmpi/include;/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -- MPI_CXX_LIBRARIES : /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi_cxx.so;/usr/lib/riscv64-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/riscv64-linux-gnu/libX11.so -- Looking for XOpenDisplay in /usr/lib/riscv64-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/riscv64-linux-gnu/libX11.so;/usr/lib/riscv64-linux-gnu/libm.so -- Found FFTW -- FFTW_PATH: /usr/include -- FFTW_INCLUDES: /usr/include -- FFTW_LIBRARIES: /usr/lib/riscv64-linux-gnu/libfftw3f.so;/usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for sincos -- Looking for sincos - found -- Looking for __sincos -- Looking for __sincos - not found -- Found TIFF: /usr/lib/riscv64-linux-gnu/libtiff.so (found version "4.5.0") -- Found ZLIB: /usr/lib/riscv64-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 -j8 -C build make[2]: Entering directory '/<>/build' /usr/bin/cmake -S/<> -B/<>/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/build/CMakeFiles /<>/build//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/<>/build' /usr/bin/make -f CMakeFiles/copy_scripts.dir/build.make CMakeFiles/copy_scripts.dir/depend /usr/bin/make -f src/apps/CMakeFiles/relion_lib.dir/build.make src/apps/CMakeFiles/relion_lib.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<> /<>/build /<>/build /<>/build/CMakeFiles/copy_scripts.dir/DependInfo.cmake --color= make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/relion_lib.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f CMakeFiles/copy_scripts.dir/build.make CMakeFiles/copy_scripts.dir/build make[4]: Entering directory '/<>/build' /usr/bin/cmake -E copy /<>/scripts/star_printtable /<>/build/bin/relion_star_printtable make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/relion_lib.dir/build.make src/apps/CMakeFiles/relion_lib.dir/build /usr/bin/cmake -E copy /<>/scripts/star_plottable /<>/build/bin/relion_star_plottable make[4]: Entering directory '/<>/build' /usr/bin/cmake -E copy /<>/scripts/star_loopheader /<>/build/bin/relion_star_loopheader [ 1%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/CPlot2D.cpp.o [ 1%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/args.cpp.o [ 1%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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 [ 2%] 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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 cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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 [ 2%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/__/macros.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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 cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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 [ 2%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/assembly.cpp.o /usr/bin/cmake -E copy /<>/scripts/star_datablock_stack /<>/build/bin/relion_star_datablock_stack cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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 [ 3%] 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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 /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' [ 3%] Built target copy_scripts [ 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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.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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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 ‘void CPlot2D::ComputeLabelTickSpacing(double, double, double*, double*, double*, int, std::string)’: /<>/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 ‘int sprintf(char*, const char*, ...)’, inlined from ‘void CPlot2D::ComputeLabelTickSpacing(double, double, double*, double*, double*, int, std::string)’ at /<>/src/CPlot2D.cpp:743:16: /usr/include/riscv64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___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 ‘void CPlot2D::ComputeLabelTickSpacing(double, double, double*, double*, double*, int, std::string)’: /<>/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 ‘int sprintf(char*, const char*, ...)’, inlined from ‘void CPlot2D::ComputeLabelTickSpacing(double, double, double*, double*, double*, int, std::string)’ at /<>/src/CPlot2D.cpp:733:16: /usr/include/riscv64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___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 ()); | ~~~~~~~~~~~~~~~~~ [ 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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 [ 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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 [ 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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 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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/__/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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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 [ 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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 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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/__/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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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 [ 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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 [ 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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 [ 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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 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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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.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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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_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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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 [ 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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 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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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 [ 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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 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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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_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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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 [ 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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.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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/riscv64-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 ‘void std::__new_allocator<_Tp>::deallocate(_Tp*, size_type) [with _Tp = double]’, inlined from ‘static void std::allocator_traits >::deallocate(allocator_type&, pointer, size_type) [with _Tp = double]’ at /usr/include/c++/12/bits/alloc_traits.h:496:23, inlined from ‘void std::_Vector_base<_Tp, _Alloc>::_M_deallocate(pointer, std::size_t) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:387:19, inlined from ‘std::_Vector_base<_Tp, _Alloc>::~_Vector_base() [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:366:15, inlined from ‘std::vector<_Tp, _Alloc>::~vector() [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:733:7, inlined from ‘MetaDataTable 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: ‘void operator delete(void*)’ called on pointer ‘’ with nonzero offset [1, 9223372036854775807] [-Wfree-nonheap-object] 158 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In member function ‘_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = double]’, inlined from ‘static _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = double]’ at /usr/include/c++/12/bits/alloc_traits.h:464:28, inlined from ‘std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:378:33, inlined from ‘void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:395:44, inlined from ‘std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:332:26, inlined from ‘std::vector<_Tp, _Alloc>::vector(size_type, const value_type&, const allocator_type&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:566:47, inlined from ‘MetaDataTable 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 ‘void* operator new(std::size_t)’ 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ 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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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 [ 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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 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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/parallel.cpp.o -MF CMakeFiles/relion_lib.dir/__/parallel.cpp.o.d -o CMakeFiles/relion_lib.dir/__/parallel.cpp.o -c /<>/src/parallel.cpp [ 16%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/particle_subtractor.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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 file included from /<>/src/numerical_recipes.h:48, from /<>/src/numerical_recipes.cpp:49: In function ‘void free_Tvector(T*&, int, int) [with T = double]’, inlined from ‘double 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: ‘void free(void*)’ called on pointer ‘xt’ with nonzero offset 8 [-Wfree-nonheap-object] 74 | free((char*)(v + nl)); | ~~~~^~~~~~~~~~~~~~~~~ /<>/src/numerical_recipes.cpp: In function ‘double brent(double, double, double, double (*)(double*, void*), void*, double, double*, int, double*, double*)’: /<>/src/numerical_recipes.cpp:579:13: note: declared here 579 | RFLOAT *xt=NULL; | ^~ In function ‘void free_Tvector(T*&, int, int) [with T = double]’, inlined from ‘void 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: ‘void free(void*)’ called on pointer ‘xit’ with nonzero offset 8 [-Wfree-nonheap-object] 74 | free((char*)(v + nl)); | ~~~~^~~~~~~~~~~~~~~~~ /<>/src/numerical_recipes.cpp: In function ‘void 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 ‘void free_Tvector(T*&, int, int) [with T = double]’, inlined from ‘void 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: ‘void free(void*)’ called on pointer ‘ptt’ with nonzero offset 8 [-Wfree-nonheap-object] 74 | free((char*)(v + nl)); | ~~~~^~~~~~~~~~~~~~~~~ /<>/src/numerical_recipes.cpp: In function ‘void 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 ‘void free_Tvector(T*&, int, int) [with T = double]’, inlined from ‘void 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: ‘void free(void*)’ called on pointer ‘pt’ with nonzero offset 8 [-Wfree-nonheap-object] 74 | free((char*)(v + nl)); | ~~~~^~~~~~~~~~~~~~~~~ /<>/src/numerical_recipes.cpp: In function ‘void 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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 [ 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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 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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/__/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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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 [ 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 18%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/preprocessing_mpi.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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 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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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 cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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 [ 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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 [ 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/__/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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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 [ 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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 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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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 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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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 [ 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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 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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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 [ 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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 /<>/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()); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 23%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/Fourier_helper.cpp.o [ 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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 cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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 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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/complex_io.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/complex_io.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/complex_io.cpp.o -c /<>/src/jaz/complex_io.cpp [ 25%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/convolution_helper.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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 [ 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/damage_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/damage_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/damage_helper.cpp.o -c /<>/src/jaz/damage_helper.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 26%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/distribution_helper.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/distribution_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/distribution_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/distribution_helper.cpp.o -c /<>/src/jaz/distribution_helper.cpp [ 26%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/fftw_helper.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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 [ 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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 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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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 [ 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/new_ft.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/new_ft.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/new_ft.cpp.o -c /<>/src/jaz/new_ft.cpp [ 30%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/noise_helper.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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 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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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 [ 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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 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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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 [ 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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 [ 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/volume_integration.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/volume_integration.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/volume_integration.cpp.o -c /<>/src/jaz/volume_integration.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 35%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/vtk_helper.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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_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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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 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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 36%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/lbfgs.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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 [ 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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 [ 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/delocalisation_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/delocalisation_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/delocalisation_helper.cpp.o -c /<>/src/jaz/ctf/delocalisation_helper.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/ctf/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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_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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /<>/src/image.h:455, from /<>/src/jaz/obs_model.h:24, from /<>/src/ctf.h:50, from /<>/src/jaz/ctf/defocus_helper.h:24, from /<>/src/jaz/ctf/defocus_helper.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_helper.cpp.o -c /<>/src/jaz/ctf/magnification_helper.cpp [ 41%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/modular_ctf_optimisation.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/modular_ctf_optimisation.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/modular_ctf_optimisation.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/modular_ctf_optimisation.cpp.o -c /<>/src/jaz/ctf/modular_ctf_optimisation.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/ctf/magnification_estimator.h:28, from /<>/src/jaz/ctf/magnification_estimator.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /<>/src/image.h:455, from /<>/src/jaz/obs_model.h:24, from /<>/src/ctf.h:50, from /<>/src/jaz/ctf/magnification_helper.h:24, from /<>/src/jaz/ctf/magnification_helper.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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 [ 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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 [ 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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 [ 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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 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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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 [ 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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 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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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.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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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 [ 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/color_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/img_proc/color_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/img_proc/color_helper.cpp.o -c /<>/src/jaz/img_proc/color_helper.cpp [ 46%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/filter_helper.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/filter_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/img_proc/filter_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/img_proc/filter_helper.cpp.o -c /<>/src/jaz/img_proc/filter_helper.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 47%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/image_op.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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 [ 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-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 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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/tomo_stack.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/tomo/tomo_stack.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/tomo/tomo_stack.cpp.o -c /<>/src/jaz/tomo/tomo_stack.cpp [ 49%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/io/star_converter.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/io/star_converter.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/io/star_converter.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/io/star_converter.cpp.o -c /<>/src/jaz/io/star_converter.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/tomo/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevq3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevq3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevq3.c.o -c /<>/src/jaz/d3x3/dsyevq3.c [ 51%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevv3.c.o cd /<>/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevv3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevv3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevv3.c.o -c /<>/src/jaz/d3x3/dsyevv3.c [ 52%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsytrd3.c.o cd /<>/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsytrd3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsytrd3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsytrd3.c.o -c /<>/src/jaz/d3x3/dsytrd3.c [ 52%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/slvsec3.c.o cd /<>/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/slvsec3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/slvsec3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/slvsec3.c.o -c /<>/src/jaz/d3x3/slvsec3.c [ 53%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/lbfgs/lbfgs.c.o cd /<>/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-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 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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /<>/src/image.h:455, from /<>/src/jaz/io/star_converter.h:5, from /<>/src/jaz/io/star_converter.cpp:1: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 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 CMakeFiles/relion_lib.dir/__/autopicker.cpp.o CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o CMakeFiles/relion_lib.dir/__/backprojector.cpp.o CMakeFiles/relion_lib.dir/__/complex.cpp.o CMakeFiles/relion_lib.dir/__/ctf.cpp.o CMakeFiles/relion_lib.dir/__/ctffind_runner.cpp.o CMakeFiles/relion_lib.dir/__/ctffind_runner_mpi.cpp.o CMakeFiles/relion_lib.dir/__/error.cpp.o CMakeFiles/relion_lib.dir/__/euler.cpp.o CMakeFiles/relion_lib.dir/__/exp_model.cpp.o 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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 cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/autopick.dir/autopick.cpp.o -MF CMakeFiles/autopick.dir/autopick.cpp.o.d -o CMakeFiles/autopick.dir/autopick.cpp.o -c /<>/src/apps/autopick.cpp cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/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 [ 54%] Building CXX object src/apps/CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o [ 54%] Building CXX object src/apps/CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o [ 55%] 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/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 cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/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 [ 55%] Building CXX object src/apps/CMakeFiles/convert_star.dir/convert_star.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/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 cd /<>/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/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 [ 55%] 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/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/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /<>/src/image.h:455, from /<>/src/jaz/io/star_converter.h:5, from /<>/src/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /<>/src/image.h:455, from /<>/src/tiff_converter.h:24, from /<>/src/apps/convert_to_tiff.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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /<>/src/image.h:455, from /<>/src/tiff_converter.h:24, from /<>/src/apps/convert_to_tiff_mpi.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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 /<>/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 55%] 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=/<>=. -fstack-protector-strong -Wformat -Werror=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 -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/riscv64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 56%] 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=/<>=. -fstack-protector-strong -Wformat -Werror=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 -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/riscv64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 56%] 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=/<>=. -fstack-protector-strong -Wformat -Werror=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 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/autopick.dir/autopick.cpp.o -o ../../bin/relion_autopick ../../lib/librelion_lib.a /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 56%] 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=/<>=. -fstack-protector-strong -Wformat -Werror=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 -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/riscv64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/<>/build' [ 56%] 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' [ 56%] 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/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 [ 57%] 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=/<>=. -fstack-protector-strong -Wformat -Werror=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 -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/riscv64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/<>/build' [ 57%] Built target convert_star /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' [ 57%] 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/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 make[4]: Leaving directory '/<>/build' [ 57%] Built target convert_to_tiff_mpi /usr/bin/make -f src/apps/CMakeFiles/ctf_toolbox.dir/build.make src/apps/CMakeFiles/ctf_toolbox.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/ctf_toolbox.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/ctf_toolbox.dir/build.make src/apps/CMakeFiles/ctf_toolbox.dir/build make[4]: Entering directory '/<>/build' [ 58%] 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/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/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 59%] 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=/<>=. -fstack-protector-strong -Wformat -Werror=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 -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/riscv64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /<>/src/image.h:455, from /<>/src/jaz/obs_model.h:24, from /<>/src/jaz/ctf/ctf_refiner.h:24, from /<>/src/jaz/ctf/ctf_refiner_mpi.h:26, from /<>/src/apps/ctf_refine_mpi.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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=/<>=. -fstack-protector-strong -Wformat -Werror=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 -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/riscv64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 60%] 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=/<>=. -fstack-protector-strong -Wformat -Werror=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 -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/riscv64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/<>/build' [ 60%] Built target autopick [ 61%] 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/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 make[4]: Leaving directory '/<>/build' [ 61%] 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' [ 61%] 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/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 make[4]: Leaving directory '/<>/build' [ 61%] Built target autopick_mpi /usr/bin/make -f src/apps/CMakeFiles/estimate_gain.dir/build.make src/apps/CMakeFiles/estimate_gain.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/estimate_gain.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/estimate_gain.dir/build.make src/apps/CMakeFiles/estimate_gain.dir/build make[4]: Entering directory '/<>/build' [ 61%] 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/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 make[4]: Leaving directory '/<>/build' [ 61%] Built target align_symmetry /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' [ 62%] 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/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 [ 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=/<>=. -fstack-protector-strong -Wformat -Werror=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 -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/riscv64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/<>/build' [ 62%] Built target ctf_refine [ 62%] 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/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 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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/__/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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/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 make[4]: Leaving directory '/<>/build' [ 62%] Linking CXX executable ../../bin/relion_ctf_toolbox [ 62%] Built target ctf_refine_mpi cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/ctf_toolbox.dir/link.txt --verbose=1 /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= /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=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 -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/riscv64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 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' [ 62%] 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/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 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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/<>/build' [ 62%] Built target ctf_toolbox /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' [ 62%] 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/flex_analyse.dir/flex_analyse.cpp.o -MF CMakeFiles/flex_analyse.dir/flex_analyse.cpp.o.d -o CMakeFiles/flex_analyse.dir/flex_analyse.cpp.o -c /<>/src/apps/flex_analyse.cpp In file included from /<>/src/image.h:455, from /<>/src/exp_model.h:24, from /<>/src/apps/../flex_analyser.h:24, from /<>/src/apps/flex_analyse.cpp:22: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 63%] 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/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 [ 63%] 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=/<>=. -fstack-protector-strong -Wformat -Werror=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 -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/riscv64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 64%] 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=/<>=. -fstack-protector-strong -Wformat -Werror=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 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/demodulate.dir/demodulate.cpp.o -o ../../bin/relion_demodulate ../../lib/librelion_lib.a /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 64%] 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=/<>=. -fstack-protector-strong -Wformat -Werror=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 -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/riscv64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/<>/build' [ 64%] Built target estimate_gain /usr/bin/make -f src/apps/CMakeFiles/flex_analyse_mpi.dir/build.make src/apps/CMakeFiles/flex_analyse_mpi.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/flex_analyse_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/flex_analyse_mpi.dir/build.make src/apps/CMakeFiles/flex_analyse_mpi.dir/build make[4]: Entering directory '/<>/build' [ 64%] 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/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 [ 65%] 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=/<>=. -fstack-protector-strong -Wformat -Werror=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 -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/riscv64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/<>/build' [ 65%] 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' [ 66%] 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/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 make[4]: Leaving directory '/<>/build' [ 66%] Built target demodulate /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' [ 67%] 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/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 [ 67%] 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/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/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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' [ 67%] Built target find_tiltpairs /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' [ 67%] 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/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/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/../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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 68%] Linking CXX executable ../../bin/relion_flex_analyse cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/flex_analyse.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=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 -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/riscv64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 68%] 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=/<>=. -fstack-protector-strong -Wformat -Werror=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 -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/riscv64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/<>/build' [ 68%] Built target helix_inimodel2d /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' [ 68%] 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/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 [ 69%] 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/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 [ 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=/<>=. -fstack-protector-strong -Wformat -Werror=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 -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/riscv64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /<>/src/image.h:455, from /<>/src/jaz/obs_model.h:24, from /<>/src/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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' [ 69%] Built target flex_analyse /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' [ 70%] 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/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 /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' [ 71%] 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/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 /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' [ 71%] 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/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 [ 71%] 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' [ 71%] Built target relion_gui_lib /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' [ 72%] 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/merge_particles.dir/merge_particles.cpp.o -MF CMakeFiles/merge_particles.dir/merge_particles.cpp.o.d -o CMakeFiles/merge_particles.dir/merge_particles.cpp.o -c /<>/src/apps/merge_particles.cpp In file included from /<>/src/image.h:455, from /<>/src/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 72%] 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=/<>=. -fstack-protector-strong -Wformat -Werror=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 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/localsym.dir/localsym.cpp.o -o ../../bin/relion_localsym ../../lib/librelion_lib.a /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/<>/build' [ 72%] Built target flex_analyse_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' [ 73%] 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/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 [ 73%] 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=/<>=. -fstack-protector-strong -Wformat -Werror=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 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/import.dir/import.cpp.o -o ../../bin/relion_import ../../lib/librelion_lib.a /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 73%] Linking CXX executable ../../bin/relion_localsym_mpi cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/localsym_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=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 -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/riscv64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/riscv64-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/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' [ 73%] 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/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 [ 73%] 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=/<>=. -fstack-protector-strong -Wformat -Werror=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 -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/riscv64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /<>/src/image.h:455, from /<>/src/jaz/obs_model.h:24, from /<>/src/ctf.h:50, from /<>/src/jaz/motion/motion_refiner.h:25, from /<>/src/apps/motion_refine.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 73%] Linking CXX executable ../../bin/relion_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=/<>=. -fstack-protector-strong -Wformat -Werror=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 -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/riscv64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/<>/build' [ 73%] Built target merge_particles /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' [ 73%] 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/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 make[4]: Leaving directory '/<>/build' [ 73%] Built target localsym /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' [ 74%] 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o -MF CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o.d -o CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o -c /<>/src/apps/particle_FCC.cpp In file included from /<>/src/image.h:455, from /<>/src/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 74%] 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=/<>=. -fstack-protector-strong -Wformat -Werror=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 -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/riscv64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 75%] 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=/<>=. -fstack-protector-strong -Wformat -Werror=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 -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/riscv64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 75%] 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=/<>=. -fstack-protector-strong -Wformat -Werror=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 -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/riscv64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/<>/build' [ 75%] Built target localsym_mpi /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' [ 76%] 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/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/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/<>/build' [ 76%] Built target helix_toolbox /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' [ 76%] 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/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 make[4]: Leaving directory '/<>/build' [ 76%] Built target image_handler /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' [ 76%] 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/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 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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 77%] 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=/<>=. -fstack-protector-strong -Wformat -Werror=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 -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/riscv64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 77%] 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=/<>=. -fstack-protector-strong -Wformat -Werror=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 -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/riscv64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 77%] 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=/<>=. -fstack-protector-strong -Wformat -Werror=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 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/mrc2vtk.dir/mrc2vtk.cpp.o -o ../../bin/relion_mrc2vtk ../../lib/librelion_lib.a /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/<>/build' [ 77%] Built target mask_create /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' [ 77%] 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/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.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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /<>/src/image.h:455, from /<>/src/jaz/obs_model.h:24, from /<>/src/ctf.h:50, from /<>/src/jaz/stack_helper.h:24, from /<>/src/apps/particle_select.cpp:1: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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 mrc2vtk /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' [ 78%] 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/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 make[4]: Leaving directory '/<>/build' [ 78%] Built target motion_refine /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' [ 78%] 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/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 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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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' [ 78%] Built target particle_FCC /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' [ 78%] 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/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 [ 79%] 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=/<>=. -fstack-protector-strong -Wformat -Werror=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 -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/riscv64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /<>/src/image.h:455, from /<>/src/jaz/obs_model.h:24, from /<>/src/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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' [ 79%] Built target motion_refine_mpi /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' [ 79%] 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/postprocess.dir/postprocess.cpp.o -MF CMakeFiles/postprocess.dir/postprocess.cpp.o.d -o CMakeFiles/postprocess.dir/postprocess.cpp.o -c /<>/src/apps/postprocess.cpp In file included from /<>/src/image.h:455, from /<>/src/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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' [ 79%] Built target particle_select /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' [ 80%] 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/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 [ 80%] 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=/<>=. -fstack-protector-strong -Wformat -Werror=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 -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/riscv64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 81%] 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=/<>=. -fstack-protector-strong -Wformat -Werror=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 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/pipeliner.dir/pipeliner.cpp.o -o ../../bin/relion_pipeliner ../../lib/librelion_lib.a /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/riscv64-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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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 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=/<>=. -fstack-protector-strong -Wformat -Werror=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 -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/riscv64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 83%] 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 make[4]: Leaving directory '/<>/build' /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=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 -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/riscv64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 83%] Built target particle_symmetry_expand /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' [ 83%] 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/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 [ 83%] 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=/<>=. -fstack-protector-strong -Wformat -Werror=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 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/postprocess.dir/postprocess.cpp.o -o ../../bin/relion_postprocess ../../lib/librelion_lib.a /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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_postprocess_mpi cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/postprocess_mpi.dir/link.txt --verbose=1 [ 83%] 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=/<>=. -fstack-protector-strong -Wformat -Werror=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 -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/riscv64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=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 -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/riscv64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/<>/build' [ 83%] Built target plot_delocalisation /usr/bin/make -f src/apps/CMakeFiles/preprocess.dir/build.make src/apps/CMakeFiles/preprocess.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/preprocess.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/preprocess.dir/build.make src/apps/CMakeFiles/preprocess.dir/build make[4]: Entering directory '/<>/build' [ 83%] 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/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' [ 83%] Built target postprocess /usr/bin/make -f src/apps/CMakeFiles/preprocess_mpi.dir/build.make src/apps/CMakeFiles/preprocess_mpi.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/preprocess_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/preprocess_mpi.dir/build.make src/apps/CMakeFiles/preprocess_mpi.dir/build make[4]: Entering directory '/<>/build' [ 83%] 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/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 make[4]: Leaving directory '/<>/build' [ 83%] 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' [ 84%] 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/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 [ 84%] 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=/<>=. -fstack-protector-strong -Wformat -Werror=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 -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/riscv64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /<>/src/image.h:455, from /<>/src/preprocessing.h:29, from /<>/src/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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_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=/<>=. -fstack-protector-strong -Wformat -Werror=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 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/preprocess.dir/preprocess.cpp.o -o ../../bin/relion_preprocess ../../lib/librelion_lib.a /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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' [ 85%] Built target particle_subtract /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' [ 85%] 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/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 [ 85%] 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=/<>=. -fstack-protector-strong -Wformat -Werror=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 -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/riscv64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/<>/build' [ 85%] Built target particle_subtract_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' [ 85%] 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o -MF CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o.d -o CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o -c /<>/src/apps/reconstruct_mpi.cpp In file included from /<>/src/image.h:455, from /<>/src/projector.h:25, from /<>/src/backprojector.h:33, from /<>/src/reconstructor.h:23, from /<>/src/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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' [ 85%] Built target preprocess /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' [ 85%] 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/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 make[4]: Leaving directory '/<>/build' [ 85%] Built target pipeliner /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' [ 86%] 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/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/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/<>/build' [ 86%] Built target particle_reposition /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' [ 86%] 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/reposition.dir/reposition.cpp.o -MF CMakeFiles/reposition.dir/reposition.cpp.o.d -o CMakeFiles/reposition.dir/reposition.cpp.o -c /<>/src/apps/reposition.cpp In file included from /<>/src/image.h:455, from /<>/src/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/<>/build' [ 86%] Built target preprocess_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= [ 87%] Linking CXX executable ../../bin/relion_reconstruct make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/run_ctffind.dir/build.make src/apps/CMakeFiles/run_ctffind.dir/build cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/reconstruct.dir/link.txt --verbose=1 make[4]: Entering directory '/<>/build' /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=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 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/reconstruct.dir/reconstruct.cpp.o -o ../../bin/relion_reconstruct ../../lib/librelion_lib.a /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 87%] 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/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/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /<>/src/image.h:455, from /<>/src/jaz/obs_model.h:24, from /<>/src/apps/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 88%] 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=/<>=. -fstack-protector-strong -Wformat -Werror=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 -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/riscv64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 88%] 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=/<>=. -fstack-protector-strong -Wformat -Werror=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 -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/riscv64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/<>/build' [ 88%] Built target reconstruct /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' [ 89%] 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/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 [ 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=/<>=. -fstack-protector-strong -Wformat -Werror=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 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/project.dir/project.cpp.o -o ../../bin/relion_project ../../lib/librelion_lib.a /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 90%] 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=/<>=. -fstack-protector-strong -Wformat -Werror=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 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/reposition.dir/reposition.cpp.o -o ../../bin/relion_reposition ../../lib/librelion_lib.a /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/<>/build' [ 90%] 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' [ 91%] 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/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 [ 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=/<>=. -fstack-protector-strong -Wformat -Werror=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 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/refine.dir/refine.cpp.o -o ../../bin/relion_refine ../../lib/librelion_lib.a /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff 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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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' [ 91%] Built target reconstruct_mpi /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' [ 91%] 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/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 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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 91%] 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=/<>=. -fstack-protector-strong -Wformat -Werror=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 -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/riscv64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/<>/build' [ 91%] Built target reposition /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' [ 91%] 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/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 [ 91%] 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=/<>=. -fstack-protector-strong -Wformat -Werror=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 -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/riscv64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 92%] 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=/<>=. -fstack-protector-strong -Wformat -Werror=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 -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/riscv64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/riscv64-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/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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 project /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= [ 92%] Linking CXX executable ../../bin/relion_run_motioncorr make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/stack_create.dir/build.make src/apps/CMakeFiles/stack_create.dir/build cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/run_motioncorr.dir/link.txt --verbose=1 make[4]: Entering directory '/<>/build' /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=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 -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/riscv64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 93%] 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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' [ 93%] Built target prepare_subtomo /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' [ 94%] 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/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 make[4]: Leaving directory '/<>/build' [ 94%] Built target run_ctffind_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' [ 94%] 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o -MF CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o.d -o CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o -c /<>/src/apps/tiltpair_plot.cpp In file included from /<>/src/image.h:455, from /<>/src/apps/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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_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=/<>=. -fstack-protector-strong -Wformat -Werror=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 -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/riscv64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/<>/build' [ 95%] Built target refine /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' [ 95%] Built target run_motioncorr /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/tomo_test.dir/build.make src/apps/CMakeFiles/tomo_test.dir/build make[4]: Entering directory '/<>/build' 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' [ 95%] 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/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 [ 95%] 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/relion-3.1.3-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/display.dir/display.cpp.o -MF CMakeFiles/display.dir/display.cpp.o.d -o CMakeFiles/display.dir/display.cpp.o -c /<>/src/apps/display.cpp In file included from /<>/src/image.h:455, from /<>/src/apps/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/<>/build' [ 95%] Built target run_motioncorr_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' [ 95%] 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/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/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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/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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-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_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=/<>=. -fstack-protector-strong -Wformat -Werror=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 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/scheduler.dir/scheduler.cpp.o -o ../../bin/relion_scheduler ../../lib/librelion_lib.a /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/<>/build' [ 95%] Built target refine_mpi /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' [ 95%] 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/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/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 [ 96%] 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=/<>=. -fstack-protector-strong -Wformat -Werror=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 -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/riscv64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 97%] 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=/<>=. -fstack-protector-strong -Wformat -Werror=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 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/display.dir/display.cpp.o -o ../../bin/relion_display ../../lib/librelion_lib.a /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gui_lib.a /usr/lib/riscv64-linux-gnu/libfltk_images.so /usr/lib/riscv64-linux-gnu/libfltk_forms.so /usr/lib/riscv64-linux-gnu/libfltk.so -lX11 -lm -ltiff ../../lib/librelion_lib.a -lfftw3f -lfftw3 -ltiff 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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/<>/build' [ 97%] Built target tiltpair_plot 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/riscv64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/riscv64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 98%] 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=/<>=. -fstack-protector-strong -Wformat -Werror=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 -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/riscv64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/<>/build' [ 98%] Built target display [ 99%] 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=/<>=. -fstack-protector-strong -Wformat -Werror=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 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/relion.dir/maingui.cpp.o -o ../../bin/relion ../../lib/librelion_lib.a /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gui_lib.a /usr/lib/riscv64-linux-gnu/libfltk_images.so /usr/lib/riscv64-linux-gnu/libfltk_forms.so /usr/lib/riscv64-linux-gnu/libfltk.so -lX11 -lm -ltiff ../../lib/librelion_lib.a -lfftw3f -lfftw3 -ltiff [ 99%] 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=/<>=. -fstack-protector-strong -Wformat -Werror=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 -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/riscv64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [100%] 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=/<>=. -fstack-protector-strong -Wformat -Werror=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 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/manualpick.dir/manualpick.cpp.o -o ../../bin/relion_manualpick ../../lib/librelion_lib.a /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gui_lib.a /usr/lib/riscv64-linux-gnu/libfltk_images.so /usr/lib/riscv64-linux-gnu/libfltk_forms.so /usr/lib/riscv64-linux-gnu/libfltk.so -lX11 -lm -ltiff ../../lib/librelion_lib.a -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/<>/build' [100%] Built target tomo_test make[4]: Leaving directory '/<>/build' [100%] Built target stack_create make[4]: Leaving directory '/<>/build' [100%] Built target manualpick [100%] 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=/<>=. -fstack-protector-strong -Wformat -Werror=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 -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/riscv64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/<>/build' [100%] Built target star_handler make[4]: Leaving directory '/<>/build' [100%] Built target scheduler make[4]: Leaving directory '/<>/build' [100%] Built target relion 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_convert_to_tiff -- Installing: /<>/debian/tmp/cli/usr/bin/relion_postprocess -- Installing: /<>/debian/tmp/cli/usr/bin/relion_find_tiltpairs -- Installing: /<>/debian/tmp/cli/usr/bin/relion_ctf_refine_mpi -- Installing: /<>/debian/tmp/cli/usr/bin/relion_tiltpair_plot -- Installing: /<>/debian/tmp/cli/usr/bin/relion_import -- Installing: /<>/debian/tmp/cli/usr/bin/relion_run_ctffind_mpi -- Installing: /<>/debian/tmp/cli/usr/bin/relion_star_printtable -- Installing: /<>/debian/tmp/cli/usr/bin/relion_star_datablock_ctfdat -- Installing: /<>/debian/tmp/cli/usr/bin/relion_run_motioncorr_mpi -- Installing: /<>/debian/tmp/cli/usr/bin/relion_particle_reposition -- Installing: /<>/debian/tmp/cli/usr/bin/relion_mask_create -- Installing: /<>/debian/tmp/cli/usr/bin/relion_run_ctffind -- Installing: /<>/debian/tmp/cli/usr/bin/relion_postprocess_mpi -- Installing: /<>/debian/tmp/cli/usr/bin/relion_star_datablock_stack -- Installing: /<>/debian/tmp/cli/usr/bin/relion_demodulate -- Installing: /<>/debian/tmp/cli/usr/bin/relion_helix_toolbox -- Installing: /<>/debian/tmp/cli/usr/bin/relion_reconstruct_mpi -- Installing: /<>/debian/tmp/cli/usr/bin/relion_estimate_gain -- Installing: /<>/debian/tmp/cli/usr/bin/relion_particle_subtract_mpi -- Installing: /<>/debian/tmp/cli/usr/bin/relion_star_datablock_singlefiles -- Installing: /<>/debian/tmp/cli/usr/bin/relion_refine -- Installing: /<>/debian/tmp/cli/usr/bin/relion_flex_analyse_mpi -- Installing: /<>/debian/tmp/cli/usr/bin/relion_particle_subtract -- Installing: /<>/debian/tmp/cli/usr/bin/relion_localsym -- Installing: /<>/debian/tmp/cli/usr/bin/relion_ctf_refine -- Installing: /<>/debian/tmp/cli/usr/bin/relion_flex_analyse -- Installing: /<>/debian/tmp/cli/usr/bin/relion_align_symmetry -- Installing: /<>/debian/tmp/cli/usr/bin/relion_prepare_subtomo -- Installing: /<>/debian/tmp/cli/usr/bin/relion_scheduler -- Installing: /<>/debian/tmp/cli/usr/bin/relion_convert_star -- Installing: /<>/debian/tmp/cli/usr/bin/relion_particle_select -- Installing: /<>/debian/tmp/cli/usr/bin/relion_preprocess_mpi -- Installing: /<>/debian/tmp/cli/usr/bin/relion_convert_to_tiff_mpi -- Installing: /<>/debian/tmp/cli/usr/bin/relion_autopick -- Installing: /<>/debian/tmp/cli/usr/bin/relion_star_handler -- Installing: /<>/debian/tmp/cli/usr/bin/relion_plot_delocalisation -- Installing: /<>/debian/tmp/cli/usr/bin/relion_motion_refine_mpi -- Installing: /<>/debian/tmp/cli/usr/bin/relion_project -- Installing: /<>/debian/tmp/cli/usr/bin/relion_star_loopheader -- Installing: /<>/debian/tmp/cli/usr/bin/relion_ctf_toolbox -- Installing: /<>/debian/tmp/cli/usr/bin/relion_manualpick -- Installing: /<>/debian/tmp/cli/usr/bin/relion_image_handler -- Installing: /<>/debian/tmp/cli/usr/bin/relion_reposition -- Installing: /<>/debian/tmp/cli/usr/bin/relion_tomo_test -- Installing: /<>/debian/tmp/cli/usr/bin/relion -- Installing: /<>/debian/tmp/cli/usr/bin/relion_localsym_mpi -- Installing: /<>/debian/tmp/cli/usr/bin/relion_run_motioncorr -- Installing: /<>/debian/tmp/cli/usr/bin/relion_mrc2vtk -- Installing: /<>/debian/tmp/cli/usr/bin/relion_motion_refine -- Installing: /<>/debian/tmp/cli/usr/bin/relion_stack_create -- Installing: /<>/debian/tmp/cli/usr/bin/relion_merge_particles -- Installing: /<>/debian/tmp/cli/usr/bin/relion_autopick_mpi -- Installing: /<>/debian/tmp/cli/usr/bin/relion_refine_mpi -- Installing: /<>/debian/tmp/cli/usr/bin/relion_particle_symmetry_expand -- Installing: /<>/debian/tmp/cli/usr/bin/relion_star_plottable -- Installing: /<>/debian/tmp/cli/usr/bin/relion_pipeliner -- Installing: /<>/debian/tmp/cli/usr/bin/relion_helix_inimodel2d -- Installing: /<>/debian/tmp/cli/usr/bin/relion_reconstruct -- Installing: /<>/debian/tmp/cli/usr/bin/relion_display -- Installing: /<>/debian/tmp/cli/usr/bin/relion_preprocess -- Installing: /<>/debian/tmp/cli/usr/bin/relion_external_reconstruct -- Installing: /<>/debian/tmp/cli/usr/bin/relion_qsub.csh -- Installing: /<>/debian/tmp/cli/usr/bin/relion_ctf_mask_test -- Installing: /<>/debian/tmp/cli/usr/bin/relion_particle_FCC -- 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_0x1f20 debugedit: debian/relion/usr/bin/relion_convert_to_tiff: Unknown DWARF DW_FORM_0x1f20 2244cf69e18c82aa88fadda7fd68ed872ef75fc9 8036fd24e83c3eb228fa3c9ebb5451e712ae3b07 debugedit: debian/relion/usr/bin/relion_postprocess: Unknown DWARF DW_FORM_0x1f20 debugedit: debian/relion-gui/usr/bin/relion: Unknown DWARF DW_FORM_0x1f20 7b77fa720bde373b7434ab1990d71af3885eb3e4 3b13b32520f874e7dd09521cee1b3a7e0f5c2736 debugedit: debian/relion/usr/bin/relion_find_tiltpairs: Unknown DWARF DW_FORM_0x1f20 6d1e3afeb1c5b742de51c2896dccd6a71663af93 debugedit: debian/relion/usr/bin/relion_ctf_refine_mpi: Unknown DWARF DW_FORM_0x1f20 d4b47b88497d7adfd59fabbbb98ae849a882f26e debugedit: debian/relion-gui/usr/bin/relion_display: Unknown DWARF DW_FORM_0x1f21 4d15e70bfa09821049625c426c40af2815ecc98c debugedit: debian/relion/usr/bin/relion_tiltpair_plot: Unknown DWARF DW_FORM_0x1f20 05e251fd81246a5d8649901f8867fc59d2c5cc4d debugedit: debian/relion/usr/bin/relion_import: Unknown DWARF DW_FORM_0x1f21 e69499a189f956ab5f73ba9594b42f7813f84f28 debugedit: debian/relion/usr/bin/relion_run_ctffind_mpi: Unknown DWARF DW_FORM_0x1f20 2882b40506bb6288b35f05c2e61d550a8847bdce debugedit: debian/relion/usr/bin/relion_run_motioncorr_mpi: Unknown DWARF DW_FORM_0x1f20 d0a62468aee9377ef1f49be1a3d15da7ee9f4a2b debugedit: debian/relion/usr/bin/relion_particle_reposition: Unknown DWARF DW_FORM_0x1f21 34326c7de61ec374dee0484ffe423fc5a9b50079 debugedit: debian/relion/usr/bin/relion_mask_create: Unknown DWARF DW_FORM_0x1f20 f9a4c02e76766552f2db5b8161d7928ce35bedfb debugedit: debian/relion/usr/bin/relion_run_ctffind: Unknown DWARF DW_FORM_0x1f21 d19f0d94440e9e426f34b21358386ac339111411 debugedit: debian/relion/usr/bin/relion_postprocess_mpi: Unknown DWARF DW_FORM_0x1f20 d4c3b123f25d2148b9d6cd42e6cd36921e97961e debugedit: debian/relion/usr/bin/relion_demodulate: Unknown DWARF DW_FORM_0x1f21 85d5fde78e651c37ec9de4e1991edfde72ebbcfd debugedit: debian/relion/usr/bin/relion_helix_toolbox: Unknown DWARF DW_FORM_0x1f20 b2472b21c0de7c926d7d65ab5874987e30c46275 debugedit: debian/relion/usr/bin/relion_reconstruct_mpi: Unknown DWARF DW_FORM_0x1f21 bdaa31b0f4411aa10ed12b1c3777983acb294c56 debugedit: debian/relion/usr/bin/relion_estimate_gain: Unknown DWARF DW_FORM_0x1f20 1469ced8eb2744f47a3c90a91504b0fcc56db806 debugedit: debian/relion/usr/bin/relion_particle_subtract_mpi: Unknown DWARF DW_FORM_0x1f21 ee3f40b1974687c135d21ea0674de7ada3492bab debugedit: debian/relion/usr/bin/relion_refine: Unknown DWARF DW_FORM_0x1f21 683f550e8957b4b80c6fd8e40d765846b2c7120d debugedit: debian/relion/usr/bin/relion_flex_analyse_mpi: Unknown DWARF DW_FORM_0x1f20 77880ba6200c29c8f8ff6dca8da9c5f836dfbfc6 debugedit: debian/relion/usr/bin/relion_particle_subtract: Unknown DWARF DW_FORM_0x1f21 b9cd1196afe37528f432f9c47c3fa2e290c609e9 debugedit: debian/relion/usr/bin/relion_localsym: Unknown DWARF DW_FORM_0x1f20 dacbbe91b9a580795a2e29bd0ba416e6c375d5bc debugedit: debian/relion/usr/bin/relion_ctf_refine: Unknown DWARF DW_FORM_0x1f20 2b5ee953cf9d87afa28fbf5fd81c7bcfa4bf64ca debugedit: debian/relion/usr/bin/relion_flex_analyse: Unknown DWARF DW_FORM_0x1f20 8538231d28adac82711b8d000a057d879fef14f4 debugedit: debian/relion/usr/bin/relion_align_symmetry: Unknown DWARF DW_FORM_0x1f20 07d02abdb220a69feb9a45b9b210441a351de728 debugedit: debian/relion/usr/bin/relion_prepare_subtomo: Unknown DWARF DW_FORM_0x1f20 057f7bda22d35cd14811428ad78710c99b4a8406 debugedit: debian/relion/usr/bin/relion_scheduler: Unknown DWARF DW_FORM_0x1f20 46252e03e341a9f4515b94915a6a812457c3a18c debugedit: debian/relion/usr/bin/relion_convert_star: Unknown DWARF DW_FORM_0x1f21 6f8a75a3802c2dc8b8b4c128ae2b8fa1a8e282ca debugedit: debian/relion/usr/bin/relion_particle_select: Unknown DWARF DW_FORM_0x1f21 8af90dd6cb688f68b6c384f9890e9d9d7540f8a2 debugedit: debian/relion/usr/bin/relion_preprocess_mpi: Unknown DWARF DW_FORM_0x1f20 60a2a3d641ac6d4f7b6b78944a7aad064ec054ca debugedit: debian/relion/usr/bin/relion_convert_to_tiff_mpi: Unknown DWARF DW_FORM_0x1f20 6bf827863cdda1accaca3e2e1c34c8892b7beb9f debugedit: debian/relion/usr/bin/relion_autopick: Unknown DWARF DW_FORM_0x1f20 1eb2fde91501f5137811e40f5abf28a75f59a0ee debugedit: debian/relion/usr/bin/relion_star_handler: Unknown DWARF DW_FORM_0x1f21 4489075c5fa3afabcf8e1abbbb3502918b38f9d6 debugedit: debian/relion/usr/bin/relion_plot_delocalisation: Unknown DWARF DW_FORM_0x1f20 0c9462dda3e3ee2adb661cae00a2216abd52b017 debugedit: debian/relion/usr/bin/relion_motion_refine_mpi: Unknown DWARF DW_FORM_0x1f20 83170ae3e180450becb377708032e60767c8e941 debugedit: debian/relion/usr/bin/relion_project: Unknown DWARF DW_FORM_0x1f20 f45112bb12c9c44b8e4f91ae4ed158ed312b2ce5 debugedit: debian/relion/usr/bin/relion_ctf_toolbox: Unknown DWARF DW_FORM_0x1f21 b9a53979f3117af803147fe5e2ff1785fa5e0d80 debugedit: debian/relion/usr/bin/relion_image_handler: Unknown DWARF DW_FORM_0x1f20 0a3b98d2a91182c70d28b02dea9e37be446c1c79 debugedit: debian/relion/usr/bin/relion_reposition: Unknown DWARF DW_FORM_0x1f20 37ec571cd7df166ad996454a11bce67270f0c434 debugedit: debian/relion/usr/bin/relion_tomo_test: Unknown DWARF DW_FORM_0x1f20 aaf4238d84bb15514f458bf60a7f89347280c0e1 debugedit: debian/relion/usr/bin/relion_localsym_mpi: Unknown DWARF DW_FORM_0x1f20 b59a711d54ef5b62b6d407ea34fd884f259f2304 debugedit: debian/relion/usr/bin/relion_run_motioncorr: Unknown DWARF DW_FORM_0x1f21 729e36ce3e15aea393cdcaaafe05b3017ef53435 debugedit: debian/relion/usr/bin/relion_mrc2vtk: Unknown DWARF DW_FORM_0x1f20 73451d902c960a69fe923ed62dc96af6c44f5dc4 debugedit: debian/relion/usr/bin/relion_motion_refine: Unknown DWARF DW_FORM_0x1f21 7ff0ded08543d5c4e8d33a025e82a2195c13ba70 debugedit: debian/relion/usr/bin/relion_stack_create: Unknown DWARF DW_FORM_0x1f20 767acc421685aa8f160f4fe0299e12fe8dc3cb69 debugedit: debian/relion/usr/bin/relion_merge_particles: Unknown DWARF DW_FORM_0x1f21 2f08ee98cf55cb7cbb86e201cbb0c2e74c0128eb debugedit: debian/relion/usr/bin/relion_autopick_mpi: Unknown DWARF DW_FORM_0x1f20 8cbffbb19688dbb98f503a11b816cac501e8d5eb debugedit: debian/relion/usr/bin/relion_refine_mpi: Unknown DWARF DW_FORM_0x1f20 acbf7c06b68db63aaeb86fadcf83cac52375178c debugedit: debian/relion/usr/bin/relion_particle_symmetry_expand: Unknown DWARF DW_FORM_0x1f20 9a83d8d27f8b06f94939d97087e251ebc8276861 debugedit: debian/relion/usr/bin/relion_pipeliner: Unknown DWARF DW_FORM_0x1f20 1e704b869d403a21e19bf06b14f714ba723ab976 debugedit: debian/relion/usr/bin/relion_helix_inimodel2d: Unknown DWARF DW_FORM_0x1f20 9eeead99ff03b50b78e644c22afdf91f82434376 debugedit: debian/relion/usr/bin/relion_reconstruct: Unknown DWARF DW_FORM_0x1f20 dda8485a1077bbe4d23288534179241cfa3f73ec debugedit: debian/relion/usr/bin/relion_preprocess: Unknown DWARF DW_FORM_0x1f20 2471d7d1ea2f0e054f8c9eaacdfad5a081bf89bb debugedit: debian/relion/usr/bin/relion_external_reconstruct: Unknown DWARF DW_FORM_0x1f20 c46d02a30dbb5e3c875597891fb2c4796458555a debugedit: debian/relion/usr/bin/relion_ctf_mask_test: Unknown DWARF DW_FORM_0x1f20 b10a39a54d1f5af69c00ef77d9b4c9f52c5d9244 debugedit: debian/relion/usr/bin/relion_particle_FCC: Unknown DWARF DW_FORM_0x1f20 9249d866f609761ae268da6c4c165b12a8b45d0e dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a INFO: pkgstriptranslations version 151 INFO: pkgstriptranslations version 151 INFO: pkgstriptranslations version 151 INFO: pkgstriptranslations version 151 pkgstriptranslations: processing relion (in debian/relion); do_strip: , oemstrip: pkgstriptranslations: processing relion-gui (in debian/relion-gui); do_strip: , oemstrip: pkgstriptranslations: processing relion-gui-dbgsym (in debian/.debhelper/relion-gui/dbgsym-root); do_strip: , oemstrip: pkgstriptranslations: processing relion-dbgsym (in debian/.debhelper/relion/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: processing control file: debian/relion-gui/DEBIAN/control, package relion-gui, directory debian/relion-gui pkgstripfiles: Running PNG optimization (using 8 cpus) for package relion ... pkgstripfiles: processing control file: debian/.debhelper/relion-gui/dbgsym-root/DEBIAN/control, package relion-gui-dbgsym, directory debian/.debhelper/relion-gui/dbgsym-root INFO: pkgstripfiles: waiting for lock (relion-gui) ... pkgstripfiles: No PNG files. dpkg-deb: building package 'relion-gui-dbgsym' in 'debian/.debhelper/scratch-space/build-relion-gui/relion-gui-dbgsym_3.1.3-3build1_riscv64.deb'. dpkg-deb: building package 'relion' in '../relion_3.1.3-3build1_riscv64.deb'. 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_riscv64.deb'. Searching for duplicated docs in dependency relion... symlinking changelog.Debian.gz in relion-gui to file in relion pkgstripfiles: Running PNG optimization (using 8 cpus) for package relion-gui ... pkgstripfiles: No PNG files. dpkg-deb: building package 'relion-gui' in '../relion-gui_3.1.3-3build1_riscv64.deb'. Renaming relion-gui-dbgsym_3.1.3-3build1_riscv64.deb to relion-gui-dbgsym_3.1.3-3build1_riscv64.ddeb Renaming relion-dbgsym_3.1.3-3build1_riscv64.deb to relion-dbgsym_3.1.3-3build1_riscv64.ddeb dpkg-genbuildinfo --build=any -O../relion_3.1.3-3build1_riscv64.buildinfo dpkg-genchanges --build=any -mLaunchpad Build Daemon -O../relion_3.1.3-3build1_riscv64.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 2023-02-04T14:37:51Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ relion_3.1.3-3build1_riscv64.changes: ------------------------------------- Format: 1.8 Date: Sat, 04 Feb 2023 07:33:54 -0500 Source: relion Binary: relion relion-gui Built-For-Profiles: noudeb Architecture: riscv64 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: af473709c1710a65bc5fb56dbbe17274a2e4a969 192357886 relion-dbgsym_3.1.3-3build1_riscv64.ddeb 798213bf835747708d2215d819cb008d3f9bbf77 11868490 relion-gui-dbgsym_3.1.3-3build1_riscv64.ddeb 8470ab6943ed3d55139071a677c22b381a695367 1142216 relion-gui_3.1.3-3build1_riscv64.deb 3ca08bb993cede805287bf2860f54affaed99e5c 10973 relion_3.1.3-3build1_riscv64.buildinfo d6ffeb81c61aadc4f635177349b340c72cffc96b 12936296 relion_3.1.3-3build1_riscv64.deb Checksums-Sha256: 193d59eae6ca5a4da96fd5e5f78dfb372b2e2fde557fdf7623367d729c53a06a 192357886 relion-dbgsym_3.1.3-3build1_riscv64.ddeb 2ca61ab8f74f137dce6a26dc69f507f1b23e25200c2dc8a6ca39955b3a7594f6 11868490 relion-gui-dbgsym_3.1.3-3build1_riscv64.ddeb faa7879fea8cee76656e31323087bf4b03767d49a6a5d7fe45f3a8bf006a6a3e 1142216 relion-gui_3.1.3-3build1_riscv64.deb f95831437acb21782d578a98202447f8016a3f8ca2922b07c947266728d05fff 10973 relion_3.1.3-3build1_riscv64.buildinfo a38935869adcb3e43635f3e3842e58bab43909f73488215bd6b4205765598f19 12936296 relion_3.1.3-3build1_riscv64.deb Files: 97a17223cd9399d36dacf540a2ecf2de 192357886 debug optional relion-dbgsym_3.1.3-3build1_riscv64.ddeb 580d9c270f26614fdb3627544bfc643a 11868490 debug optional relion-gui-dbgsym_3.1.3-3build1_riscv64.ddeb b7535007dc68aa6deb512b05eb78d861 1142216 science optional relion-gui_3.1.3-3build1_riscv64.deb 87292e01bd22f33543ce8262f5a2d419 10973 science optional relion_3.1.3-3build1_riscv64.buildinfo d75c9430e77f3ccabcb644fc291da292 12936296 science optional relion_3.1.3-3build1_riscv64.deb /<>/relion_3.1.3-3build1_riscv64.changes.new could not be renamed to /<>/relion_3.1.3-3build1_riscv64.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: relion Binary: relion relion-dbgsym relion-gui relion-gui-dbgsym Architecture: riscv64 Version: 3.1.3-3build1 Checksums-Md5: 97a17223cd9399d36dacf540a2ecf2de 192357886 relion-dbgsym_3.1.3-3build1_riscv64.ddeb 580d9c270f26614fdb3627544bfc643a 11868490 relion-gui-dbgsym_3.1.3-3build1_riscv64.ddeb b7535007dc68aa6deb512b05eb78d861 1142216 relion-gui_3.1.3-3build1_riscv64.deb d75c9430e77f3ccabcb644fc291da292 12936296 relion_3.1.3-3build1_riscv64.deb Checksums-Sha1: af473709c1710a65bc5fb56dbbe17274a2e4a969 192357886 relion-dbgsym_3.1.3-3build1_riscv64.ddeb 798213bf835747708d2215d819cb008d3f9bbf77 11868490 relion-gui-dbgsym_3.1.3-3build1_riscv64.ddeb 8470ab6943ed3d55139071a677c22b381a695367 1142216 relion-gui_3.1.3-3build1_riscv64.deb d6ffeb81c61aadc4f635177349b340c72cffc96b 12936296 relion_3.1.3-3build1_riscv64.deb Checksums-Sha256: 193d59eae6ca5a4da96fd5e5f78dfb372b2e2fde557fdf7623367d729c53a06a 192357886 relion-dbgsym_3.1.3-3build1_riscv64.ddeb 2ca61ab8f74f137dce6a26dc69f507f1b23e25200c2dc8a6ca39955b3a7594f6 11868490 relion-gui-dbgsym_3.1.3-3build1_riscv64.ddeb faa7879fea8cee76656e31323087bf4b03767d49a6a5d7fe45f3a8bf006a6a3e 1142216 relion-gui_3.1.3-3build1_riscv64.deb a38935869adcb3e43635f3e3842e58bab43909f73488215bd6b4205765598f19 12936296 relion_3.1.3-3build1_riscv64.deb Build-Origin: Ubuntu Build-Architecture: riscv64 Build-Date: Sat, 04 Feb 2023 14:37:27 +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-riscv64-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), libjansson4 (= 2.14-2), libjbig-dev (= 2.1-6ubuntu1), libjbig0 (= 2.1-6ubuntu1), libjpeg-dev (= 8c-2ubuntu10), libjpeg-turbo8 (= 2.1.2-0ubuntu1), libjpeg-turbo8-dev (= 2.1.2-0ubuntu1), libjpeg8 (= 8c-2ubuntu10), libjpeg8-dev (= 8c-2ubuntu10), libjs-jquery (= 3.6.1+dfsg+~3.5.14-1), libjs-jquery-ui (= 1.13.2+dfsg-1), libjsoncpp25 (= 1.9.5-4), libk5crypto3 (= 1.20.1-1build1), libkeyutils1 (= 1.6.3-2), libkrb5-3 (= 1.20.1-1build1), libkrb5support0 (= 1.20.1-1build1), libldap2 (= 2.6.3+dfsg-1~exp1ubuntu1), liblerc-dev (= 4.0.0+ds-2ubuntu2), liblerc4 (= 4.0.0+ds-2ubuntu2), libllvm15 (= 1:15.0.7-1), 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), 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), 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="nocheck parallel=8" 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_riscv64.deb ------------------------------------ new Debian package, version 2.0. size 1142216 bytes: control archive=988 bytes. 1218 bytes, 23 lines control 308 bytes, 5 lines md5sums Package: relion-gui Source: relion Version: 3.1.3-3build1 Architecture: riscv64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 3979 Depends: relion (= 3.1.3-3build1), libc6 (>= 2.34), libfftw3-double3 (>= 3.3.5), libfltk1.3 (>= 1.3.4), libgcc-s1 (>= 3.4), 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 2228720 2023-02-04 12:33 ./usr/bin/relion -rwxr-xr-x root/root 983816 2023-02-04 12:33 ./usr/bin/relion_display -rwxr-xr-x root/root 840120 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_riscv64.deb -------------------------------- new Debian package, version 2.0. size 12936296 bytes: control archive=2659 bytes. 1233 bytes, 23 lines control 4218 bytes, 66 lines md5sums Package: relion Version: 3.1.3-3build1 Architecture: riscv64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 69723 Depends: openmpi-gcc | openmpi-bin, libc6 (>= 2.34), libfftw3-double3 (>= 3.3.5), libfftw3-single3 (>= 3.3.5), libgcc-s1 (>= 3.4), 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 700752 2023-02-04 12:33 ./usr/bin/relion_align_symmetry -rwxr-xr-x root/root 1556976 2023-02-04 12:33 ./usr/bin/relion_autopick -rwxr-xr-x root/root 1644416 2023-02-04 12:33 ./usr/bin/relion_autopick_mpi -rwxr-xr-x root/root 1118752 2023-02-04 12:33 ./usr/bin/relion_convert_star -rwxr-xr-x root/root 823800 2023-02-04 12:33 ./usr/bin/relion_convert_to_tiff -rwxr-xr-x root/root 886536 2023-02-04 12:33 ./usr/bin/relion_convert_to_tiff_mpi -rwxr-xr-x root/root 1249752 2023-02-04 12:33 ./usr/bin/relion_ctf_mask_test -rwxr-xr-x root/root 1823296 2023-02-04 12:33 ./usr/bin/relion_ctf_refine -rwxr-xr-x root/root 1906640 2023-02-04 12:33 ./usr/bin/relion_ctf_refine_mpi -rwxr-xr-x root/root 831872 2023-02-04 12:33 ./usr/bin/relion_ctf_toolbox -rwxr-xr-x root/root 1167800 2023-02-04 12:33 ./usr/bin/relion_demodulate -rwxr-xr-x root/root 643464 2023-02-04 12:33 ./usr/bin/relion_estimate_gain -rwxr-xr-x root/root 811376 2023-02-04 12:33 ./usr/bin/relion_external_reconstruct -rwxr-xr-x root/root 470928 2023-02-04 12:33 ./usr/bin/relion_find_tiltpairs -rwxr-xr-x root/root 1853288 2023-02-04 12:33 ./usr/bin/relion_flex_analyse -rwxr-xr-x root/root 1853304 2023-02-04 12:33 ./usr/bin/relion_flex_analyse_mpi -rwxr-xr-x root/root 868736 2023-02-04 12:33 ./usr/bin/relion_helix_inimodel2d -rwxr-xr-x root/root 1212896 2023-02-04 12:33 ./usr/bin/relion_helix_toolbox -rwxr-xr-x root/root 954776 2023-02-04 12:33 ./usr/bin/relion_image_handler -rwxr-xr-x root/root 803072 2023-02-04 12:33 ./usr/bin/relion_import -rwxr-xr-x root/root 1470984 2023-02-04 12:33 ./usr/bin/relion_localsym -rwxr-xr-x root/root 1611696 2023-02-04 12:33 ./usr/bin/relion_localsym_mpi -rwxr-xr-x root/root 1176016 2023-02-04 12:33 ./usr/bin/relion_mask_create -rwxr-xr-x root/root 758000 2023-02-04 12:33 ./usr/bin/relion_merge_particles -rwxr-xr-x root/root 2175688 2023-02-04 12:33 ./usr/bin/relion_motion_refine -rwxr-xr-x root/root 2259032 2023-02-04 12:33 ./usr/bin/relion_motion_refine_mpi -rwxr-xr-x root/root 577736 2023-02-04 12:33 ./usr/bin/relion_mrc2vtk -rwxr-xr-x root/root 1409560 2023-02-04 12:33 ./usr/bin/relion_particle_FCC -rwxr-xr-x root/root 2339472 2023-02-04 12:33 ./usr/bin/relion_particle_reposition -rwxr-xr-x root/root 1135032 2023-02-04 12:33 ./usr/bin/relion_particle_select -rwxr-xr-x root/root 2355856 2023-02-04 12:33 ./usr/bin/relion_particle_subtract -rwxr-xr-x root/root 2426800 2023-02-04 12:33 ./usr/bin/relion_particle_subtract_mpi -rwxr-xr-x root/root 856400 2023-02-04 12:33 ./usr/bin/relion_particle_symmetry_expand -rwxr-xr-x root/root 1101784 2023-02-04 12:33 ./usr/bin/relion_pipeliner 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root/root 968496 2023-02-04 12:33 ./usr/bin/relion_run_ctffind_mpi -rwxr-xr-x root/root 1110560 2023-02-04 12:33 ./usr/bin/relion_run_motioncorr -rwxr-xr-x root/root 1193904 2023-02-04 12:33 ./usr/bin/relion_run_motioncorr_mpi -rwxr-xr-x root/root 1614288 2023-02-04 12:33 ./usr/bin/relion_scheduler -rwxr-xr-x root/root 852352 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 901432 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 520128 2023-02-04 12:33 ./usr/bin/relion_tiltpair_plot -rwxr-xr-x root/root 1089904 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: riscv64 Build Type: any Build-Space: 4200036 Build-Time: 5073 Distribution: lunar-proposed Host Architecture: riscv64 Install-Time: 363 Job: relion_3.1.3-3build1.dsc Machine Architecture: riscv64 Package: relion Package-Time: 5466 Source-Version: 3.1.3-3build1 Space: 4200036 Status: successful Version: 3.1.3-3build1 -------------------------------------------------------------------------------- Finished at 2023-02-04T14:37:51Z Build needed 01:31:06, 4200036k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=lunar --arch=riscv64 PACKAGEBUILD-25549283 Scanning for processes to kill in build PACKAGEBUILD-25549283 RUN: /usr/share/launchpad-buildd/bin/in-target umount-chroot --backend=chroot --series=lunar --arch=riscv64 PACKAGEBUILD-25549283 Stopping target for build PACKAGEBUILD-25549283 RUN: /usr/share/launchpad-buildd/bin/in-target remove-build --backend=chroot --series=lunar --arch=riscv64 PACKAGEBUILD-25549283 Removing build PACKAGEBUILD-25549283