https://launchpad.net/ubuntu/+source/relion-cuda/3.1.3-1/+build/24619634 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux lcy02-amd64-007 5.4.0-131-generic #147-Ubuntu SMP Fri Oct 14 17:07:22 UTC 2022 x86_64 Buildd toolchain package versions: launchpad-buildd_223~593~ubuntu20.04.1 python3-lpbuildd_223~593~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.6 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1. Syncing the system clock with the buildd NTP service... 6 Nov 07:56:23 ntpdate[1767]: adjust time server 10.131.248.1 offset -0.001460 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=lunar --arch=amd64 PACKAGEBUILD-24619634 --image-type chroot /home/buildd/filecache-default/93056656ffca866e6c2a454f453b424a388b800f Creating target for build PACKAGEBUILD-24619634 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=lunar --arch=amd64 PACKAGEBUILD-24619634 Starting target for build PACKAGEBUILD-24619634 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=lunar --arch=amd64 PACKAGEBUILD-24619634 'deb http://ftpmaster.internal/ubuntu lunar main restricted universe multiverse' 'deb http://ftpmaster.internal/ubuntu lunar-security main restricted universe multiverse' 'deb http://ftpmaster.internal/ubuntu lunar-updates main restricted universe multiverse' 'deb http://ftpmaster.internal/ubuntu lunar-proposed main restricted universe multiverse' Overriding sources.list in build-PACKAGEBUILD-24619634 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=lunar --arch=amd64 PACKAGEBUILD-24619634 Updating target for build PACKAGEBUILD-24619634 Get:1 http://ftpmaster.internal/ubuntu lunar InRelease [224 kB] Get:2 http://ftpmaster.internal/ubuntu lunar-security InRelease [74.9 kB] Get:3 http://ftpmaster.internal/ubuntu lunar-updates InRelease [74.9 kB] Get:4 http://ftpmaster.internal/ubuntu lunar-proposed InRelease [74.9 kB] Get:5 http://ftpmaster.internal/ubuntu lunar/main amd64 Packages [1390 kB] Get:6 http://ftpmaster.internal/ubuntu lunar/main Translation-en [510 kB] Get:7 http://ftpmaster.internal/ubuntu lunar/restricted amd64 Packages [124 kB] Get:8 http://ftpmaster.internal/ubuntu lunar/restricted Translation-en [18.2 kB] Get:9 http://ftpmaster.internal/ubuntu lunar/universe amd64 Packages [14.5 MB] Get:10 http://ftpmaster.internal/ubuntu lunar/universe Translation-en [5791 kB] Get:11 http://ftpmaster.internal/ubuntu lunar/multiverse amd64 Packages [236 kB] Get:12 http://ftpmaster.internal/ubuntu lunar/multiverse Translation-en [112 kB] Get:13 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 Packages [374 kB] Get:14 http://ftpmaster.internal/ubuntu lunar-proposed/main Translation-en [141 kB] Get:15 http://ftpmaster.internal/ubuntu lunar-proposed/restricted amd64 Packages [69.6 kB] Get:16 http://ftpmaster.internal/ubuntu lunar-proposed/restricted Translation-en [12.8 kB] Get:17 http://ftpmaster.internal/ubuntu lunar-proposed/universe amd64 Packages [2311 kB] Get:18 http://ftpmaster.internal/ubuntu lunar-proposed/universe Translation-en [1000 kB] Get:19 http://ftpmaster.internal/ubuntu lunar-proposed/multiverse amd64 Packages [2448 B] Get:20 http://ftpmaster.internal/ubuntu lunar-proposed/multiverse Translation-en [1932 B] Fetched 27.0 MB in 2s (11.6 MB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libperl5.34 perl-modules-5.34 sgml-base Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: libperl5.36 perl-modules-5.36 The following packages will be upgraded: apt base-files base-passwd bash binutils binutils-common binutils-x86-64-linux-gnu cpp-12 debianutils fakeroot g++-12 gcc-12 gcc-12-base gpg gpg-agent gpgconf gpgv grep init init-system-helpers libapparmor1 libapt-pkg6.0 libasan8 libassuan0 libatomic1 libaudit-common libaudit1 libbinutils libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcc1-0 libcrypt-dev libcrypt1 libctf-nobfd0 libctf0 libfakeroot libffi8 libgcc-12-dev libgcc-s1 libgdbm-compat4 libgdbm6 libgnutls30 libgomp1 libgpg-error0 libgprofng0 libidn2-0 libitm1 libjson-c5 liblsan0 liblz4-1 liblzma5 libp11-kit0 libpng16-16 libquadmath0 libreadline8 libseccomp2 libselinux1 libsemanage-common libsemanage2 libsqlite3-0 libstdc++-12-dev libstdc++6 libsystemd-shared libsystemd0 libtasn1-6 libtsan2 libubsan1 libudev1 libunistring2 linux-libc-dev lto-disabled-list perl perl-base readline-common sgml-base systemd systemd-sysv tzdata usrmerge xz-utils zlib1g 84 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 92.2 MB of archives. After this operation, 47.4 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libcrypt-dev amd64 1:4.4.30-1 [112 kB] Get:2 http://ftpmaster.internal/ubuntu lunar/main amd64 libc6-dev amd64 2.36-0ubuntu4 [2088 kB] Get:3 http://ftpmaster.internal/ubuntu lunar/main amd64 libc-dev-bin amd64 2.36-0ubuntu4 [20.0 kB] Get:4 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libcrypt1 amd64 1:4.4.30-1 [80.7 kB] Get:5 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 linux-libc-dev amd64 5.19.0-23.24 [1345 kB] Get:6 http://ftpmaster.internal/ubuntu lunar/main amd64 libcc1-0 amd64 12.2.0-9ubuntu1 [46.4 kB] Get:7 http://ftpmaster.internal/ubuntu lunar/main amd64 gcc-12-base amd64 12.2.0-9ubuntu1 [19.5 kB] Get:8 http://ftpmaster.internal/ubuntu lunar/main amd64 libgcc-s1 amd64 12.2.0-9ubuntu1 [54.2 kB] Get:9 http://ftpmaster.internal/ubuntu lunar/main amd64 libgomp1 amd64 12.2.0-9ubuntu1 [125 kB] Get:10 http://ftpmaster.internal/ubuntu lunar/main amd64 libitm1 amd64 12.2.0-9ubuntu1 [29.4 kB] Get:11 http://ftpmaster.internal/ubuntu lunar/main amd64 libatomic1 amd64 12.2.0-9ubuntu1 [10.4 kB] Get:12 http://ftpmaster.internal/ubuntu lunar/main amd64 libasan8 amd64 12.2.0-9ubuntu1 [2433 kB] Get:13 http://ftpmaster.internal/ubuntu lunar/main amd64 liblsan0 amd64 12.2.0-9ubuntu1 [1060 kB] Get:14 http://ftpmaster.internal/ubuntu lunar/main amd64 libtsan2 amd64 12.2.0-9ubuntu1 [2456 kB] Get:15 http://ftpmaster.internal/ubuntu lunar/main amd64 libubsan1 amd64 12.2.0-9ubuntu1 [969 kB] Get:16 http://ftpmaster.internal/ubuntu lunar/main amd64 libquadmath0 amd64 12.2.0-9ubuntu1 [152 kB] Get:17 http://ftpmaster.internal/ubuntu lunar/main amd64 g++-12 amd64 12.2.0-9ubuntu1 [12.0 MB] Get:18 http://ftpmaster.internal/ubuntu lunar/main amd64 libstdc++-12-dev amd64 12.2.0-9ubuntu1 [2158 kB] Get:19 http://ftpmaster.internal/ubuntu lunar/main amd64 libgcc-12-dev amd64 12.2.0-9ubuntu1 [2577 kB] Get:20 http://ftpmaster.internal/ubuntu lunar/main amd64 gcc-12 amd64 12.2.0-9ubuntu1 [21.4 MB] Get:21 http://ftpmaster.internal/ubuntu lunar/main amd64 cpp-12 amd64 12.2.0-9ubuntu1 [10.6 MB] Get:22 http://ftpmaster.internal/ubuntu lunar/main amd64 libstdc++6 amd64 12.2.0-9ubuntu1 [678 kB] Get:23 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 zlib1g amd64 1:1.2.11.dfsg-4.1ubuntu2 [58.8 kB] Get:24 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libgprofng0 amd64 2.39-8ubuntu2 [897 kB] Get:25 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libctf0 amd64 2.39-8ubuntu2 [97.4 kB] Get:26 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libctf-nobfd0 amd64 2.39-8ubuntu2 [99.9 kB] Get:27 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libbinutils amd64 2.39-8ubuntu2 [610 kB] Get:28 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 binutils-common amd64 2.39-8ubuntu2 [233 kB] Get:29 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 binutils amd64 2.39-8ubuntu2 [3240 B] Get:30 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 binutils-x86-64-linux-gnu amd64 2.39-8ubuntu2 [2402 kB] Get:31 http://ftpmaster.internal/ubuntu lunar/main amd64 libc6 amd64 2.36-0ubuntu4 [3163 kB] Get:32 http://ftpmaster.internal/ubuntu lunar/main amd64 base-files amd64 12.3ubuntu1 [73.4 kB] Get:33 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 debianutils amd64 5.7-0.4 [103 kB] Get:34 http://ftpmaster.internal/ubuntu lunar/main amd64 bash amd64 5.2-1ubuntu2 [788 kB] Get:35 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 grep amd64 3.8-3 [159 kB] Get:36 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 perl-modules-5.36 all 5.36.0-4ubuntu2 [2984 kB] Get:37 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libperl5.36 amd64 5.36.0-4ubuntu2 [4808 kB] Get:38 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 perl amd64 5.36.0-4ubuntu2 [235 kB] Get:39 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 perl-base amd64 5.36.0-4ubuntu2 [1779 kB] Get:40 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libgdbm6 amd64 1.23-3 [33.2 kB] Get:41 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libgdbm-compat4 amd64 1.23-3 [6524 B] Get:42 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libselinux1 amd64 3.4-1build1 [77.9 kB] Get:43 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 base-passwd amd64 3.6.1 [49.9 kB] Get:44 http://ftpmaster.internal/ubuntu lunar/main amd64 usrmerge all 29ubuntu2 [55.8 kB] Get:45 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 init-system-helpers all 1.65.2 [38.1 kB] Get:46 http://ftpmaster.internal/ubuntu lunar/main amd64 libc-bin amd64 2.36-0ubuntu4 [675 kB] Get:47 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 liblz4-1 amd64 1.9.4-1 [63.1 kB] Get:48 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 liblzma5 amd64 5.2.7-0.1 [101 kB] Get:49 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libapparmor1 amd64 3.0.7-1ubuntu3 [36.8 kB] Get:50 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libaudit-common all 1:3.0.7-1ubuntu2 [5018 B] Get:51 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libcap-ng0 amd64 0.8.3-1build1 [15.2 kB] Get:52 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libaudit1 amd64 1:3.0.7-1ubuntu2 [45.4 kB] Get:53 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libseccomp2 amd64 2.5.4-1ubuntu2 [46.2 kB] Get:54 http://ftpmaster.internal/ubuntu lunar/main amd64 systemd-sysv amd64 251.4-1ubuntu7 [11.2 kB] Get:55 http://ftpmaster.internal/ubuntu lunar/main amd64 systemd amd64 251.4-1ubuntu7 [2808 kB] Get:56 http://ftpmaster.internal/ubuntu lunar/main amd64 libsystemd-shared amd64 251.4-1ubuntu7 [1703 kB] Get:57 http://ftpmaster.internal/ubuntu lunar/main amd64 libsystemd0 amd64 251.4-1ubuntu7 [323 kB] Get:58 http://ftpmaster.internal/ubuntu lunar/main amd64 libudev1 amd64 251.4-1ubuntu7 [79.8 kB] Get:59 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libapt-pkg6.0 amd64 2.5.4 [902 kB] Get:60 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libgpg-error0 amd64 1.46-1 [68.9 kB] Get:61 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 gpgv amd64 2.2.40-1ubuntu1 [137 kB] Get:62 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libunistring2 amd64 1.0-2 [536 kB] Get:63 http://ftpmaster.internal/ubuntu lunar/main amd64 libidn2-0 amd64 2.3.3-1build1 [62.9 kB] Get:64 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libffi8 amd64 3.4.4-1 [23.8 kB] Get:65 http://ftpmaster.internal/ubuntu lunar/main amd64 libp11-kit0 amd64 0.24.1-1ubuntu2 [246 kB] Get:66 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libtasn1-6 amd64 4.19.0-2 [43.9 kB] Get:67 http://ftpmaster.internal/ubuntu lunar/main amd64 libgnutls30 amd64 3.7.7-2ubuntu2 [976 kB] Get:68 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 apt amd64 2.5.4 [1378 kB] Get:69 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 init amd64 1.65.2 [4808 B] Get:70 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 sgml-base all 1.31 [11.4 kB] Get:71 http://ftpmaster.internal/ubuntu lunar/main amd64 libsemanage-common all 3.4-1build1 [9544 B] Get:72 http://ftpmaster.internal/ubuntu lunar/main amd64 libsemanage2 amd64 3.4-1build1 [93.2 kB] Get:73 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libjson-c5 amd64 0.16-2 [32.8 kB] Get:74 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 readline-common all 8.2-1.1 [55.1 kB] Get:75 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libreadline8 amd64 8.2-1.1 [150 kB] Get:76 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libsqlite3-0 amd64 3.39.4-1 [656 kB] Get:77 http://ftpmaster.internal/ubuntu lunar/main amd64 tzdata all 2022f-0ubuntu1 [400 kB] Get:78 http://ftpmaster.internal/ubuntu lunar/main amd64 libpng16-16 amd64 1.6.38-2 [186 kB] Get:79 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 xz-utils amd64 5.2.7-0.1 [142 kB] Get:80 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libfakeroot amd64 1.30.1-1ubuntu1 [30.9 kB] Get:81 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 fakeroot amd64 1.30.1-1ubuntu1 [60.1 kB] Get:82 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libassuan0 amd64 2.5.5-5 [37.2 kB] Get:83 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 gpg amd64 2.2.40-1ubuntu1 [523 kB] Get:84 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 gpgconf amd64 2.2.40-1ubuntu1 [93.8 kB] Get:85 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 gpg-agent amd64 2.2.40-1ubuntu1 [217 kB] Get:86 http://ftpmaster.internal/ubuntu lunar/main amd64 lto-disabled-list all 35 [12.2 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 92.2 MB in 1s (149 MB/s) (Reading database ... 13569 files and directories currently installed.) 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Setting up binutils-x86-64-linux-gnu (2.39-8ubuntu2) ... Setting up gpg-agent (2.2.40-1ubuntu1) ... Setting up libstdc++-12-dev:amd64 (12.2.0-9ubuntu1) ... Setting up binutils (2.39-8ubuntu2) ... Setting up perl (5.36.0-4ubuntu2) ... Setting up gcc-12 (12.2.0-9ubuntu1) ... Setting up g++-12 (12.2.0-9ubuntu1) ... Processing triggers for debianutils (5.7-0.4) ... Processing triggers for libc-bin (2.36-0ubuntu4) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-24619634 amd64 lunar-proposed -c chroot:build-PACKAGEBUILD-24619634 --arch=amd64 --dist=lunar-proposed --nolog -A relion-cuda_3.1.3-1.dsc Initiating build PACKAGEBUILD-24619634 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-131-generic #147-Ubuntu SMP Fri Oct 14 17:07:22 UTC 2022 x86_64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on lcy02-amd64-007.buildd +==============================================================================+ | relion-cuda 3.1.3-1 (amd64) Sun, 06 Nov 2022 07:56:41 +0000 | +==============================================================================+ Package: relion-cuda Version: 3.1.3-1 Source Version: 3.1.3-1 Distribution: lunar-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: binary I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-24619634/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/relion-cuda-xjHFRg/resolver-uJupsd' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- relion-cuda_3.1.3-1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/relion-cuda-xjHFRg/relion-cuda-3.1.3' with '<>' I: NOTICE: Log filtering will replace 'build/relion-cuda-xjHFRg' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: cmake, debhelper-compat (= 13), libfftw3-dev, libfltk1.3-dev, libopenmpi-dev, libtiff-dev, nvidia-cuda-toolkit-gcc, fluid, build-essential, fakeroot Filtered Build-Depends: cmake, debhelper-compat (= 13), libfftw3-dev, libfltk1.3-dev, libopenmpi-dev, libtiff-dev, nvidia-cuda-toolkit-gcc, 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 [421 B] Get:5 copy:/<>/apt_archive ./ Packages [503 B] Fetched 1881 B in 0s (0 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libperl5.34 perl-modules-5.34 Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils cmake cmake-data cpp-10 debhelper debugedit dh-autoreconf dh-elpa-helper dh-strip-nondeterminism dwz emacsen-common file fluid fontconfig-config fonts-dejavu-core g++-10 gcc-10 gcc-10-base gcc-11-base gettext gettext-base gfortran-12 groff-base ibverbs-providers intltool-debian libaccinj64-11.5 libarchive-zip-perl libarchive13 libasan6 libbrotli1 libbsd0 libcairo2 libcbor0.8 libcub-dev libcublas11 libcublaslt11 libcudart11.0 libcufft10 libcufftw10 libcuinj64-11.5 libcupti-dev libcupti11.5 libcurand10 libcurl3-gnutls libcurl4 libcusolver11 libcusolvermg11 libcusparse11 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-quad3 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 libgcc-10-dev 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 libldap-2.5-0 liblerc-dev liblerc3 libllvm15 libltdl-dev libltdl7 liblzma-dev libmagic-mgc libmagic1 libmd0 libnghttp2-14 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnppc11 libnppial11 libnppicc11 libnppidei11 libnppif11 libnppig11 libnppim11 libnppist11 libnppisu11 libnppitc11 libnpps11 libnuma-dev libnuma1 libnvblas11 libnvidia-compute-510 libnvidia-ml-dev libnvjpeg11 libnvrtc-builtins11.5 libnvrtc11.2 libnvtoolsext1 libnvvm4 libopenmpi-dev libopenmpi3 libpciaccess0 libpipeline1 libpixman-1-0 libpmix-dev libpmix2 libpsl5 libpsm-infinipath1 libpsm2-2 libpthread-stubs0-dev librdmacm1 librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libssh-4 libstdc++-10-dev libsub-override-perl libthrust-dev libtiff-dev libtiff5 libtiffxx5 libtool libtsan0 libuchardet0 libucx0 libuv1 libwebp7 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 m4 man-db nvidia-cuda-dev nvidia-cuda-toolkit nvidia-cuda-toolkit-gcc nvidia-opencl-dev nvidia-profiler ocl-icd-libopencl1 ocl-icd-opencl-dev opencl-c-headers opencl-clhpp-headers openmpi-bin openmpi-common openssh-client po-debconf ucf x11proto-dev xorg-sgml-doctools xtrans-dev zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc cmake-doc ninja-build cmake-format gcc-10-locales dh-make g++-10-multilib gcc-10-doc gcc-10-multilib gettext-doc libasprintf-dev libgettextpo-dev gfortran-12-multilib gfortran-12-doc libcoarrays-dev groff lrzip libfftw3-doc fltk1.3-doc libcairo2-dev libpng-dev libxext-dev libxft-dev libxinerama-dev libhwloc-contrib-plugins libjs-jquery-ui-docs libtool-doc liblzma-doc openmpi-doc pciutils lm-sensors libstdc++-10-doc gcj-jdk libx11-doc libxcb-doc m4-doc apparmor less www-browser opencl-clhpp-headers-doc gfortran | fortran-compiler keychain libpam-ssh monkeysphere ssh-askpass libmail-box-perl Recommended packages: fltk1.3-doc curl | wget | lynx libcupti-doc libarchive-cpio-perl libgl-dev libglu1-mesa-dev | libglu-dev libgl1-amber-dri javascript-common libldap-common libcoarrays-openmpi-dev publicsuffix libsasl2-modules libtbb-dev libgl1-mesa-dev | libgl-dev libvdpau-dev libnvcuvid1 nvidia-cuda-toolkit-doc nvidia-cuda-gdb nvidia-visual-profiler nsight-compute nsight-systems xauth libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils cmake cmake-data cpp-10 debhelper debugedit dh-autoreconf dh-elpa-helper dh-strip-nondeterminism dwz emacsen-common file fluid fontconfig-config fonts-dejavu-core g++-10 gcc-10 gcc-10-base gcc-11-base gettext gettext-base gfortran-12 groff-base ibverbs-providers intltool-debian libaccinj64-11.5 libarchive-zip-perl libarchive13 libasan6 libbrotli1 libbsd0 libcairo2 libcbor0.8 libcub-dev libcublas11 libcublaslt11 libcudart11.0 libcufft10 libcufftw10 libcuinj64-11.5 libcupti-dev libcupti11.5 libcurand10 libcurl3-gnutls libcurl4 libcusolver11 libcusolvermg11 libcusparse11 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-quad3 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 libgcc-10-dev 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 libldap-2.5-0 liblerc-dev liblerc3 libllvm15 libltdl-dev libltdl7 liblzma-dev libmagic-mgc libmagic1 libmd0 libnghttp2-14 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnppc11 libnppial11 libnppicc11 libnppidei11 libnppif11 libnppig11 libnppim11 libnppist11 libnppisu11 libnppitc11 libnpps11 libnuma-dev libnuma1 libnvblas11 libnvidia-compute-510 libnvidia-ml-dev libnvjpeg11 libnvrtc-builtins11.5 libnvrtc11.2 libnvtoolsext1 libnvvm4 libopenmpi-dev libopenmpi3 libpciaccess0 libpipeline1 libpixman-1-0 libpmix-dev libpmix2 libpsl5 libpsm-infinipath1 libpsm2-2 libpthread-stubs0-dev librdmacm1 librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libssh-4 libstdc++-10-dev libsub-override-perl libthrust-dev libtiff-dev libtiff5 libtiffxx5 libtool libtsan0 libuchardet0 libucx0 libuv1 libwebp7 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 m4 man-db nvidia-cuda-dev nvidia-cuda-toolkit nvidia-cuda-toolkit-gcc nvidia-opencl-dev nvidia-profiler ocl-icd-libopencl1 ocl-icd-opencl-dev opencl-c-headers opencl-clhpp-headers openmpi-bin openmpi-common openssh-client po-debconf sbuild-build-depends-main-dummy ucf x11proto-dev xorg-sgml-doctools xtrans-dev zlib1g-dev 0 upgraded, 228 newly installed, 0 to remove and 0 not upgraded. Need to get 1549 MB of archives. After this operation, 4554 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [724 B] Get:2 http://ftpmaster.internal/ubuntu lunar/main amd64 libmd0 amd64 1.0.4-2 [22.7 kB] Get:3 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libbsd0 amd64 0.11.7-1 [43.9 kB] Get:4 http://ftpmaster.internal/ubuntu lunar/main amd64 libelf1 amd64 0.187-4 [50.9 kB] Get:5 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libexpat1 amd64 2.5.0-1 [84.2 kB] Get:6 http://ftpmaster.internal/ubuntu lunar/main amd64 libicu71 amd64 71.1-3ubuntu1 [10.6 MB] Get:7 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libxml2 amd64 2.9.14+dfsg-1.1 [762 kB] Get:8 http://ftpmaster.internal/ubuntu lunar/main amd64 ucf all 3.0043 [56.1 kB] Get:9 http://ftpmaster.internal/ubuntu lunar/main amd64 bsdextrautils amd64 2.38-4ubuntu1 [71.1 kB] Get:10 http://ftpmaster.internal/ubuntu lunar/main amd64 libmagic-mgc amd64 1:5.41-4 [257 kB] Get:11 http://ftpmaster.internal/ubuntu lunar/main amd64 libmagic1 amd64 1:5.41-4 [87.3 kB] Get:12 http://ftpmaster.internal/ubuntu lunar/main amd64 file amd64 1:5.41-4 [21.5 kB] Get:13 http://ftpmaster.internal/ubuntu lunar/main amd64 gettext-base amd64 0.21-8 [37.8 kB] Get:14 http://ftpmaster.internal/ubuntu lunar/main amd64 libuchardet0 amd64 0.0.7-1build2 [76.9 kB] Get:15 http://ftpmaster.internal/ubuntu lunar/main amd64 groff-base amd64 1.22.4-8build1 [955 kB] Get:16 http://ftpmaster.internal/ubuntu lunar/main amd64 libcbor0.8 amd64 0.8.0-2ubuntu1 [24.6 kB] Get:17 http://ftpmaster.internal/ubuntu lunar/main amd64 libdrm-common all 2.4.113-2 [5324 B] Get:18 http://ftpmaster.internal/ubuntu lunar/main amd64 libdrm2 amd64 2.4.113-2 [38.3 kB] Get:19 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libedit2 amd64 3.1-20221030-1 [95.2 kB] Get:20 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libfido2-1 amd64 1.12.0-1 [84.7 kB] Get:21 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libnghttp2-14 amd64 1.50.0-1 [73.7 kB] Get:22 http://ftpmaster.internal/ubuntu lunar/main amd64 libnuma1 amd64 2.0.14-3ubuntu2 [22.5 kB] Get:23 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libpipeline1 amd64 1.5.6-3 [23.4 kB] Get:24 http://ftpmaster.internal/ubuntu lunar/main amd64 libpsl5 amd64 0.21.0-1.2build2 [58.4 kB] Get:25 http://ftpmaster.internal/ubuntu lunar/main amd64 libuv1 amd64 1.44.2-1 [91.0 kB] Get:26 http://ftpmaster.internal/ubuntu lunar/main amd64 libxau6 amd64 1:1.0.9-1build5 [7634 B] Get:27 http://ftpmaster.internal/ubuntu lunar/main amd64 libxdmcp6 amd64 1:1.1.3-0ubuntu5 [10.9 kB] Get:28 http://ftpmaster.internal/ubuntu lunar/main amd64 libxcb1 amd64 1.15-1 [48.0 kB] Get:29 http://ftpmaster.internal/ubuntu lunar/main amd64 libx11-data all 2:1.8.1-2 [118 kB] Get:30 http://ftpmaster.internal/ubuntu lunar/main amd64 libx11-6 amd64 2:1.8.1-2 [650 kB] Get:31 http://ftpmaster.internal/ubuntu lunar/main amd64 libxext6 amd64 2:1.3.4-1build1 [31.8 kB] Get:32 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 man-db amd64 2.11.0-1 [1182 kB] Get:33 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 openssh-client amd64 1:9.0p1-1ubuntu8 [876 kB] Get:34 http://ftpmaster.internal/ubuntu lunar/main amd64 m4 amd64 1.4.19-1 [244 kB] Get:35 http://ftpmaster.internal/ubuntu lunar/main amd64 autoconf all 2.71-2 [338 kB] Get:36 http://ftpmaster.internal/ubuntu lunar/main amd64 autotools-dev all 20220109.1 [44.9 kB] Get:37 http://ftpmaster.internal/ubuntu lunar/main amd64 automake all 1:1.16.5-1.3 [558 kB] Get:38 http://ftpmaster.internal/ubuntu lunar/main amd64 autopoint all 0.21-8 [421 kB] Get:39 http://ftpmaster.internal/ubuntu lunar/main amd64 libarchive13 amd64 3.6.0-1ubuntu1 [368 kB] Get:40 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libbrotli1 amd64 1.0.9-2build7 [309 kB] Get:41 http://ftpmaster.internal/ubuntu lunar/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-6ubuntu2 [20.3 kB] Get:42 http://ftpmaster.internal/ubuntu lunar/main amd64 libsasl2-2 amd64 2.1.28+dfsg-6ubuntu2 [56.6 kB] Get:43 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-1ubuntu2 [184 kB] Get:44 http://ftpmaster.internal/ubuntu lunar/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2build4 [58.2 kB] Get:45 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libssh-4 amd64 0.10.4-2 [185 kB] Get:46 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libcurl4 amd64 7.86.0-1 [293 kB] Get:47 http://ftpmaster.internal/ubuntu lunar/main amd64 libjsoncpp25 amd64 1.9.5-4 [80.3 kB] Get:48 http://ftpmaster.internal/ubuntu lunar/main amd64 librhash0 amd64 1.4.2-1ubuntu1 [125 kB] Get:49 http://ftpmaster.internal/ubuntu lunar/main amd64 dh-elpa-helper all 2.0.9ubuntu1 [7610 B] Get:50 http://ftpmaster.internal/ubuntu lunar/main amd64 emacsen-common all 3.0.4 [14.9 kB] Get:51 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 cmake-data all 3.24.3-1ubuntu1 [2025 kB] Get:52 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 cmake amd64 3.24.3-1ubuntu1 [8979 kB] Get:53 http://ftpmaster.internal/ubuntu lunar/universe amd64 gcc-10-base amd64 10.4.0-5ubuntu2 [20.1 kB] Get:54 http://ftpmaster.internal/ubuntu lunar/universe amd64 cpp-10 amd64 10.4.0-5ubuntu2 [9296 kB] Get:55 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libdebhelper-perl all 13.10.1ubuntu1 [67.1 kB] Get:56 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 gcc-11-base amd64 11.3.0-9ubuntu1 [20.1 kB] Get:57 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libasan6 amd64 11.3.0-9ubuntu1 [2259 kB] Get:58 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libtsan0 amd64 11.3.0-9ubuntu1 [2245 kB] Get:59 http://ftpmaster.internal/ubuntu lunar/universe amd64 libgcc-10-dev amd64 10.4.0-5ubuntu2 [2456 kB] Get:60 http://ftpmaster.internal/ubuntu lunar/universe amd64 gcc-10 amd64 10.4.0-5ubuntu2 [18.9 MB] Get:61 http://ftpmaster.internal/ubuntu lunar/main amd64 libtool all 2.4.7-4 [166 kB] Get:62 http://ftpmaster.internal/ubuntu lunar/main amd64 dh-autoreconf all 20 [16.1 kB] Get:63 http://ftpmaster.internal/ubuntu lunar/main amd64 libarchive-zip-perl all 1.68-1 [90.2 kB] Get:64 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libsub-override-perl all 0.09-4 [8706 B] Get:65 http://ftpmaster.internal/ubuntu lunar/main amd64 libfile-stripnondeterminism-perl all 1.13.0-1 [18.1 kB] Get:66 http://ftpmaster.internal/ubuntu lunar/main amd64 dh-strip-nondeterminism all 1.13.0-1 [5344 B] Get:67 http://ftpmaster.internal/ubuntu lunar/main amd64 libdw1 amd64 0.187-4 [248 kB] Get:68 http://ftpmaster.internal/ubuntu lunar/main amd64 debugedit amd64 1:5.0-5 [46.1 kB] Get:69 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 dwz amd64 0.14+20220924-2 [112 kB] Get:70 http://ftpmaster.internal/ubuntu lunar/main amd64 gettext amd64 0.21-8 [867 kB] Get:71 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] Get:72 http://ftpmaster.internal/ubuntu lunar/main amd64 po-debconf all 1.0.21+nmu1 [233 kB] Get:73 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 debhelper all 13.10.1ubuntu1 [924 kB] Get:74 http://ftpmaster.internal/ubuntu lunar/main amd64 libfreetype6 amd64 2.12.1+dfsg-3 [387 kB] Get:75 http://ftpmaster.internal/ubuntu lunar/main amd64 fonts-dejavu-core all 2.37-2build1 [1041 kB] Get:76 http://ftpmaster.internal/ubuntu lunar/main amd64 fontconfig-config all 2.13.1-4.4ubuntu1 [28.2 kB] Get:77 http://ftpmaster.internal/ubuntu lunar/main amd64 libfontconfig1 amd64 2.13.1-4.4ubuntu1 [129 kB] Get:78 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libxfixes3 amd64 1:6.0.0-2 [10.9 kB] Get:79 http://ftpmaster.internal/ubuntu lunar/main amd64 libxrender1 amd64 1:0.9.10-1.1 [20.0 kB] Get:80 http://ftpmaster.internal/ubuntu lunar/main amd64 libxcursor1 amd64 1:1.2.1-1 [21.4 kB] Get:81 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libxft2 amd64 2.3.6-1 [44.5 kB] Get:82 http://ftpmaster.internal/ubuntu lunar/main amd64 libxinerama1 amd64 2:1.1.4-3 [7382 B] Get:83 http://ftpmaster.internal/ubuntu lunar-proposed/universe amd64 libfltk1.3 amd64 1.3.8-5 [606 kB] Get:84 http://ftpmaster.internal/ubuntu lunar-proposed/universe amd64 libfltk-forms1.3 amd64 1.3.8-5 [13.8 kB] Get:85 http://ftpmaster.internal/ubuntu lunar/main amd64 libjpeg-turbo8 amd64 2.1.2-0ubuntu1 [134 kB] Get:86 http://ftpmaster.internal/ubuntu lunar/main amd64 libjpeg8 amd64 8c-2ubuntu10 [2264 B] Get:87 http://ftpmaster.internal/ubuntu lunar-proposed/universe amd64 libfltk-images1.3 amd64 1.3.8-5 [27.8 kB] Get:88 http://ftpmaster.internal/ubuntu lunar-proposed/universe amd64 fluid amd64 1.3.8-5 [208 kB] Get:89 http://ftpmaster.internal/ubuntu lunar/universe amd64 libstdc++-10-dev amd64 10.4.0-5ubuntu2 [1863 kB] Get:90 http://ftpmaster.internal/ubuntu lunar/universe amd64 g++-10 amd64 10.4.0-5ubuntu2 [10.5 MB] Get:91 http://ftpmaster.internal/ubuntu lunar/main amd64 libgfortran5 amd64 12.2.0-9ubuntu1 [875 kB] Get:92 http://ftpmaster.internal/ubuntu lunar/main amd64 libgfortran-12-dev amd64 12.2.0-9ubuntu1 [929 kB] Get:93 http://ftpmaster.internal/ubuntu lunar/main amd64 gfortran-12 amd64 12.2.0-9ubuntu1 [11.1 MB] Get:94 http://ftpmaster.internal/ubuntu lunar/main amd64 libnl-3-200 amd64 3.7.0-0.2 [57.4 kB] Get:95 http://ftpmaster.internal/ubuntu lunar/main amd64 libnl-route-3-200 amd64 3.7.0-0.2 [189 kB] Get:96 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libibverbs1 amd64 43.0-1 [67.2 kB] Get:97 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 ibverbs-providers amd64 43.0-1 [360 kB] Get:98 http://ftpmaster.internal/ubuntu lunar/multiverse amd64 libcupti11.5 amd64 11.5.114~11.5.2-1ubuntu1 [7582 kB] Get:99 http://ftpmaster.internal/ubuntu lunar/multiverse amd64 libaccinj64-11.5 amd64 11.5.114~11.5.2-1ubuntu1 [838 kB] Get:100 http://ftpmaster.internal/ubuntu lunar/main amd64 libpixman-1-0 amd64 0.40.0-1build4 [264 kB] Get:101 http://ftpmaster.internal/ubuntu lunar/main amd64 libxcb-render0 amd64 1.15-1 [16.3 kB] Get:102 http://ftpmaster.internal/ubuntu lunar/main amd64 libxcb-shm0 amd64 1.15-1 [5740 B] Get:103 http://ftpmaster.internal/ubuntu lunar/main amd64 libcairo2 amd64 1.16.0-5ubuntu2 [628 kB] Get:104 http://ftpmaster.internal/ubuntu lunar/universe amd64 libcub-dev all 1.16.0-1 [227 kB] Get:105 http://ftpmaster.internal/ubuntu lunar/multiverse amd64 libcublaslt11 amd64 11.7.4.6~11.5.2-1ubuntu1 [148 MB] Get:106 http://ftpmaster.internal/ubuntu lunar/multiverse amd64 libcublas11 amd64 11.7.4.6~11.5.2-1ubuntu1 [77.9 MB] Get:107 http://ftpmaster.internal/ubuntu lunar/multiverse amd64 libcudart11.0 amd64 11.5.117~11.5.2-1ubuntu1 [173 kB] Get:108 http://ftpmaster.internal/ubuntu lunar/multiverse amd64 libcufft10 amd64 11.1.1+~10.6.0.107~11.5.2-1ubuntu1 [70.3 MB] Get:109 http://ftpmaster.internal/ubuntu lunar/multiverse amd64 libcufftw10 amd64 11.1.1+~10.6.0.107~11.5.2-1ubuntu1 [205 kB] Get:110 http://ftpmaster.internal/ubuntu lunar/restricted amd64 libnvidia-compute-510 amd64 510.85.02-0ubuntu2 [57.7 MB] Get:111 http://ftpmaster.internal/ubuntu lunar/multiverse amd64 libcuinj64-11.5 amd64 11.5.114~11.5.2-1ubuntu1 [996 kB] Get:112 http://ftpmaster.internal/ubuntu lunar/multiverse amd64 libcurand10 amd64 11.1.1+~10.2.7.107~11.5.2-1ubuntu1 [41.8 MB] Get:113 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libcurl3-gnutls amd64 7.86.0-1 [288 kB] Get:114 http://ftpmaster.internal/ubuntu lunar/multiverse amd64 libcusolver11 amd64 11.3.2.107~11.5.2-1ubuntu1 [31.2 MB] Get:115 http://ftpmaster.internal/ubuntu lunar/multiverse amd64 libcusolvermg11 amd64 11.3.2.107~11.5.2-1ubuntu1 [17.8 MB] Get:116 http://ftpmaster.internal/ubuntu lunar/multiverse amd64 libcusparse11 amd64 11.7.0.107~11.5.2-1ubuntu1 [95.9 MB] Get:117 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libdeflate0 amd64 1.14-1 [64.8 kB] Get:118 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libdeflate-dev amd64 1.14-1 [55.4 kB] Get:119 http://ftpmaster.internal/ubuntu lunar/main amd64 libdrm-amdgpu1 amd64 2.4.113-2 [20.0 kB] Get:120 http://ftpmaster.internal/ubuntu lunar/main amd64 libdrm-nouveau2 amd64 2.4.113-2 [17.6 kB] Get:121 http://ftpmaster.internal/ubuntu lunar/main amd64 libdrm-radeon1 amd64 2.4.113-2 [21.0 kB] Get:122 http://ftpmaster.internal/ubuntu lunar/main amd64 libevent-2.1-7a amd64 2.1.12-stable-5ubuntu1 [144 kB] Get:123 http://ftpmaster.internal/ubuntu lunar/main amd64 libevent-core-2.1-7a amd64 2.1.12-stable-5ubuntu1 [91.2 kB] Get:124 http://ftpmaster.internal/ubuntu lunar/main amd64 libevent-extra-2.1-7 amd64 2.1.12-stable-5ubuntu1 [64.2 kB] Get:125 http://ftpmaster.internal/ubuntu lunar/main amd64 libevent-pthreads-2.1-7 amd64 2.1.12-stable-5ubuntu1 [7694 B] Get:126 http://ftpmaster.internal/ubuntu lunar/main amd64 libevent-openssl-2.1-7 amd64 2.1.12-stable-5ubuntu1 [15.4 kB] Get:127 http://ftpmaster.internal/ubuntu lunar/main amd64 libevent-dev amd64 2.1.12-stable-5ubuntu1 [275 kB] Get:128 http://ftpmaster.internal/ubuntu lunar-proposed/universe amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.2 [181 kB] Get:129 http://ftpmaster.internal/ubuntu lunar-proposed/universe amd64 libpsm2-2 amd64 11.2.185-2 [196 kB] Get:130 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 librdmacm1 amd64 43.0-1 [69.9 kB] Get:131 http://ftpmaster.internal/ubuntu lunar/universe amd64 libfabric1 amd64 1.11.0-3 [558 kB] Get:132 http://ftpmaster.internal/ubuntu lunar/main amd64 libfftw3-double3 amd64 3.3.8-2ubuntu8 [770 kB] Get:133 http://ftpmaster.internal/ubuntu lunar/main amd64 libfftw3-long3 amd64 3.3.8-2ubuntu8 [335 kB] Get:134 http://ftpmaster.internal/ubuntu lunar/main amd64 libfftw3-quad3 amd64 3.3.8-2ubuntu8 [614 kB] Get:135 http://ftpmaster.internal/ubuntu lunar/main amd64 libfftw3-single3 amd64 3.3.8-2ubuntu8 [800 kB] Get:136 http://ftpmaster.internal/ubuntu lunar/main amd64 libfftw3-bin amd64 3.3.8-2ubuntu8 [35.5 kB] Get:137 http://ftpmaster.internal/ubuntu lunar/main amd64 libfftw3-dev amd64 3.3.8-2ubuntu8 [2101 kB] Get:138 http://ftpmaster.internal/ubuntu lunar-proposed/universe amd64 libfltk-cairo1.3 amd64 1.3.8-5 [6700 B] Get:139 http://ftpmaster.internal/ubuntu lunar/main amd64 libglvnd0 amd64 1.5.0-1 [68.1 kB] Get:140 http://ftpmaster.internal/ubuntu lunar/main amd64 libglapi-mesa amd64 22.2.1-1ubuntu1 [32.3 kB] Get:141 http://ftpmaster.internal/ubuntu lunar/main amd64 libx11-xcb1 amd64 2:1.8.1-2 [7768 B] Get:142 http://ftpmaster.internal/ubuntu lunar/main amd64 libxcb-dri2-0 amd64 1.15-1 [7276 B] Get:143 http://ftpmaster.internal/ubuntu lunar/main amd64 libxcb-dri3-0 amd64 1.15-1 [7174 B] Get:144 http://ftpmaster.internal/ubuntu lunar/main amd64 libxcb-glx0 amd64 1.15-1 [24.6 kB] Get:145 http://ftpmaster.internal/ubuntu lunar/main amd64 libxcb-present0 amd64 1.15-1 [5708 B] Get:146 http://ftpmaster.internal/ubuntu lunar/main amd64 libxcb-sync1 amd64 1.15-1 [9358 B] Get:147 http://ftpmaster.internal/ubuntu lunar/main amd64 libxcb-xfixes0 amd64 1.15-1 [10.2 kB] Get:148 http://ftpmaster.internal/ubuntu lunar/main amd64 libxshmfence1 amd64 1.3-1build4 [5394 B] Get:149 http://ftpmaster.internal/ubuntu lunar/main amd64 libxxf86vm1 amd64 1:1.1.4-1build3 [10.4 kB] Get:150 http://ftpmaster.internal/ubuntu lunar/main amd64 libllvm15 amd64 1:15.0.2-1 [25.2 MB] Get:151 http://ftpmaster.internal/ubuntu lunar/main amd64 libsensors-config all 1:3.6.0-7ubuntu1 [5274 B] Get:152 http://ftpmaster.internal/ubuntu lunar/main amd64 libsensors5 amd64 1:3.6.0-7ubuntu1 [26.3 kB] Get:153 http://ftpmaster.internal/ubuntu lunar/main amd64 libgl1-mesa-dri amd64 22.2.1-1ubuntu1 [7616 kB] Get:154 http://ftpmaster.internal/ubuntu lunar/main amd64 libglx-mesa0 amd64 22.2.1-1ubuntu1 [154 kB] Get:155 http://ftpmaster.internal/ubuntu lunar/main amd64 libglx0 amd64 1.5.0-1 [38.0 kB] Get:156 http://ftpmaster.internal/ubuntu lunar/main amd64 libgl1 amd64 1.5.0-1 [103 kB] Get:157 http://ftpmaster.internal/ubuntu lunar-proposed/universe amd64 libfltk-gl1.3 amd64 1.3.8-5 [43.4 kB] Get:158 http://ftpmaster.internal/ubuntu lunar/main amd64 xorg-sgml-doctools all 1:1.11-1.1 [10.9 kB] Get:159 http://ftpmaster.internal/ubuntu lunar/main amd64 x11proto-dev all 2022.1-1 [605 kB] Get:160 http://ftpmaster.internal/ubuntu lunar/main amd64 libxau-dev amd64 1:1.0.9-1build5 [9724 B] Get:161 http://ftpmaster.internal/ubuntu lunar/main amd64 libxdmcp-dev amd64 1:1.1.3-0ubuntu5 [26.5 kB] Get:162 http://ftpmaster.internal/ubuntu lunar/main amd64 xtrans-dev all 1.4.0-1 [68.9 kB] Get:163 http://ftpmaster.internal/ubuntu lunar/main amd64 libpthread-stubs0-dev amd64 0.4-1build2 [5516 B] Get:164 http://ftpmaster.internal/ubuntu lunar/main amd64 libxcb1-dev amd64 1.15-1 [85.8 kB] Get:165 http://ftpmaster.internal/ubuntu lunar/main amd64 libx11-dev amd64 2:1.8.1-2 [733 kB] Get:166 http://ftpmaster.internal/ubuntu lunar-proposed/universe amd64 libfltk1.3-dev amd64 1.3.8-5 [903 kB] Get:167 http://ftpmaster.internal/ubuntu lunar/universe amd64 libhwloc15 amd64 2.8.0-1 [160 kB] Get:168 http://ftpmaster.internal/ubuntu lunar/main amd64 libjpeg-turbo8-dev amd64 2.1.2-0ubuntu1 [257 kB] Get:169 http://ftpmaster.internal/ubuntu lunar/main amd64 libjpeg8-dev amd64 8c-2ubuntu10 [1476 B] Get:170 http://ftpmaster.internal/ubuntu lunar/main amd64 libjpeg-dev amd64 8c-2ubuntu10 [1472 B] Get:171 http://ftpmaster.internal/ubuntu lunar/main amd64 libjs-jquery all 3.6.0+dfsg+~3.5.13-1 [321 kB] Get:172 http://ftpmaster.internal/ubuntu lunar/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] Get:173 http://ftpmaster.internal/ubuntu lunar/main amd64 liblerc3 amd64 3.0+ds-1ubuntu1 [128 kB] Get:174 http://ftpmaster.internal/ubuntu lunar/main amd64 liblerc-dev amd64 3.0+ds-1ubuntu1 [125 kB] Get:175 http://ftpmaster.internal/ubuntu lunar/main amd64 libltdl7 amd64 2.4.7-4 [40.3 kB] Get:176 http://ftpmaster.internal/ubuntu lunar/main amd64 libltdl-dev amd64 2.4.7-4 [169 kB] Get:177 http://ftpmaster.internal/ubuntu lunar/main amd64 libnl-3-dev amd64 3.7.0-0.2 [101 kB] Get:178 http://ftpmaster.internal/ubuntu lunar/main amd64 libnl-route-3-dev amd64 3.7.0-0.2 [216 kB] Get:179 http://ftpmaster.internal/ubuntu lunar/multiverse amd64 libnppc11 amd64 11.5.1.107~11.5.2-1ubuntu1 [423 kB] Get:180 http://ftpmaster.internal/ubuntu lunar/multiverse amd64 libnppial11 amd64 11.5.1.107~11.5.2-1ubuntu1 [5188 kB] Get:181 http://ftpmaster.internal/ubuntu lunar/multiverse amd64 libnppicc11 amd64 11.5.1.107~11.5.2-1ubuntu1 [2344 kB] Get:182 http://ftpmaster.internal/ubuntu lunar/multiverse amd64 libnppidei11 amd64 11.5.1.107~11.5.2-1ubuntu1 [2560 kB] Get:183 http://ftpmaster.internal/ubuntu lunar/multiverse amd64 libnppif11 amd64 11.5.1.107~11.5.2-1ubuntu1 [33.6 MB] Get:184 http://ftpmaster.internal/ubuntu lunar/multiverse amd64 libnppig11 amd64 11.5.1.107~11.5.2-1ubuntu1 [14.5 MB] Get:185 http://ftpmaster.internal/ubuntu lunar/multiverse amd64 libnppim11 amd64 11.5.1.107~11.5.2-1ubuntu1 [3010 kB] Get:186 http://ftpmaster.internal/ubuntu lunar/multiverse amd64 libnppist11 amd64 11.5.1.107~11.5.2-1ubuntu1 [13.7 MB] Get:187 http://ftpmaster.internal/ubuntu lunar/multiverse amd64 libnppisu11 amd64 11.5.1.107~11.5.2-1ubuntu1 [172 kB] Get:188 http://ftpmaster.internal/ubuntu lunar/multiverse amd64 libnppitc11 amd64 11.5.1.107~11.5.2-1ubuntu1 [1276 kB] Get:189 http://ftpmaster.internal/ubuntu lunar/multiverse amd64 libnpps11 amd64 11.5.1.107~11.5.2-1ubuntu1 [7079 kB] Get:190 http://ftpmaster.internal/ubuntu lunar/multiverse amd64 libnvblas11 amd64 11.7.4.6~11.5.2-1ubuntu1 [185 kB] Get:191 http://ftpmaster.internal/ubuntu lunar/multiverse amd64 libnvidia-ml-dev amd64 11.5.50~11.5.2-1ubuntu1 [68.9 kB] Get:192 http://ftpmaster.internal/ubuntu lunar/multiverse amd64 libnvjpeg11 amd64 11.5.4.107~11.5.2-1ubuntu1 [1840 kB] Get:193 http://ftpmaster.internal/ubuntu lunar/multiverse amd64 libnvrtc-builtins11.5 amd64 11.5.119~11.5.2-1ubuntu1 [114 kB] Get:194 http://ftpmaster.internal/ubuntu lunar/multiverse amd64 libnvrtc11.2 amd64 11.5.119~11.5.2-1ubuntu1 [15.7 MB] Get:195 http://ftpmaster.internal/ubuntu lunar/multiverse amd64 libnvvm4 amd64 11.5.119~11.5.2-1ubuntu1 [8665 kB] Get:196 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libpciaccess0 amd64 0.17-1 [18.5 kB] Get:197 http://ftpmaster.internal/ubuntu lunar/main amd64 libxnvctrl0 amd64 510.47.03-0ubuntu1 [11.5 kB] Get:198 http://ftpmaster.internal/ubuntu lunar-proposed/universe amd64 ocl-icd-libopencl1 amd64 2.3.1-1 [37.6 kB] Get:199 http://ftpmaster.internal/ubuntu lunar/universe amd64 libhwloc-plugins amd64 2.8.0-1 [15.6 kB] Get:200 http://ftpmaster.internal/ubuntu lunar/universe amd64 libpmix2 amd64 4.1.2-2ubuntu2 [607 kB] Get:201 http://ftpmaster.internal/ubuntu lunar/universe amd64 libucx0 amd64 1.13.0-1 [911 kB] Get:202 http://ftpmaster.internal/ubuntu lunar/universe amd64 libopenmpi3 amd64 4.1.4-2ubuntu2 [2586 kB] Get:203 http://ftpmaster.internal/ubuntu lunar/main amd64 libnuma-dev amd64 2.0.14-3ubuntu2 [35.9 kB] Get:204 http://ftpmaster.internal/ubuntu lunar/universe amd64 libhwloc-dev amd64 2.8.0-1 [256 kB] Get:205 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-4.1ubuntu2 [164 kB] Get:206 http://ftpmaster.internal/ubuntu lunar/universe amd64 libpmix-dev amd64 4.1.2-2ubuntu2 [805 kB] Get:207 http://ftpmaster.internal/ubuntu lunar/main amd64 libjbig0 amd64 2.1-3.1build3 [28.9 kB] Get:208 http://ftpmaster.internal/ubuntu lunar/main amd64 libjbig-dev amd64 2.1-3.1build3 [27.3 kB] Get:209 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 liblzma-dev amd64 5.2.7-0.1 [158 kB] Get:210 http://ftpmaster.internal/ubuntu lunar/main amd64 libwebp7 amd64 1.2.2-2 [206 kB] Get:211 http://ftpmaster.internal/ubuntu lunar/main amd64 libtiff5 amd64 4.4.0-4ubuntu3 [190 kB] Get:212 http://ftpmaster.internal/ubuntu lunar/main amd64 libtiffxx5 amd64 4.4.0-4ubuntu3 [5732 B] Get:213 http://ftpmaster.internal/ubuntu lunar/main amd64 libtiff-dev amd64 4.4.0-4ubuntu3 [324 kB] Get:214 http://ftpmaster.internal/ubuntu lunar/multiverse amd64 nvidia-profiler amd64 11.5.114~11.5.2-1ubuntu1 [1720 kB] Get:215 http://ftpmaster.internal/ubuntu lunar/multiverse amd64 libnvtoolsext1 amd64 11.5.114~11.5.2-1ubuntu1 [27.8 kB] Get:216 http://ftpmaster.internal/ubuntu lunar/multiverse amd64 libcupti-dev amd64 11.5.114~11.5.2-1ubuntu1 [7801 kB] Get:217 http://ftpmaster.internal/ubuntu lunar/multiverse amd64 libthrust-dev all 1.16.0-1 [418 kB] Get:218 http://ftpmaster.internal/ubuntu lunar/multiverse amd64 nvidia-cuda-dev amd64 11.5.2-1ubuntu1 [664 MB] Get:219 http://ftpmaster.internal/ubuntu lunar-proposed/universe amd64 opencl-c-headers all 3.0~2022.09.30-1 [45.1 kB] Get:220 http://ftpmaster.internal/ubuntu lunar/universe amd64 opencl-clhpp-headers all 3.0~2022.05.18-1ubuntu1 [45.2 kB] Get:221 http://ftpmaster.internal/ubuntu lunar-proposed/universe amd64 ocl-icd-opencl-dev amd64 2.3.1-1 [2434 B] Get:222 http://ftpmaster.internal/ubuntu lunar/multiverse amd64 nvidia-opencl-dev amd64 11.5.2-1ubuntu1 [17.8 kB] Get:223 http://ftpmaster.internal/ubuntu lunar/multiverse amd64 nvidia-cuda-toolkit amd64 11.5.2-1ubuntu1 [62.7 MB] Get:224 http://ftpmaster.internal/ubuntu lunar/multiverse amd64 nvidia-cuda-toolkit-gcc amd64 11.5.2-1ubuntu1 [16.3 kB] Get:225 http://ftpmaster.internal/ubuntu lunar/universe amd64 openmpi-common all 4.1.4-2ubuntu2 [163 kB] Get:226 http://ftpmaster.internal/ubuntu lunar/universe amd64 openmpi-bin amd64 4.1.4-2ubuntu2 [115 kB] Get:227 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libibverbs-dev amd64 43.0-1 [661 kB] Get:228 http://ftpmaster.internal/ubuntu lunar/universe amd64 libopenmpi-dev amd64 4.1.4-2ubuntu2 [864 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 1549 MB in 13s (123 MB/s) Selecting previously unselected package libmd0:amd64. (Reading database ... 15539 files and directories currently installed.) Preparing to unpack .../000-libmd0_1.0.4-2_amd64.deb ... Unpacking libmd0:amd64 (1.0.4-2) ... Selecting previously unselected package libbsd0:amd64. Preparing to unpack .../001-libbsd0_0.11.7-1_amd64.deb ... Unpacking libbsd0:amd64 (0.11.7-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../002-libelf1_0.187-4_amd64.deb ... Unpacking libelf1:amd64 (0.187-4) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../003-libexpat1_2.5.0-1_amd64.deb ... Unpacking libexpat1:amd64 (2.5.0-1) ... Selecting previously unselected package libicu71:amd64. Preparing to unpack .../004-libicu71_71.1-3ubuntu1_amd64.deb ... Unpacking libicu71:amd64 (71.1-3ubuntu1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../005-libxml2_2.9.14+dfsg-1.1_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.1) ... Selecting previously unselected package ucf. Preparing to unpack .../006-ucf_3.0043_all.deb ... Moving old data out of the way Unpacking ucf (3.0043) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../007-bsdextrautils_2.38-4ubuntu1_amd64.deb ... Unpacking bsdextrautils (2.38-4ubuntu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../008-libmagic-mgc_1%3a5.41-4_amd64.deb ... Unpacking libmagic-mgc (1:5.41-4) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../009-libmagic1_1%3a5.41-4_amd64.deb ... Unpacking libmagic1:amd64 (1:5.41-4) ... Selecting previously unselected package file. Preparing to unpack .../010-file_1%3a5.41-4_amd64.deb ... Unpacking file (1:5.41-4) ... Selecting previously unselected package gettext-base. Preparing to unpack .../011-gettext-base_0.21-8_amd64.deb ... Unpacking gettext-base (0.21-8) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../012-libuchardet0_0.0.7-1build2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1build2) ... Selecting previously unselected package groff-base. Preparing to unpack .../013-groff-base_1.22.4-8build1_amd64.deb ... Unpacking groff-base (1.22.4-8build1) ... Selecting previously unselected package libcbor0.8:amd64. Preparing to unpack .../014-libcbor0.8_0.8.0-2ubuntu1_amd64.deb ... Unpacking libcbor0.8:amd64 (0.8.0-2ubuntu1) ... Selecting previously unselected package libdrm-common. Preparing to unpack .../015-libdrm-common_2.4.113-2_all.deb ... Unpacking libdrm-common (2.4.113-2) ... Selecting previously unselected package libdrm2:amd64. Preparing to unpack .../016-libdrm2_2.4.113-2_amd64.deb ... Unpacking libdrm2:amd64 (2.4.113-2) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../017-libedit2_3.1-20221030-1_amd64.deb ... Unpacking libedit2:amd64 (3.1-20221030-1) ... Selecting previously unselected package libfido2-1:amd64. Preparing to unpack .../018-libfido2-1_1.12.0-1_amd64.deb ... Unpacking libfido2-1:amd64 (1.12.0-1) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../019-libnghttp2-14_1.50.0-1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.50.0-1) ... Selecting previously unselected package libnuma1:amd64. Preparing to unpack .../020-libnuma1_2.0.14-3ubuntu2_amd64.deb ... Unpacking libnuma1:amd64 (2.0.14-3ubuntu2) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../021-libpipeline1_1.5.6-3_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.6-3) ... Selecting previously unselected package libpsl5:amd64. Preparing to unpack .../022-libpsl5_0.21.0-1.2build2_amd64.deb ... Unpacking libpsl5:amd64 (0.21.0-1.2build2) ... Selecting previously unselected package libuv1:amd64. Preparing to unpack .../023-libuv1_1.44.2-1_amd64.deb ... Unpacking libuv1:amd64 (1.44.2-1) ... Selecting previously unselected package libxau6:amd64. 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Selecting previously unselected package libarchive13:amd64. Preparing to unpack .../037-libarchive13_3.6.0-1ubuntu1_amd64.deb ... Unpacking libarchive13:amd64 (3.6.0-1ubuntu1) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../038-libbrotli1_1.0.9-2build7_amd64.deb ... Unpacking libbrotli1:amd64 (1.0.9-2build7) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../039-libsasl2-modules-db_2.1.28+dfsg-6ubuntu2_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg-6ubuntu2) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../040-libsasl2-2_2.1.28+dfsg-6ubuntu2_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg-6ubuntu2) ... Selecting previously unselected package libldap-2.5-0:amd64. Preparing to unpack .../041-libldap-2.5-0_2.5.13+dfsg-1ubuntu2_amd64.deb ... Unpacking libldap-2.5-0:amd64 (2.5.13+dfsg-1ubuntu2) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../042-librtmp1_2.4+20151223.gitfa8646d.1-2build4_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2build4) ... Selecting previously unselected package libssh-4:amd64. Preparing to unpack .../043-libssh-4_0.10.4-2_amd64.deb ... Unpacking libssh-4:amd64 (0.10.4-2) ... Selecting previously unselected package libcurl4:amd64. Preparing to unpack .../044-libcurl4_7.86.0-1_amd64.deb ... Unpacking libcurl4:amd64 (7.86.0-1) ... Selecting previously unselected package libjsoncpp25:amd64. Preparing to unpack .../045-libjsoncpp25_1.9.5-4_amd64.deb ... Unpacking libjsoncpp25:amd64 (1.9.5-4) ... Selecting previously unselected package librhash0:amd64. Preparing to unpack .../046-librhash0_1.4.2-1ubuntu1_amd64.deb ... Unpacking librhash0:amd64 (1.4.2-1ubuntu1) ... Selecting previously unselected package dh-elpa-helper. Preparing to unpack .../047-dh-elpa-helper_2.0.9ubuntu1_all.deb ... Unpacking dh-elpa-helper (2.0.9ubuntu1) ... Selecting previously unselected package emacsen-common. Preparing to unpack .../048-emacsen-common_3.0.4_all.deb ... Unpacking emacsen-common (3.0.4) ... Selecting previously unselected package cmake-data. Preparing to unpack .../049-cmake-data_3.24.3-1ubuntu1_all.deb ... Unpacking cmake-data (3.24.3-1ubuntu1) ... Selecting previously unselected package cmake. Preparing to unpack .../050-cmake_3.24.3-1ubuntu1_amd64.deb ... Unpacking cmake (3.24.3-1ubuntu1) ... Selecting previously unselected package gcc-10-base:amd64. Preparing to unpack .../051-gcc-10-base_10.4.0-5ubuntu2_amd64.deb ... Unpacking gcc-10-base:amd64 (10.4.0-5ubuntu2) ... Selecting previously unselected package cpp-10. Preparing to unpack .../052-cpp-10_10.4.0-5ubuntu2_amd64.deb ... Unpacking cpp-10 (10.4.0-5ubuntu2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../053-libdebhelper-perl_13.10.1ubuntu1_all.deb ... 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Setting up libcurand10:amd64 (11.1.1+~10.2.7.107~11.5.2-1ubuntu1) ... Setting up libevent-pthreads-2.1-7:amd64 (2.1.12-stable-5ubuntu1) ... Setting up libnvrtc-builtins11.5:amd64 (11.5.119~11.5.2-1ubuntu1) ... Setting up libtsan0:amd64 (11.3.0-9ubuntu1) ... Setting up libjpeg8:amd64 (8c-2ubuntu10) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.0-1) ... Setting up libdw1:amd64 (0.187-4) ... Setting up libnppidei11:amd64 (11.5.1.107~11.5.2-1ubuntu1) ... Setting up libjpeg-turbo8-dev:amd64 (2.1.2-0ubuntu1) ... Setting up libxdmcp6:amd64 (1:1.1.3-0ubuntu5) ... Setting up libevent-extra-2.1-7:amd64 (2.1.12-stable-5ubuntu1) ... Setting up libxcb1:amd64 (1.15-1) ... Setting up gettext (0.21-8) ... Setting up libthrust-dev (1.16.0-1) ... Setting up libnppial11:amd64 (11.5.1.107~11.5.2-1ubuntu1) ... Setting up libnppif11:amd64 (11.5.1.107~11.5.2-1ubuntu1) ... Setting up libxcb-xfixes0:amd64 (1.15-1) ... Setting up libcuinj64-11.5:amd64 (11.5.114~11.5.2-1ubuntu1) ... Setting up libcufftw10:amd64 (11.1.1+~10.6.0.107~11.5.2-1ubuntu1) ... Setting up libcublas11:amd64 (11.7.4.6~11.5.2-1ubuntu1) ... Setting up libnvidia-ml-dev:amd64 (11.5.50~11.5.2-1ubuntu1) ... Setting up libtool (2.4.7-4) ... Setting up libarchive13:amd64 (3.6.0-1ubuntu1) ... Setting up libxcb-render0:amd64 (1.15-1) ... Setting up libfftw3-bin (3.3.8-2ubuntu8) ... Setting up fontconfig-config (2.13.1-4.4ubuntu1) ... Setting up libxcb-glx0:amd64 (1.15-1) ... Setting up libgcc-10-dev:amd64 (10.4.0-5ubuntu2) ... Setting up libedit2:amd64 (3.1-20221030-1) ... Setting up libcupti-dev:amd64 (11.5.114~11.5.2-1ubuntu1) ... Setting up libjbig-dev:amd64 (2.1-3.1build3) ... Setting up libgfortran-12-dev:amd64 (12.2.0-9ubuntu1) ... Setting up libxcb-shm0:amd64 (1.15-1) ... Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-1ubuntu2) ... Setting up nvidia-profiler (11.5.114~11.5.2-1ubuntu1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnuma-dev:amd64 (2.0.14-3ubuntu2) ... Setting up libnl-route-3-200:amd64 (3.7.0-0.2) ... Setting up libxcb-present0:amd64 (1.15-1) ... Setting up dh-autoreconf (20) ... Setting up libltdl-dev:amd64 (2.4.7-4) ... Setting up libnvblas11:amd64 (11.7.4.6~11.5.2-1ubuntu1) ... Setting up gfortran-12 (12.2.0-9ubuntu1) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libxcb-sync1:amd64 (1.15-1) ... Setting up libcusolver11:amd64 (11.3.2.107~11.5.2-1ubuntu1) ... Setting up libnvrtc11.2:amd64 (11.5.119~11.5.2-1ubuntu1) ... Setting up opencl-clhpp-headers (3.0~2022.05.18-1ubuntu1) ... Setting up libevent-dev (2.1.12-stable-5ubuntu1) ... Setting up libcusolvermg11:amd64 (11.3.2.107~11.5.2-1ubuntu1) ... Setting up gcc-10 (10.4.0-5ubuntu2) ... Setting up ocl-icd-opencl-dev:amd64 (2.3.1-1) ... Setting up libxcb-dri2-0:amd64 (1.15-1) ... Setting up dh-strip-nondeterminism (1.13.0-1) ... Setting up libdrm2:amd64 (2.4.113-2) ... Setting up dwz (0.14+20220924-2) ... Setting up libnl-3-dev:amd64 (3.7.0-0.2) ... Setting up groff-base (1.22.4-8build1) ... Setting up libllvm15:amd64 (1:15.0.2-1) ... Setting up debugedit (1:5.0-5) ... Setting up libcurl4:amd64 (7.86.0-1) ... Setting up libx11-6:amd64 (2:1.8.1-2) ... Setting up libhwloc-dev:amd64 (2.8.0-1) ... Setting up libtiff5:amd64 (4.4.0-4ubuntu3) ... Setting up libjpeg8-dev:amd64 (8c-2ubuntu10) ... Setting up libfftw3-dev:amd64 (3.3.8-2ubuntu8) ... Setting up libtiffxx5:amd64 (4.4.0-4ubuntu3) ... Setting up libdrm-amdgpu1:amd64 (2.4.113-2) ... Setting up libxcb-dri3-0:amd64 (1.15-1) ... Setting up libx11-xcb1:amd64 (2:1.8.1-2) ... Setting up libibverbs1:amd64 (43.0-1) ... Setting up libdrm-nouveau2:amd64 (2.4.113-2) ... Setting up libstdc++-10-dev:amd64 (10.4.0-5ubuntu2) ... Setting up g++-10 (10.4.0-5ubuntu2) ... Setting up libxrender1:amd64 (1:0.9.10-1.1) ... Setting up ibverbs-providers:amd64 (43.0-1) ... Setting up libdrm-radeon1:amd64 (2.4.113-2) ... 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 nvidia-cuda-dev:amd64 (11.5.2-1ubuntu1) ... Setting up libgl1-mesa-dri:amd64 (22.2.1-1ubuntu1) ... Setting up libjpeg-dev:amd64 (8c-2ubuntu10) ... Setting up libxext6:amd64 (2:1.3.4-1build1) ... Setting up libcurl3-gnutls:amd64 (7.86.0-1) ... Setting up man-db (2.11.0-1) ... 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 libxxf86vm1:amd64 (1:1.1.4-1build3) ... Setting up libxnvctrl0:amd64 (510.47.03-0ubuntu1) ... Setting up libnl-route-3-dev:amd64 (3.7.0-0.2) ... Setting up libtiff-dev:amd64 (4.4.0-4ubuntu3) ... Setting up libxfixes3:amd64 (1:6.0.0-2) ... Setting up nvidia-cuda-toolkit (11.5.2-1ubuntu1) ... Setting up libxinerama1:amd64 (2:1.1.4-3) ... Setting up nvidia-opencl-dev:amd64 (11.5.2-1ubuntu1) ... Setting up nvidia-cuda-toolkit-gcc (11.5.2-1ubuntu1) ... Setting up cmake (3.24.3-1ubuntu1) ... Setting up librdmacm1:amd64 (43.0-1) ... Setting up libucx0:amd64 (1.13.0-1) ... Setting up libglx-mesa0:amd64 (22.2.1-1ubuntu1) ... Setting up libglx0:amd64 (1.5.0-1) ... Setting up libxcursor1:amd64 (1:1.2.1-1) ... Setting up debhelper (13.10.1ubuntu1) ... Setting up libibverbs-dev:amd64 (43.0-1) ... Setting up libhwloc-plugins:amd64 (2.8.0-1) ... Setting up libgl1:amd64 (1.5.0-1) ... Setting up libfabric1:amd64 (1.11.0-3) ... Setting up libpmix2:amd64 (4.1.2-2ubuntu2) ... Setting up libopenmpi3:amd64 (4.1.4-2ubuntu2) ... Setting up libpmix-dev:amd64 (4.1.2-2ubuntu2) ... Setting up openmpi-bin (4.1.4-2ubuntu2) ... 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:amd64 (4.1.4-2ubuntu2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openmpi/include to provide /usr/include/x86_64-linux-gnu/mpi (mpi-x86_64-linux-gnu) in auto mode Processing triggers for libc-bin (2.36-0ubuntu4) ... Processing triggers for sgml-base (1.31) ... Setting up libfontconfig1:amd64 (2.13.1-4.4ubuntu1) ... Setting up x11proto-dev (2022.1-1) ... Setting up libxft2:amd64 (2.3.6-1) ... Setting up libxau-dev:amd64 (1:1.0.9-1build5) ... Setting up libfltk1.3:amd64 (1.3.8-5) ... Setting up libfltk-gl1.3:amd64 (1.3.8-5) ... Setting up libfltk-images1.3:amd64 (1.3.8-5) ... Setting up libcairo2:amd64 (1.16.0-5ubuntu2) ... Setting up libxdmcp-dev:amd64 (1:1.1.3-0ubuntu5) ... Setting up libfltk-forms1.3:amd64 (1.3.8-5) ... Setting up libxcb1-dev:amd64 (1.15-1) ... Setting up libx11-dev:amd64 (2:1.8.1-2) ... Setting up libfltk-cairo1.3:amd64 (1.3.8-5) ... Setting up fluid (1.3.8-5) ... Setting up libfltk1.3-dev:amd64 (1.3.8-5) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.36-0ubuntu4) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-131-generic #147-Ubuntu SMP Fri Oct 14 17:07:22 UTC 2022 amd64 (x86_64) Toolchain package versions: binutils_2.39-8ubuntu2 dpkg-dev_1.21.9ubuntu1 g++-10_10.4.0-5ubuntu2 g++-12_12.2.0-9ubuntu1 gcc-10_10.4.0-5ubuntu2 gcc-12_12.2.0-9ubuntu1 libc6-dev_2.36-0ubuntu4 libstdc++-10-dev_10.4.0-5ubuntu2 libstdc++-12-dev_12.2.0-9ubuntu1 libstdc++6_12.2.0-9ubuntu1 linux-libc-dev_5.19.0-23.24 Package versions: adduser_3.121ubuntu1 advancecomp_2.3-1 apt_2.5.4 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-8 autotools-dev_20220109.1 base-files_12.3ubuntu1 base-passwd_3.6.1 bash_5.2-1ubuntu2 binutils_2.39-8ubuntu2 binutils-common_2.39-8ubuntu2 binutils-x86-64-linux-gnu_2.39-8ubuntu2 bsdextrautils_2.38-4ubuntu1 bsdutils_1:2.38-4ubuntu1 build-essential_12.9ubuntu3 bzip2_1.0.8-5build1 ca-certificates_20211016 cmake_3.24.3-1ubuntu1 cmake-data_3.24.3-1ubuntu1 coreutils_8.32-4.1ubuntu1 cpp_4:12.2.0-1ubuntu1 cpp-10_10.4.0-5ubuntu2 cpp-12_12.2.0-9ubuntu1 dash_0.5.11+git20210903+057cd650a4ed-8ubuntu1 debconf_1.5.79ubuntu1 debhelper_13.10.1ubuntu1 debianutils_5.7-0.4 debugedit_1:5.0-5 dh-autoreconf_20 dh-elpa-helper_2.0.9ubuntu1 dh-strip-nondeterminism_1.13.0-1 diffutils_1:3.8-1 dpkg_1.21.9ubuntu1 dpkg-dev_1.21.9ubuntu1 dwz_0.14+20220924-2 e2fsprogs_1.46.5-2ubuntu2 emacsen-common_3.0.4 fakeroot_1.30.1-1ubuntu1 file_1:5.41-4 findutils_4.9.0-3ubuntu1 fluid_1.3.8-5 fontconfig-config_2.13.1-4.4ubuntu1 fonts-dejavu-core_2.37-2build1 g++_4:12.2.0-1ubuntu1 g++-10_10.4.0-5ubuntu2 g++-12_12.2.0-9ubuntu1 gcc_4:12.2.0-1ubuntu1 gcc-10_10.4.0-5ubuntu2 gcc-10-base_10.4.0-5ubuntu2 gcc-11-base_11.3.0-9ubuntu1 gcc-12_12.2.0-9ubuntu1 gcc-12-base_12.2.0-9ubuntu1 gettext_0.21-8 gettext-base_0.21-8 gfortran-12_12.2.0-9ubuntu1 gpg_2.2.40-1ubuntu1 gpg-agent_2.2.40-1ubuntu1 gpgconf_2.2.40-1ubuntu1 gpgv_2.2.40-1ubuntu1 grep_3.8-3 groff-base_1.22.4-8build1 gzip_1.12-1ubuntu1 hostname_3.23ubuntu2 ibverbs-providers_43.0-1 init_1.65.2 init-system-helpers_1.65.2 intltool-debian_0.35.0+20060710.6 libaccinj64-11.5_11.5.114~11.5.2-1ubuntu1 libacl1_2.3.1-1 libapparmor1_3.0.7-1ubuntu3 libapt-pkg6.0_2.5.4 libarchive-zip-perl_1.68-1 libarchive13_3.6.0-1ubuntu1 libargon2-1_0~20171227-0.3 libasan6_11.3.0-9ubuntu1 libasan8_12.2.0-9ubuntu1 libassuan0_2.5.5-5 libatomic1_12.2.0-9ubuntu1 libattr1_1:2.5.1-1build1 libaudit-common_1:3.0.7-1ubuntu2 libaudit1_1:3.0.7-1ubuntu2 libbinutils_2.39-8ubuntu2 libblkid1_2.38-4ubuntu1 libbrotli1_1.0.9-2build7 libbsd0_0.11.7-1 libbz2-1.0_1.0.8-5build1 libc-bin_2.36-0ubuntu4 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+------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: relion-cuda Binary: relion-cuda, relion-gui-cuda Architecture: any Version: 3.1.3-1 Maintainer: Debian Med Packaging Team Uploaders: Roland Fehrenbacher 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, nvidia-cuda-toolkit-gcc, fluid Package-List: relion-cuda deb contrib/science optional arch=any relion-gui-cuda deb contrib/science optional arch=any Checksums-Sha1: c6ca397db6c711f87305bd803f672345f7487bae 2345487 relion-cuda_3.1.3.orig.tar.gz 1299d7eafefba5149b8c8f01581787b428ef9f84 12128 relion-cuda_3.1.3-1.debian.tar.xz 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[ 1%] Building NVCC (Device) object src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_autopicker.cu.o cd /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda && /usr/bin/cmake -E make_directory /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/. cd /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda && /usr/bin/cmake -E make_directory /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/. /usr/bin/cmake -E copy /<>/scripts/star_plottable /<>/build/bin/relion_star_plottable cd /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/cuda_kernels && /usr/bin/cmake -D verbose:BOOL=1 -D build_configuration:STRING=Release -D generated_file:STRING=/<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/cuda_kernels/./relion_gpu_util_generated_helper.cu.o -D generated_cubin_file:STRING=/<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/cuda_kernels/./relion_gpu_util_generated_helper.cu.o.cubin.txt -P /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/cuda_kernels/relion_gpu_util_generated_helper.cu.o.Release.cmake cd /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda && /usr/bin/cmake -D verbose:BOOL=1 -D build_configuration:STRING=Release -D generated_file:STRING=/<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/./relion_gpu_util_generated_cuda_projector_plan.cu.o -D generated_cubin_file:STRING=/<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/./relion_gpu_util_generated_cuda_projector_plan.cu.o.cubin.txt -P /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_projector_plan.cu.o.Release.cmake cd /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda && /usr/bin/cmake -D verbose:BOOL=1 -D build_configuration:STRING=Release -D generated_file:STRING=/<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/./relion_gpu_util_generated_cuda_autopicker.cu.o -D 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/<>/scripts/star_datablock_singlefiles /<>/build/bin/relion_star_datablock_singlefiles /usr/bin/cmake -E rm -f /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/./relion_gpu_util_generated_cuda_autopicker.cu.o /usr/bin/cmake -E rm -f /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/./relion_gpu_util_generated_cuda_projector_plan.cu.o /usr/bin/cmake -E copy /<>/scripts/star_datablock_ctfdat /<>/build/bin/relion_star_datablock_ctfdat -- Generating dependency file: /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/cuda_kernels/relion_gpu_util_generated_helper.cu.o.NVCC-depend -- Generating dependency file: /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_autopicker.cu.o.NVCC-depend /usr/bin/cmake -E copy /<>/scripts/qsub.csh /<>/build/bin/relion_qsub.csh /usr/bin/nvcc -M -D__CUDACC__ /<>/src/acc/cuda/cuda_kernels/helper.cu -o 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/<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_autopicker.cu.o.NVCC-depend -ccbin /usr/bin/cuda-gcc -m64 -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -DACC_CUDA=2 -DACC_CPU=1 -DCUDA -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -Xcompiler ,\"-g\",\"-O2\",\"-ffile-prefix-map=/<>=.\",\"-fstack-protector-strong\",\"-Wformat\",\"-Werror=format-security\",\"-Wdate-time\",\"-D_FORTIFY_SOURCE=2\",\"-O3\",\"-DNDEBUG\" -arch=sm_35 -D__INTEL_COMPILER --default-stream per-thread --disable-warnings -DNVCC -I/usr/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -I/usr/include/x86_64-linux-gnu make[4]: Leaving directory '/<>/build' nvcc warning : The 'compute_35', 'compute_37', 'compute_50', 'sm_35', 'sm_37' and 'sm_50' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning). nvcc warning : The 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warning : The 'compute_35', 'compute_37', 'compute_50', 'sm_35', 'sm_37' and 'sm_50' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning). [ 1%] Built target copy_scripts [ 1%] Building NVCC (Device) object src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_backprojector.cu.o cd /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda && /usr/bin/cmake -E make_directory /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/. cd /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda && /usr/bin/cmake -D verbose:BOOL=1 -D build_configuration:STRING=Release -D generated_file:STRING=/<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/./relion_gpu_util_generated_cuda_backprojector.cu.o -D generated_cubin_file:STRING=/<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/./relion_gpu_util_generated_cuda_backprojector.cu.o.cubin.txt -P /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_backprojector.cu.o.Release.cmake -- Removing 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-I/usr/include/x86_64-linux-gnu nvcc warning : The 'compute_35', 'compute_37', 'compute_50', 'sm_35', 'sm_37' and 'sm_50' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning). /usr/bin/nvcc /<>/src/acc/cuda/cuda_kernels/helper.cu -c -o /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/cuda_kernels/./relion_gpu_util_generated_helper.cu.o -ccbin /usr/bin/cuda-gcc -m64 -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -DACC_CUDA=2 -DACC_CPU=1 -DCUDA -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -Xcompiler ,\"-g\",\"-O2\",\"-ffile-prefix-map=/<>=.\",\"-fstack-protector-strong\",\"-Wformat\",\"-Werror=format-security\",\"-Wdate-time\",\"-D_FORTIFY_SOURCE=2\",\"-O3\",\"-DNDEBUG\" -arch=sm_35 -D__INTEL_COMPILER --default-stream per-thread --disable-warnings -DNVCC -I/usr/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -I/usr/include/x86_64-linux-gnu nvcc warning : The 'compute_35', 'compute_37', 'compute_50', 'sm_35', 'sm_37' and 'sm_50' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning). -- Generating temporary cmake readable file: /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_projector_plan.cu.o.depend.tmp /usr/bin/cmake -D input_file:FILEPATH=/<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_projector_plan.cu.o.NVCC-depend -D output_file:FILEPATH=/<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_projector_plan.cu.o.depend.tmp -D verbose=1 -P /usr/share/cmake-3.24/Modules/FindCUDA/make2cmake.cmake -- Copy if different /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_projector_plan.cu.o.depend.tmp to 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deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning). -- Generating temporary cmake readable file: /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_autopicker.cu.o.depend.tmp /usr/bin/cmake -D input_file:FILEPATH=/<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_autopicker.cu.o.NVCC-depend -D output_file:FILEPATH=/<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_autopicker.cu.o.depend.tmp -D verbose=1 -P /usr/share/cmake-3.24/Modules/FindCUDA/make2cmake.cmake -- Copy if different /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_autopicker.cu.o.depend.tmp to /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_autopicker.cu.o.depend /usr/bin/cmake -E copy_if_different 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[ 2%] Building NVCC (Device) object src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_benchmark_utils.cu.o cd /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda && /usr/bin/cmake -E make_directory /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/. cd /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda && /usr/bin/cmake -D verbose:BOOL=1 -D build_configuration:STRING=Release -D generated_file:STRING=/<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/./relion_gpu_util_generated_cuda_benchmark_utils.cu.o -D generated_cubin_file:STRING=/<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/./relion_gpu_util_generated_cuda_benchmark_utils.cu.o.cubin.txt -P /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_benchmark_utils.cu.o.Release.cmake -- Removing /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/./relion_gpu_util_generated_cuda_benchmark_utils.cu.o 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-I/usr/include/x86_64-linux-gnu nvcc warning : The 'compute_35', 'compute_37', 'compute_50', 'sm_35', 'sm_37' and 'sm_50' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning). Generated /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/./relion_gpu_util_generated_cuda_benchmark_utils.cu.o successfully. [ 2%] Building NVCC (Device) object src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_helper_functions.cu.o cd /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda && /usr/bin/cmake -E make_directory /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/. cd /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda && /usr/bin/cmake -D verbose:BOOL=1 -D build_configuration:STRING=Release -D generated_file:STRING=/<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/./relion_gpu_util_generated_cuda_helper_functions.cu.o -D generated_cubin_file:STRING=/<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/./relion_gpu_util_generated_cuda_helper_functions.cu.o.cubin.txt -P /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_helper_functions.cu.o.Release.cmake -- Removing /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/./relion_gpu_util_generated_cuda_helper_functions.cu.o /usr/bin/cmake -E rm -f /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/./relion_gpu_util_generated_cuda_helper_functions.cu.o -- Generating dependency file: /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_helper_functions.cu.o.NVCC-depend /usr/bin/nvcc -M -D__CUDACC__ /<>/src/acc/cuda/cuda_helper_functions.cu -o /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_helper_functions.cu.o.NVCC-depend -ccbin /usr/bin/cuda-gcc -m64 -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -DACC_CUDA=2 -DACC_CPU=1 -DCUDA -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -Xcompiler ,\"-g\",\"-O2\",\"-ffile-prefix-map=/<>=.\",\"-fstack-protector-strong\",\"-Wformat\",\"-Werror=format-security\",\"-Wdate-time\",\"-D_FORTIFY_SOURCE=2\",\"-O3\",\"-DNDEBUG\" -arch=sm_35 -D__INTEL_COMPILER --default-stream per-thread --disable-warnings -DNVCC -I/usr/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -I/usr/include/x86_64-linux-gnu nvcc warning : The 'compute_35', 'compute_37', 'compute_50', 'sm_35', 'sm_37' and 'sm_50' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning). Generated /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/cuda_kernels/./relion_gpu_util_generated_helper.cu.o successfully. [ 3%] Building NVCC (Device) object src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_ml_optimiser.cu.o cd /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda && /usr/bin/cmake -E make_directory /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/. cd /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda && /usr/bin/cmake -D verbose:BOOL=1 -D build_configuration:STRING=Release -D generated_file:STRING=/<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/./relion_gpu_util_generated_cuda_ml_optimiser.cu.o -D generated_cubin_file:STRING=/<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/./relion_gpu_util_generated_cuda_ml_optimiser.cu.o.cubin.txt -P /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_ml_optimiser.cu.o.Release.cmake -- Removing /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/./relion_gpu_util_generated_cuda_ml_optimiser.cu.o /usr/bin/cmake 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and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning). Generated /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/./relion_gpu_util_generated_cuda_projector_plan.cu.o successfully. [ 3%] Building NVCC (Device) object src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_projector.cu.o cd /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda && /usr/bin/cmake -E make_directory /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/. cd /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda && /usr/bin/cmake -D verbose:BOOL=1 -D build_configuration:STRING=Release -D generated_file:STRING=/<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/./relion_gpu_util_generated_cuda_projector.cu.o -D generated_cubin_file:STRING=/<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/./relion_gpu_util_generated_cuda_projector.cu.o.cubin.txt -P /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_projector.cu.o.Release.cmake -- Removing /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/./relion_gpu_util_generated_cuda_projector.cu.o /usr/bin/cmake -E rm -f /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/./relion_gpu_util_generated_cuda_projector.cu.o -- Generating dependency file: /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_projector.cu.o.NVCC-depend /usr/bin/nvcc -M -D__CUDACC__ /<>/src/acc/cuda/cuda_projector.cu -o /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_projector.cu.o.NVCC-depend -ccbin /usr/bin/cuda-gcc -m64 -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -DACC_CUDA=2 -DACC_CPU=1 -DCUDA -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -Xcompiler ,\"-g\",\"-O2\",\"-ffile-prefix-map=/<>=.\",\"-fstack-protector-strong\",\"-Wformat\",\"-Werror=format-security\",\"-Wdate-time\",\"-D_FORTIFY_SOURCE=2\",\"-O3\",\"-DNDEBUG\" -arch=sm_35 -D__INTEL_COMPILER --default-stream per-thread --disable-warnings -DNVCC -I/usr/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -I/usr/include/x86_64-linux-gnu nvcc warning : The 'compute_35', 'compute_37', 'compute_50', 'sm_35', 'sm_37' and 'sm_50' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning). -- Generating temporary cmake readable file: /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_projector.cu.o.depend.tmp /usr/bin/cmake -D input_file:FILEPATH=/<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_projector.cu.o.NVCC-depend -D output_file:FILEPATH=/<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_projector.cu.o.depend.tmp -D verbose=1 -P /usr/share/cmake-3.24/Modules/FindCUDA/make2cmake.cmake -- Copy if different /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_projector.cu.o.depend.tmp to /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_projector.cu.o.depend /usr/bin/cmake -E copy_if_different /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_projector.cu.o.depend.tmp /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_projector.cu.o.depend -- Removing /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_projector.cu.o.depend.tmp and /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_projector.cu.o.NVCC-depend /usr/bin/cmake -E rm -f /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_projector.cu.o.depend.tmp /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_projector.cu.o.NVCC-depend -- Generating /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/./relion_gpu_util_generated_cuda_projector.cu.o /usr/bin/nvcc /<>/src/acc/cuda/cuda_projector.cu -c -o /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/./relion_gpu_util_generated_cuda_projector.cu.o -ccbin /usr/bin/cuda-gcc -m64 -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -DACC_CUDA=2 -DACC_CPU=1 -DCUDA -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -Xcompiler ,\"-g\",\"-O2\",\"-ffile-prefix-map=/<>=.\",\"-fstack-protector-strong\",\"-Wformat\",\"-Werror=format-security\",\"-Wdate-time\",\"-D_FORTIFY_SOURCE=2\",\"-O3\",\"-DNDEBUG\" -arch=sm_35 -D__INTEL_COMPILER --default-stream per-thread --disable-warnings -DNVCC -I/usr/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -I/usr/include/x86_64-linux-gnu nvcc warning : The 'compute_35', 'compute_37', 'compute_50', 'sm_35', 'sm_37' and 'sm_50' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning). Generated /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/./relion_gpu_util_generated_cuda_projector.cu.o successfully. Generated /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/./relion_gpu_util_generated_cuda_autopicker.cu.o successfully. Generated /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/./relion_gpu_util_generated_cuda_helper_functions.cu.o successfully. Generated /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/./relion_gpu_util_generated_cuda_ml_optimiser.cu.o successfully. cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/relion_gpu_util.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/relion_gpu_util.dir/build.make src/apps/CMakeFiles/relion_gpu_util.dir/build make[4]: Entering directory '/<>/build' [ 3%] Linking CXX static library ../../lib/librelion_gpu_util.a cd /<>/build/src/apps && /usr/bin/cmake -P CMakeFiles/relion_gpu_util.dir/cmake_clean_target.cmake cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/relion_gpu_util.dir/link.txt --verbose=1 /usr/bin/ar qc ../../lib/librelion_gpu_util.a CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_autopicker.cu.o CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_backprojector.cu.o CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_benchmark_utils.cu.o CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_helper_functions.cu.o CMakeFiles/relion_gpu_util.dir/__/acc/cuda/cuda_kernels/relion_gpu_util_generated_helper.cu.o CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_ml_optimiser.cu.o CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_projector.cu.o CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_projector_plan.cu.o /usr/bin/ranlib ../../lib/librelion_gpu_util.a make[4]: Leaving directory '/<>/build' [ 3%] Built target relion_gpu_util /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' [ 4%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/CPlot2D.cpp.o [ 4%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/assembly.cpp.o [ 4%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/__/macros.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/__/macros.cpp.o -MF CMakeFiles/relion_lib.dir/__/__/macros.cpp.o.d -o CMakeFiles/relion_lib.dir/__/__/macros.cpp.o -c /<>/build/macros.cpp cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 4%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/args.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 5%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/autopicker.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/autopicker.cpp.o -MF CMakeFiles/relion_lib.dir/__/autopicker.cpp.o.d -o CMakeFiles/relion_lib.dir/__/autopicker.cpp.o -c /<>/src/autopicker.cpp In file included from /<>/src/image.h:455, from /<>/src/autopicker.h:10, from /<>/src/autopicker.cpp:20: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 5%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o -c /<>/src/autopicker_mpi.cpp /<>/src/CPlot2D.cpp: In member function ‘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/x86_64-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/x86_64-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 ()); | ~~~~~~~~~~~~~~~~~ [ 5%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/backprojector.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/backprojector.cpp.o -MF CMakeFiles/relion_lib.dir/__/backprojector.cpp.o.d -o CMakeFiles/relion_lib.dir/__/backprojector.cpp.o -c /<>/src/backprojector.cpp In file included from /<>/src/image.h:455, from /<>/src/autopicker.h:10, from /<>/src/autopicker_mpi.h:12, from /<>/src/autopicker_mpi.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /<>/src/image.h:455, from /<>/src/projector.h:25, from /<>/src/backprojector.h:33, from /<>/src/backprojector.cpp:27: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/complex.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctf.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/ctf.cpp.o -MF CMakeFiles/relion_lib.dir/__/ctf.cpp.o.d -o CMakeFiles/relion_lib.dir/__/ctf.cpp.o -c /<>/src/ctf.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/obs_model.h:24, from /<>/src/ctf.h:50, from /<>/src/ctf.cpp:45: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 7%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner.cpp.o -MF CMakeFiles/relion_lib.dir/__/ctffind_runner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/ctffind_runner.cpp.o -c /<>/src/ctffind_runner.cpp In file included from /<>/src/image.h:455, from /<>/src/ctffind_runner.h:31, from /<>/src/ctffind_runner.cpp:20: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 7%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner_mpi.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/ctffind_runner_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/ctffind_runner_mpi.cpp.o -c /<>/src/ctffind_runner_mpi.cpp In file included from /<>/src/image.h:455, from /<>/src/ctffind_runner.h:31, from /<>/src/ctffind_runner_mpi.h:25, from /<>/src/ctffind_runner_mpi.cpp:20: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 7%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/error.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 8%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/euler.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 8%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/exp_model.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/exp_model.cpp.o -MF CMakeFiles/relion_lib.dir/__/exp_model.cpp.o.d -o CMakeFiles/relion_lib.dir/__/exp_model.cpp.o -c /<>/src/exp_model.cpp In file included from /<>/src/image.h:455, from /<>/src/exp_model.h:24, from /<>/src/exp_model.cpp:20: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 8%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/fftw.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 9%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/filename.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 9%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/flex_analyser.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 9%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/funcs.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 10%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/healpix_sampling.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/healpix_sampling.cpp.o -MF CMakeFiles/relion_lib.dir/__/healpix_sampling.cpp.o.d -o CMakeFiles/relion_lib.dir/__/healpix_sampling.cpp.o -c /<>/src/healpix_sampling.cpp In file included from /<>/src/image.h:455, from /<>/src/helix.h:30, from /<>/src/healpix_sampling.h:31, from /<>/src/healpix_sampling.cpp:20: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 10%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/helix.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/helix.cpp.o -MF CMakeFiles/relion_lib.dir/__/helix.cpp.o.d -o CMakeFiles/relion_lib.dir/__/helix.cpp.o -c /<>/src/helix.cpp In file included from /<>/src/image.h:455, from /<>/src/helix.h:30, from /<>/src/helix.cpp:22: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 11%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/helix_inimodel2d.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/helix_inimodel2d.cpp.o -MF CMakeFiles/relion_lib.dir/__/helix_inimodel2d.cpp.o.d -o CMakeFiles/relion_lib.dir/__/helix_inimodel2d.cpp.o -c /<>/src/helix_inimodel2d.cpp In file included from /<>/src/image.h:455, from /<>/src/helix_inimodel2d.h:29, from /<>/src/helix_inimodel2d.cpp:22: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 11%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/image.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/image.cpp.o -MF CMakeFiles/relion_lib.dir/__/image.cpp.o.d -o CMakeFiles/relion_lib.dir/__/image.cpp.o -c /<>/src/image.cpp In file included from /<>/src/image.h:455, from /<>/src/image.cpp:20: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 11%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/local_symmetry.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 12%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/local_symmetry_mpi.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/local_symmetry_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/local_symmetry_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/local_symmetry_mpi.cpp.o -c /<>/src/local_symmetry_mpi.cpp In file included from /<>/src/image.h:455, from /<>/src/local_symmetry.h:30, from /<>/src/local_symmetry.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /<>/src/image.h:455, from /<>/src/local_symmetry.h:30, from /<>/src/local_symmetry_mpi.h:5, from /<>/src/local_symmetry_mpi.cpp:1: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 12%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/mask.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 12%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/matrix1d.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 13%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/matrix2d.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 13%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/memory.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 14%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/metadata_container.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 14%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/metadata_label.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 14%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/metadata_table.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 15%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/micrograph_model.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/micrograph_model.cpp.o -MF CMakeFiles/relion_lib.dir/__/micrograph_model.cpp.o.d -o CMakeFiles/relion_lib.dir/__/micrograph_model.cpp.o -c /<>/src/micrograph_model.cpp In file included from /<>/src/image.h:455, from /<>/src/micrograph_model.cpp:23: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /usr/include/x86_64-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))); | ^ [ 15%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ml_model.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 15%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ml_optimiser.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/ml_optimiser.cpp.o -MF CMakeFiles/relion_lib.dir/__/ml_optimiser.cpp.o.d -o CMakeFiles/relion_lib.dir/__/ml_optimiser.cpp.o -c /<>/src/ml_optimiser.cpp In file included from /<>/src/image.h:455, from /<>/src/projector.h:25, from /<>/src/ml_model.h:23, from /<>/src/ml_model.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /<>/src/image.h:455, from /<>/src/projector.h:25, from /<>/src/ml_model.h:23, from /<>/src/ml_optimiser.h:35, from /<>/src/ml_optimiser.cpp:44: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 16%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ml_optimiser_mpi.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/ml_optimiser_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/ml_optimiser_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/ml_optimiser_mpi.cpp.o -c /<>/src/ml_optimiser_mpi.cpp In file included from /<>/src/image.h:455, from /<>/src/projector.h:25, from /<>/src/ml_model.h:23, from /<>/src/ml_optimiser.h:35, from /<>/src/ml_optimiser_mpi.h:24, from /<>/src/ml_optimiser_mpi.cpp:20: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 16%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/motioncorr_runner.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/motioncorr_runner.cpp.o -MF CMakeFiles/relion_lib.dir/__/motioncorr_runner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/motioncorr_runner.cpp.o -c /<>/src/motioncorr_runner.cpp In file included from /<>/src/image.h:455, from /<>/src/motioncorr_runner.h:32, from /<>/src/motioncorr_runner.cpp:22: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 16%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/motioncorr_runner_mpi.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/motioncorr_runner_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/motioncorr_runner_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/motioncorr_runner_mpi.cpp.o -c /<>/src/motioncorr_runner_mpi.cpp In file included from /<>/src/image.h:455, from /<>/src/motioncorr_runner.h:32, from /<>/src/motioncorr_runner_mpi.h:25, from /<>/src/motioncorr_runner_mpi.cpp:20: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 17%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/mpi.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 17%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/multidim_array.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 18%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/numerical_recipes.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 18%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/parallel.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/parallel.cpp.o -MF CMakeFiles/relion_lib.dir/__/parallel.cpp.o.d -o CMakeFiles/relion_lib.dir/__/parallel.cpp.o -c /<>/src/parallel.cpp In file included from /<>/src/numerical_recipes.h:48, from /<>/src/numerical_recipes.cpp:49: In function ‘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; | ^~ [ 18%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/particle_subtractor.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/particle_subtractor.cpp.o -MF CMakeFiles/relion_lib.dir/__/particle_subtractor.cpp.o.d -o CMakeFiles/relion_lib.dir/__/particle_subtractor.cpp.o -c /<>/src/particle_subtractor.cpp In function ‘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; | ^~ [ 19%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/pipeline_control.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/pipeline_control.cpp.o -MF CMakeFiles/relion_lib.dir/__/pipeline_control.cpp.o.d -o CMakeFiles/relion_lib.dir/__/pipeline_control.cpp.o -c /<>/src/pipeline_control.cpp In file included from /<>/src/image.h:455, from /<>/src/projector.h:25, from /<>/src/ml_model.h:23, from /<>/src/ml_optimiser.h:35, from /<>/src/particle_subtractor.h:24, from /<>/src/particle_subtractor.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 19%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/pipeline_jobs.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 19%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/pipeliner.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 20%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/postprocessing.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/postprocessing.cpp.o -MF CMakeFiles/relion_lib.dir/__/postprocessing.cpp.o.d -o CMakeFiles/relion_lib.dir/__/postprocessing.cpp.o -c /<>/src/postprocessing.cpp In file included from /<>/src/image.h:455, from /<>/src/postprocessing.h:24, from /<>/src/postprocessing.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 20%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/preprocessing.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/preprocessing.cpp.o -MF CMakeFiles/relion_lib.dir/__/preprocessing.cpp.o.d -o CMakeFiles/relion_lib.dir/__/preprocessing.cpp.o -c /<>/src/preprocessing.cpp In file included from /<>/src/image.h:455, from /<>/src/preprocessing.h:29, from /<>/src/preprocessing.cpp:20: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 20%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/preprocessing_mpi.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 21%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/projector.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/projector.cpp.o -MF CMakeFiles/relion_lib.dir/__/projector.cpp.o.d -o CMakeFiles/relion_lib.dir/__/projector.cpp.o -c /<>/src/projector.cpp In file included from /<>/src/image.h:455, from /<>/src/preprocessing.h:29, from /<>/src/preprocessing_mpi.h:24, from /<>/src/preprocessing_mpi.cpp:20: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /<>/src/image.h:455, from /<>/src/projector.h:25, from /<>/src/projector.cpp:20: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 21%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/reconstructor.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/reconstructor.cpp.o -MF CMakeFiles/relion_lib.dir/__/reconstructor.cpp.o.d -o CMakeFiles/relion_lib.dir/__/reconstructor.cpp.o -c /<>/src/reconstructor.cpp In file included from /<>/src/image.h:455, from /<>/src/projector.h:25, from /<>/src/backprojector.h:33, from /<>/src/reconstructor.h:23, from /<>/src/reconstructor.cpp:20: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 22%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/reconstructor_mpi.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/reconstructor_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/reconstructor_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/reconstructor_mpi.cpp.o -c /<>/src/reconstructor_mpi.cpp In file included from /<>/src/image.h:455, from /<>/src/projector.h:25, from /<>/src/backprojector.h:33, from /<>/src/reconstructor.h:23, from /<>/src/reconstructor_mpi.h:25, from /<>/src/reconstructor_mpi.cpp:20: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 22%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/renderEER.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 22%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/scheduler.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/scheduler.cpp.o -MF CMakeFiles/relion_lib.dir/__/scheduler.cpp.o.d -o CMakeFiles/relion_lib.dir/__/scheduler.cpp.o -c /<>/src/scheduler.cpp In file included from /<>/src/image.h:455, from /<>/src/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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /<>/src/image.h:455, from /<>/src/jaz/obs_model.h:24, from /<>/src/scheduler.h:26, from /<>/src/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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | 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); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 23%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/strings.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 23%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/symmetries.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 23%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/tabfuncs.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 24%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/tiff_converter.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/tiff_converter.cpp.o -MF CMakeFiles/relion_lib.dir/__/tiff_converter.cpp.o.d -o CMakeFiles/relion_lib.dir/__/tiff_converter.cpp.o -c /<>/src/tiff_converter.cpp In file included from /<>/src/image.h:455, from /<>/src/tiff_converter.cpp:24: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/tiff_converter.cpp: In member function ‘void TIFFConverter::estimate(FileName)’: /<>/src/tiff_converter.cpp:141:101: warning: format ‘%d’ expects argument of type ‘int’, but argument 7 has type ‘long int’ [-Wformat=] 141 | printf(" %s Frame %03d #Changed %10d #Mismatch %10d, #Negative %10d, #Unreliable %10d / %10d\n", | ~~~^ | | | int | %10ld /<>/src/tiff_converter.cpp:141:108: warning: format ‘%d’ expects argument of type ‘int’, but argument 8 has type ‘long int’ [-Wformat=] 141 | printf(" %s Frame %03d #Changed %10d #Mismatch %10d, #Negative %10d, #Unreliable %10d / %10d\n", | ~~~^ | | | int | %10ld /<>/src/tiff_converter.cpp: In member function ‘int TIFFConverter::checkMRCtype(FileName)’: /<>/src/tiff_converter.cpp:309:14: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 309 | fread(headers, sizeof(int), 24, mrcin); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/tiff_converter.cpp: In member function ‘void TIFFConverter::initialise(int, int)’: /<>/src/tiff_converter.cpp:367:23: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | system(("mkdir -p " + fn_out.beforeLastOf("/")).c_str()); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/tiff_converter.cpp: In member function ‘void TIFFConverter::run()’: /<>/src/tiff_converter.cpp:530:31: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | system(("mkdir -p " + fn_tiff.beforeLastOf("/")).c_str()); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 24%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/time.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 25%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/transformations.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 25%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/Healpix_2.15a/cxxutils.cc.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 25%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/Healpix_2.15a/healpix_base.cc.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 26%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/Fourier_helper.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 26%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/Gaussian_pyramid.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 26%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/aberration_fit.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 27%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/complex_io.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/complex_io.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/complex_io.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/complex_io.cpp.o -c /<>/src/jaz/complex_io.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/Fourier_helper.h:24, from /<>/src/jaz/Fourier_helper.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /<>/src/image.h:455, from /<>/src/jaz/aberration_fit.h:24, from /<>/src/jaz/aberration_fit.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 27%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/convolution_helper.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/convolution_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/convolution_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/convolution_helper.cpp.o -c /<>/src/jaz/convolution_helper.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/complex_io.h:24, from /<>/src/jaz/complex_io.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 27%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf_helper.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf_helper.cpp.o -c /<>/src/jaz/ctf_helper.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/convolution_helper.h:24, from /<>/src/jaz/convolution_helper.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 28%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/damage_helper.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /<>/src/image.h:455, from /<>/src/jaz/obs_model.h:24, from /<>/src/ctf.h:50, from /<>/src/jaz/fsc_helper.h:24, from /<>/src/jaz/damage_helper.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 28%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/distribution_helper.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 29%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/fftw_helper.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/fftw_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/fftw_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/fftw_helper.cpp.o -c /<>/src/jaz/fftw_helper.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/distribution_helper.h:25, from /<>/src/jaz/distribution_helper.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 29%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/fsc_helper.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/fsc_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/fsc_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/fsc_helper.cpp.o -c /<>/src/jaz/fsc_helper.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/obs_model.h:24, from /<>/src/ctf.h:50, from /<>/src/jaz/fsc_helper.h:24, from /<>/src/jaz/fsc_helper.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 29%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/image_log.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/image_log.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/image_log.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/image_log.cpp.o -c /<>/src/jaz/image_log.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/image_log.h:24, from /<>/src/jaz/image_log.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 30%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/interpolation.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/interpolation.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/interpolation.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/interpolation.cpp.o -c /<>/src/jaz/interpolation.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/interpolation.h:24, from /<>/src/jaz/interpolation.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 30%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/jaz_config.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 30%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/legacy_obs_model.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 31%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/local_motion_fit.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 31%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/micrograph_handler.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 31%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/new_ft.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/new_ft.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/new_ft.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/new_ft.cpp.o -c /<>/src/jaz/new_ft.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /<>/src/image.h:455, from /<>/src/jaz/micrograph_handler.h:31, from /<>/src/jaz/micrograph_handler.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 32%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/noise_helper.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 32%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/obs_model.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/obs_model.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/obs_model.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/obs_model.cpp.o -c /<>/src/jaz/obs_model.cpp In file included from /<>/src/image.h:455, from /<>/src/projector.h:25, from /<>/src/jaz/noise_helper.h:25, from /<>/src/jaz/noise_helper.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | 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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 33%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/parallel_ft.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 33%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/reference_map.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/reference_map.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/reference_map.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/reference_map.cpp.o -c /<>/src/jaz/reference_map.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/reference_map.h:24, from /<>/src/jaz/reference_map.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 33%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/refinement_helper.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 34%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/resampling_helper.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 34%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/slice_helper.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/slice_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/slice_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/slice_helper.cpp.o -c /<>/src/jaz/slice_helper.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/obs_model.h:24, from /<>/src/ctf.h:50, from /<>/src/jaz/refinement_helper.h:24, from /<>/src/jaz/refinement_helper.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | 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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 34%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/spectral_helper.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 35%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/stack_helper.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/stack_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/stack_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/stack_helper.cpp.o -c /<>/src/jaz/stack_helper.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/spectral_helper.h:24, from /<>/src/jaz/spectral_helper.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /<>/src/image.h:455, from /<>/src/jaz/obs_model.h:24, from /<>/src/ctf.h:50, from /<>/src/jaz/stack_helper.h:24, from /<>/src/jaz/stack_helper.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 35%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/structure_tensor.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 35%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/svd_helper.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/svd_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/svd_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/svd_helper.cpp.o -c /<>/src/jaz/svd_helper.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/img_proc/filter_helper.h:24, from /<>/src/jaz/structure_tensor.cpp:22: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 36%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/t_complex.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 36%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/volume_converter.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 37%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/volume_integration.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/volume_integration.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/volume_integration.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/volume_integration.cpp.o -c /<>/src/jaz/volume_integration.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/volume_converter.h:25, from /<>/src/jaz/volume_converter.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 37%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/vtk_helper.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/vtk_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/vtk_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/vtk_helper.cpp.o -c /<>/src/jaz/vtk_helper.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/volume_integration.h:26, from /<>/src/jaz/volume_integration.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 37%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/gradient_descent.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 38%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/lbfgs.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 38%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/nelder_mead.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 38%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/optimization.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 39%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/aberration_estimator.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 39%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/bfactor_refiner.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/bfactor_refiner.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/bfactor_refiner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/bfactor_refiner.cpp.o -c /<>/src/jaz/ctf/bfactor_refiner.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/ctf/aberration_estimator.h:4, from /<>/src/jaz/ctf/aberration_estimator.cpp:1: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 40%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner.cpp.o -c /<>/src/jaz/ctf/ctf_refiner.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/ctf/bfactor_refiner.h:4, from /<>/src/jaz/ctf/bfactor_refiner.cpp:1: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | 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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 40%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner_mpi.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner_mpi.cpp.o -c /<>/src/jaz/ctf/ctf_refiner_mpi.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/obs_model.h:24, from /<>/src/jaz/ctf/ctf_refiner.h:24, from /<>/src/jaz/ctf/ctf_refiner_mpi.h:26, from /<>/src/jaz/ctf/ctf_refiner_mpi.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 40%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_estimator.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 41%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_helper.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 41%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/delocalisation_helper.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/delocalisation_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/delocalisation_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/delocalisation_helper.cpp.o -c /<>/src/jaz/ctf/delocalisation_helper.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/ctf/defocus_estimator.h:24, from /<>/src/jaz/ctf/defocus_estimator.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | 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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | 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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 41%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/equation2x2.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 42%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_estimator.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 42%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_helper.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 42%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/modular_ctf_optimisation.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | 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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /<>/src/image.h:455, from /<>/src/jaz/ctf/modular_ctf_optimisation.h:5, from /<>/src/jaz/ctf/modular_ctf_optimisation.cpp:1: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 43%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_estimator.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_estimator.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_estimator.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_estimator.cpp.o -c /<>/src/jaz/ctf/tilt_estimator.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/ctf/tilt_estimator.h:24, from /<>/src/jaz/ctf/tilt_estimator.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 43%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_helper.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_helper.cpp.o -c /<>/src/jaz/ctf/tilt_helper.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/obs_model.h:24, from /<>/src/ctf.h:50, from /<>/src/jaz/ctf/tilt_helper.h:24, from /<>/src/jaz/ctf/tilt_helper.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 44%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/alignment_set.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 44%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/frame_recombiner.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/frame_recombiner.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/frame_recombiner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/frame_recombiner.cpp.o -c /<>/src/jaz/motion/frame_recombiner.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/motion/frame_recombiner.h:24, from /<>/src/jaz/motion/frame_recombiner.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 44%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/gp_motion_fit.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/gp_motion_fit.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/gp_motion_fit.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/gp_motion_fit.cpp.o -c /<>/src/jaz/motion/gp_motion_fit.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/motion/gp_motion_fit.h:24, from /<>/src/jaz/motion/gp_motion_fit.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 45%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_estimator.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 45%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_helper.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 45%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_param_estimator.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_param_estimator.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/motion_param_estimator.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_param_estimator.cpp.o -c /<>/src/jaz/motion/motion_param_estimator.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/motion/motion_estimator.h:24, from /<>/src/jaz/motion/motion_estimator.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | 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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /<>/src/image.h:455, from /<>/src/jaz/motion/alignment_set.h:24, from /<>/src/jaz/motion/motion_param_estimator.h:24, from /<>/src/jaz/motion/motion_param_estimator.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 46%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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/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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 46%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner_mpi.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner_mpi.cpp.o -c /<>/src/jaz/motion/motion_refiner_mpi.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/obs_model.h:24, from /<>/src/ctf.h:50, from /<>/src/jaz/motion/motion_refiner.h:25, from /<>/src/jaz/motion/motion_refiner_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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 46%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/three_hyperparameter_fit.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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/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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 47%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/two_hyperparameter_fit.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 47%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/math/Zernike.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 48%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/color_helper.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 48%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/filter_helper.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 48%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/image_op.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 49%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/backprojection_helper.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/backprojection_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/tomo/backprojection_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/tomo/backprojection_helper.cpp.o -c /<>/src/jaz/tomo/backprojection_helper.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/img_proc/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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | 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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /<>/src/image.h:455, from /<>/src/jaz/tomo/backprojection_helper.h:24, from /<>/src/jaz/tomo/backprojection_helper.cpp:23: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 49%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/imod_helper.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 49%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/projection_helper.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 50%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/tomo_stack.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 50%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/io/star_converter.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/io/star_converter.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/io/star_converter.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/io/star_converter.cpp.o -c /<>/src/jaz/io/star_converter.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/tomo/tomo_stack.h:25, from /<>/src/jaz/tomo/tomo_stack.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | 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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 51%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyev2.c.o cd /<>/build/src/apps && /usr/bin/mpicc -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 51%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevc3.c.o cd /<>/build/src/apps && /usr/bin/mpicc -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 51%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevd3.c.o cd /<>/build/src/apps && /usr/bin/mpicc -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 52%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevh3.c.o cd /<>/build/src/apps && /usr/bin/mpicc -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 52%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevj3.c.o cd /<>/build/src/apps && /usr/bin/mpicc -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 52%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevq3.c.o cd /<>/build/src/apps && /usr/bin/mpicc -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 53%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevv3.c.o cd /<>/build/src/apps && /usr/bin/mpicc -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 53%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsytrd3.c.o cd /<>/build/src/apps && /usr/bin/mpicc -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 53%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/slvsec3.c.o cd /<>/build/src/apps && /usr/bin/mpicc -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 54%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/lbfgs/lbfgs.c.o cd /<>/build/src/apps && /usr/bin/mpicc -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 54%] 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 CMakeFiles/relion_lib.dir/__/fftw.cpp.o CMakeFiles/relion_lib.dir/__/filename.cpp.o 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CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_estimator.cpp.o CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_helper.cpp.o CMakeFiles/relion_lib.dir/__/jaz/motion/alignment_set.cpp.o CMakeFiles/relion_lib.dir/__/jaz/motion/frame_recombiner.cpp.o CMakeFiles/relion_lib.dir/__/jaz/motion/gp_motion_fit.cpp.o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_estimator.cpp.o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_helper.cpp.o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_param_estimator.cpp.o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner.cpp.o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner_mpi.cpp.o CMakeFiles/relion_lib.dir/__/jaz/motion/three_hyperparameter_fit.cpp.o CMakeFiles/relion_lib.dir/__/jaz/motion/two_hyperparameter_fit.cpp.o CMakeFiles/relion_lib.dir/__/jaz/math/Zernike.cpp.o CMakeFiles/relion_lib.dir/__/jaz/img_proc/color_helper.cpp.o CMakeFiles/relion_lib.dir/__/jaz/img_proc/filter_helper.cpp.o CMakeFiles/relion_lib.dir/__/jaz/img_proc/image_op.cpp.o CMakeFiles/relion_lib.dir/__/jaz/tomo/backprojection_helper.cpp.o CMakeFiles/relion_lib.dir/__/jaz/tomo/imod_helper.cpp.o CMakeFiles/relion_lib.dir/__/jaz/tomo/projection_helper.cpp.o CMakeFiles/relion_lib.dir/__/jaz/tomo/tomo_stack.cpp.o CMakeFiles/relion_lib.dir/__/jaz/io/star_converter.cpp.o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyev2.c.o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevc3.c.o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevd3.c.o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevh3.c.o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevj3.c.o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevq3.c.o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevv3.c.o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsytrd3.c.o CMakeFiles/relion_lib.dir/__/jaz/d3x3/slvsec3.c.o CMakeFiles/relion_lib.dir/__/jaz/lbfgs/lbfgs.c.o /usr/bin/ranlib ../../lib/librelion_lib.a make[4]: Leaving directory '/<>/build' [ 54%] Built target relion_lib /usr/bin/make -f src/apps/CMakeFiles/relion_gui_lib.dir/build.make src/apps/CMakeFiles/relion_gui_lib.dir/depend /usr/bin/make -f src/apps/CMakeFiles/align_symmetry.dir/build.make src/apps/CMakeFiles/align_symmetry.dir/depend /usr/bin/make -f src/apps/CMakeFiles/autopick.dir/build.make src/apps/CMakeFiles/autopick.dir/depend /usr/bin/make -f src/apps/CMakeFiles/autopick_mpi.dir/build.make src/apps/CMakeFiles/autopick_mpi.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/relion_gui_lib.dir/DependInfo.cmake --color= make[4]: Entering directory '/<>/build' make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/align_symmetry.dir/DependInfo.cmake --color= cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/autopick.dir/DependInfo.cmake --color= make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/autopick_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/align_symmetry.dir/build.make src/apps/CMakeFiles/align_symmetry.dir/build /usr/bin/make -f src/apps/CMakeFiles/autopick.dir/build.make src/apps/CMakeFiles/autopick.dir/build make[4]: Entering directory '/<>/build' make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/relion_gui_lib.dir/build.make src/apps/CMakeFiles/relion_gui_lib.dir/build make[4]: Entering directory '/<>/build' make[4]: Entering directory '/<>/build' 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' [ 55%] Building CXX object src/apps/CMakeFiles/autopick.dir/autopick.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 55%] Building CXX object src/apps/CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o -MF CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o.d -o CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o -c /<>/src/apps/align_symmetry.cpp [ 55%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 55%] Building CXX object src/apps/CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o -MF CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o.d -o CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o -c /<>/src/apps/autopick_mpi.cpp In file included from /<>/src/image.h:455, from /<>/src/projector.h:25, from /<>/src/apps/align_symmetry.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | 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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /<>/src/image.h:455, from /<>/src/autopicker.h:10, from /<>/src/autopicker_mpi.h:12, from /<>/src/apps/autopick_mpi.cpp:20: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ 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 | ^~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 56%] 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 -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -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 -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff make[4]: Leaving directory '/<>/build' [ 56%] 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' [ 56%] Building CXX object src/apps/CMakeFiles/convert_star.dir/convert_star.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 make[4]: Leaving directory '/<>/build' [ 56%] Built target autopick /usr/bin/make -f src/apps/CMakeFiles/convert_to_tiff.dir/build.make src/apps/CMakeFiles/convert_to_tiff.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/convert_to_tiff.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/convert_to_tiff.dir/build.make src/apps/CMakeFiles/convert_to_tiff.dir/build make[4]: Entering directory '/<>/build' [ 57%] Building CXX object src/apps/CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o -MF CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o.d -o CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o -c /<>/src/apps/convert_to_tiff.cpp In file included from /<>/src/image.h:455, from /<>/src/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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | 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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 57%] 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 -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff make[4]: Leaving directory '/<>/build' [ 57%] Linking CXX executable ../../bin/relion_convert_star cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/convert_star.dir/link.txt --verbose=1 [ 57%] 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= /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build.make src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build make[4]: Entering directory '/<>/build' [ 58%] Building CXX object src/apps/CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o -MF CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o.d -o CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o -c /<>/src/apps/convert_to_tiff_mpi.cpp In file included from /<>/src/image.h:455, from /<>/src/tiff_converter.h:24, from /<>/src/apps/convert_to_tiff_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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/<>/build' [ 58%] Built target convert_star /usr/bin/make -f src/apps/CMakeFiles/ctf_mask_test.dir/build.make src/apps/CMakeFiles/ctf_mask_test.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/ctf_mask_test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/ctf_mask_test.dir/build.make src/apps/CMakeFiles/ctf_mask_test.dir/build make[4]: Entering directory '/<>/build' [ 58%] Building CXX object src/apps/CMakeFiles/ctf_mask_test.dir/ctf_mask_test.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 58%] 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 -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff 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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 58%] Linking CXX executable ../../bin/relion_convert_to_tiff_mpi cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/convert_to_tiff_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff make[4]: Leaving directory '/<>/build' [ 58%] Built target align_symmetry /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' [ 58%] Building CXX object src/apps/CMakeFiles/ctf_refine.dir/ctf_refine.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 make[4]: Leaving directory '/<>/build' [ 58%] Built target convert_to_tiff_mpi /usr/bin/make -f src/apps/CMakeFiles/ctf_refine_mpi.dir/build.make src/apps/CMakeFiles/ctf_refine_mpi.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/ctf_refine_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/ctf_refine_mpi.dir/build.make src/apps/CMakeFiles/ctf_refine_mpi.dir/build make[4]: Entering directory '/<>/build' [ 59%] Building CXX object src/apps/CMakeFiles/ctf_refine_mpi.dir/ctf_refine_mpi.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/ctf_refine_mpi.dir/ctf_refine_mpi.cpp.o -MF CMakeFiles/ctf_refine_mpi.dir/ctf_refine_mpi.cpp.o.d -o CMakeFiles/ctf_refine_mpi.dir/ctf_refine_mpi.cpp.o -c /<>/src/apps/ctf_refine_mpi.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/obs_model.h:24, from /<>/src/jaz/ctf/ctf_refiner.h:24, from /<>/src/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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | 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/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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 59%] 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 -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff make[4]: Leaving directory '/<>/build' [ 59%] Built target ctf_refine /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' [ 59%] Building CXX object src/apps/CMakeFiles/ctf_toolbox.dir/ctf_toolbox.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 59%] 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 -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff 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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 60%] 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 make[4]: Leaving directory '/<>/build' /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff [ 60%] Built target ctf_refine_mpi /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' [ 60%] Building CXX object src/apps/CMakeFiles/demodulate.dir/demodulate.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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' [ 60%] Built target ctf_mask_test /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= 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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ 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 -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/estimate_gain.dir/estimate_gain.cpp.o -MF CMakeFiles/estimate_gain.dir/estimate_gain.cpp.o.d -o CMakeFiles/estimate_gain.dir/estimate_gain.cpp.o -c /<>/src/apps/estimate_gain.cpp In file included from /<>/src/image.h:455, from /<>/src/apps/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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 62%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 63%] Linking CXX executable ../../bin/relion_ctf_toolbox cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/ctf_toolbox.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff [ 63%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 make[4]: Leaving directory '/<>/build' [ 63%] Built target ctf_toolbox /usr/bin/make -f src/apps/CMakeFiles/external_reconstruct.dir/build.make src/apps/CMakeFiles/external_reconstruct.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/external_reconstruct.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/external_reconstruct.dir/build.make src/apps/CMakeFiles/external_reconstruct.dir/build make[4]: Entering directory '/<>/build' [ 63%] Building CXX object src/apps/CMakeFiles/external_reconstruct.dir/external_reconstruct.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 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 -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff [ 64%] 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 -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff 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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/<>/build' [ 64%] Built target estimate_gain /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' [ 64%] Building CXX object src/apps/CMakeFiles/find_tiltpairs.dir/find_tiltpairs.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/find_tiltpairs.dir/find_tiltpairs.cpp.o -MF CMakeFiles/find_tiltpairs.dir/find_tiltpairs.cpp.o.d -o CMakeFiles/find_tiltpairs.dir/find_tiltpairs.cpp.o -c /<>/src/apps/find_tiltpairs.cpp make[4]: Leaving directory '/<>/build' [ 64%] Built target demodulate /usr/bin/make -f src/apps/CMakeFiles/flex_analyse.dir/build.make src/apps/CMakeFiles/flex_analyse.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/flex_analyse.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/flex_analyse.dir/build.make src/apps/CMakeFiles/flex_analyse.dir/build make[4]: Entering directory '/<>/build' [ 65%] Building CXX object src/apps/CMakeFiles/flex_analyse.dir/flex_analyse.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /<>/src/numerical_recipes.h:48, from /<>/src/funcs.h:59, from /<>/src/args.h:56, from /<>/src/apps/find_tiltpairs.cpp:20: In function ‘void free_Tvector(T*&, int, int) [with T = int]’, inlined from ‘void gaussj(T*, int, T*, int) [with T = double]’ at /<>/src/numerical_recipes.h:262:17: /<>/src/memory.h:74:13: warning: ‘void free(void*)’ called on pointer ‘ipiv’ with nonzero offset 4 [-Wfree-nonheap-object] 74 | free((char*)(v + nl)); | ~~~~^~~~~~~~~~~~~~~~~ /<>/src/numerical_recipes.h: In function ‘void gaussj(T*, int, T*, int) [with T = double]’: /<>/src/numerical_recipes.h:198:26: note: declared here 198 | int *indxc, *indxr, *ipiv; | ^~~~ In function ‘void free_Tvector(T*&, int, int) [with T = int]’, inlined from ‘void gaussj(T*, int, T*, int) [with T = double]’ at /<>/src/numerical_recipes.h:262:17: /<>/src/memory.h:74:13: warning: ‘void free(void*)’ called on pointer ‘ipiv’ with nonzero offset 4 [-Wfree-nonheap-object] 74 | free((char*)(v + nl)); | ~~~~^~~~~~~~~~~~~~~~~ /<>/src/numerical_recipes.h: In function ‘void gaussj(T*, int, T*, int) [with T = double]’: /<>/src/numerical_recipes.h:198:26: note: declared here 198 | int *indxc, *indxr, *ipiv; | ^~~~ [ 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 -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff make[4]: Leaving directory '/<>/build' [ 65%] Built target find_tiltpairs /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' [ 66%] Building CXX object src/apps/CMakeFiles/flex_analyse_mpi.dir/flex_analyse_mpi.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 67%] 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 -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff [ 67%] 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 -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff [ 67%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o -MF CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o.d -o CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o -c /<>/src/gui_mainwindow.cpp In file included from /<>/src/image.h:455, from /<>/src/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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/<>/build' [ 67%] Built target external_reconstruct /usr/bin/make -f src/apps/CMakeFiles/helix_inimodel2d.dir/build.make src/apps/CMakeFiles/helix_inimodel2d.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/helix_inimodel2d.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/helix_inimodel2d.dir/build.make src/apps/CMakeFiles/helix_inimodel2d.dir/build make[4]: Entering directory '/<>/build' [ 67%] Building CXX object src/apps/CMakeFiles/helix_inimodel2d.dir/helix_inimodel2d.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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' [ 67%] Built target flex_analyse /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 -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o -MF CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o.d -o CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o -c /<>/src/apps/helix_toolbox.cpp In file included from /<>/src/image.h:455, from /<>/src/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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | 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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | 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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | 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 -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff make[4]: Leaving directory '/<>/build' [ 68%] Built target helix_inimodel2d /usr/bin/make -f src/apps/CMakeFiles/image_handler.dir/build.make src/apps/CMakeFiles/image_handler.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/image_handler.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/image_handler.dir/build.make src/apps/CMakeFiles/image_handler.dir/build make[4]: Entering directory '/<>/build' [ 69%] Building CXX object src/apps/CMakeFiles/image_handler.dir/image_handler.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 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 -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/<>/build' [ 69%] Built target flex_analyse_mpi /usr/bin/make -f src/apps/CMakeFiles/import.dir/build.make src/apps/CMakeFiles/import.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/import.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/import.dir/build.make src/apps/CMakeFiles/import.dir/build make[4]: Entering directory '/<>/build' [ 70%] Building CXX object src/apps/CMakeFiles/import.dir/import.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/import.dir/import.cpp.o -MF CMakeFiles/import.dir/import.cpp.o.d -o CMakeFiles/import.dir/import.cpp.o -c /<>/src/apps/import.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/obs_model.h:24, from /<>/src/apps/import.cpp:22: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 70%] Linking CXX executable ../../bin/relion_import cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/import.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff make[4]: Leaving directory '/<>/build' [ 70%] 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' [ 70%] Building CXX object src/apps/CMakeFiles/localsym.dir/localsym.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/localsym.dir/localsym.cpp.o -MF CMakeFiles/localsym.dir/localsym.cpp.o.d -o CMakeFiles/localsym.dir/localsym.cpp.o -c /<>/src/apps/localsym.cpp In file included from /<>/src/image.h:455, from /<>/src/local_symmetry.h:30, from /<>/src/apps/localsym.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 71%] Linking CXX executable ../../bin/relion_localsym cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/localsym.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff make[4]: Leaving directory '/<>/build' [ 71%] 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' [ 71%] Building CXX object src/apps/CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 72%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/manualpicker.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/manualpicker.cpp.o -MF CMakeFiles/relion_gui_lib.dir/__/manualpicker.cpp.o.d -o CMakeFiles/relion_gui_lib.dir/__/manualpicker.cpp.o -c /<>/src/manualpicker.cpp In file included from /<>/src/image.h:455, from /<>/src/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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 72%] 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 -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff 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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/<>/build' [ 72%] Built target helix_toolbox /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' [ 72%] Building CXX object src/apps/CMakeFiles/mask_create.dir/mask_create.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 72%] 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 -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff 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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/<>/build' [ 72%] Built target localsym_mpi /usr/bin/make -f src/apps/CMakeFiles/merge_particles.dir/build.make src/apps/CMakeFiles/merge_particles.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/merge_particles.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/merge_particles.dir/build.make src/apps/CMakeFiles/merge_particles.dir/build make[4]: Entering directory '/<>/build' [ 72%] Building CXX object src/apps/CMakeFiles/merge_particles.dir/merge_particles.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 72%] Linking CXX executable ../../bin/relion_image_handler cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/image_handler.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/<>/build' [ 72%] Built target image_handler /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' [ 72%] Building CXX object src/apps/CMakeFiles/motion_refine.dir/motion_refine.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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_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 -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/<>/build' [ 73%] Built target merge_particles /usr/bin/make -f src/apps/CMakeFiles/motion_refine_mpi.dir/build.make src/apps/CMakeFiles/motion_refine_mpi.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/motion_refine_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/motion_refine_mpi.dir/build.make src/apps/CMakeFiles/motion_refine_mpi.dir/build make[4]: Entering directory '/<>/build' [ 74%] Building CXX object src/apps/CMakeFiles/motion_refine_mpi.dir/motion_refine_mpi.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/motion_refine_mpi.dir/motion_refine_mpi.cpp.o -MF CMakeFiles/motion_refine_mpi.dir/motion_refine_mpi.cpp.o.d -o CMakeFiles/motion_refine_mpi.dir/motion_refine_mpi.cpp.o -c /<>/src/apps/motion_refine_mpi.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/obs_model.h:24, from /<>/src/ctf.h:50, from /<>/src/jaz/motion/motion_refiner.h:25, from /<>/src/jaz/motion/motion_refiner_mpi.h:27, from /<>/src/apps/motion_refine_mpi.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 74%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/cxxutils.cc.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 74%] 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 -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff [ 75%] Linking CXX executable ../../bin/relion_mask_create cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/mask_create.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff make[4]: Leaving directory '/<>/build' [ 75%] Built target mask_create /usr/bin/make -f src/apps/CMakeFiles/mrc2vtk.dir/build.make src/apps/CMakeFiles/mrc2vtk.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/mrc2vtk.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/mrc2vtk.dir/build.make src/apps/CMakeFiles/mrc2vtk.dir/build make[4]: Entering directory '/<>/build' [ 75%] Building CXX object src/apps/CMakeFiles/mrc2vtk.dir/mrc2vtk.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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' [ 75%] Built target motion_refine /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' [ 75%] Building CXX object src/apps/CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o -MF CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o.d -o CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o -c /<>/src/apps/particle_FCC.cpp In file included from /<>/src/image.h:455, from /<>/src/apps/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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 75%] 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 -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff In file included from /<>/src/image.h:455, from /<>/src/apps/particle_FCC.cpp:7: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 76%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 make[4]: Leaving directory '/<>/build' [ 76%] Built target motion_refine_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' [ 77%] Building CXX object src/apps/CMakeFiles/particle_reposition.dir/particle_reposition.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 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 -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff 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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 78%] Linking CXX executable ../../bin/relion_mrc2vtk cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/mrc2vtk.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff [ 78%] 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 make[4]: Leaving directory '/<>/build' make[4]: Leaving directory '/<>/build' [ 78%] Built target mrc2vtk /usr/bin/make -f src/apps/CMakeFiles/particle_select.dir/build.make src/apps/CMakeFiles/particle_select.dir/depend /usr/bin/ranlib ../../lib/librelion_gui_lib.a [ 78%] Built target particle_FCC /usr/bin/make -f src/apps/CMakeFiles/particle_subtract.dir/build.make src/apps/CMakeFiles/particle_subtract.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/particle_select.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/particle_subtract.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]: 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]: Entering directory '/<>/build' [ 79%] Building CXX object src/apps/CMakeFiles/particle_select.dir/particle_select.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 79%] Building CXX object src/apps/CMakeFiles/particle_subtract.dir/particle_subtract.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 make[4]: Leaving directory '/<>/build' [ 79%] Built target relion_gui_lib /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' [ 79%] Building CXX object src/apps/CMakeFiles/particle_subtract_mpi.dir/particle_subtract_mpi.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | 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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /<>/src/image.h:455, from /<>/src/projector.h:25, from /<>/src/ml_model.h:23, from /<>/src/ml_optimiser.h:35, from /<>/src/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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 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 -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff make[4]: Leaving directory '/<>/build' [ 79%] Built target particle_select /usr/bin/make -f src/apps/CMakeFiles/particle_symmetry_expand.dir/build.make src/apps/CMakeFiles/particle_symmetry_expand.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/particle_symmetry_expand.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/particle_symmetry_expand.dir/build.make src/apps/CMakeFiles/particle_symmetry_expand.dir/build make[4]: Entering directory '/<>/build' [ 80%] Building CXX object src/apps/CMakeFiles/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o -MF CMakeFiles/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o.d -o CMakeFiles/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o -c /<>/src/apps/particle_symmetry_expand.cpp In file included from /<>/src/image.h:455, from /<>/src/jaz/obs_model.h:24, from /<>/src/apps/particle_symmetry_expand.cpp:26: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 81%] 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 -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff make[4]: Leaving directory '/<>/build' [ 81%] Built target particle_subtract /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' [ 82%] Building CXX object src/apps/CMakeFiles/pipeliner.dir/pipeliner.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 82%] Linking CXX executable ../../bin/relion_particle_subtract_mpi cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_subtract_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff [ 82%] 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 -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff make[4]: Leaving directory '/<>/build' [ 82%] Built target particle_subtract_mpi /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' [ 82%] Building CXX object src/apps/CMakeFiles/plot_delocalisation.dir/plot_delocalisation.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 make[4]: Leaving directory '/<>/build' [ 82%] Built target particle_symmetry_expand /usr/bin/make -f src/apps/CMakeFiles/postprocess.dir/build.make src/apps/CMakeFiles/postprocess.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/postprocess.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/postprocess.dir/build.make src/apps/CMakeFiles/postprocess.dir/build make[4]: Entering directory '/<>/build' [ 82%] Building CXX object src/apps/CMakeFiles/postprocess.dir/postprocess.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | 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.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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 82%] 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 -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff make[4]: Leaving directory '/<>/build' [ 82%] Built target pipeliner /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' [ 83%] Building CXX object src/apps/CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 83%] 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 -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff [ 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 -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff 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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 84%] Linking CXX executable ../../bin/relion_plot_delocalisation cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/plot_delocalisation.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff make[4]: Leaving directory '/<>/build' [ 84%] Built target postprocess /usr/bin/make -f src/apps/CMakeFiles/prepare_subtomo.dir/build.make src/apps/CMakeFiles/prepare_subtomo.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/prepare_subtomo.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/prepare_subtomo.dir/build.make src/apps/CMakeFiles/prepare_subtomo.dir/build make[4]: Entering directory '/<>/build' [ 84%] Building CXX object src/apps/CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 make[4]: Leaving directory '/<>/build' [ 84%] Built target particle_reposition /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' [ 84%] Building CXX object src/apps/CMakeFiles/preprocess.dir/preprocess.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/preprocess.dir/preprocess.cpp.o -MF CMakeFiles/preprocess.dir/preprocess.cpp.o.d -o CMakeFiles/preprocess.dir/preprocess.cpp.o -c /<>/src/apps/preprocess.cpp In file included from /<>/src/image.h:455, from /<>/src/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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/<>/build' /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 84%] Built target plot_delocalisation /usr/bin/make -f src/apps/CMakeFiles/preprocess_mpi.dir/build.make src/apps/CMakeFiles/preprocess_mpi.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/preprocess_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/preprocess_mpi.dir/build.make src/apps/CMakeFiles/preprocess_mpi.dir/build make[4]: Entering directory '/<>/build' [ 84%] Building CXX object src/apps/CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o -MF CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o.d -o CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o -c /<>/src/apps/preprocess_mpi.cpp In file included from /<>/src/image.h:455, from /<>/src/preprocessing.h:29, from /<>/src/apps/preprocess.cpp:20: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 84%] Linking CXX executable ../../bin/relion_postprocess_mpi cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/postprocess_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff make[4]: Leaving directory '/<>/build' [ 84%] 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' [ 85%] Building CXX object src/apps/CMakeFiles/project.dir/project.cpp.o 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 | ^~~~~ cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/project.dir/project.cpp.o -MF CMakeFiles/project.dir/project.cpp.o.d -o CMakeFiles/project.dir/project.cpp.o -c /<>/src/apps/project.cpp In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 86%] 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 -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/<>/build' [ 86%] Built target preprocess /usr/bin/make -f src/apps/CMakeFiles/reconstruct.dir/build.make src/apps/CMakeFiles/reconstruct.dir/depend make[4]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/reconstruct.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/reconstruct.dir/build.make src/apps/CMakeFiles/reconstruct.dir/build make[4]: Entering directory '/<>/build' [ 86%] Building CXX object src/apps/CMakeFiles/reconstruct.dir/reconstruct.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 86%] 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 -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff 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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | 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/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' [ 86%] Building CXX object src/apps/CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o -MF CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o.d -o CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o -c /<>/src/apps/reconstruct_mpi.cpp In file included from /<>/src/image.h:455, from /<>/src/projector.h:25, from /<>/src/backprojector.h:33, from /<>/src/reconstructor.h:23, from /<>/src/reconstructor_mpi.h:25, from /<>/src/apps/reconstruct_mpi.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 87%] Linking CXX executable ../../bin/relion_reconstruct cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/reconstruct.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff make[4]: Leaving directory '/<>/build' [ 87%] Built target reconstruct /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' [ 88%] Building CXX object src/apps/CMakeFiles/refine.dir/refine.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/refine.dir/refine.cpp.o -MF CMakeFiles/refine.dir/refine.cpp.o.d -o CMakeFiles/refine.dir/refine.cpp.o -c /<>/src/apps/refine.cpp In file included from /<>/src/image.h:455, from /<>/src/projector.h:25, from /<>/src/ml_model.h:23, from /<>/src/ml_optimiser.h:35, from /<>/src/apps/refine.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | 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 -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff make[4]: Leaving directory '/<>/build' [ 88%] Built target reconstruct_mpi /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' [ 89%] Building CXX object src/apps/CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o -MF CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o.d -o CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o -c /<>/src/apps/refine_mpi.cpp In file included from /<>/src/image.h:455, from /<>/src/projector.h:25, from /<>/src/ml_model.h:23, from /<>/src/ml_optimiser.h:35, from /<>/src/ml_optimiser_mpi.h:24, from /<>/src/apps/refine_mpi.cpp:21: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 89%] 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 -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff [ 89%] Linking CXX executable ../../bin/relion_project cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/project.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff make[4]: Leaving directory '/<>/build' [ 89%] Built target refine /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' [ 90%] Building CXX object src/apps/CMakeFiles/reposition.dir/reposition.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 make[4]: Leaving directory '/<>/build' [ 90%] Built target project /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' [ 90%] Building CXX object src/apps/CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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/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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | 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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 90%] 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 -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff [ 91%] 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 -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff make[4]: Leaving directory '/<>/build' [ 91%] Built target refine_mpi /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' [ 91%] Building CXX object src/apps/CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 make[4]: Leaving directory '/<>/build' [ 91%] 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' [ 92%] Building CXX object src/apps/CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 93%] 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 -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | 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/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' [ 93%] Building CXX object src/apps/CMakeFiles/run_motioncorr_mpi.dir/run_motioncorr_mpi.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 93%] Linking CXX executable ../../bin/relion_reposition cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/reposition.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 93%] Linking CXX executable ../../bin/relion_run_motioncorr cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/run_motioncorr.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff make[4]: Leaving directory '/<>/build' [ 93%] 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' [ 93%] Building CXX object src/apps/CMakeFiles/scheduler.dir/scheduler.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 93%] 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 -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff make[4]: Leaving directory '/<>/build' [ 93%] Built target run_motioncorr /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' [ 93%] Building CXX object src/apps/CMakeFiles/stack_create.dir/stack_create.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 make[4]: Leaving directory '/<>/build' [ 93%] Built target run_ctffind_mpi /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= 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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ 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 -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 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 -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff 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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | 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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | 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/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' [ 95%] Building CXX object src/apps/CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o -MF CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o.d -o CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o -c /<>/src/apps/tiltpair_plot.cpp In file included from /<>/src/image.h:455, from /<>/src/apps/tiltpair_plot.cpp:25: /<>/src/rwTIFF.h: In member function ‘int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)’: /<>/src/rwTIFF.h:43:16: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 96%] Linking CXX executable ../../bin/relion_scheduler cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/scheduler.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff [ 97%] 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 -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff make[4]: Leaving directory '/<>/build' [ 97%] 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' [ 97%] Building CXX object src/apps/CMakeFiles/tomo_test.dir/tomo_test.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 make[4]: Leaving directory '/<>/build' [ 97%] Built target scheduler /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' [ 97%] Building CXX object src/apps/CMakeFiles/display.dir/display.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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/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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ 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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 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 -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a ../../lib/librelion_gui_lib.a /usr/lib/x86_64-linux-gnu/libfltk_images.so /usr/lib/x86_64-linux-gnu/libfltk_forms.so /usr/lib/x86_64-linux-gnu/libfltk.so -lX11 -lm -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -ltiff -Wl,-Bstatic -lcudart_static -Wl,-Bdynamic -ldl -Wl,-Bstatic -lrt -Wl,-Bdynamic -lcufft [ 97%] 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 -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff make[4]: Leaving directory '/<>/build' [ 97%] Built target display /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' [ 97%] Building CXX object src/apps/CMakeFiles/relion.dir/maingui.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 make[4]: Leaving directory '/<>/build' [ 97%] Built target stack_create /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' [ 98%] Building CXX object src/apps/CMakeFiles/manualpick.dir/manualpick.cpp.o cd /<>/build/src/apps && /usr/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DALLOW_CTF_IN_SGD -DCUDA -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/<>/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<> -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 99%] 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 -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ 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/x86_64-linux-gnu/tiffio.h:31, from /<>/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:43:23: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:16: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:30: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:44:45: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:32: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:185:43: warning: ‘uint32’ is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:84:38: note: declared here 84 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:32: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /<>/src/rwTIFF.h:186:50: warning: ‘uint16’ is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:81:38: note: declared here 81 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/<>/build' [ 99%] Built target tomo_test [ 99%] 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 -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a ../../lib/librelion_gui_lib.a /usr/lib/x86_64-linux-gnu/libfltk_images.so /usr/lib/x86_64-linux-gnu/libfltk_forms.so /usr/lib/x86_64-linux-gnu/libfltk.so -lX11 -lm -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -ltiff -Wl,-Bstatic -lcudart_static -Wl,-Bdynamic -ldl -Wl,-Bstatic -lrt -Wl,-Bdynamic -lcufft [100%] 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 -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a ../../lib/librelion_gui_lib.a /usr/lib/x86_64-linux-gnu/libfltk_images.so /usr/lib/x86_64-linux-gnu/libfltk_forms.so /usr/lib/x86_64-linux-gnu/libfltk.so -lX11 -lm -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -ltiff -Wl,-Bstatic -lcudart_static -Wl,-Bdynamic -ldl -Wl,-Bstatic -lrt -Wl,-Bdynamic -lcufft make[4]: Leaving directory '/<>/build' [100%] Built target manualpick make[4]: Leaving directory '/<>/build' [100%] Built target relion [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 -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff make[4]: Leaving directory '/<>/build' [100%] Built target star_handler 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 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 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. -- 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 -- CUDA enabled - Building CUDA-accelerated version of RELION -- Setting cpu precision to double -- Setting accelerated code precision to single -- Using cuda wrapper to compile.... -- Cuda version is >= 7.5 and single-precision build, enable double usage warning. -- MPI_INCLUDE_PATH : /usr/lib/x86_64-linux-gnu/openmpi/include;/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -- MPI_LIBRARIES : /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -- MPI_CXX_INCLUDE_PATH : /usr/lib/x86_64-linux-gnu/openmpi/include;/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -- MPI_CXX_LIBRARIES : /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -- CMAKE_C_COMPILER : /usr/bin/cc -- CMAKE_CXX_COMPILER : /usr/bin/c++ -- MPI_C_COMPILER : /usr/bin/mpicc -- MPI_CXX_COMPILER : /usr/bin/mpicxx -- CMAKE_CXX_COMPILER_ID : GNU -- X11 and FLTK were found -- FLTK_LIBRARIES: fltk_images;fltk_forms;fltk;/usr/lib/x86_64-linux-gnu/libX11.so;/usr/lib/x86_64-linux-gnu/libm.so -- Found FFTW -- FFTW_PATH: /usr/include -- FFTW_INCLUDES: /usr/include -- FFTW_LIBRARIES: /usr/lib/x86_64-linux-gnu/libfftw3f.so;/usr/lib/x86_64-linux-gnu/libfftw3.so -- 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 -- Configuring done -- Generating done -- Build files have been written to: /<>/build /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 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CMakeFiles/relion_gpu_util.dir/cmake_clean_target.cmake cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/relion_gpu_util.dir/link.txt --verbose=1 /usr/bin/ar qc ../../lib/librelion_gpu_util.a CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_autopicker.cu.o CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_backprojector.cu.o CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_benchmark_utils.cu.o CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_helper_functions.cu.o CMakeFiles/relion_gpu_util.dir/__/acc/cuda/cuda_kernels/relion_gpu_util_generated_helper.cu.o CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_ml_optimiser.cu.o CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_projector.cu.o CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_projector_plan.cu.o /usr/bin/ranlib 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-Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/autopick.dir/autopick.cpp.o -o ../../bin/relion_autopick ../../lib/librelion_lib.a -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff make[4]: Leaving directory '/<>/build' [ 58%] 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= Consolidate compiler generated dependencies of target autopick_mpi make[4]: Leaving directory '/<>/build' /usr/bin/make -f 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-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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff make[4]: Leaving directory '/<>/build' [ 61%] 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= Consolidate compiler generated dependencies of target ctf_mask_test make[4]: Leaving directory '/<>/build' /usr/bin/make 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-fstack-protector-strong -Wformat -Werror=format-security -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff make[4]: Leaving directory '/<>/build' [ 67%] 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 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-ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff 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= Consolidate compiler generated dependencies of target pipeliner make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/pipeliner.dir/build.make src/apps/CMakeFiles/pipeliner.dir/build make[4]: Entering directory '/<>/build' [ 83%] 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 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/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff 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= Consolidate compiler generated dependencies of target postprocess 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' [ 85%] Linking CXX executable ../../bin/relion_postprocess cd /<>/build/src/apps && /usr/bin/cmake 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/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff 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= Consolidate compiler generated dependencies of target prepare_subtomo 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' [ 87%] Linking CXX executable ../../bin/relion_prepare_subtomo cd 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/usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/apps /<>/build /<>/build/src/apps /<>/build/src/apps/CMakeFiles/preprocess.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target preprocess 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' [ 88%] 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 -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff 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= Consolidate compiler generated dependencies of target preprocess_mpi 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' [ 88%] 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 -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff 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 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-ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff 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 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-ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff 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= Consolidate 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/usr/bin/make -f src/apps/CMakeFiles/scheduler.dir/build.make src/apps/CMakeFiles/scheduler.dir/build make[4]: Entering directory '/<>/build' [ 97%] 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 -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff make[4]: Leaving directory '/<>/build' [ 97%] 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= Consolidate compiler generated dependencies of target stack_create make[4]: Leaving directory '/<>/build' /usr/bin/make -f src/apps/CMakeFiles/stack_create.dir/build.make src/apps/CMakeFiles/stack_create.dir/build make[4]: Entering directory '/<>/build' [ 97%] 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 -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff 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= Consolidate compiler generated dependencies of target star_handler 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' [ 97%] 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 -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff 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= Consolidate compiler generated dependencies of target tiltpair_plot 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' [ 99%] Linking CXX executable ../../bin/relion_tiltpair_plot cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiltpair_plot.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff 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= Consolidate compiler generated dependencies of target tomo_test 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' [100%] Linking CXX executable ../../bin/relion_tomo_test cd /<>/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/tomo_test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -lcufft /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gpu_util.a -ltiff ../../lib/librelion_lib.a ../../lib/librelion_gpu_util.a -lfftw3f -lfftw3 -lcurand -Wl,-Bstatic -lcudart_static -lrt -Wl,-Bdynamic -lcufft -ldl -ltiff 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_tomo_test -- Installing: /<>/debian/tmp/cli/usr/bin/relion_stack_create -- Installing: /<>/debian/tmp/cli/usr/bin/relion_refine -- Installing: /<>/debian/tmp/cli/usr/bin/relion_scheduler -- Installing: /<>/debian/tmp/cli/usr/bin/relion_mrc2vtk -- Installing: /<>/debian/tmp/cli/usr/bin/relion_helix_toolbox -- Installing: /<>/debian/tmp/cli/usr/bin/relion_qsub.csh -- Installing: /<>/debian/tmp/cli/usr/bin/relion_star_datablock_singlefiles -- Installing: /<>/debian/tmp/cli/usr/bin/relion_run_ctffind_mpi -- Installing: /<>/debian/tmp/cli/usr/bin/relion_postprocess -- Installing: /<>/debian/tmp/cli/usr/bin/relion_star_plottable -- Installing: /<>/debian/tmp/cli/usr/bin/relion_tiltpair_plot -- Installing: /<>/debian/tmp/cli/usr/bin/relion_preprocess -- Installing: /<>/debian/tmp/cli/usr/bin/relion_ctf_toolbox -- Installing: /<>/debian/tmp/cli/usr/bin/relion_manualpick -- Installing: /<>/debian/tmp/cli/usr/bin/relion_localsym -- Installing: /<>/debian/tmp/cli/usr/bin/relion_pipeliner -- Installing: /<>/debian/tmp/cli/usr/bin/relion_star_handler -- Installing: /<>/debian/tmp/cli/usr/bin/relion_run_motioncorr -- Installing: /<>/debian/tmp/cli/usr/bin/relion_display -- Installing: /<>/debian/tmp/cli/usr/bin/relion_ctf_mask_test -- Installing: /<>/debian/tmp/cli/usr/bin/relion_particle_symmetry_expand -- Installing: /<>/debian/tmp/cli/usr/bin/relion_particle_reposition -- Installing: /<>/debian/tmp/cli/usr/bin/relion_particle_select -- Installing: /<>/debian/tmp/cli/usr/bin/relion_reconstruct_mpi -- Installing: /<>/debian/tmp/cli/usr/bin/relion_star_loopheader -- Installing: /<>/debian/tmp/cli/usr/bin/relion_reconstruct -- Installing: /<>/debian/tmp/cli/usr/bin/relion_project -- Installing: /<>/debian/tmp/cli/usr/bin/relion_image_handler -- Installing: /<>/debian/tmp/cli/usr/bin/relion_flex_analyse_mpi -- Installing: /<>/debian/tmp/cli/usr/bin/relion_align_symmetry -- Installing: /<>/debian/tmp/cli/usr/bin/relion_demodulate -- Installing: /<>/debian/tmp/cli/usr/bin/relion_star_printtable -- Installing: /<>/debian/tmp/cli/usr/bin/relion_motion_refine_mpi -- Installing: /<>/debian/tmp/cli/usr/bin/relion_postprocess_mpi -- Installing: /<>/debian/tmp/cli/usr/bin/relion_autopick_mpi -- Installing: /<>/debian/tmp/cli/usr/bin/relion_convert_to_tiff_mpi -- Installing: /<>/debian/tmp/cli/usr/bin/relion_find_tiltpairs -- Installing: /<>/debian/tmp/cli/usr/bin/relion_autopick -- Installing: /<>/debian/tmp/cli/usr/bin/relion_particle_subtract_mpi -- Installing: /<>/debian/tmp/cli/usr/bin/relion_estimate_gain -- Installing: /<>/debian/tmp/cli/usr/bin/relion_mask_create -- Installing: /<>/debian/tmp/cli/usr/bin/relion_particle_subtract -- Installing: /<>/debian/tmp/cli/usr/bin/relion_helix_inimodel2d -- Installing: /<>/debian/tmp/cli/usr/bin/relion_run_ctffind -- 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_motion_refine -- Installing: /<>/debian/tmp/cli/usr/bin/relion_prepare_subtomo -- Installing: /<>/debian/tmp/cli/usr/bin/relion_convert_to_tiff -- Installing: /<>/debian/tmp/cli/usr/bin/relion_particle_FCC -- Installing: /<>/debian/tmp/cli/usr/bin/relion_localsym_mpi -- Installing: /<>/debian/tmp/cli/usr/bin/relion_preprocess_mpi -- Installing: /<>/debian/tmp/cli/usr/bin/relion_star_datablock_stack -- Installing: /<>/debian/tmp/cli/usr/bin/relion_ctf_refine -- Installing: /<>/debian/tmp/cli/usr/bin/relion_external_reconstruct -- Installing: /<>/debian/tmp/cli/usr/bin/relion_convert_star -- Installing: /<>/debian/tmp/cli/usr/bin/relion_merge_particles -- Installing: /<>/debian/tmp/cli/usr/bin/relion_refine_mpi -- Installing: /<>/debian/tmp/cli/usr/bin/relion_plot_delocalisation -- Installing: /<>/debian/tmp/cli/usr/bin/relion_reposition -- Installing: /<>/debian/tmp/cli/usr/bin/relion_flex_analyse -- Installing: /<>/debian/tmp/cli/usr/bin/relion_import -- Installing: /<>/debian/tmp/cli/usr/bin/relion -- Installing: /<>/debian/tmp/cli/usr/bin/relion_ctf_refine_mpi -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_align_symmetry -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_autopick -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_autopick_mpi -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_convert_star -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_convert_to_tiff -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_convert_to_tiff_mpi -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_ctf_mask_test -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_ctf_refine -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_ctf_refine_mpi -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_ctf_toolbox -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_demodulate -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_display -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_estimate_gain -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_external_reconstruct -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_find_tiltpairs -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_flex_analyse -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_flex_analyse_mpi -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_helix_inimodel2d -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_helix_toolbox -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_image_handler -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_import -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_localsym -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_localsym_mpi -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_manualpick -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_mask_create -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_merge_particles -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_motion_refine -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_motion_refine_mpi -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_mrc2vtk -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_particle_FCC -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_particle_reposition -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_particle_select -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_particle_subtract -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_particle_subtract_mpi -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_particle_symmetry_expand -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_pipeliner -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_plot_delocalisation -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_postprocess -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_postprocess_mpi -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_prepare_subtomo -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_preprocess -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_preprocess_mpi -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_project -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_reconstruct -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_reconstruct_mpi -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_refine -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_refine_mpi -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_reposition -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_run_ctffind -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_run_ctffind_mpi -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_run_motioncorr -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_run_motioncorr_mpi -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_scheduler -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_stack_create -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_star_handler -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_tiltpair_plot -- Up-to-date: /<>/debian/tmp/cli/usr/bin/relion_tomo_test make[2]: Leaving directory '/<>/build' mkdir -p /<>/debian/tmp/gui/usr/bin rm /<>/debian/tmp/cli/usr/bin/*.csh # Useless ... set -e; for prog in relion relion_display relion_manualpick; do \ mv /<>/debian/tmp/cli/usr/bin/$prog \ /<>/debian/tmp/gui/usr/bin; done make[1]: Leaving directory '/<>' dh_install dh_installdocs dh_installchangelogs dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a debugedit: debian/relion-gui-cuda/usr/bin/relion_manualpick: Unknown DWARF DW_FORM_0x1f21 debugedit: debian/relion-cuda/usr/bin/relion_tomo_test: Unknown DWARF DW_FORM_0x1f20 52fcb6e154b13d30a70ee7d9b764674c802174fe c57531cc21319dcac91b8a79a999a7994fe06754 debugedit: debian/relion-gui-cuda/usr/bin/relion_display: Unknown DWARF DW_FORM_0x1f20 3183fdba373b36caa33039713e045961d12bc0c0 debugedit: debian/relion-cuda/usr/bin/relion_stack_create: Unknown DWARF DW_FORM_0x1f20 7728e2c8870d1bafcdd9bd059175d7012b2b53e6 debugedit: debian/relion-gui-cuda/usr/bin/relion: Unknown DWARF DW_FORM_0x1f20 debugedit: debian/relion-cuda/usr/bin/relion_refine: Unknown DWARF DW_FORM_0x1f20 f24a59da72186b7680535bfd324daa44ab7e689f b3f3126d2c8f4ba6fcee3010c284003e7aaa78b7 debugedit: debian/relion-cuda/usr/bin/relion_scheduler: Unknown DWARF DW_FORM_0x1f20 5249a8d9b42c42b936872fcf4014a9afdd5c4795 debugedit: debian/relion-cuda/usr/bin/relion_mrc2vtk: Unknown DWARF DW_FORM_0x1f20 dcd132793e54b55c0869e6b461098f5459c6129d debugedit: debian/relion-cuda/usr/bin/relion_helix_toolbox: Unknown DWARF DW_FORM_0x1f20 de1c9b31ab670547c465976bbbb07bc9b5eca2da debugedit: debian/relion-cuda/usr/bin/relion_run_ctffind_mpi: Unknown DWARF DW_FORM_0x1f21 4c6849cd18c6467bab03cd9ffe49885a4c4f2ce2 debugedit: debian/relion-cuda/usr/bin/relion_postprocess: Unknown DWARF DW_FORM_0x1f20 0137aa9951a21feb36e3cf081dc83053ff7a6ed2 debugedit: debian/relion-cuda/usr/bin/relion_tiltpair_plot: Unknown DWARF DW_FORM_0x1f20 530e6d9447b2e88d91ab545aca67ee6efe02ea6c debugedit: debian/relion-cuda/usr/bin/relion_preprocess: Unknown DWARF DW_FORM_0x1f20 28465f6d2d64600f328ad32c45d31006d39aeaa8 debugedit: debian/relion-cuda/usr/bin/relion_ctf_toolbox: Unknown DWARF DW_FORM_0x1f20 2f8799e0b3fec30dc4dc033dd9a5ba88d86cfdcc debugedit: debian/relion-cuda/usr/bin/relion_localsym: Unknown DWARF DW_FORM_0x1f21 83db63afd04c75cb61f93a9578aa47959e1382dc debugedit: debian/relion-cuda/usr/bin/relion_pipeliner: Unknown DWARF DW_FORM_0x1f20 f18d01c4aae8f35596e83c6833ece8bf926e31f7 debugedit: debian/relion-cuda/usr/bin/relion_star_handler: Unknown DWARF DW_FORM_0x1f20 7537df73bf452436c6b57dc416f2413f9c96cc7f debugedit: debian/relion-cuda/usr/bin/relion_run_motioncorr: Unknown DWARF DW_FORM_0x1f21 3f3d9a341c4da31dabe81a10254b465925c4b9cf debugedit: debian/relion-cuda/usr/bin/relion_ctf_mask_test: Unknown DWARF DW_FORM_0x1f20 faa11460cf5b656cff66085a8fda54344dc34611 debugedit: debian/relion-cuda/usr/bin/relion_particle_symmetry_expand: Unknown DWARF DW_FORM_0x1f20 568f9dfafefa22f41c11a12db7f53ca2f76c0832 debugedit: debian/relion-cuda/usr/bin/relion_particle_reposition: Unknown DWARF DW_FORM_0x1f20 5a379dc1e254aa55bca1bb38ad955651872da0f6 debugedit: debian/relion-cuda/usr/bin/relion_particle_select: Unknown DWARF DW_FORM_0x1f20 e78e922c1fcfe39a8de389f92222e1fb218f10fc debugedit: debian/relion-cuda/usr/bin/relion_reconstruct_mpi: Unknown DWARF DW_FORM_0x1f20 0e2b281c9a85fc01095ddfd998796ec7a3f51dff debugedit: debian/relion-cuda/usr/bin/relion_reconstruct: Unknown DWARF DW_FORM_0x1f20 e346fcc4662166d90bb28eb0b12b8b709ecc4739 debugedit: debian/relion-cuda/usr/bin/relion_project: Unknown DWARF DW_FORM_0x1f20 abd96119d9846cd32287a18ce246e6d08708f8de debugedit: debian/relion-cuda/usr/bin/relion_image_handler: Unknown DWARF DW_FORM_0x1f20 8cc4503ca22fdf19503ae88adaea8fc8250de053 debugedit: debian/relion-cuda/usr/bin/relion_flex_analyse_mpi: Unknown DWARF DW_FORM_0x1f20 3f64ce47627709bf6ccb51e6ec6ace892a739679 debugedit: debian/relion-cuda/usr/bin/relion_align_symmetry: Unknown DWARF DW_FORM_0x1f20 0774fb3f5848ed728e76161da0959c4851806bfe debugedit: debian/relion-cuda/usr/bin/relion_demodulate: Unknown DWARF DW_FORM_0x1f20 69c77bcc71215dee0dcad0dcf045c9b0a5cad3c1 debugedit: debian/relion-cuda/usr/bin/relion_motion_refine_mpi: Unknown DWARF DW_FORM_0x1f20 9ff8793e3be428a74374cb1e89c433a794c50ab6 debugedit: debian/relion-cuda/usr/bin/relion_postprocess_mpi: Unknown DWARF DW_FORM_0x1f20 7e8317853f49023fd70cdbc73f67a8de1b64942a debugedit: debian/relion-cuda/usr/bin/relion_autopick_mpi: Unknown DWARF DW_FORM_0x1f20 36b11c2a8cdbbe783ac6a29f25945ee78dfd4b8f debugedit: debian/relion-cuda/usr/bin/relion_convert_to_tiff_mpi: Unknown DWARF DW_FORM_0x1f20 eab197f4b6185e194b8b5d76512400e684c91e78 debugedit: debian/relion-cuda/usr/bin/relion_find_tiltpairs: Unknown DWARF DW_FORM_0x1f20 48dcd1b51bce4afba23a9ffef5507c93005b102b debugedit: debian/relion-cuda/usr/bin/relion_autopick: Unknown DWARF DW_FORM_0x1f20 27059ec969f71de7e33cefcb39cc8503a45040e3 debugedit: debian/relion-cuda/usr/bin/relion_particle_subtract_mpi: Unknown DWARF DW_FORM_0x1f20 92906deb654dd095d0d3808f4dcbb78ad4d18e8d debugedit: debian/relion-cuda/usr/bin/relion_estimate_gain: Unknown DWARF DW_FORM_0x1f20 74f3949aeb0a2b2a11d5ab30a0857bbe9f96d1eb debugedit: debian/relion-cuda/usr/bin/relion_mask_create: Unknown DWARF DW_FORM_0x1f20 bde7c0b73959884a42bc28d391074725b88584b5 debugedit: debian/relion-cuda/usr/bin/relion_particle_subtract: Unknown DWARF DW_FORM_0x1f20 f45718f22aaac93f141c9b5097b0f24b419b2aaa debugedit: debian/relion-cuda/usr/bin/relion_helix_inimodel2d: Unknown DWARF DW_FORM_0x1f20 d1ac55690b84bb24b9e8a8ab8c7bdc1123279685 debugedit: debian/relion-cuda/usr/bin/relion_run_ctffind: Unknown DWARF DW_FORM_0x1f21 c29537a5cedd5ae9b0d135403e936ee6fdd45ea3 debugedit: debian/relion-cuda/usr/bin/relion_run_motioncorr_mpi: Unknown DWARF DW_FORM_0x1f21 c6d93ac050508cdee074e7a071b521877c8b783e debugedit: debian/relion-cuda/usr/bin/relion_motion_refine: Unknown DWARF DW_FORM_0x1f21 567d1fb0d71f2084e1a5522aa2710272ea088d10 debugedit: debian/relion-cuda/usr/bin/relion_prepare_subtomo: Unknown DWARF DW_FORM_0x1f21 34c31011192bf894c0fe7b0ef5d746012911dd97 debugedit: debian/relion-cuda/usr/bin/relion_convert_to_tiff: Unknown DWARF DW_FORM_0x1f20 4af5f295d7a7207c2336bb2e1b24fe36d317f108 debugedit: debian/relion-cuda/usr/bin/relion_particle_FCC: Unknown DWARF DW_FORM_0x1f21 4e5a0fa7d416159744c1cec4a67571fb348f7a62 debugedit: debian/relion-cuda/usr/bin/relion_localsym_mpi: Unknown DWARF DW_FORM_0x1f20 be31d98303f310983c71ee561aca46f850940ca2 debugedit: debian/relion-cuda/usr/bin/relion_preprocess_mpi: Unknown DWARF DW_FORM_0x1f20 8b4ccfd9a81440221140458bc9f8f63a01ee7739 debugedit: debian/relion-cuda/usr/bin/relion_ctf_refine: Unknown DWARF DW_FORM_0x1f20 daf4a82ec1acf5adca03f02a5f9eca023f17cf21 debugedit: debian/relion-cuda/usr/bin/relion_external_reconstruct: Unknown DWARF DW_FORM_0x1f20 6d841567c8359b32fabf2d23f31054c1d0f91c4e debugedit: debian/relion-cuda/usr/bin/relion_convert_star: Unknown DWARF DW_FORM_0x1f21 15f58d708a85398367ac02f3e0a73ea79083e1d7 debugedit: debian/relion-cuda/usr/bin/relion_merge_particles: Unknown DWARF DW_FORM_0x1f20 f6d9e168e743c60f0ad2d7fdd10686cf47ff1941 debugedit: debian/relion-cuda/usr/bin/relion_refine_mpi: Unknown DWARF DW_FORM_0x1f20 138a3bd96156fd031c6853da080744201dbfd7fc debugedit: debian/relion-cuda/usr/bin/relion_plot_delocalisation: Unknown DWARF DW_FORM_0x1f21 c573199f2861aa399dbbdb327ff02362334c339a debugedit: debian/relion-cuda/usr/bin/relion_reposition: Unknown DWARF DW_FORM_0x1f21 c3ad85e4e50f365cf501b7a386b4921852c171d6 debugedit: debian/relion-cuda/usr/bin/relion_flex_analyse: Unknown DWARF DW_FORM_0x1f20 64506b610b3db13896a1530fcb2670582f73b675 debugedit: debian/relion-cuda/usr/bin/relion_import: Unknown DWARF DW_FORM_0x1f20 2d3dd22ab8a00beaf509102470f90c7e550be8b5 debugedit: debian/relion-cuda/usr/bin/relion_ctf_refine_mpi: Unknown DWARF DW_FORM_0x1f20 a9836e982a9075ff23a56d6de974da521f5eeaa6 dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb INFO: pkgstriptranslations version 149 INFO: pkgstriptranslations version 149 INFO: pkgstriptranslations version 149 INFO: pkgstriptranslations version 149 pkgstriptranslations: processing relion-gui-cuda (in debian/relion-gui-cuda); do_strip: , oemstrip: pkgstriptranslations: processing relion-cuda (in debian/relion-cuda); do_strip: , oemstrip: pkgstriptranslations: processing relion-gui-cuda-dbgsym (in debian/.debhelper/relion-gui-cuda/dbgsym-root); do_strip: , oemstrip: pkgstriptranslations: processing relion-cuda-dbgsym (in debian/.debhelper/relion-cuda/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/.debhelper/relion-gui-cuda/dbgsym-root/DEBIAN/control, package relion-gui-cuda-dbgsym, directory debian/.debhelper/relion-gui-cuda/dbgsym-root dpkg-deb: building package 'relion-gui-cuda-dbgsym' in 'debian/.debhelper/scratch-space/build-relion-gui-cuda/relion-gui-cuda-dbgsym_3.1.3-1_amd64.deb'. pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/relion-gui-cuda/DEBIAN/control, package relion-gui-cuda, directory debian/relion-gui-cuda INFO: pkgstripfiles: waiting for lock (relion-gui-cuda) ... INFO: pkgstripfiles: waiting for lock (relion-gui-cuda) ... INFO: pkgstripfiles: waiting for lock (relion-gui-cuda) ... INFO: pkgstripfiles: waiting for lock (relion-gui-cuda) ... INFO: pkgstripfiles: waiting for lock (relion-gui-cuda) ... INFO: pkgstripfiles: waiting for lock (relion-gui-cuda) ... INFO: pkgstripfiles: waiting for lock (relion-gui-cuda) ... INFO: pkgstripfiles: waiting for lock (relion-gui-cuda) ... INFO: pkgstripfiles: waiting for lock (relion-gui-cuda) ... INFO: pkgstripfiles: waiting for lock (relion-gui-cuda) ... pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/.debhelper/relion-cuda/dbgsym-root/DEBIAN/control, package relion-cuda-dbgsym, directory debian/.debhelper/relion-cuda/dbgsym-root dpkg-deb: building package 'relion-cuda-dbgsym' in 'debian/.debhelper/scratch-space/build-relion-cuda/relion-cuda-dbgsym_3.1.3-1_amd64.deb'. INFO: pkgstripfiles: waiting for lock (relion-gui-cuda) ... INFO: pkgstripfiles: waiting for lock (relion-gui-cuda) ... Renaming relion-gui-cuda-dbgsym_3.1.3-1_amd64.deb to relion-gui-cuda-dbgsym_3.1.3-1_amd64.ddeb INFO: pkgstripfiles: waiting for lock (relion-gui-cuda) ... INFO: pkgstripfiles: waiting for lock (relion-gui-cuda) ... INFO: pkgstripfiles: waiting for lock (relion-gui-cuda) ... INFO: pkgstripfiles: waiting for lock (relion-gui-cuda) ... INFO: pkgstripfiles: waiting for lock (relion-gui-cuda) ... INFO: pkgstripfiles: waiting for lock (relion-gui-cuda) ... INFO: pkgstripfiles: waiting for lock (relion-gui-cuda) ... INFO: pkgstripfiles: waiting for lock (relion-gui-cuda) ... INFO: pkgstripfiles: waiting for lock (relion-gui-cuda) ... INFO: pkgstripfiles: waiting for lock (relion-gui-cuda) ... INFO: pkgstripfiles: waiting for lock (relion-gui-cuda) ... INFO: pkgstripfiles: waiting for lock (relion-gui-cuda) ... INFO: pkgstripfiles: waiting for lock (relion-gui-cuda) ... pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/relion-cuda/DEBIAN/control, package relion-cuda, directory debian/relion-cuda pkgstripfiles: Running PNG optimization (using 4 cpus) for package relion-cuda ... pkgstripfiles: No PNG files. dpkg-deb: building package 'relion-cuda' in '../relion-cuda_3.1.3-1_amd64.deb'. Searching for duplicated docs in dependency relion-cuda... symlinking changelog.Debian.gz in relion-gui-cuda to file in relion-cuda pkgstripfiles: Running PNG optimization (using 4 cpus) for package relion-gui-cuda ... pkgstripfiles: No PNG files. dpkg-deb: building package 'relion-gui-cuda' in '../relion-gui-cuda_3.1.3-1_amd64.deb'. Renaming relion-cuda-dbgsym_3.1.3-1_amd64.deb to relion-cuda-dbgsym_3.1.3-1_amd64.ddeb dpkg-genbuildinfo --build=binary -O../relion-cuda_3.1.3-1_amd64.buildinfo dpkg-genchanges --build=binary -mLaunchpad Build Daemon -O../relion-cuda_3.1.3-1_amd64.changes dpkg-genchanges: warning: the current version (3.1.3-1) is earlier than the previous one (3.1.3-2) dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2022-11-06T08:10:29Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ relion-cuda_3.1.3-1_amd64.changes: ---------------------------------- Format: 1.8 Date: Thu, 29 Sep 2022 14:56:00 +0200 Source: relion-cuda Binary: relion-cuda relion-gui-cuda Built-For-Profiles: noudeb Architecture: amd64 Version: 3.1.3-1 Distribution: lunar-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Andreas Beckmann Description: relion-cuda - parallel toolkit for 3D reconstructions in cryo-electron microsco relion-gui-cuda - toolkit for 3D reconstructions in cryo-electron microscopy (gui a Changes: relion-cuda (3.1.3-1) unstable; urgency=medium . * Team upload. * New upstream version. * Build using cuda-gcc. Checksums-Sha1: 10cd69c3b424b79468088a94df8b01add740f3cd 729292096 relion-cuda-dbgsym_3.1.3-1_amd64.ddeb 49fa64f239c04d1bab3523835efd9fc92cf66545 13546 relion-cuda_3.1.3-1_amd64.buildinfo 8358a9cae14b7e5292102c2122a034b545341e11 81222036 relion-cuda_3.1.3-1_amd64.deb eebd7646040a0e716bf4c712111cb4e232fbedd4 52422840 relion-gui-cuda-dbgsym_3.1.3-1_amd64.ddeb 76a99b7c71be70d420cf7674d5f0decb0e4a8d94 6669172 relion-gui-cuda_3.1.3-1_amd64.deb Checksums-Sha256: 60cabdd583d03eb9a0caf8f69f6d9e6aeeef1922153c60869e91b69f2efc749d 729292096 relion-cuda-dbgsym_3.1.3-1_amd64.ddeb 80c68bc0bcaf631545010a54124e6279a6cbdd71a96f35acf08838476b18ca56 13546 relion-cuda_3.1.3-1_amd64.buildinfo c4cd67a02848bda31dc069d15b2c73d1280897e8e4c1ea9e5ae69bbcc676e9fb 81222036 relion-cuda_3.1.3-1_amd64.deb e28603db6596228655c29d3ce31c668e1b99ed77cd70ed19802a21131a18d74c 52422840 relion-gui-cuda-dbgsym_3.1.3-1_amd64.ddeb c3071f44002e23fed059fce98f82c78dcf9c7a452b3a84aa80e6503dc7edab6e 6669172 relion-gui-cuda_3.1.3-1_amd64.deb Files: ab135ce2c2c8ba3063f207555d37b962 729292096 contrib/debug optional relion-cuda-dbgsym_3.1.3-1_amd64.ddeb d51e6bf6088654865a3dd8eba90d3215 13546 contrib/science optional relion-cuda_3.1.3-1_amd64.buildinfo 75805ad1243b6c4c6d773761cf4bcecc 81222036 contrib/science optional relion-cuda_3.1.3-1_amd64.deb 3232ca2465391b7124b40ebc6fdcacde 52422840 contrib/debug optional relion-gui-cuda-dbgsym_3.1.3-1_amd64.ddeb 2298879a32f43b2fea5e28834a2df254 6669172 contrib/science optional relion-gui-cuda_3.1.3-1_amd64.deb /<>/relion-cuda_3.1.3-1_amd64.changes.new could not be renamed to /<>/relion-cuda_3.1.3-1_amd64.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: relion-cuda Binary: relion-cuda relion-cuda-dbgsym relion-gui-cuda relion-gui-cuda-dbgsym Architecture: amd64 Version: 3.1.3-1 Checksums-Md5: ab135ce2c2c8ba3063f207555d37b962 729292096 relion-cuda-dbgsym_3.1.3-1_amd64.ddeb 75805ad1243b6c4c6d773761cf4bcecc 81222036 relion-cuda_3.1.3-1_amd64.deb 3232ca2465391b7124b40ebc6fdcacde 52422840 relion-gui-cuda-dbgsym_3.1.3-1_amd64.ddeb 2298879a32f43b2fea5e28834a2df254 6669172 relion-gui-cuda_3.1.3-1_amd64.deb Checksums-Sha1: 10cd69c3b424b79468088a94df8b01add740f3cd 729292096 relion-cuda-dbgsym_3.1.3-1_amd64.ddeb 8358a9cae14b7e5292102c2122a034b545341e11 81222036 relion-cuda_3.1.3-1_amd64.deb eebd7646040a0e716bf4c712111cb4e232fbedd4 52422840 relion-gui-cuda-dbgsym_3.1.3-1_amd64.ddeb 76a99b7c71be70d420cf7674d5f0decb0e4a8d94 6669172 relion-gui-cuda_3.1.3-1_amd64.deb Checksums-Sha256: 60cabdd583d03eb9a0caf8f69f6d9e6aeeef1922153c60869e91b69f2efc749d 729292096 relion-cuda-dbgsym_3.1.3-1_amd64.ddeb c4cd67a02848bda31dc069d15b2c73d1280897e8e4c1ea9e5ae69bbcc676e9fb 81222036 relion-cuda_3.1.3-1_amd64.deb e28603db6596228655c29d3ce31c668e1b99ed77cd70ed19802a21131a18d74c 52422840 relion-gui-cuda-dbgsym_3.1.3-1_amd64.ddeb c3071f44002e23fed059fce98f82c78dcf9c7a452b3a84aa80e6503dc7edab6e 6669172 relion-gui-cuda_3.1.3-1_amd64.deb Build-Origin: Ubuntu Build-Architecture: amd64 Build-Date: Sun, 06 Nov 2022 08:10:21 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: adduser (= 3.121ubuntu1), autoconf (= 2.71-2), automake (= 1:1.16.5-1.3), autopoint (= 0.21-8), autotools-dev (= 20220109.1), base-files (= 12.3ubuntu1), base-passwd (= 3.6.1), bash (= 5.2-1ubuntu2), binutils (= 2.39-8ubuntu2), binutils-common (= 2.39-8ubuntu2), binutils-x86-64-linux-gnu (= 2.39-8ubuntu2), bsdextrautils (= 2.38-4ubuntu1), bsdutils (= 1:2.38-4ubuntu1), build-essential (= 12.9ubuntu3), bzip2 (= 1.0.8-5build1), cmake (= 3.24.3-1ubuntu1), cmake-data (= 3.24.3-1ubuntu1), coreutils (= 8.32-4.1ubuntu1), cpp (= 4:12.2.0-1ubuntu1), cpp-10 (= 10.4.0-5ubuntu2), cpp-12 (= 12.2.0-9ubuntu1), dash (= 0.5.11+git20210903+057cd650a4ed-8ubuntu1), debconf (= 1.5.79ubuntu1), debhelper (= 13.10.1ubuntu1), debianutils (= 5.7-0.4), debugedit (= 1:5.0-5), dh-autoreconf (= 20), dh-elpa-helper (= 2.0.9ubuntu1), dh-strip-nondeterminism (= 1.13.0-1), diffutils (= 1:3.8-1), dpkg (= 1.21.9ubuntu1), dpkg-dev (= 1.21.9ubuntu1), dwz (= 0.14+20220924-2), emacsen-common (= 3.0.4), file (= 1:5.41-4), findutils (= 4.9.0-3ubuntu1), fluid (= 1.3.8-5), fontconfig-config (= 2.13.1-4.4ubuntu1), fonts-dejavu-core (= 2.37-2build1), g++ (= 4:12.2.0-1ubuntu1), g++-10 (= 10.4.0-5ubuntu2), g++-12 (= 12.2.0-9ubuntu1), gcc (= 4:12.2.0-1ubuntu1), gcc-10 (= 10.4.0-5ubuntu2), gcc-10-base (= 10.4.0-5ubuntu2), gcc-11-base (= 11.3.0-9ubuntu1), gcc-12 (= 12.2.0-9ubuntu1), gcc-12-base (= 12.2.0-9ubuntu1), gettext (= 0.21-8), gettext-base (= 0.21-8), gfortran-12 (= 12.2.0-9ubuntu1), grep (= 3.8-3), groff-base (= 1.22.4-8build1), gzip (= 1.12-1ubuntu1), hostname (= 3.23ubuntu2), ibverbs-providers (= 43.0-1), init-system-helpers (= 1.65.2), intltool-debian (= 0.35.0+20060710.6), libaccinj64-11.5 (= 11.5.114~11.5.2-1ubuntu1), libacl1 (= 2.3.1-1), libarchive-zip-perl (= 1.68-1), libarchive13 (= 3.6.0-1ubuntu1), libasan6 (= 11.3.0-9ubuntu1), libasan8 (= 12.2.0-9ubuntu1), libatomic1 (= 12.2.0-9ubuntu1), libattr1 (= 1:2.5.1-1build1), libaudit-common (= 1:3.0.7-1ubuntu2), libaudit1 (= 1:3.0.7-1ubuntu2), libbinutils (= 2.39-8ubuntu2), libblkid1 (= 2.38-4ubuntu1), libbrotli1 (= 1.0.9-2build7), libbsd0 (= 0.11.7-1), libbz2-1.0 (= 1.0.8-5build1), libc-bin (= 2.36-0ubuntu4), libc-dev-bin (= 2.36-0ubuntu4), libc6 (= 2.36-0ubuntu4), libc6-dev (= 2.36-0ubuntu4), libcairo2 (= 1.16.0-5ubuntu2), libcap-ng0 (= 0.8.3-1build1), libcap2 (= 1:2.44-1build3), libcbor0.8 (= 0.8.0-2ubuntu1), libcc1-0 (= 12.2.0-9ubuntu1), libcom-err2 (= 1.46.5-2ubuntu2), libcrypt-dev (= 1:4.4.30-1), libcrypt1 (= 1:4.4.30-1), libctf-nobfd0 (= 2.39-8ubuntu2), libctf0 (= 2.39-8ubuntu2), libcub-dev (= 1.16.0-1), libcublas11 (= 11.7.4.6~11.5.2-1ubuntu1), libcublaslt11 (= 11.7.4.6~11.5.2-1ubuntu1), libcudart11.0 (= 11.5.117~11.5.2-1ubuntu1), libcufft10 (= 11.1.1+~10.6.0.107~11.5.2-1ubuntu1), libcufftw10 (= 11.1.1+~10.6.0.107~11.5.2-1ubuntu1), libcuinj64-11.5 (= 11.5.114~11.5.2-1ubuntu1), libcupti-dev (= 11.5.114~11.5.2-1ubuntu1), libcupti11.5 (= 11.5.114~11.5.2-1ubuntu1), libcurand10 (= 11.1.1+~10.2.7.107~11.5.2-1ubuntu1), libcurl3-gnutls (= 7.86.0-1), libcurl4 (= 7.86.0-1), libcusolver11 (= 11.3.2.107~11.5.2-1ubuntu1), libcusolvermg11 (= 11.3.2.107~11.5.2-1ubuntu1), libcusparse11 (= 11.7.0.107~11.5.2-1ubuntu1), libdb5.3 (= 5.3.28+dfsg1-0.10), libdebconfclient0 (= 0.264ubuntu1), libdebhelper-perl (= 13.10.1ubuntu1), libdeflate-dev (= 1.14-1), libdeflate0 (= 1.14-1), libdpkg-perl (= 1.21.9ubuntu1), libdrm-amdgpu1 (= 2.4.113-2), libdrm-common (= 2.4.113-2), libdrm-nouveau2 (= 2.4.113-2), libdrm-radeon1 (= 2.4.113-2), libdrm2 (= 2.4.113-2), libdw1 (= 0.187-4), libedit2 (= 3.1-20221030-1), libelf1 (= 0.187-4), 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 (= 1.11.0-3), 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-quad3 (= 3.3.8-2ubuntu8), libfftw3-single3 (= 3.3.8-2ubuntu8), libfido2-1 (= 1.12.0-1), libfile-stripnondeterminism-perl (= 1.13.0-1), 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 (= 2.13.1-4.4ubuntu1), libfreetype6 (= 2.12.1+dfsg-3), libgcc-10-dev (= 10.4.0-5ubuntu2), libgcc-12-dev (= 12.2.0-9ubuntu1), libgcc-s1 (= 12.2.0-9ubuntu1), libgcrypt20 (= 1.10.1-2ubuntu1), libgdbm-compat4 (= 1.23-3), libgdbm6 (= 1.23-3), libgfortran-12-dev (= 12.2.0-9ubuntu1), libgfortran5 (= 12.2.0-9ubuntu1), libgl1 (= 1.5.0-1), libgl1-mesa-dri (= 22.2.1-1ubuntu1), libglapi-mesa (= 22.2.1-1ubuntu1), libglvnd0 (= 1.5.0-1), libglx-mesa0 (= 22.2.1-1ubuntu1), libglx0 (= 1.5.0-1), libgmp10 (= 2:6.2.1+dfsg1-1ubuntu2), libgnutls30 (= 3.7.7-2ubuntu2), libgomp1 (= 12.2.0-9ubuntu1), libgpg-error0 (= 1.46-1), libgprofng0 (= 2.39-8ubuntu2), libgssapi-krb5-2 (= 1.20-1), libhogweed6 (= 3.8.1-2), libhwloc-dev (= 2.8.0-1), libhwloc-plugins (= 2.8.0-1), libhwloc15 (= 2.8.0-1), libibverbs-dev (= 43.0-1), libibverbs1 (= 43.0-1), libicu71 (= 71.1-3ubuntu1), libidn2-0 (= 2.3.3-1build1), libisl23 (= 0.25-1), libitm1 (= 12.2.0-9ubuntu1), libjbig-dev (= 2.1-3.1build3), libjbig0 (= 2.1-3.1build3), 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 (= 3.6.0+dfsg+~3.5.13-1), libjs-jquery-ui (= 1.13.2+dfsg-1), libjsoncpp25 (= 1.9.5-4), libk5crypto3 (= 1.20-1), libkeyutils1 (= 1.6.3-1), libkrb5-3 (= 1.20-1), libkrb5support0 (= 1.20-1), libldap-2.5-0 (= 2.5.13+dfsg-1ubuntu2), liblerc-dev (= 3.0+ds-1ubuntu1), liblerc3 (= 3.0+ds-1ubuntu1), libllvm15 (= 1:15.0.2-1), liblsan0 (= 12.2.0-9ubuntu1), libltdl-dev (= 2.4.7-4), libltdl7 (= 2.4.7-4), liblz4-1 (= 1.9.4-1), liblzma-dev (= 5.2.7-0.1), liblzma5 (= 5.2.7-0.1), libmagic-mgc (= 1:5.41-4), libmagic1 (= 1:5.41-4), libmd0 (= 1.0.4-2), libmount1 (= 2.38-4ubuntu1), libmpc3 (= 1.2.1-2build1), libmpfr6 (= 4.1.0-3build3), libncurses6 (= 6.3+20220423-2), libncursesw6 (= 6.3+20220423-2), libnettle8 (= 3.8.1-2), libnghttp2-14 (= 1.50.0-1), 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), libnppc11 (= 11.5.1.107~11.5.2-1ubuntu1), libnppial11 (= 11.5.1.107~11.5.2-1ubuntu1), libnppicc11 (= 11.5.1.107~11.5.2-1ubuntu1), libnppidei11 (= 11.5.1.107~11.5.2-1ubuntu1), libnppif11 (= 11.5.1.107~11.5.2-1ubuntu1), libnppig11 (= 11.5.1.107~11.5.2-1ubuntu1), libnppim11 (= 11.5.1.107~11.5.2-1ubuntu1), libnppist11 (= 11.5.1.107~11.5.2-1ubuntu1), libnppisu11 (= 11.5.1.107~11.5.2-1ubuntu1), libnppitc11 (= 11.5.1.107~11.5.2-1ubuntu1), libnpps11 (= 11.5.1.107~11.5.2-1ubuntu1), libnsl-dev (= 1.3.0-2build2), libnsl2 (= 1.3.0-2build2), libnuma-dev (= 2.0.14-3ubuntu2), libnuma1 (= 2.0.14-3ubuntu2), libnvblas11 (= 11.7.4.6~11.5.2-1ubuntu1), libnvidia-compute-510 (= 510.85.02-0ubuntu2), libnvidia-ml-dev (= 11.5.50~11.5.2-1ubuntu1), libnvjpeg11 (= 11.5.4.107~11.5.2-1ubuntu1), libnvrtc-builtins11.5 (= 11.5.119~11.5.2-1ubuntu1), libnvrtc11.2 (= 11.5.119~11.5.2-1ubuntu1), libnvtoolsext1 (= 11.5.114~11.5.2-1ubuntu1), libnvvm4 (= 11.5.119~11.5.2-1ubuntu1), libopenmpi-dev (= 4.1.4-2ubuntu2), libopenmpi3 (= 4.1.4-2ubuntu2), libp11-kit0 (= 0.24.1-1ubuntu2), libpam-modules (= 1.5.2-2ubuntu1), libpam-modules-bin (= 1.5.2-2ubuntu1), libpam-runtime (= 1.5.2-2ubuntu1), libpam0g (= 1.5.2-2ubuntu1), libpciaccess0 (= 0.17-1), libpcre2-8-0 (= 10.40-1ubuntu1), libperl5.36 (= 5.36.0-4ubuntu2), libpipeline1 (= 1.5.6-3), libpixman-1-0 (= 0.40.0-1build4), libpmix-dev (= 4.1.2-2ubuntu2), libpmix2 (= 4.1.2-2ubuntu2), libpng16-16 (= 1.6.38-2), libprocps8 (= 2:3.3.17-7ubuntu1), libpsl5 (= 0.21.0-1.2build2), libpsm-infinipath1 (= 3.3+20.604758e7-6.2), libpsm2-2 (= 11.2.185-2), libpthread-stubs0-dev (= 0.4-1build2), libquadmath0 (= 12.2.0-9ubuntu1), librdmacm1 (= 43.0-1), librhash0 (= 1.4.2-1ubuntu1), librtmp1 (= 2.4+20151223.gitfa8646d.1-2build4), libsasl2-2 (= 2.1.28+dfsg-6ubuntu2), libsasl2-modules-db (= 2.1.28+dfsg-6ubuntu2), libseccomp2 (= 2.5.4-1ubuntu2), libselinux1 (= 3.4-1build1), libsemanage-common (= 3.4-1build1), libsemanage2 (= 3.4-1build1), libsensors-config (= 1:3.6.0-7ubuntu1), libsensors5 (= 1:3.6.0-7ubuntu1), libsepol2 (= 3.4-2), libsmartcols1 (= 2.38-4ubuntu1), libssh-4 (= 0.10.4-2), libssl3 (= 3.0.5-2ubuntu1), libstdc++-10-dev (= 10.4.0-5ubuntu2), libstdc++-12-dev (= 12.2.0-9ubuntu1), libstdc++6 (= 12.2.0-9ubuntu1), libsub-override-perl (= 0.09-4), libsystemd0 (= 251.4-1ubuntu7), libtasn1-6 (= 4.19.0-2), libthrust-dev (= 1.16.0-1), libtiff-dev (= 4.4.0-4ubuntu3), libtiff5 (= 4.4.0-4ubuntu3), libtiffxx5 (= 4.4.0-4ubuntu3), libtinfo6 (= 6.3+20220423-2), libtirpc-common (= 1.3.3+ds-1), libtirpc-dev (= 1.3.3+ds-1), libtirpc3 (= 1.3.3+ds-1), libtool (= 2.4.7-4), libtsan0 (= 11.3.0-9ubuntu1), libtsan2 (= 12.2.0-9ubuntu1), libubsan1 (= 12.2.0-9ubuntu1), libuchardet0 (= 0.0.7-1build2), libucx0 (= 1.13.0-1), libudev1 (= 251.4-1ubuntu7), libunistring2 (= 1.0-2), libuuid1 (= 2.38-4ubuntu1), libuv1 (= 1.44.2-1), libwebp7 (= 1.2.2-2), libx11-6 (= 2:1.8.1-2), libx11-data (= 2:1.8.1-2), libx11-dev (= 2:1.8.1-2), libx11-xcb1 (= 2:1.8.1-2), 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), libzstd1 (= 1.5.2+dfsg-1), linux-libc-dev (= 5.19.0-23.24), login (= 1:4.11.1+dfsg1-2ubuntu1), lsb-base (= 11.2ubuntu1), lto-disabled-list (= 35), m4 (= 1.4.19-1), make (= 4.3-4.1build1), man-db (= 2.11.0-1), mawk (= 1.3.4.20200120-3.1), ncurses-base (= 6.3+20220423-2), ncurses-bin (= 6.3+20220423-2), nvidia-cuda-dev (= 11.5.2-1ubuntu1), nvidia-cuda-toolkit (= 11.5.2-1ubuntu1), nvidia-cuda-toolkit-gcc (= 11.5.2-1ubuntu1), nvidia-opencl-dev (= 11.5.2-1ubuntu1), nvidia-profiler (= 11.5.114~11.5.2-1ubuntu1), ocl-icd-libopencl1 (= 2.3.1-1), ocl-icd-opencl-dev (= 2.3.1-1), opencl-c-headers (= 3.0~2022.09.30-1), opencl-clhpp-headers (= 3.0~2022.05.18-1ubuntu1), openmpi-bin (= 4.1.4-2ubuntu2), openmpi-common (= 4.1.4-2ubuntu2), openssh-client (= 1:9.0p1-1ubuntu8), passwd (= 1:4.11.1+dfsg1-2ubuntu1), patch (= 2.7.6-7build2), perl (= 5.36.0-4ubuntu2), perl-base (= 5.36.0-4ubuntu2), perl-modules-5.36 (= 5.36.0-4ubuntu2), po-debconf (= 1.0.21+nmu1), procps (= 2:3.3.17-7ubuntu1), rpcsvc-proto (= 1.4.2-0ubuntu6), sed (= 4.8-1ubuntu2), sensible-utils (= 0.0.17), sgml-base (= 1.31), sysvinit-utils (= 3.04-1ubuntu1), tar (= 1.34+dfsg-1build3), ucf (= 3.0043), usrmerge (= 29ubuntu2), util-linux (= 2.38-4ubuntu1), util-linux-extra (= 2.38-4ubuntu1), x11proto-dev (= 2022.1-1), xorg-sgml-doctools (= 1:1.11-1.1), xtrans-dev (= 1.4.0-1), xz-utils (= 5.2.7-0.1), zlib1g (= 1:1.2.11.dfsg-4.1ubuntu2), zlib1g-dev (= 1:1.2.11.dfsg-4.1ubuntu2) Environment: DEB_BUILD_OPTIONS="parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1664456160" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ relion-cuda_3.1.3-1_amd64.deb ----------------------------- new Debian package, version 2.0. size 81222036 bytes: control archive=2665 bytes. 1257 bytes, 23 lines control 4243 bytes, 66 lines md5sums Package: relion-cuda Version: 3.1.3-1 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 392675 Depends: openmpi-gcc | openmpi-bin, libc6 (>= 2.34), libcufft10, libfftw3-double3 (>= 3.3.5), libfftw3-single3 (>= 3.3.5), libgcc-s1 (>= 3.0), libgomp1 (>= 4.9), libopenmpi3 (>= 4.1.4), libstdc++6 (>= 11), libtiff5 (>= 4.0.3) Conflicts: relion 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: contrib/science Priority: optional Homepage: https://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page Description: parallel 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-cuda provides the serial and parallel (MPI) command-line tools with CUDA/GPU support. drwxr-xr-x root/root 0 2022-09-29 12:56 ./ drwxr-xr-x root/root 0 2022-09-29 12:56 ./usr/ drwxr-xr-x root/root 0 2022-09-29 12:56 ./usr/bin/ -rwxr-xr-x root/root 8379400 2022-09-29 12:56 ./usr/bin/relion_align_symmetry -rwxr-xr-x root/root 9485344 2022-09-29 12:56 ./usr/bin/relion_autopick -rwxr-xr-x root/root 9489440 2022-09-29 12:56 ./usr/bin/relion_autopick_mpi -rwxr-xr-x root/root 8789000 2022-09-29 12:56 ./usr/bin/relion_convert_star -rwxr-xr-x root/root 1161856 2022-09-29 12:56 ./usr/bin/relion_convert_to_tiff -rwxr-xr-x root/root 1239680 2022-09-29 12:56 ./usr/bin/relion_convert_to_tiff_mpi -rwxr-xr-x root/root 8993800 2022-09-29 12:56 ./usr/bin/relion_ctf_mask_test -rwxr-xr-x root/root 9542632 2022-09-29 12:56 ./usr/bin/relion_ctf_refine -rwxr-xr-x root/root 9546728 2022-09-29 12:56 ./usr/bin/relion_ctf_refine_mpi -rwxr-xr-x root/root 8379400 2022-09-29 12:56 ./usr/bin/relion_ctf_toolbox -rwxr-xr-x root/root 8883208 2022-09-29 12:56 ./usr/bin/relion_demodulate -rwxr-xr-x root/root 879240 2022-09-29 12:56 ./usr/bin/relion_estimate_gain -rwxr-xr-x root/root 8371208 2022-09-29 12:56 ./usr/bin/relion_external_reconstruct -rwxr-xr-x root/root 633480 2022-09-29 12:56 ./usr/bin/relion_find_tiltpairs -rwxr-xr-x root/root 8469512 2022-09-29 12:56 ./usr/bin/relion_flex_analyse -rwxr-xr-x root/root 8469512 2022-09-29 12:56 ./usr/bin/relion_flex_analyse_mpi -rwxr-xr-x root/root 8461320 2022-09-29 12:56 ./usr/bin/relion_helix_inimodel2d -rwxr-xr-x root/root 8436744 2022-09-29 12:56 ./usr/bin/relion_helix_toolbox -rwxr-xr-x root/root 8453128 2022-09-29 12:56 ./usr/bin/relion_image_handler -rwxr-xr-x root/root 8350696 2022-09-29 12:56 ./usr/bin/relion_import -rwxr-xr-x root/root 8305672 2022-09-29 12:56 ./usr/bin/relion_localsym -rwxr-xr-x root/root 8399880 2022-09-29 12:56 ./usr/bin/relion_localsym_mpi -rwxr-xr-x root/root 8379400 2022-09-29 12:56 ./usr/bin/relion_mask_create -rwxr-xr-x root/root 8317928 2022-09-29 12:56 ./usr/bin/relion_merge_particles -rwxr-xr-x root/root 10050568 2022-09-29 12:56 ./usr/bin/relion_motion_refine -rwxr-xr-x root/root 10062856 2022-09-29 12:56 ./usr/bin/relion_motion_refine_mpi -rwxr-xr-x root/root 789096 2022-09-29 12:56 ./usr/bin/relion_mrc2vtk -rwxr-xr-x root/root 8961000 2022-09-29 12:56 ./usr/bin/relion_particle_FCC -rwxr-xr-x root/root 8416264 2022-09-29 12:56 ./usr/bin/relion_particle_reposition -rwxr-xr-x root/root 8842248 2022-09-29 12:56 ./usr/bin/relion_particle_select -rwxr-xr-x root/root 8449000 2022-09-29 12:56 ./usr/bin/relion_particle_subtract -rwxr-xr-x root/root 8453128 2022-09-29 12:56 ./usr/bin/relion_particle_subtract_mpi -rwxr-xr-x root/root 8334312 2022-09-29 12:56 ./usr/bin/relion_particle_symmetry_expand -rwxr-xr-x root/root 1550952 2022-09-29 12:56 ./usr/bin/relion_pipeliner -rwxr-xr-x root/root 8846344 2022-09-29 12:56 ./usr/bin/relion_plot_delocalisation -rwxr-xr-x root/root 1030784 2022-09-29 12:56 ./usr/bin/relion_postprocess -rwxr-xr-x root/root 1030784 2022-09-29 12:56 ./usr/bin/relion_postprocess_mpi -rwxr-xr-x root/root 912008 2022-09-29 12:56 ./usr/bin/relion_prepare_subtomo -rwxr-xr-x root/root 8457192 2022-09-29 12:56 ./usr/bin/relion_preprocess -rwxr-xr-x root/root 8469480 2022-09-29 12:56 ./usr/bin/relion_preprocess_mpi -rwxr-xr-x root/root 8408072 2022-09-29 12:56 ./usr/bin/relion_project -rwxr-xr-x root/root 8453096 2022-09-29 12:56 ./usr/bin/relion_reconstruct -rwxr-xr-x root/root 8469480 2022-09-29 12:56 ./usr/bin/relion_reconstruct_mpi -rwxr-xr-x root/root 8338440 2022-09-29 12:56 ./usr/bin/relion_refine -rwxr-xr-x root/root 8510472 2022-09-29 12:56 ./usr/bin/relion_refine_mpi -rwxr-xr-x root/root 8981480 2022-09-29 12:56 ./usr/bin/relion_reposition -rwxr-xr-x root/root 8453128 2022-09-29 12:56 ./usr/bin/relion_run_ctffind -rwxr-xr-x root/root 8465416 2022-09-29 12:56 ./usr/bin/relion_run_ctffind_mpi -rwxr-xr-x root/root 8780808 2022-09-29 12:56 ./usr/bin/relion_run_motioncorr -rwxr-xr-x root/root 8793096 2022-09-29 12:56 ./usr/bin/relion_run_motioncorr_mpi -rwxr-xr-x root/root 9522152 2022-09-29 12:56 ./usr/bin/relion_scheduler -rwxr-xr-x root/root 8375304 2022-09-29 12:56 ./usr/bin/relion_stack_create -rwxr-xr-x root/root 1055 2022-09-29 12:56 ./usr/bin/relion_star_datablock_ctfdat -rwxr-xr-x root/root 714 2022-09-29 12:56 ./usr/bin/relion_star_datablock_singlefiles -rwxr-xr-x root/root 767 2022-09-29 12:56 ./usr/bin/relion_star_datablock_stack -rwxr-xr-x root/root 8481800 2022-09-29 12:56 ./usr/bin/relion_star_handler -rwxr-xr-x root/root 675 2022-09-29 12:56 ./usr/bin/relion_star_loopheader -rwxr-xr-x root/root 1217 2022-09-29 12:56 ./usr/bin/relion_star_plottable -rwxr-xr-x root/root 2263 2022-09-29 12:56 ./usr/bin/relion_star_printtable -rwxr-xr-x root/root 711304 2022-09-29 12:56 ./usr/bin/relion_tiltpair_plot -rwxr-xr-x root/root 8809448 2022-09-29 12:56 ./usr/bin/relion_tomo_test drwxr-xr-x root/root 0 2022-09-29 12:56 ./usr/share/ drwxr-xr-x root/root 0 2022-09-29 12:56 ./usr/share/doc/ drwxr-xr-x root/root 0 2022-09-29 12:56 ./usr/share/doc/relion-cuda/ -rw-r--r-- root/root 1433 2021-08-31 10:17 ./usr/share/doc/relion-cuda/AUTHORS -rw-r--r-- root/root 2810 2021-08-31 10:17 ./usr/share/doc/relion-cuda/README.md.gz -rw-r--r-- root/root 1205 2022-09-29 12:56 ./usr/share/doc/relion-cuda/changelog.Debian.gz -rw-r--r-- root/root 7540 2022-09-29 12:56 ./usr/share/doc/relion-cuda/copyright drwxr-xr-x root/root 0 2022-09-29 12:56 ./usr/share/lintian/ drwxr-xr-x root/root 0 2022-09-29 12:56 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 15 2022-09-29 12:56 ./usr/share/lintian/overrides/relion-cuda relion-gui-cuda_3.1.3-1_amd64.deb --------------------------------- new Debian package, version 2.0. size 6669172 bytes: control archive=996 bytes. 1261 bytes, 23 lines control 318 bytes, 5 lines md5sums Package: relion-gui-cuda Source: relion-cuda Version: 3.1.3-1 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 26521 Depends: relion-cuda (= 3.1.3-1), libc6 (>= 2.34), libcufft10, libfftw3-double3 (>= 3.3.5), libfltk1.3 (>= 1.3.4), libgcc-s1 (>= 3.0), libgomp1 (>= 4.9), libopenmpi3 (>= 4.1.4), libstdc++6 (>= 11), libtiff5 (>= 4.0.3) Conflicts: relion-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: contrib/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-cuda provides the graphical user interface with CUDA/GPU support. drwxr-xr-x root/root 0 2022-09-29 12:56 ./ drwxr-xr-x root/root 0 2022-09-29 12:56 ./usr/ drwxr-xr-x root/root 0 2022-09-29 12:56 ./usr/bin/ -rwxr-xr-x root/root 10172776 2022-09-29 12:56 ./usr/bin/relion -rwxr-xr-x root/root 8563688 2022-09-29 12:56 ./usr/bin/relion_display -rwxr-xr-x root/root 8399848 2022-09-29 12:56 ./usr/bin/relion_manualpick drwxr-xr-x root/root 0 2022-09-29 12:56 ./usr/share/ drwxr-xr-x root/root 0 2022-09-29 12:56 ./usr/share/doc/ drwxr-xr-x root/root 0 2022-09-29 12:56 ./usr/share/doc/relion-gui-cuda/ lrwxrwxrwx root/root 0 2022-09-29 12:56 ./usr/share/doc/relion-gui-cuda/changelog.Debian.gz -> ../relion-cuda/changelog.Debian.gz -rw-r--r-- root/root 7540 2022-09-29 12:56 ./usr/share/doc/relion-gui-cuda/copyright drwxr-xr-x root/root 0 2022-09-29 12:56 ./usr/share/lintian/ drwxr-xr-x root/root 0 2022-09-29 12:56 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 15 2022-09-29 12:56 ./usr/share/lintian/overrides/relion-gui-cuda +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: binary Build-Space: 9826184 Build-Time: 786 Distribution: lunar-proposed Host Architecture: amd64 Install-Time: 41 Job: relion-cuda_3.1.3-1.dsc Machine Architecture: amd64 Package: relion-cuda Package-Time: 828 Source-Version: 3.1.3-1 Space: 9826184 Status: successful Version: 3.1.3-1 -------------------------------------------------------------------------------- Finished at 2022-11-06T08:10:29Z Build needed 00:13:48, 9826184k disk space Adding user buildd to group lxd RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=lunar --arch=amd64 PACKAGEBUILD-24619634 Scanning for processes to kill in build PACKAGEBUILD-24619634