Sun Nov 10 02:59:12 UTC 2024 I: starting to build relion/unstable/amd64 on jenkins on '2024-11-10 02:58' Sun Nov 10 02:59:12 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_37/36557/console.log Sun Nov 10 02:59:12 UTC 2024 I: Downloading source for unstable/relion=3.1.3-4 --2024-11-10 02:59:12-- http://deb.debian.org/debian/pool/main/r/relion/relion_3.1.3-4.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2141 (2.1K) [text/prs.lines.tag] Saving to: ‘relion_3.1.3-4.dsc’ 0K .. 100% 209M=0s 2024-11-10 02:59:12 (209 MB/s) - ‘relion_3.1.3-4.dsc’ saved [2141/2141] Sun Nov 10 02:59:12 UTC 2024 I: relion_3.1.3-4.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: relion Binary: relion, relion-gui Architecture: any Version: 3.1.3-4 Maintainer: Debian Med Packaging Team Uploaders: Roland Fehrenbacher , Andreas Tille , Homepage: https://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page Standards-Version: 4.7.0 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, mpi-default-dev, libtiff-dev, fluid Package-List: relion deb science optional arch=any relion-gui deb science optional arch=any Checksums-Sha1: c6ca397db6c711f87305bd803f672345f7487bae 2345487 relion_3.1.3.orig.tar.gz cbd977bd73a6270bab2fc9aca5779296c528315b 12056 relion_3.1.3-4.debian.tar.xz Checksums-Sha256: f10934058e0670807b7004899d7b5103c21ad77841219352c66a33f98586d42e 2345487 relion_3.1.3.orig.tar.gz 5dfd505bf26bb03602300ad0b21ed1e6459f97491725abdb5dfa79427972a46a 12056 relion_3.1.3-4.debian.tar.xz Files: 5ddaf9afe51d743c5f58f625d9fd1cb7 2345487 relion_3.1.3.orig.tar.gz d7e1621d2cf43aa84fc9c84f31ece31b 12056 relion_3.1.3-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmcvqOQUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdq5XhAAi2JZBOvwNQepfXxfokEG0B/f52Qh wjokzJyLMtdn4jOCMucgKwDkLiYKE3IhijrB7PHEHvbLUwa7pOU/mkxf36uYwY58 53e/zJrYmmdfnGO2DCtHCmSagbTU5NB2PI8rWi7ZOPPxkDKHzXJj+SN6nTXvSZb9 bEH9lBVbsgpxiUo40SN24unL1SrIqBDaOMvaiXJvSu50cF+ibeXhWISXyDS3etuS 9ARzfN8JltyeC/fp0Pawcan+OxytEvsIG1QMzNy3v2NAy98H1HeOL/hm7A4TgRgP R3fhOdfqloOTZAvdL2TVSJS+LznwoPUfPNlRjUEjPjIXj27Q8IRVakt9ENyaEVjK AXk4DtOaSEqx2qWa/M4GND1tBc5VqtefeVA+5+epFvCABbnBD2nJcHgmkZc95VDy hsYGbps6xzHnhTSc+Fq5VR1/rym7Q/LFFTc1qk2QU9YEXr7oONP+e0gZmhiUGSxE 2yOc60ihgvr1MT6uksq+C8OPQDB9Tsk22clT2xresUVIGXQxg9HI0L+tlrqkcxz1 +uTI9RzkxQz+bvULKvNmdBjMYhTBoRv7+0pvycVzqO4c2MTlRXc7jE8PvEI66S0m V7FYN/n2Jh4eksRWSC9dFPIIKhnYm1nlXz3JIKgFXeRThQ20tixfQTeoKYKZ8SdE cjIJ+ooqY1d8WUs= =+RH5 -----END PGP SIGNATURE----- Sun Nov 10 02:59:12 UTC 2024 I: Checking whether the package is not for us Sun Nov 10 02:59:12 UTC 2024 I: Starting 1st build on remote node infom01-amd64.debian.net. Sun Nov 10 02:59:12 UTC 2024 I: Preparing to do remote build '1' on infom01-amd64.debian.net. Sun Nov 10 03:09:16 UTC 2024 I: Deleting $TMPDIR on infom01-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sat Nov 9 14:59:14 -12 2024 I: pbuilder-time-stamp: 1731207554 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [relion_3.1.3-4.dsc] I: copying [./relion_3.1.3.orig.tar.gz] I: copying [./relion_3.1.3-4.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Nov 9 18:24:36 2024 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./relion_3.1.3-4.dsc: no acceptable signature found dpkg-source: info: extracting relion in relion-3.1.3 dpkg-source: info: unpacking relion_3.1.3.orig.tar.gz dpkg-source: info: unpacking relion_3.1.3-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 0001-Repair-wrong-comment-sign-pointed-out-by-Alexey-Roma.patch dpkg-source: info: applying typos.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2452736/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='caf226e3750c4c7599515620e7468bb1' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='2452736' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.NsZJyNAm/pbuilderrc_W8HD --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.NsZJyNAm/b1 --logfile b1/build.log relion_3.1.3-4.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' I: uname -a Linux infom01-amd64 6.1.0-26-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.112-1 (2024-09-30) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2452736/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: cmake, debhelper-compat (= 13), libfftw3-dev, libfltk1.3-dev, mpi-default-dev, libtiff-dev, fluid dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19970 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on libfftw3-dev; however: Package libfftw3-dev is not installed. pbuilder-satisfydepends-dummy depends on libfltk1.3-dev; however: Package libfltk1.3-dev is not installed. pbuilder-satisfydepends-dummy depends on mpi-default-dev; however: Package mpi-default-dev is not installed. pbuilder-satisfydepends-dummy depends on libtiff-dev; however: Package libtiff-dev is not installed. pbuilder-satisfydepends-dummy depends on fluid; however: Package fluid is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} fluid{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gettext{a} gettext-base{a} gfortran-14{a} gfortran-14-x86-64-linux-gnu{a} groff-base{a} ibverbs-providers{a} intltool-debian{a} libamd-comgr2{a} libamdhip64-5{a} libarchive-zip-perl{a} libarchive13t64{a} libbrotli1{a} libcairo2{a} libcbor0.10{a} libcom-err2{a} libcurl4t64{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-intel1{a} libdrm-radeon1{a} libdrm2{a} libedit2{a} libelf1t64{a} libevent-2.1-7t64{a} libevent-core-2.1-7t64{a} libevent-dev{a} libevent-extra-2.1-7t64{a} libevent-openssl-2.1-7t64{a} libevent-pthreads-2.1-7t64{a} libexpat1{a} libfabric1{a} libfftw3-bin{a} libfftw3-dev{a} libfftw3-double3{a} libfftw3-long3{a} libfftw3-quad3{a} libfftw3-single3{a} libfido2-1{a} libfile-stripnondeterminism-perl{a} libfltk-cairo1.3t64{a} libfltk-forms1.3t64{a} libfltk-gl1.3t64{a} libfltk-images1.3t64{a} libfltk1.3-dev{a} libfltk1.3t64{a} libfontconfig1{a} libfreetype6{a} libgbm1{a} libgfortran-14-dev{a} libgfortran5{a} libgl1{a} libgl1-mesa-dri{a} libglapi-mesa{a} libglvnd0{a} libglx-mesa0{a} libglx0{a} libgssapi-krb5-2{a} libhsa-runtime64-1{a} libhsakmt1{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc15{a} libibmad5{a} libibumad3{a} libibverbs-dev{a} libibverbs1{a} libicu72{a} libjbig-dev{a} libjbig0{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libjs-jquery{a} libjs-jquery-ui{a} libjsoncpp26{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.5-0{a} liblerc-dev{a} liblerc4{a} libllvm17t64{a} libllvm19{a} libltdl-dev{a} libltdl7{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libmunge2{a} libnghttp2-14{a} libnl-3-200{a} libnl-3-dev{a} libnl-route-3-200{a} libnl-route-3-dev{a} libnuma-dev{a} libnuma1{a} libopenmpi-dev{a} libopenmpi3t64{a} libpciaccess0{a} libpipeline1{a} libpixman-1-0{a} libpmix-dev{a} libpmix2t64{a} libpng16-16t64{a} libproc2-0{a} libpsl5t64{a} libpsm-infinipath1{a} libpsm2-2{a} librdmacm1t64{a} librhash1{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsensors-config{a} libsensors5{a} libsharpyuv-dev{a} libsharpyuv0{a} libssh2-1t64{a} libtiff-dev{a} libtiff6{a} libtiffxx6{a} libtool{a} libuchardet0{a} libucx0{a} libuv1t64{a} libvulkan1{a} libwayland-server0{a} libwebp-dev{a} libwebp7{a} libwebpdecoder3{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libx11-dev{a} libx11-xcb1{a} libxau-dev{a} libxau6{a} libxcb-dri2-0{a} libxcb-dri3-0{a} libxcb-glx0{a} libxcb-present0{a} libxcb-randr0{a} libxcb-render0{a} libxcb-shm0{a} libxcb-sync1{a} libxcb-xfixes0{a} libxcb1{a} libxcb1-dev{a} libxcursor1{a} libxdmcp-dev{a} libxdmcp6{a} libxext6{a} libxfixes3{a} libxft2{a} libxinerama1{a} libxml2{a} libxnvctrl0{a} libxrender1{a} libxshmfence1{a} libxxf86vm1{a} libz3-4{a} libzstd-dev{a} m4{a} man-db{a} mesa-libgallium{a} mpi-default-dev{a} ocl-icd-libopencl1{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} po-debconf{a} procps{a} sensible-utils{a} x11proto-dev{a} xorg-sgml-doctools{a} xtrans-dev{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl fltk1.3-doc javascript-common krb5-locales libarchive-cpio-perl libcoarrays-openmpi-dev libgl-dev libglu1-mesa-dev libldap-common libmail-sendmail-perl libsasl2-modules linux-sysctl-defaults lynx mesa-vulkan-drivers psmisc publicsuffix wget xauth 0 packages upgraded, 198 newly installed, 0 to remove and 0 not upgraded. Need to get 177 MB of archives. After unpacking 724 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-6 [64.8 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-6 [879 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.2-10 [97.2 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20240808-1 [93.9 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 libcbor0.10 amd64 0.10.2-2 [28.3 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 libfido2-1 amd64 1.15.0-1+b1 [78.7 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.1-1+b1 [23.2 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 20 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 openssh-client amd64 1:9.9p1-3 [991 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 cmake-data all 3.30.5-1 [2223 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.1 [699 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libarchive13t64 amd64 3.7.4-1.1 [349 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b5 [307 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-3+b1 [188 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.11.0-1 [351 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 libjsoncpp26 amd64 1.9.6-2 [81.6 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 librhash1 amd64 1.4.5-1 [132 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libuv1t64 amd64 1.48.0-7 [148 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 cmake amd64 3.30.5-1 [11.4 MB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-8 [517 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 52 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.20 [915 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.44-2 [280 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.15.0-1.1+b1 [318 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-1.1+b1 [391 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.2-3+b2 [24.4 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 libxfixes3 amd64 1:6.0.0-2+b2 [20.3 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.10-1.1+b2 [27.8 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 libxcursor1 amd64 1:1.2.2-1+b1 [37.6 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b2 [50.5 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libxft2 amd64 2.3.6-1+b2 [54.5 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 libxinerama1 amd64 2:1.1.4-3+b2 [16.0 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 libfltk1.3t64 amd64 1.3.8-6.1+b1 [556 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 libfltk-forms1.3t64 amd64 1.3.8-6.1+b1 [36.7 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 libfltk-images1.3t64 amd64 1.3.8-6.1+b1 [50.2 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 fluid amd64 1.3.8-6.1+b1 [220 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.2.0-8 [836 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libgfortran-14-dev amd64 14.2.0-8 [878 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 gfortran-14-x86-64-linux-gnu amd64 14.2.0-8 [11.7 MB] Get: 83 http://deb.debian.org/debian unstable/main amd64 gfortran-14 amd64 14.2.0-8 [12.2 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 libnl-3-200 amd64 3.7.0-0.3+b1 [59.4 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 libnl-route-3-200 amd64 3.7.0-0.3+b1 [182 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 libibverbs1 amd64 52.0-2+b1 [62.2 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 ibverbs-providers amd64 52.0-2+b1 [343 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 libllvm17t64 amd64 1:17.0.6-18 [23.6 MB] Get: 90 http://deb.debian.org/debian unstable/main amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3+b2 [13.0 MB] Get: 91 http://deb.debian.org/debian unstable/main amd64 libdrm-common all 2.4.123-1 [8084 B] Get: 92 http://deb.debian.org/debian unstable/main amd64 libdrm2 amd64 2.4.123-1 [38.7 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 libdrm-amdgpu1 amd64 2.4.123-1 [22.3 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 libnuma1 amd64 2.0.18-1+b1 [22.3 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 libhsakmt1 amd64 6.1.2+ds-1 [59.8 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 libhsa-runtime64-1 amd64 6.1.2-2 [535 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 libamdhip64-5 amd64 5.7.1-5 [8877 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 libcairo2 amd64 1.18.2-2 [535 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.22-1 [47.3 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 libdeflate-dev amd64 1.22-1 [55.8 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 libpciaccess0 amd64 0.17-3+b2 [51.9 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 libdrm-intel1 amd64 2.4.123-1 [63.7 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 libdrm-radeon1 amd64 2.4.123-1 [22.3 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10+b1 [132 kB] Get: 109 http://deb.debian.org/debian unstable/main amd64 libevent-extra-2.1-7t64 amd64 2.1.12-stable-10+b1 [108 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10+b1 [54.3 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 libevent-openssl-2.1-7t64 amd64 2.1.12-stable-10+b1 [61.1 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 libevent-dev amd64 2.1.12-stable-10+b1 [305 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.3 [170 kB] Get: 114 http://deb.debian.org/debian unstable/main amd64 libpsm2-2 amd64 11.2.185-2.1 [181 kB] Get: 115 http://deb.debian.org/debian unstable/main amd64 librdmacm1t64 amd64 52.0-2+b1 [70.4 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 libfabric1 amd64 1.17.0-3.1 [631 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 libfftw3-double3 amd64 3.3.10-2 [781 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 libfftw3-long3 amd64 3.3.10-2 [347 kB] Get: 119 http://deb.debian.org/debian unstable/main amd64 libfftw3-quad3 amd64 3.3.10-2 [617 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 libfftw3-single3 amd64 3.3.10-2 [809 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 libfftw3-bin amd64 3.3.10-2 [51.0 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 libfftw3-dev amd64 3.3.10-2 [2113 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 libfltk-cairo1.3t64 amd64 1.3.8-6.1+b1 [30.0 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 libglvnd0 amd64 1.7.0-1+b2 [52.0 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 libglapi-mesa amd64 24.2.6-1 [38.0 kB] Get: 126 http://deb.debian.org/debian unstable/main amd64 libx11-xcb1 amd64 2:1.8.10-2 [241 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 libxcb-dri2-0 amd64 1.17.0-2+b1 [107 kB] Get: 128 http://deb.debian.org/debian unstable/main amd64 libxcb-dri3-0 amd64 1.17.0-2+b1 [107 kB] Get: 129 http://deb.debian.org/debian unstable/main amd64 libxcb-glx0 amd64 1.17.0-2+b1 [122 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 libxcb-present0 amd64 1.17.0-2+b1 [106 kB] Get: 131 http://deb.debian.org/debian unstable/main amd64 libxcb-randr0 amd64 1.17.0-2+b1 [117 kB] Get: 132 http://deb.debian.org/debian unstable/main amd64 libxcb-sync1 amd64 1.17.0-2+b1 [109 kB] Get: 133 http://deb.debian.org/debian unstable/main amd64 libxcb-xfixes0 amd64 1.17.0-2+b1 [109 kB] Get: 134 http://deb.debian.org/debian unstable/main amd64 libxshmfence1 amd64 1.3-1+b2 [8848 B] Get: 135 http://deb.debian.org/debian unstable/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b3 [19.3 kB] Get: 136 http://deb.debian.org/debian unstable/main amd64 libllvm19 amd64 1:19.1.3-1 [26.0 MB] Get: 137 http://deb.debian.org/debian unstable/main amd64 libsensors-config all 1:3.6.0-10 [14.6 kB] Get: 138 http://deb.debian.org/debian unstable/main amd64 libsensors5 amd64 1:3.6.0-10+b1 [35.1 kB] Get: 139 http://deb.debian.org/debian unstable/main amd64 mesa-libgallium amd64 24.2.6-1 [9185 kB] Get: 140 http://deb.debian.org/debian unstable/main amd64 libvulkan1 amd64 1.3.296.0-1 [126 kB] Get: 141 http://deb.debian.org/debian unstable/main amd64 libwayland-server0 amd64 1.23.0-1+b1 [34.2 kB] Get: 142 http://deb.debian.org/debian unstable/main amd64 libgbm1 amd64 24.2.6-1 [42.8 kB] Get: 143 http://deb.debian.org/debian unstable/main amd64 libgl1-mesa-dri amd64 24.2.6-1 [43.9 kB] Get: 144 http://deb.debian.org/debian unstable/main amd64 libglx-mesa0 amd64 24.2.6-1 [154 kB] Get: 145 http://deb.debian.org/debian unstable/main amd64 libglx0 amd64 1.7.0-1+b2 [34.9 kB] Get: 146 http://deb.debian.org/debian unstable/main amd64 libgl1 amd64 1.7.0-1+b2 [89.5 kB] Get: 147 http://deb.debian.org/debian unstable/main amd64 libfltk-gl1.3t64 amd64 1.3.8-6.1+b1 [63.0 kB] Get: 148 http://deb.debian.org/debian unstable/main amd64 xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB] Get: 149 http://deb.debian.org/debian unstable/main amd64 x11proto-dev all 2024.1-1 [603 kB] Get: 150 http://deb.debian.org/debian unstable/main amd64 libxau-dev amd64 1:1.0.11-1 [23.6 kB] Get: 151 http://deb.debian.org/debian unstable/main amd64 libxdmcp-dev amd64 1:1.1.2-3+b2 [40.8 kB] Get: 152 http://deb.debian.org/debian unstable/main amd64 xtrans-dev all 1.4.0-1 [98.7 kB] Get: 153 http://deb.debian.org/debian unstable/main amd64 libxcb1-dev amd64 1.17.0-2+b1 [181 kB] Get: 154 http://deb.debian.org/debian unstable/main amd64 libx11-dev amd64 2:1.8.10-2 [891 kB] Get: 155 http://deb.debian.org/debian unstable/main amd64 libfltk1.3-dev amd64 1.3.8-6.1+b1 [849 kB] Get: 156 http://deb.debian.org/debian unstable/main amd64 libhwloc15 amd64 2.11.2-1 [164 kB] Get: 157 http://deb.debian.org/debian unstable/main amd64 libnuma-dev amd64 2.0.18-1+b1 [36.6 kB] Get: 158 http://deb.debian.org/debian unstable/main amd64 libltdl7 amd64 2.4.7-8 [393 kB] Get: 159 http://deb.debian.org/debian unstable/main amd64 libltdl-dev amd64 2.4.7-8 [165 kB] Get: 160 http://deb.debian.org/debian unstable/main amd64 libhwloc-dev amd64 2.11.2-1 [254 kB] Get: 161 http://deb.debian.org/debian unstable/main amd64 libxnvctrl0 amd64 535.171.04-1+b1 [14.2 kB] Get: 162 http://deb.debian.org/debian unstable/main amd64 ocl-icd-libopencl1 amd64 2.3.2-1+b2 [40.2 kB] Get: 163 http://deb.debian.org/debian unstable/main amd64 libhwloc-plugins amd64 2.11.2-1 [18.1 kB] Get: 164 http://deb.debian.org/debian unstable/main amd64 libibumad3 amd64 52.0-2+b1 [28.2 kB] Get: 165 http://deb.debian.org/debian unstable/main amd64 libibmad5 amd64 52.0-2+b1 [43.4 kB] Get: 166 http://deb.debian.org/debian unstable/main amd64 libnl-3-dev amd64 3.7.0-0.3+b1 [100 kB] Get: 167 http://deb.debian.org/debian unstable/main amd64 libnl-route-3-dev amd64 3.7.0-0.3+b1 [200 kB] Get: 168 http://deb.debian.org/debian unstable/main amd64 libibverbs-dev amd64 52.0-2+b1 [636 kB] Get: 169 http://deb.debian.org/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get: 170 http://deb.debian.org/debian unstable/main amd64 libjbig-dev amd64 2.1-6.1+b2 [31.4 kB] Get: 171 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo-dev amd64 1:2.1.5-3+b1 [292 kB] Get: 172 http://deb.debian.org/debian unstable/main amd64 libjpeg-dev amd64 1:2.1.5-3+b1 [72.2 kB] Get: 173 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 174 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 175 http://deb.debian.org/debian unstable/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get: 176 http://deb.debian.org/debian unstable/main amd64 liblerc-dev amd64 4.0.0+ds-5 [183 kB] Get: 177 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.6.3-1+b1 [316 kB] Get: 178 http://deb.debian.org/debian unstable/main amd64 libmunge2 amd64 0.5.15-4+b1 [20.0 kB] Get: 179 http://deb.debian.org/debian unstable/main amd64 libpmix2t64 amd64 5.0.3-2+b1 [662 kB] Get: 180 http://deb.debian.org/debian unstable/main amd64 libucx0 amd64 1.17.0+ds-3 [1130 kB] Get: 181 http://deb.debian.org/debian unstable/main amd64 libopenmpi3t64 amd64 5.0.5-3 [2007 kB] Get: 182 http://deb.debian.org/debian unstable/main amd64 openmpi-common all 5.0.5-3 [95.0 kB] Get: 183 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 184 http://deb.debian.org/debian unstable/main amd64 libpmix-dev amd64 5.0.3-2+b1 [3958 kB] Get: 185 http://deb.debian.org/debian unstable/main amd64 openmpi-bin amd64 5.0.5-3 [168 kB] Get: 186 http://deb.debian.org/debian unstable/main amd64 libopenmpi-dev amd64 5.0.5-3 [1087 kB] Get: 187 http://deb.debian.org/debian unstable/main amd64 libsharpyuv0 amd64 1.4.0-0.1+b1 [113 kB] Get: 188 http://deb.debian.org/debian unstable/main amd64 libsharpyuv-dev amd64 1.4.0-0.1+b1 [117 kB] Get: 189 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.6+dfsg-1+b1 [365 kB] Get: 190 http://deb.debian.org/debian unstable/main amd64 libwebp7 amd64 1.4.0-0.1+b1 [313 kB] Get: 191 http://deb.debian.org/debian unstable/main amd64 libwebpdemux2 amd64 1.4.0-0.1+b1 [111 kB] Get: 192 http://deb.debian.org/debian unstable/main amd64 libwebpmux3 amd64 1.4.0-0.1+b1 [123 kB] Get: 193 http://deb.debian.org/debian unstable/main amd64 libwebpdecoder3 amd64 1.4.0-0.1+b1 [204 kB] Get: 194 http://deb.debian.org/debian unstable/main amd64 libwebp-dev amd64 1.4.0-0.1+b1 [442 kB] Get: 195 http://deb.debian.org/debian unstable/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get: 196 http://deb.debian.org/debian unstable/main amd64 libtiffxx6 amd64 4.5.1+git230720-5 [149 kB] Get: 197 http://deb.debian.org/debian unstable/main amd64 libtiff-dev amd64 4.5.1+git230720-5 [463 kB] Get: 198 http://deb.debian.org/debian unstable/main amd64 mpi-default-dev amd64 1.17 [3148 B] Fetched 177 MB in 2s (105 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libproc2-0:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19970 files and directories currently installed.) Preparing to unpack .../000-libproc2-0_2%3a4.0.4-6_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-6) ... Selecting previously unselected package procps. Preparing to unpack .../001-procps_2%3a4.0.4-6_amd64.deb ... Unpacking procps (2:4.0.4-6) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../002-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../003-libmagic-mgc_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../004-libmagic1t64_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../005-file_1%3a5.45-3+b1_amd64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../006-gettext-base_0.22.5-2_amd64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../007-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../008-groff-base_1.23.0-5_amd64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../009-bsdextrautils_2.40.2-10_amd64.deb ... Unpacking bsdextrautils (2.40.2-10) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../010-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../011-man-db_2.13.0-1_amd64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../012-libedit2_3.1-20240808-1_amd64.deb ... Unpacking libedit2:amd64 (3.1-20240808-1) ... Selecting previously unselected package libcbor0.10:amd64. Preparing to unpack .../013-libcbor0.10_0.10.2-2_amd64.deb ... Unpacking libcbor0.10:amd64 (0.10.2-2) ... Selecting previously unselected package libfido2-1:amd64. Preparing to unpack .../014-libfido2-1_1.15.0-1+b1_amd64.deb ... Unpacking libfido2-1:amd64 (1.15.0-1+b1) ... 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Unpacking libgssapi-krb5-2:amd64 (1.21.3-3) ... Selecting previously unselected package openssh-client. Preparing to unpack .../021-openssh-client_1%3a9.9p1-3_amd64.deb ... Unpacking openssh-client (1:9.9p1-3) ... Selecting previously unselected package m4. Preparing to unpack .../022-m4_1.4.19-4_amd64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../023-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../024-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../025-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../026-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package cmake-data. 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Setting up libtiff6:amd64 (4.5.1+git230720-5) ... Setting up libxcb-randr0:amd64 (1.17.0-2+b1) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up procps (2:4.0.4-6) ... Setting up libnl-3-200:amd64 (3.7.0-0.3+b1) ... Setting up libpsm2-2 (11.2.185-2.1) ... Setting up openmpi-common (5.0.5-3) ... Setting up libx11-6:amd64 (2:1.8.10-2) ... Setting up xorg-sgml-doctools (1:1.11-1.1) ... Setting up cmake-data (3.30.5-1) ... Setting up librhash1:amd64 (1.4.5-1) ... Setting up libkrb5-3:amd64 (1.21.3-3) ... Setting up libevent-core-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up libpsm-infinipath1 (3.3+20.604758e7-6.3) ... update-alternatives: using /usr/lib/libpsm1/libpsm_infinipath.so.1.16 to provide /usr/lib/x86_64-linux-gnu/libpsm_infinipath.so.1 (libpsm_infinipath.so.1) in auto mode Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libfido2-1:amd64 (1.15.0-1+b1) ... 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Setting up openmpi-bin (5.0.5-3) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: warning: skip creation of /usr/share/man/man1/mpirun.1.gz because associated file /usr/share/man/man1/mpirun.openmpi.1.gz (of link group mpirun) doesn't exist update-alternatives: warning: skip creation of /usr/share/man/man1/mpiexec.1.gz because associated file /usr/share/man/man1/mpiexec.openmpi.1.gz (of link group mpirun) doesn't exist update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up libfltk1.3-dev:amd64 (1.3.8-6.1+b1) ... Setting up libopenmpi-dev:amd64 (5.0.5-3) ... 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 Setting up mpi-default-dev (1.17) ... Processing triggers for libc-bin (2.40-3) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/relion-3.1.3/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../relion_3.1.3-4_source.changes dpkg-buildpackage: info: source package relion dpkg-buildpackage: info: source version 3.1.3-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/relion-3.1.3' dh_clean rm -rf build make[1]: Leaving directory '/build/reproducible-path/relion-3.1.3' debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/relion-3.1.3' mkdir /build/reproducible-path/relion-3.1.3/build cd /build/reproducible-path/relion-3.1.3/build; \ CC=gcc CXX=g++ cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_SKIP_RPATH=TRUE -DDoublePrec_GPU=ON -DGUI=ON -DCUDA=OFF /build/reproducible-path/relion-3.1.3 CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. CMake Warning (dev) at /usr/share/cmake-3.30/Modules/CMakeDetermineCompilerId.cmake:96 (if): Policy CMP0054 is not set: Only interpret if() arguments as variables or keywords when unquoted. Run "cmake --help-policy CMP0054" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Quoted variables like "CUDA" will no longer be dereferenced when the policy is set to NEW. Since the policy is not set the OLD behavior will be used. Call Stack (most recent call first): /usr/share/cmake-3.30/Modules/CMakeDetermineCCompiler.cmake:123 (CMAKE_DETERMINE_COMPILER_ID) CMakeLists.txt:6 (project) This warning is for project developers. Use -Wno-dev to suppress it. -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- BUILD TYPE set to the default type: 'Release' -- Setting fallback CUDA_ARCH=35 -- ALLOW_CTF_IN_SAGD enabled - This build of RELION allows modulation of particle images by a contrast transfer function inside stochastic average gradient descent, as specified in Claim 1 of patent US10,282,513B2 -- Setting cpu precision to double -- Setting accelerated code precision to single -- Using non-cuda compilation.... -- Found MPI_C: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") -- 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.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.so -- CMAKE_C_COMPILER : /usr/bin/gcc -- CMAKE_CXX_COMPILER : /usr/bin/g++ -- MPI_C_COMPILER : /usr/bin/mpicc -- MPI_CXX_COMPILER : /usr/bin/mpicxx -- CMAKE_CXX_COMPILER_ID : GNU -- Found X11: /usr/include -- Looking for XOpenDisplay in /usr/lib/x86_64-linux-gnu/libX11.so -- Looking for XOpenDisplay in /usr/lib/x86_64-linux-gnu/libX11.so - found -- Looking for gethostbyname -- Looking for gethostbyname - found -- Looking for connect -- Looking for connect - found -- Looking for remove -- Looking for remove - found -- Looking for shmat -- Looking for shmat - found -- Found FLTK: fltk_images;fltk_forms;fltk -- X11 and FLTK were found -- FLTK_LIBRARIES: fltk_images;fltk_forms;fltk;/usr/lib/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 -- Looking for sincos -- Looking for sincos - found -- Looking for __sincos -- Looking for __sincos - not found -- Found TIFF: /usr/lib/x86_64-linux-gnu/libtiff.so (found version "4.5.1") -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.3.1") -- 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/reproducible-path/relion-3.1.3/build -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Configuring done (11.4s) -- Generating done (0.2s) CMake Warning: Manually-specified variables were not used by the project: DoublePrec_GPU -- Build files have been written to: /build/reproducible-path/relion-3.1.3/build make[1]: Leaving directory '/build/reproducible-path/relion-3.1.3' debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/relion-3.1.3' /usr/bin/make -j12 -C build make[2]: Entering directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/cmake -S/build/reproducible-path/relion-3.1.3 -B/build/reproducible-path/relion-3.1.3/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/relion-3.1.3/build/CMakeFiles /build/reproducible-path/relion-3.1.3/build//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/make -f CMakeFiles/copy_scripts.dir/build.make CMakeFiles/copy_scripts.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/CMakeFiles/copy_scripts.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/apps/CMakeFiles/relion_lib.dir/build.make src/apps/CMakeFiles/relion_lib.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/relion_lib.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/make -f CMakeFiles/copy_scripts.dir/build.make CMakeFiles/copy_scripts.dir/build make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/cmake -E copy /build/reproducible-path/relion-3.1.3/scripts/star_printtable /build/reproducible-path/relion-3.1.3/build/bin/relion_star_printtable /usr/bin/make -f src/apps/CMakeFiles/relion_lib.dir/build.make src/apps/CMakeFiles/relion_lib.dir/build make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/cmake -E copy /build/reproducible-path/relion-3.1.3/scripts/star_plottable /build/reproducible-path/relion-3.1.3/build/bin/relion_star_plottable [ 0%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/__/macros.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/relion-3.1.3/build/macros.cpp /usr/bin/cmake -E copy /build/reproducible-path/relion-3.1.3/scripts/star_loopheader /build/reproducible-path/relion-3.1.3/build/bin/relion_star_loopheader [ 1%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/CPlot2D.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/CPlot2D.cpp [ 1%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/assembly.cpp.o [ 1%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/args.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/args.cpp /usr/bin/cmake -E copy /build/reproducible-path/relion-3.1.3/scripts/star_datablock_stack /build/reproducible-path/relion-3.1.3/build/bin/relion_star_datablock_stack [ 2%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/autopicker.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/assembly.cpp cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/autopicker.cpp /usr/bin/cmake -E copy /build/reproducible-path/relion-3.1.3/scripts/star_datablock_singlefiles /build/reproducible-path/relion-3.1.3/build/bin/relion_star_datablock_singlefiles /usr/bin/cmake -E copy /build/reproducible-path/relion-3.1.3/scripts/star_datablock_ctfdat /build/reproducible-path/relion-3.1.3/build/bin/relion_star_datablock_ctfdat [ 2%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o [ 3%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/backprojector.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/autopicker_mpi.cpp /usr/bin/cmake -E copy /build/reproducible-path/relion-3.1.3/scripts/qsub.csh /build/reproducible-path/relion-3.1.3/build/bin/relion_qsub.csh cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/backprojector.cpp make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 3%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/complex.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/complex.cpp [ 3%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctf.cpp.o [ 3%] Built target copy_scripts cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/ctf.cpp [ 4%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner.cpp.o [ 4%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/error.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/error.cpp cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/ctffind_runner.cpp [ 4%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner_mpi.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/ctffind_runner_mpi.cpp [ 5%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/euler.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/euler.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/ctffind_runner.h:31, from /build/reproducible-path/relion-3.1.3/src/ctffind_runner.cpp:20: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 5%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/exp_model.cpp.o In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/projector.h:25, from /build/reproducible-path/relion-3.1.3/src/backprojector.h:33, from /build/reproducible-path/relion-3.1.3/src/backprojector.cpp:27: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/exp_model.cpp [ 6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/fftw.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/fftw.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/autopicker.h:10, from /build/reproducible-path/relion-3.1.3/src/autopicker.cpp:20: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/exp_model.h:24, from /build/reproducible-path/relion-3.1.3/src/exp_model.cpp:20: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, from /build/reproducible-path/relion-3.1.3/src/ctf.h:50, from /build/reproducible-path/relion-3.1.3/src/ctf.cpp:45: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/autopicker.h:10, from /build/reproducible-path/relion-3.1.3/src/autopicker_mpi.h:12, from /build/reproducible-path/relion-3.1.3/src/autopicker_mpi.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/ctffind_runner.h:31, from /build/reproducible-path/relion-3.1.3/src/ctffind_runner_mpi.h:25, from /build/reproducible-path/relion-3.1.3/src/ctffind_runner_mpi.cpp:20: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/filename.cpp.o /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/filename.cpp [ 6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/flex_analyser.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/flex_analyser.cpp [ 7%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/funcs.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/funcs.cpp [ 7%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/healpix_sampling.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/healpix_sampling.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/exp_model.h:24, from /build/reproducible-path/relion-3.1.3/src/flex_analyser.h:24, from /build/reproducible-path/relion-3.1.3/src/flex_analyser.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 7%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/helix.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/helix.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/helix.h:30, from /build/reproducible-path/relion-3.1.3/src/healpix_sampling.h:31, from /build/reproducible-path/relion-3.1.3/src/healpix_sampling.cpp:20: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 8%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/helix_inimodel2d.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/helix_inimodel2d.cpp [ 8%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/image.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/image.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/helix.h:30, from /build/reproducible-path/relion-3.1.3/src/helix.cpp:22: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/helix_inimodel2d.h:29, from /build/reproducible-path/relion-3.1.3/src/helix_inimodel2d.cpp:22: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/image.cpp:20: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 9%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/local_symmetry.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/local_symmetry.cpp [ 9%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/local_symmetry_mpi.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/local_symmetry_mpi.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/local_symmetry.h:30, from /build/reproducible-path/relion-3.1.3/src/local_symmetry.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/local_symmetry.h:30, from /build/reproducible-path/relion-3.1.3/src/local_symmetry_mpi.h:5, from /build/reproducible-path/relion-3.1.3/src/local_symmetry_mpi.cpp:1: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 9%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/mask.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/mask.cpp [ 10%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/matrix1d.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/matrix1d.cpp [ 10%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/matrix2d.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/matrix2d.cpp [ 11%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/memory.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/memory.cpp [ 11%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/metadata_container.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/metadata_container.cpp [ 11%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/metadata_label.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/metadata_label.cpp [ 12%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/metadata_table.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/metadata_table.cpp [ 12%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/micrograph_model.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/micrograph_model.cpp [ 12%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ml_model.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/ml_model.cpp [ 13%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ml_optimiser.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/ml_optimiser.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/micrograph_model.cpp:23: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/projector.h:25, from /build/reproducible-path/relion-3.1.3/src/ml_model.h:23, from /build/reproducible-path/relion-3.1.3/src/ml_optimiser.h:35, from /build/reproducible-path/relion-3.1.3/src/ml_optimiser.cpp:44: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/projector.h:25, from /build/reproducible-path/relion-3.1.3/src/ml_model.h:23, from /build/reproducible-path/relion-3.1.3/src/ml_model.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 13%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ml_optimiser_mpi.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/ml_optimiser_mpi.cpp [ 14%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/motioncorr_runner.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/motioncorr_runner.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/projector.h:25, from /build/reproducible-path/relion-3.1.3/src/ml_model.h:23, from /build/reproducible-path/relion-3.1.3/src/ml_optimiser.h:35, from /build/reproducible-path/relion-3.1.3/src/ml_optimiser_mpi.h:24, from /build/reproducible-path/relion-3.1.3/src/ml_optimiser_mpi.cpp:20: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 14%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/motioncorr_runner_mpi.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/motioncorr_runner_mpi.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/motioncorr_runner.h:32, from /build/reproducible-path/relion-3.1.3/src/motioncorr_runner.cpp:22: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 14%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/mpi.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/mpi.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/motioncorr_runner.h:32, from /build/reproducible-path/relion-3.1.3/src/motioncorr_runner_mpi.h:25, from /build/reproducible-path/relion-3.1.3/src/motioncorr_runner_mpi.cpp:20: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 15%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/multidim_array.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/multidim_array.cpp [ 15%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/numerical_recipes.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/numerical_recipes.cpp [ 15%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/parallel.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/parallel.cpp In file included from /build/reproducible-path/relion-3.1.3/src/numerical_recipes.h:48, from /build/reproducible-path/relion-3.1.3/src/numerical_recipes.cpp:49: In function 'void free_Tvector(T*&, int, int) [with T = double]', inlined from 'void mnbrak(double*, double*, double*, double*, double*, double*, double (*)(double*, void*), void*, int, double*, double*)' at /build/reproducible-path/relion-3.1.3/src/numerical_recipes.cpp:561:17: /build/reproducible-path/relion-3.1.3/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)); | ~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/relion-3.1.3/src/numerical_recipes.cpp: In function 'void mnbrak(double*, double*, double*, double*, double*, double*, double (*)(double*, void*), void*, int, double*, double*)': /build/reproducible-path/relion-3.1.3/src/numerical_recipes.cpp:499:13: note: declared here 499 | RFLOAT *xt=NULL; | ^~ 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 /build/reproducible-path/relion-3.1.3/src/numerical_recipes.cpp:594:25: /build/reproducible-path/relion-3.1.3/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)); | ~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/relion-3.1.3/src/numerical_recipes.cpp: In function 'double brent(double, double, double, double (*)(double*, void*), void*, double, double*, int, double*, double*)': /build/reproducible-path/relion-3.1.3/src/numerical_recipes.cpp:579:13: note: declared here 579 | RFLOAT *xt=NULL; | ^~ In function 'void free_Tvector(T*&, int, int) [with T = double]', inlined from 'void linmin(double*, double*, int, double&, double (*)(double*, void*), void*)' at /build/reproducible-path/relion-3.1.3/src/numerical_recipes.cpp:691:17: /build/reproducible-path/relion-3.1.3/src/memory.h:74:13: warning: 'void free(void*)' called on pointer 'xicom' with nonzero offset 8 [-Wfree-nonheap-object] 74 | free((char*)(v + nl)); | ~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/relion-3.1.3/src/numerical_recipes.cpp: In function 'void linmin(double*, double*, int, double&, double (*)(double*, void*), void*)': /build/reproducible-path/relion-3.1.3/src/numerical_recipes.cpp:673:13: note: declared here 673 | RFLOAT *xicom=NULL; | ^~~~~ In function 'void free_Tvector(T*&, int, int) [with T = double]', inlined from 'void linmin(double*, double*, int, double&, double (*)(double*, void*), void*)' at /build/reproducible-path/relion-3.1.3/src/numerical_recipes.cpp:692:17: /build/reproducible-path/relion-3.1.3/src/memory.h:74:13: warning: 'void free(void*)' called on pointer 'pcom' with nonzero offset 8 [-Wfree-nonheap-object] 74 | free((char*)(v + nl)); | ~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/relion-3.1.3/src/numerical_recipes.cpp: In function 'void linmin(double*, double*, int, double&, double (*)(double*, void*), void*)': /build/reproducible-path/relion-3.1.3/src/numerical_recipes.cpp:672:13: note: declared here 672 | RFLOAT *pcom=NULL; | ^~~~ In function 'void free_Tvector(T*&, int, int) [with T = double]', inlined from 'void powell(double*, double*, int, double, int&, double&, double (*)(double*, void*), void*, bool)' at /build/reproducible-path/relion-3.1.3/src/numerical_recipes.cpp:767:25: /build/reproducible-path/relion-3.1.3/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)); | ~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/relion-3.1.3/src/numerical_recipes.cpp: In function 'void powell(double*, double*, int, double, int&, double&, double (*)(double*, void*), void*, bool)': /build/reproducible-path/relion-3.1.3/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 /build/reproducible-path/relion-3.1.3/src/numerical_recipes.cpp:768:25: /build/reproducible-path/relion-3.1.3/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)); | ~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/relion-3.1.3/src/numerical_recipes.cpp: In function 'void powell(double*, double*, int, double, int&, double&, double (*)(double*, void*), void*, bool)': /build/reproducible-path/relion-3.1.3/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 /build/reproducible-path/relion-3.1.3/src/numerical_recipes.cpp:769:25: /build/reproducible-path/relion-3.1.3/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)); | ~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/relion-3.1.3/src/numerical_recipes.cpp: In function 'void powell(double*, double*, int, double, int&, double&, double (*)(double*, void*), void*, bool)': /build/reproducible-path/relion-3.1.3/src/numerical_recipes.cpp:703:13: note: declared here 703 | RFLOAT *pt, *ptt, *xit; | ^~ [ 16%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/particle_subtractor.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/particle_subtractor.cpp In function 'void free_Tvector(T*&, int, int) [with T = double]', inlined from 'void svbksb(double*, double*, double*, int, int, double*, double*)' at /build/reproducible-path/relion-3.1.3/src/numerical_recipes.cpp:1124:17: /build/reproducible-path/relion-3.1.3/src/memory.h:74:13: warning: 'void free(void*)' called on pointer 'tmp' with nonzero offset 8 [-Wfree-nonheap-object] 74 | free((char*)(v + nl)); | ~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/relion-3.1.3/src/numerical_recipes.cpp: In function 'void svbksb(double*, double*, double*, int, int, double*, double*)': /build/reproducible-path/relion-3.1.3/src/numerical_recipes.cpp:1103:16: note: declared here 1103 | RFLOAT s, *tmp; | ^~~ [ 16%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/pipeline_control.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/pipeline_control.cpp [ 17%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/pipeline_jobs.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/pipeline_jobs.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/projector.h:25, from /build/reproducible-path/relion-3.1.3/src/ml_model.h:23, from /build/reproducible-path/relion-3.1.3/src/ml_optimiser.h:35, from /build/reproducible-path/relion-3.1.3/src/particle_subtractor.h:24, from /build/reproducible-path/relion-3.1.3/src/particle_subtractor.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 17%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/pipeliner.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/pipeliner.cpp [ 17%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/postprocessing.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/postprocessing.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/postprocessing.h:24, from /build/reproducible-path/relion-3.1.3/src/postprocessing.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 18%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/preprocessing.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/preprocessing.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/preprocessing.h:29, from /build/reproducible-path/relion-3.1.3/src/preprocessing.cpp:20: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 18%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/preprocessing_mpi.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/preprocessing_mpi.cpp [ 18%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/projector.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/projector.cpp [ 19%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/reconstructor.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/reconstructor.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/preprocessing.h:29, from /build/reproducible-path/relion-3.1.3/src/preprocessing_mpi.h:24, from /build/reproducible-path/relion-3.1.3/src/preprocessing_mpi.cpp:20: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/projector.h:25, from /build/reproducible-path/relion-3.1.3/src/projector.cpp:20: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 19%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/reconstructor_mpi.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/reconstructor_mpi.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/projector.h:25, from /build/reproducible-path/relion-3.1.3/src/backprojector.h:33, from /build/reproducible-path/relion-3.1.3/src/reconstructor.h:23, from /build/reproducible-path/relion-3.1.3/src/reconstructor.cpp:20: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/projector.h:25, from /build/reproducible-path/relion-3.1.3/src/backprojector.h:33, from /build/reproducible-path/relion-3.1.3/src/reconstructor.h:23, from /build/reproducible-path/relion-3.1.3/src/reconstructor_mpi.h:25, from /build/reproducible-path/relion-3.1.3/src/reconstructor_mpi.cpp:20: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 20%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/renderEER.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/renderEER.cpp [ 20%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/scheduler.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/scheduler.cpp [ 20%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/strings.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/strings.cpp [ 21%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/symmetries.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/symmetries.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/renderEER.cpp:10: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/renderEER.cpp: In member function 'void EERRenderer::readLegacy(FILE*)': /build/reproducible-path/relion-3.1.3/src/renderEER.cpp:191:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 191 | fread(buf, sizeof(char), file_size, fh); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 21%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/tabfuncs.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/tabfuncs.cpp [ 21%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/tiff_converter.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/tiff_converter.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, from /build/reproducible-path/relion-3.1.3/src/scheduler.h:26, from /build/reproducible-path/relion-3.1.3/src/scheduler.cpp:20: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/tiff_converter.cpp:24: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/tiff_converter.cpp: In member function 'void TIFFConverter::estimate(FileName)': /build/reproducible-path/relion-3.1.3/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 /build/reproducible-path/relion-3.1.3/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 [ 22%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/time.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/time.cpp /build/reproducible-path/relion-3.1.3/src/tiff_converter.cpp: In member function 'int TIFFConverter::checkMRCtype(FileName)': /build/reproducible-path/relion-3.1.3/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); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/relion-3.1.3/src/tiff_converter.cpp: In member function 'void TIFFConverter::initialise(int, int)': /build/reproducible-path/relion-3.1.3/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()); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/relion-3.1.3/src/tiff_converter.cpp: In member function 'void TIFFConverter::run()': /build/reproducible-path/relion-3.1.3/src/tiff_converter.cpp:530:31: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | system(("mkdir -p " + fn_tiff.beforeLastOf("/")).c_str()); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 22%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/transformations.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/transformations.cpp [ 23%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/Healpix_2.15a/cxxutils.cc.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/Healpix_2.15a/cxxutils.cc [ 23%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/Healpix_2.15a/healpix_base.cc.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/Healpix_2.15a/healpix_base.cc [ 23%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/Fourier_helper.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/Fourier_helper.cpp [ 24%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/Gaussian_pyramid.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/Gaussian_pyramid.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/Fourier_helper.h:24, from /build/reproducible-path/relion-3.1.3/src/jaz/Fourier_helper.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 24%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/aberration_fit.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/aberration_fit.cpp [ 25%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/complex_io.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/complex_io.cpp [ 25%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/convolution_helper.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/convolution_helper.cpp [ 25%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf_helper.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/ctf_helper.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/complex_io.h:24, from /build/reproducible-path/relion-3.1.3/src/jaz/complex_io.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/aberration_fit.h:24, from /build/reproducible-path/relion-3.1.3/src/jaz/aberration_fit.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 26%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/damage_helper.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/damage_helper.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, from /build/reproducible-path/relion-3.1.3/src/ctf.h:50, from /build/reproducible-path/relion-3.1.3/src/jaz/ctf_helper.h:24, from /build/reproducible-path/relion-3.1.3/src/jaz/ctf_helper.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/convolution_helper.h:24, from /build/reproducible-path/relion-3.1.3/src/jaz/convolution_helper.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, from /build/reproducible-path/relion-3.1.3/src/ctf.h:50, from /build/reproducible-path/relion-3.1.3/src/jaz/fsc_helper.h:24, from /build/reproducible-path/relion-3.1.3/src/jaz/damage_helper.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 26%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/distribution_helper.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/distribution_helper.cpp [ 26%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/fftw_helper.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/fftw_helper.cpp [ 27%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/fsc_helper.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/fsc_helper.cpp [ 27%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/image_log.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/image_log.cpp [ 27%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/jaz_config.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/jaz_config.cpp [ 28%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/interpolation.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/interpolation.cpp [ 28%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/legacy_obs_model.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/legacy_obs_model.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/distribution_helper.h:25, from /build/reproducible-path/relion-3.1.3/src/jaz/distribution_helper.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 29%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/local_motion_fit.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/local_motion_fit.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, from /build/reproducible-path/relion-3.1.3/src/ctf.h:50, from /build/reproducible-path/relion-3.1.3/src/jaz/fsc_helper.h:24, from /build/reproducible-path/relion-3.1.3/src/jaz/fsc_helper.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/image_log.h:24, from /build/reproducible-path/relion-3.1.3/src/jaz/image_log.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/interpolation.h:24, from /build/reproducible-path/relion-3.1.3/src/jaz/interpolation.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/legacy_obs_model.h:4, from /build/reproducible-path/relion-3.1.3/src/jaz/legacy_obs_model.cpp:1: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 29%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/micrograph_handler.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/micrograph_handler.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/local_motion_fit.h:24, from /build/reproducible-path/relion-3.1.3/src/jaz/local_motion_fit.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/micrograph_handler.h:31, from /build/reproducible-path/relion-3.1.3/src/jaz/micrograph_handler.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 29%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/new_ft.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/new_ft.cpp [ 30%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/noise_helper.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/noise_helper.cpp [ 30%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/obs_model.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.cpp [ 31%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/parallel_ft.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/parallel_ft.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/projector.h:25, from /build/reproducible-path/relion-3.1.3/src/jaz/noise_helper.h:25, from /build/reproducible-path/relion-3.1.3/src/jaz/noise_helper.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 31%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/reference_map.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/reference_map.cpp [ 31%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/refinement_helper.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/refinement_helper.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/reference_map.h:24, from /build/reproducible-path/relion-3.1.3/src/jaz/reference_map.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 32%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/resampling_helper.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/resampling_helper.cpp [ 32%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/slice_helper.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/slice_helper.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, from /build/reproducible-path/relion-3.1.3/src/ctf.h:50, from /build/reproducible-path/relion-3.1.3/src/jaz/refinement_helper.h:24, from /build/reproducible-path/relion-3.1.3/src/jaz/refinement_helper.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 32%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/spectral_helper.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/spectral_helper.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/slice_helper.h:24, from /build/reproducible-path/relion-3.1.3/src/jaz/slice_helper.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 33%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/stack_helper.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/stack_helper.cpp [ 33%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/structure_tensor.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/structure_tensor.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/spectral_helper.h:24, from /build/reproducible-path/relion-3.1.3/src/jaz/spectral_helper.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, from /build/reproducible-path/relion-3.1.3/src/ctf.h:50, from /build/reproducible-path/relion-3.1.3/src/jaz/stack_helper.h:24, from /build/reproducible-path/relion-3.1.3/src/jaz/stack_helper.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 34%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/svd_helper.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/svd_helper.cpp [ 34%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/t_complex.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/t_complex.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/img_proc/filter_helper.h:24, from /build/reproducible-path/relion-3.1.3/src/jaz/structure_tensor.cpp:22: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 34%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/volume_converter.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/volume_converter.cpp [ 35%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/volume_integration.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/volume_integration.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/volume_converter.h:25, from /build/reproducible-path/relion-3.1.3/src/jaz/volume_converter.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 35%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/vtk_helper.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/vtk_helper.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/volume_integration.h:26, from /build/reproducible-path/relion-3.1.3/src/jaz/volume_integration.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 36%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/gradient_descent.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/optimization/gradient_descent.cpp [ 36%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/lbfgs.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/optimization/lbfgs.cpp [ 36%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/nelder_mead.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/optimization/nelder_mead.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/vtk_helper.h:24, from /build/reproducible-path/relion-3.1.3/src/jaz/vtk_helper.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 37%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/optimization.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/optimization/optimization.cpp [ 37%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/aberration_estimator.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/ctf/aberration_estimator.cpp [ 37%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/bfactor_refiner.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp [ 38%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/aberration_estimator.h:4, from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/aberration_estimator.cpp:1: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 39%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner_mpi.cpp.o [ 39%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_estimator.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.cpp cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/ctf/defocus_estimator.cpp [ 39%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_helper.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/ctf/defocus_helper.cpp [ 39%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/delocalisation_helper.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/ctf/delocalisation_helper.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/bfactor_refiner.h:4, from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:1: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, from /build/reproducible-path/relion-3.1.3/src/ctf.h:50, from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/defocus_helper.h:24, from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/defocus_helper.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/defocus_estimator.h:24, from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/defocus_estimator.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, from /build/reproducible-path/relion-3.1.3/src/ctf.h:50, from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/delocalisation_helper.h:4, from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/delocalisation_helper.cpp:1: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.h:26, from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 40%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/equation2x2.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/ctf/equation2x2.cpp [ 40%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_estimator.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/ctf/magnification_estimator.cpp [ 40%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_helper.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/ctf/magnification_helper.cpp [ 41%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/modular_ctf_optimisation.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/magnification_estimator.h:28, from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/magnification_estimator.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 41%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_estimator.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/ctf/tilt_estimator.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, from /build/reproducible-path/relion-3.1.3/src/ctf.h:50, from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/magnification_helper.h:24, from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/magnification_helper.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.h:5, from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.cpp:1: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/tilt_estimator.h:24, from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/tilt_estimator.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 42%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_helper.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/ctf/tilt_helper.cpp [ 42%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/alignment_set.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/motion/alignment_set.cpp [ 42%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/frame_recombiner.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/motion/frame_recombiner.cpp [ 43%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/gp_motion_fit.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp [ 43%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_estimator.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/motion/motion_estimator.cpp [ 43%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_helper.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/motion/motion_helper.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, from /build/reproducible-path/relion-3.1.3/src/ctf.h:50, from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/tilt_helper.h:24, from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/tilt_helper.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/motion/gp_motion_fit.h:24, from /build/reproducible-path/relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 44%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_param_estimator.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp [ 44%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/motion/motion_refiner.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/motion/motion_estimator.h:24, from /build/reproducible-path/relion-3.1.3/src/jaz/motion/motion_estimator.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/motion/frame_recombiner.h:24, from /build/reproducible-path/relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, from /build/reproducible-path/relion-3.1.3/src/ctf.h:50, from /build/reproducible-path/relion-3.1.3/src/jaz/motion/motion_helper.h:24, from /build/reproducible-path/relion-3.1.3/src/jaz/motion/motion_helper.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 45%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner_mpi.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/reproducible-path/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, from /build/reproducible-path/relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, from /build/reproducible-path/relion-3.1.3/src/ctf.h:50, from /build/reproducible-path/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/reproducible-path/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.h:27, from /build/reproducible-path/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, from /build/reproducible-path/relion-3.1.3/src/ctf.h:50, from /build/reproducible-path/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/reproducible-path/relion-3.1.3/src/jaz/motion/motion_refiner.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 45%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/three_hyperparameter_fit.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/motion/three_hyperparameter_fit.cpp [ 45%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/two_hyperparameter_fit.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/motion/two_hyperparameter_fit.cpp [ 46%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/math/Zernike.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/math/Zernike.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/reproducible-path/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, from /build/reproducible-path/relion-3.1.3/src/jaz/motion/three_hyperparameter_fit.cpp:22: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/reproducible-path/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, from /build/reproducible-path/relion-3.1.3/src/jaz/motion/two_hyperparameter_fit.cpp:22: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 46%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/color_helper.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/img_proc/color_helper.cpp [ 46%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/filter_helper.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/img_proc/filter_helper.cpp [ 47%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/image_op.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/img_proc/image_op.cpp [ 47%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/backprojection_helper.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/tomo/backprojection_helper.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/img_proc/filter_helper.h:24, from /build/reproducible-path/relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 48%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/imod_helper.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/tomo/imod_helper.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/img_proc/color_helper.h:5, from /build/reproducible-path/relion-3.1.3/src/jaz/img_proc/color_helper.cpp:1: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 48%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/projection_helper.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/tomo/projection_helper.cpp [ 48%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/tomo_stack.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/tomo/tomo_stack.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/tomo/backprojection_helper.h:24, from /build/reproducible-path/relion-3.1.3/src/jaz/tomo/backprojection_helper.cpp:23: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 49%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/io/star_converter.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/io/star_converter.cpp [ 49%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyev2.c.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/d3x3/dsyev2.c [ 50%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevc3.c.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/d3x3/dsyevc3.c [ 50%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevd3.c.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/d3x3/dsyevd3.c [ 50%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevh3.c.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/d3x3/dsyevh3.c [ 51%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevj3.c.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/d3x3/dsyevj3.c In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/tomo/tomo_stack.h:25, from /build/reproducible-path/relion-3.1.3/src/jaz/tomo/tomo_stack.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 51%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevq3.c.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/d3x3/dsyevq3.c [ 51%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevv3.c.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/d3x3/dsyevv3.c [ 52%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsytrd3.c.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/d3x3/dsytrd3.c [ 52%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/slvsec3.c.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/d3x3/slvsec3.c [ 53%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/lbfgs/lbfgs.c.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/jaz/lbfgs/lbfgs.c In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/reproducible-path/relion-3.1.3/src/jaz/io/star_converter.cpp:1: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 53%] Linking CXX static library ../../lib/librelion_lib.a cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -P CMakeFiles/relion_lib.dir/cmake_clean_target.cmake cd /build/reproducible-path/relion-3.1.3/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 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CMakeFiles/relion_lib.dir/__/metadata_container.cpp.o CMakeFiles/relion_lib.dir/__/metadata_label.cpp.o CMakeFiles/relion_lib.dir/__/metadata_table.cpp.o CMakeFiles/relion_lib.dir/__/micrograph_model.cpp.o CMakeFiles/relion_lib.dir/__/ml_model.cpp.o CMakeFiles/relion_lib.dir/__/ml_optimiser.cpp.o CMakeFiles/relion_lib.dir/__/ml_optimiser_mpi.cpp.o CMakeFiles/relion_lib.dir/__/motioncorr_runner.cpp.o CMakeFiles/relion_lib.dir/__/motioncorr_runner_mpi.cpp.o CMakeFiles/relion_lib.dir/__/mpi.cpp.o CMakeFiles/relion_lib.dir/__/multidim_array.cpp.o CMakeFiles/relion_lib.dir/__/numerical_recipes.cpp.o CMakeFiles/relion_lib.dir/__/parallel.cpp.o CMakeFiles/relion_lib.dir/__/particle_subtractor.cpp.o CMakeFiles/relion_lib.dir/__/pipeline_control.cpp.o CMakeFiles/relion_lib.dir/__/pipeline_jobs.cpp.o CMakeFiles/relion_lib.dir/__/pipeliner.cpp.o CMakeFiles/relion_lib.dir/__/postprocessing.cpp.o CMakeFiles/relion_lib.dir/__/preprocessing.cpp.o CMakeFiles/relion_lib.dir/__/preprocessing_mpi.cpp.o 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CMakeFiles/relion_lib.dir/__/jaz/damage_helper.cpp.o CMakeFiles/relion_lib.dir/__/jaz/distribution_helper.cpp.o CMakeFiles/relion_lib.dir/__/jaz/fftw_helper.cpp.o CMakeFiles/relion_lib.dir/__/jaz/fsc_helper.cpp.o CMakeFiles/relion_lib.dir/__/jaz/image_log.cpp.o CMakeFiles/relion_lib.dir/__/jaz/interpolation.cpp.o CMakeFiles/relion_lib.dir/__/jaz/jaz_config.cpp.o CMakeFiles/relion_lib.dir/__/jaz/legacy_obs_model.cpp.o CMakeFiles/relion_lib.dir/__/jaz/local_motion_fit.cpp.o CMakeFiles/relion_lib.dir/__/jaz/micrograph_handler.cpp.o CMakeFiles/relion_lib.dir/__/jaz/new_ft.cpp.o CMakeFiles/relion_lib.dir/__/jaz/noise_helper.cpp.o CMakeFiles/relion_lib.dir/__/jaz/obs_model.cpp.o CMakeFiles/relion_lib.dir/__/jaz/parallel_ft.cpp.o CMakeFiles/relion_lib.dir/__/jaz/reference_map.cpp.o CMakeFiles/relion_lib.dir/__/jaz/refinement_helper.cpp.o CMakeFiles/relion_lib.dir/__/jaz/resampling_helper.cpp.o CMakeFiles/relion_lib.dir/__/jaz/slice_helper.cpp.o CMakeFiles/relion_lib.dir/__/jaz/spectral_helper.cpp.o CMakeFiles/relion_lib.dir/__/jaz/stack_helper.cpp.o CMakeFiles/relion_lib.dir/__/jaz/structure_tensor.cpp.o CMakeFiles/relion_lib.dir/__/jaz/svd_helper.cpp.o CMakeFiles/relion_lib.dir/__/jaz/t_complex.cpp.o CMakeFiles/relion_lib.dir/__/jaz/volume_converter.cpp.o CMakeFiles/relion_lib.dir/__/jaz/volume_integration.cpp.o CMakeFiles/relion_lib.dir/__/jaz/vtk_helper.cpp.o CMakeFiles/relion_lib.dir/__/jaz/optimization/gradient_descent.cpp.o CMakeFiles/relion_lib.dir/__/jaz/optimization/lbfgs.cpp.o CMakeFiles/relion_lib.dir/__/jaz/optimization/nelder_mead.cpp.o CMakeFiles/relion_lib.dir/__/jaz/optimization/optimization.cpp.o CMakeFiles/relion_lib.dir/__/jaz/ctf/aberration_estimator.cpp.o CMakeFiles/relion_lib.dir/__/jaz/ctf/bfactor_refiner.cpp.o CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner.cpp.o CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner_mpi.cpp.o CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_estimator.cpp.o CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_helper.cpp.o CMakeFiles/relion_lib.dir/__/jaz/ctf/delocalisation_helper.cpp.o CMakeFiles/relion_lib.dir/__/jaz/ctf/equation2x2.cpp.o CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_estimator.cpp.o CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_helper.cpp.o CMakeFiles/relion_lib.dir/__/jaz/ctf/modular_ctf_optimisation.cpp.o 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/reproducible-path/relion-3.1.3/build' [ 53%] Built target relion_lib /usr/bin/make -f src/apps/CMakeFiles/relion_gui_lib.dir/build.make src/apps/CMakeFiles/relion_gui_lib.dir/depend /usr/bin/make -f src/apps/CMakeFiles/align_symmetry.dir/build.make src/apps/CMakeFiles/align_symmetry.dir/depend /usr/bin/make -f src/apps/CMakeFiles/autopick.dir/build.make src/apps/CMakeFiles/autopick.dir/depend /usr/bin/make -f src/apps/CMakeFiles/autopick_mpi.dir/build.make src/apps/CMakeFiles/autopick_mpi.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/relion_gui_lib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/apps/CMakeFiles/convert_star.dir/build.make src/apps/CMakeFiles/convert_star.dir/depend /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/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/align_symmetry.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build.make src/apps/CMakeFiles/convert_to_tiff_mpi.dir/depend /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/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/autopick.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/ctf_refine.dir/build.make src/apps/CMakeFiles/ctf_refine.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/autopick_mpi.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/apps/CMakeFiles/ctf_refine_mpi.dir/build.make src/apps/CMakeFiles/ctf_refine_mpi.dir/depend make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/align_symmetry.dir/build.make src/apps/CMakeFiles/align_symmetry.dir/build make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/convert_star.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/ctf_toolbox.dir/build.make src/apps/CMakeFiles/ctf_toolbox.dir/depend [ 53%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/displayer.cpp make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 54%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/convert_to_tiff.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/apps/CMakeFiles/autopick.dir/build.make src/apps/CMakeFiles/autopick.dir/build cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/gui_entries.cpp make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' [ 54%] Building CXX object src/apps/CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/apps/align_symmetry.cpp make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/convert_to_tiff_mpi.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/ctf_mask_test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 55%] Building CXX object src/apps/CMakeFiles/autopick.dir/autopick.cpp.o make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/convert_star.dir/build.make src/apps/CMakeFiles/convert_star.dir/build cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/apps/autopick.cpp make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/ctf_refine.dir/DependInfo.cmake "--color=" /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/reproducible-path/relion-3.1.3/build' make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/ctf_refine_mpi.dir/DependInfo.cmake "--color=" [ 55%] Building CXX object src/apps/CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/apps/autopick_mpi.cpp make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 55%] Building CXX object src/apps/CMakeFiles/convert_star.dir/convert_star.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/apps/convert_star.cpp make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/ctf_toolbox.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/ctf_mask_test.dir/build.make src/apps/CMakeFiles/ctf_mask_test.dir/build make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 55%] Building CXX object src/apps/CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/apps/convert_to_tiff.cpp make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' [ 55%] Building CXX object src/apps/CMakeFiles/ctf_refine.dir/ctf_refine.cpp.o [ 56%] Building CXX object src/apps/CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/apps/ctf_refine.cpp cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/apps/convert_to_tiff_mpi.cpp [ 56%] Building CXX object src/apps/CMakeFiles/ctf_refine_mpi.dir/ctf_refine_mpi.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/apps/ctf_refine_mpi.cpp make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' [ 56%] Building CXX object src/apps/CMakeFiles/ctf_mask_test.dir/ctf_mask_test.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/apps/ctf_mask_test.cpp [ 57%] Building CXX object src/apps/CMakeFiles/ctf_toolbox.dir/ctf_toolbox.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/apps/ctf_toolbox.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/apps/ctf_toolbox.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/autopicker.h:10, from /build/reproducible-path/relion-3.1.3/src/apps/autopick.cpp:20: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/tiff_converter.h:24, from /build/reproducible-path/relion-3.1.3/src/apps/convert_to_tiff.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/reproducible-path/relion-3.1.3/src/apps/convert_star.cpp:24: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/reproducible-path/relion-3.1.3/src/apps/ctf_refine.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/apps/ctf_mask_test.cpp:7: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/autopicker.h:10, from /build/reproducible-path/relion-3.1.3/src/autopicker_mpi.h:12, from /build/reproducible-path/relion-3.1.3/src/apps/autopick_mpi.cpp:20: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/projector.h:25, from /build/reproducible-path/relion-3.1.3/src/apps/align_symmetry.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/displayer.h:40, from /build/reproducible-path/relion-3.1.3/src/displayer.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/reproducible-path/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.h:26, from /build/reproducible-path/relion-3.1.3/src/apps/ctf_refine_mpi.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/tiff_converter.h:24, from /build/reproducible-path/relion-3.1.3/src/apps/convert_to_tiff_mpi.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 57%] Linking CXX executable ../../bin/relion_convert_to_tiff cd /build/reproducible-path/relion-3.1.3/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=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o -o ../../bin/relion_convert_to_tiff ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 57%] Built target convert_to_tiff /usr/bin/make -f src/apps/CMakeFiles/demodulate.dir/build.make src/apps/CMakeFiles/demodulate.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' [ 58%] Linking CXX executable ../../bin/relion_convert_star cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/demodulate.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/convert_star.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/convert_star.dir/convert_star.cpp.o -o ../../bin/relion_convert_star ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/demodulate.dir/build.make src/apps/CMakeFiles/demodulate.dir/build [ 58%] Linking CXX executable ../../bin/relion_autopick cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/autopick.dir/link.txt --verbose=1 make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' [ 58%] Linking CXX executable ../../bin/relion_convert_to_tiff_mpi cd /build/reproducible-path/relion-3.1.3/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=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/autopick.dir/autopick.cpp.o -o ../../bin/relion_autopick ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 58%] Building CXX object src/apps/CMakeFiles/demodulate.dir/demodulate.cpp.o /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o -o ../../bin/relion_convert_to_tiff_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/apps/demodulate.cpp [ 59%] Linking CXX executable ../../bin/relion_ctf_refine cd /build/reproducible-path/relion-3.1.3/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=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ctf_refine.dir/ctf_refine.cpp.o -o ../../bin/relion_ctf_refine ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 59%] Built target convert_star /usr/bin/make -f src/apps/CMakeFiles/estimate_gain.dir/build.make src/apps/CMakeFiles/estimate_gain.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/estimate_gain.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/estimate_gain.dir/build.make src/apps/CMakeFiles/estimate_gain.dir/build [ 59%] Built target convert_to_tiff_mpi /usr/bin/make -f src/apps/CMakeFiles/external_reconstruct.dir/build.make src/apps/CMakeFiles/external_reconstruct.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' [ 59%] Building CXX object src/apps/CMakeFiles/estimate_gain.dir/estimate_gain.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/apps/estimate_gain.cpp make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/external_reconstruct.dir/DependInfo.cmake "--color=" [ 60%] Linking CXX executable ../../bin/relion_autopick_mpi cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/autopick_mpi.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o -o ../../bin/relion_autopick_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 61%] Building CXX object src/apps/CMakeFiles/external_reconstruct.dir/external_reconstruct.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/apps/external_reconstruct.cpp make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 61%] Linking CXX executable ../../bin/relion_ctf_refine_mpi cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/ctf_refine_mpi.dir/link.txt --verbose=1 [ 61%] Built target autopick /usr/bin/make -f src/apps/CMakeFiles/find_tiltpairs.dir/build.make src/apps/CMakeFiles/find_tiltpairs.dir/depend [ 61%] Built target ctf_refine /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ctf_refine_mpi.dir/ctf_refine_mpi.cpp.o -o ../../bin/relion_ctf_refine_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff /usr/bin/make -f src/apps/CMakeFiles/flex_analyse.dir/build.make src/apps/CMakeFiles/flex_analyse.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/find_tiltpairs.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/flex_analyse.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' [ 61%] Building CXX object src/apps/CMakeFiles/find_tiltpairs.dir/find_tiltpairs.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/apps/find_tiltpairs.cpp make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' [ 61%] Building CXX object src/apps/CMakeFiles/flex_analyse.dir/flex_analyse.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/apps/flex_analyse.cpp [ 61%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/gui_jobwindow.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/vtk_helper.h:24, from /build/reproducible-path/relion-3.1.3/src/apps/demodulate.cpp:1: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 61%] Built target autopick_mpi /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/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/flex_analyse_mpi.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' [ 61%] Building CXX object src/apps/CMakeFiles/flex_analyse_mpi.dir/flex_analyse_mpi.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/apps/flex_analyse_mpi.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/apps/external_reconstruct.cpp:24: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/apps/estimate_gain.cpp:27: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 61%] Built target ctf_refine_mpi /usr/bin/make -f src/apps/CMakeFiles/helix_inimodel2d.dir/build.make src/apps/CMakeFiles/helix_inimodel2d.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/helix_inimodel2d.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' [ 62%] Building CXX object src/apps/CMakeFiles/helix_inimodel2d.dir/helix_inimodel2d.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/apps/helix_inimodel2d.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/exp_model.h:24, from /build/reproducible-path/relion-3.1.3/src/apps/../flex_analyser.h:24, from /build/reproducible-path/relion-3.1.3/src/apps/flex_analyse.cpp:22: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/exp_model.h:24, from /build/reproducible-path/relion-3.1.3/src/apps/../flex_analyser.h:24, from /build/reproducible-path/relion-3.1.3/src/apps/flex_analyse_mpi.cpp:22: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/apps/../helix_inimodel2d.h:29, from /build/reproducible-path/relion-3.1.3/src/apps/helix_inimodel2d.cpp:22: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 62%] Linking CXX executable ../../bin/relion_helix_inimodel2d cd /build/reproducible-path/relion-3.1.3/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=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/helix_inimodel2d.dir/helix_inimodel2d.cpp.o -o ../../bin/relion_helix_inimodel2d ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 63%] Linking CXX executable ../../bin/relion_ctf_mask_test cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/ctf_mask_test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ctf_mask_test.dir/ctf_mask_test.cpp.o -o ../../bin/relion_ctf_mask_test ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /build/reproducible-path/relion-3.1.3/src/numerical_recipes.h:48, from /build/reproducible-path/relion-3.1.3/src/funcs.h:59, from /build/reproducible-path/relion-3.1.3/src/args.h:56, from /build/reproducible-path/relion-3.1.3/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 /build/reproducible-path/relion-3.1.3/src/numerical_recipes.h:262:17: /build/reproducible-path/relion-3.1.3/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)); | ~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/relion-3.1.3/src/numerical_recipes.h: In function 'void gaussj(T*, int, T*, int) [with T = double]': /build/reproducible-path/relion-3.1.3/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 /build/reproducible-path/relion-3.1.3/src/numerical_recipes.h:262:17: /build/reproducible-path/relion-3.1.3/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)); | ~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/relion-3.1.3/src/numerical_recipes.h: In function 'void gaussj(T*, int, T*, int) [with T = double]': /build/reproducible-path/relion-3.1.3/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 /build/reproducible-path/relion-3.1.3/src/numerical_recipes.h:263:17: /build/reproducible-path/relion-3.1.3/src/memory.h:74:13: warning: 'void free(void*)' called on pointer 'indxr' with nonzero offset 4 [-Wfree-nonheap-object] 74 | free((char*)(v + nl)); | ~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/relion-3.1.3/src/numerical_recipes.h: In function 'void gaussj(T*, int, T*, int) [with T = double]': /build/reproducible-path/relion-3.1.3/src/numerical_recipes.h:198:18: 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 /build/reproducible-path/relion-3.1.3/src/numerical_recipes.h:264:17: /build/reproducible-path/relion-3.1.3/src/memory.h:74:13: warning: 'void free(void*)' called on pointer 'indxc' with nonzero offset 4 [-Wfree-nonheap-object] 74 | free((char*)(v + nl)); | ~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/relion-3.1.3/src/numerical_recipes.h: In function 'void gaussj(T*, int, T*, int) [with T = double]': /build/reproducible-path/relion-3.1.3/src/numerical_recipes.h:198:10: note: declared here 198 | int *indxc, *indxr, *ipiv; | ^~~~~ make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 63%] Linking CXX executable ../../bin/relion_ctf_toolbox cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/ctf_toolbox.dir/link.txt --verbose=1 [ 63%] Built target helix_inimodel2d /usr/bin/make -f src/apps/CMakeFiles/helix_toolbox.dir/build.make src/apps/CMakeFiles/helix_toolbox.dir/depend /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ctf_toolbox.dir/ctf_toolbox.cpp.o -o ../../bin/relion_ctf_toolbox ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/helix_toolbox.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/helix_toolbox.dir/build.make src/apps/CMakeFiles/helix_toolbox.dir/build make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' [ 64%] Building CXX object src/apps/CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/apps/helix_toolbox.cpp [ 64%] Built target ctf_mask_test /usr/bin/make -f src/apps/CMakeFiles/image_handler.dir/build.make src/apps/CMakeFiles/image_handler.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/image_handler.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' [ 64%] Building CXX object src/apps/CMakeFiles/image_handler.dir/image_handler.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/apps/image_handler.cpp [ 64%] Linking CXX executable ../../bin/relion_flex_analyse_mpi cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/flex_analyse_mpi.dir/link.txt --verbose=1 [ 65%] Linking CXX executable ../../bin/relion_flex_analyse cd /build/reproducible-path/relion-3.1.3/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=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/flex_analyse_mpi.dir/flex_analyse_mpi.cpp.o -o ../../bin/relion_flex_analyse_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/flex_analyse.dir/flex_analyse.cpp.o -o ../../bin/relion_flex_analyse ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 65%] Built target ctf_toolbox /usr/bin/make -f src/apps/CMakeFiles/import.dir/build.make src/apps/CMakeFiles/import.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/import.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/import.dir/build.make src/apps/CMakeFiles/import.dir/build make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' [ 65%] Building CXX object src/apps/CMakeFiles/import.dir/import.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/apps/import.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/apps/image_handler.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/helix.h:30, from /build/reproducible-path/relion-3.1.3/src/apps/helix_toolbox.cpp:22: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 65%] Built target flex_analyse_mpi /usr/bin/make -f src/apps/CMakeFiles/localsym.dir/build.make src/apps/CMakeFiles/localsym.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/localsym.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/localsym.dir/build.make src/apps/CMakeFiles/localsym.dir/build make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 65%] Built target flex_analyse [ 66%] Building CXX object src/apps/CMakeFiles/localsym.dir/localsym.cpp.o /usr/bin/make -f src/apps/CMakeFiles/localsym_mpi.dir/build.make src/apps/CMakeFiles/localsym_mpi.dir/depend cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/apps/localsym.cpp make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/localsym_mpi.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' [ 67%] Building CXX object src/apps/CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/apps/localsym_mpi.cpp [ 68%] Linking CXX executable ../../bin/relion_find_tiltpairs cd /build/reproducible-path/relion-3.1.3/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=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/find_tiltpairs.dir/find_tiltpairs.cpp.o -o ../../bin/relion_find_tiltpairs ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 68%] Built target find_tiltpairs /usr/bin/make -f src/apps/CMakeFiles/mask_create.dir/build.make src/apps/CMakeFiles/mask_create.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/mask_create.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' [ 68%] Building CXX object src/apps/CMakeFiles/mask_create.dir/mask_create.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/apps/mask_create.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, from /build/reproducible-path/relion-3.1.3/src/apps/import.cpp:22: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 68%] Linking CXX executable ../../bin/relion_external_reconstruct In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/local_symmetry.h:30, from /build/reproducible-path/relion-3.1.3/src/apps/localsym.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ cd /build/reproducible-path/relion-3.1.3/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=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/external_reconstruct.dir/external_reconstruct.cpp.o -o ../../bin/relion_external_reconstruct ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/apps/mask_create.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/local_symmetry.h:30, from /build/reproducible-path/relion-3.1.3/src/local_symmetry_mpi.h:5, from /build/reproducible-path/relion-3.1.3/src/apps/localsym_mpi.cpp:1: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 69%] Linking CXX executable ../../bin/relion_demodulate cd /build/reproducible-path/relion-3.1.3/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=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/demodulate.dir/demodulate.cpp.o -o ../../bin/relion_demodulate ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 69%] Built target external_reconstruct /usr/bin/make -f src/apps/CMakeFiles/merge_particles.dir/build.make src/apps/CMakeFiles/merge_particles.dir/depend [ 69%] Linking CXX executable ../../bin/relion_align_symmetry cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/align_symmetry.dir/link.txt --verbose=1 [ 69%] Linking CXX executable ../../bin/relion_localsym cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/localsym.dir/link.txt --verbose=1 make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/merge_particles.dir/DependInfo.cmake "--color=" /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/localsym.dir/localsym.cpp.o -o ../../bin/relion_localsym ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o -o ../../bin/relion_align_symmetry ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' [ 70%] Building CXX object src/apps/CMakeFiles/merge_particles.dir/merge_particles.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/apps/merge_particles.cpp make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 70%] Built target align_symmetry /usr/bin/make -f src/apps/CMakeFiles/motion_refine.dir/build.make src/apps/CMakeFiles/motion_refine.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/motion_refine.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' [ 71%] Building CXX object src/apps/CMakeFiles/motion_refine.dir/motion_refine.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/apps/motion_refine.cpp make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 71%] Built target demodulate /usr/bin/make -f src/apps/CMakeFiles/motion_refine_mpi.dir/build.make src/apps/CMakeFiles/motion_refine_mpi.dir/depend make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 71%] Linking CXX executable ../../bin/relion_localsym_mpi make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/motion_refine_mpi.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/localsym_mpi.dir/link.txt --verbose=1 [ 71%] Built target localsym /usr/bin/make -f src/apps/CMakeFiles/mrc2vtk.dir/build.make src/apps/CMakeFiles/mrc2vtk.dir/depend /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o -o ../../bin/relion_localsym_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/mrc2vtk.dir/DependInfo.cmake "--color=" [ 71%] Building CXX object src/apps/CMakeFiles/motion_refine_mpi.dir/motion_refine_mpi.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/apps/motion_refine_mpi.cpp make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/mrc2vtk.dir/build.make src/apps/CMakeFiles/mrc2vtk.dir/build make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' [ 71%] Building CXX object src/apps/CMakeFiles/mrc2vtk.dir/mrc2vtk.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/apps/mrc2vtk.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/reproducible-path/relion-3.1.3/src/apps/merge_particles.cpp:2: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 71%] Linking CXX executable ../../bin/relion_estimate_gain cd /build/reproducible-path/relion-3.1.3/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=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/estimate_gain.dir/estimate_gain.cpp.o -o ../../bin/relion_estimate_gain ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, from /build/reproducible-path/relion-3.1.3/src/ctf.h:50, from /build/reproducible-path/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/reproducible-path/relion-3.1.3/src/apps/motion_refine.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 71%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/gui_mainwindow.cpp make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 71%] Built target localsym_mpi /usr/bin/make -f src/apps/CMakeFiles/particle_FCC.dir/build.make src/apps/CMakeFiles/particle_FCC.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/particle_FCC.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' [ 71%] Built target estimate_gain /usr/bin/make -f src/apps/CMakeFiles/particle_reposition.dir/build.make src/apps/CMakeFiles/particle_reposition.dir/depend [ 72%] Building CXX object src/apps/CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/particle_reposition.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/apps/particle_FCC.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/apps/mrc2vtk.cpp:1: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' [ 73%] Building CXX object src/apps/CMakeFiles/particle_reposition.dir/particle_reposition.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/apps/particle_reposition.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, from /build/reproducible-path/relion-3.1.3/src/ctf.h:50, from /build/reproducible-path/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/reproducible-path/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.h:27, from /build/reproducible-path/relion-3.1.3/src/apps/motion_refine_mpi.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 73%] Linking CXX executable ../../bin/relion_merge_particles cd /build/reproducible-path/relion-3.1.3/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=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/merge_particles.dir/merge_particles.cpp.o -o ../../bin/relion_merge_particles ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/apps/particle_FCC.cpp:7: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/projector.h:25, from /build/reproducible-path/relion-3.1.3/src/ml_model.h:23, from /build/reproducible-path/relion-3.1.3/src/ml_optimiser.h:35, from /build/reproducible-path/relion-3.1.3/src/apps/particle_reposition.cpp:22: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 73%] Built target merge_particles /usr/bin/make -f src/apps/CMakeFiles/particle_select.dir/build.make src/apps/CMakeFiles/particle_select.dir/depend In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, from /build/reproducible-path/relion-3.1.3/src/scheduler.h:26, from /build/reproducible-path/relion-3.1.3/src/gui_mainwindow.h:28, from /build/reproducible-path/relion-3.1.3/src/gui_mainwindow.cpp:22: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/particle_select.dir/DependInfo.cmake "--color=" /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/particle_select.dir/build.make src/apps/CMakeFiles/particle_select.dir/build make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' [ 73%] Building CXX object src/apps/CMakeFiles/particle_select.dir/particle_select.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/apps/particle_select.cpp [ 73%] Linking CXX executable ../../bin/relion_motion_refine cd /build/reproducible-path/relion-3.1.3/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=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/motion_refine.dir/motion_refine.cpp.o -o ../../bin/relion_motion_refine ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 73%] Linking CXX executable ../../bin/relion_import cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/import.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/import.dir/import.cpp.o -o ../../bin/relion_import ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 73%] Built target motion_refine /usr/bin/make -f src/apps/CMakeFiles/particle_subtract.dir/build.make src/apps/CMakeFiles/particle_subtract.dir/depend [ 73%] Linking CXX executable ../../bin/relion_mrc2vtk cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/mrc2vtk.dir/link.txt --verbose=1 make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/particle_subtract.dir/DependInfo.cmake "--color=" /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/mrc2vtk.dir/mrc2vtk.cpp.o -o ../../bin/relion_mrc2vtk ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/particle_subtract.dir/build.make src/apps/CMakeFiles/particle_subtract.dir/build In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, from /build/reproducible-path/relion-3.1.3/src/ctf.h:50, from /build/reproducible-path/relion-3.1.3/src/jaz/stack_helper.h:24, from /build/reproducible-path/relion-3.1.3/src/apps/particle_select.cpp:1: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' [ 73%] Building CXX object src/apps/CMakeFiles/particle_subtract.dir/particle_subtract.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/apps/particle_subtract.cpp make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 73%] Built target import /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/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/particle_subtract_mpi.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' [ 73%] Building CXX object src/apps/CMakeFiles/particle_subtract_mpi.dir/particle_subtract_mpi.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/apps/particle_subtract_mpi.cpp make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 73%] Linking CXX executable ../../bin/relion_particle_FCC cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_FCC.dir/link.txt --verbose=1 [ 73%] Built target mrc2vtk /usr/bin/make -f src/apps/CMakeFiles/particle_symmetry_expand.dir/build.make src/apps/CMakeFiles/particle_symmetry_expand.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/particle_symmetry_expand.dir/DependInfo.cmake "--color=" /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o -o ../../bin/relion_particle_FCC ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' [ 74%] Building CXX object src/apps/CMakeFiles/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/apps/particle_symmetry_expand.cpp [ 75%] Linking CXX executable ../../bin/relion_motion_refine_mpi cd /build/reproducible-path/relion-3.1.3/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=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/motion_refine_mpi.dir/motion_refine_mpi.cpp.o -o ../../bin/relion_motion_refine_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 75%] Linking CXX executable ../../bin/relion_mask_create cd /build/reproducible-path/relion-3.1.3/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=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/mask_create.dir/mask_create.cpp.o -o ../../bin/relion_mask_create ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/projector.h:25, from /build/reproducible-path/relion-3.1.3/src/ml_model.h:23, from /build/reproducible-path/relion-3.1.3/src/ml_optimiser.h:35, from /build/reproducible-path/relion-3.1.3/src/apps/../particle_subtractor.h:24, from /build/reproducible-path/relion-3.1.3/src/apps/particle_subtract.cpp:22: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/projector.h:25, from /build/reproducible-path/relion-3.1.3/src/ml_model.h:23, from /build/reproducible-path/relion-3.1.3/src/ml_optimiser.h:35, from /build/reproducible-path/relion-3.1.3/src/apps/../particle_subtractor.h:24, from /build/reproducible-path/relion-3.1.3/src/apps/particle_subtract_mpi.cpp:22: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 75%] Built target mask_create /usr/bin/make -f src/apps/CMakeFiles/pipeliner.dir/build.make src/apps/CMakeFiles/pipeliner.dir/depend [ 75%] Built target particle_FCC /usr/bin/make -f src/apps/CMakeFiles/plot_delocalisation.dir/build.make src/apps/CMakeFiles/plot_delocalisation.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/pipeliner.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/plot_delocalisation.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/pipeliner.dir/build.make src/apps/CMakeFiles/pipeliner.dir/build make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' [ 75%] Building CXX object src/apps/CMakeFiles/pipeliner.dir/pipeliner.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/apps/pipeliner.cpp [ 75%] Building CXX object src/apps/CMakeFiles/plot_delocalisation.dir/plot_delocalisation.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/apps/plot_delocalisation.cpp [ 76%] Linking CXX executable ../../bin/relion_particle_select In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, from /build/reproducible-path/relion-3.1.3/src/apps/particle_symmetry_expand.cpp:26: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_select.dir/link.txt --verbose=1 In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/particle_select.dir/particle_select.cpp.o -o ../../bin/relion_particle_select ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 76%] Built target motion_refine_mpi /usr/bin/make -f src/apps/CMakeFiles/postprocess.dir/build.make src/apps/CMakeFiles/postprocess.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/postprocess.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/postprocess.dir/build.make src/apps/CMakeFiles/postprocess.dir/build make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' [ 76%] Building CXX object src/apps/CMakeFiles/postprocess.dir/postprocess.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/apps/postprocess.cpp make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 76%] Built target particle_select /usr/bin/make -f src/apps/CMakeFiles/postprocess_mpi.dir/build.make src/apps/CMakeFiles/postprocess_mpi.dir/depend In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/apps/plot_delocalisation.cpp:7: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/postprocess_mpi.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' [ 77%] Building CXX object src/apps/CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/apps/postprocess_mpi.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/postprocessing.h:24, from /build/reproducible-path/relion-3.1.3/src/apps/postprocess.cpp:20: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 78%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/manualpicker.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/manualpicker.cpp [ 79%] Linking CXX executable ../../bin/relion_pipeliner cd /build/reproducible-path/relion-3.1.3/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=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/pipeliner.dir/pipeliner.cpp.o -o ../../bin/relion_pipeliner ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/postprocessing.h:24, from /build/reproducible-path/relion-3.1.3/src/apps/postprocess_mpi.cpp:20: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 80%] Linking CXX executable ../../bin/relion_plot_delocalisation cd /build/reproducible-path/relion-3.1.3/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=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/plot_delocalisation.dir/plot_delocalisation.cpp.o -o ../../bin/relion_plot_delocalisation ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 80%] Linking CXX executable ../../bin/relion_particle_symmetry_expand cd /build/reproducible-path/relion-3.1.3/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=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o -o ../../bin/relion_particle_symmetry_expand ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 80%] Built target pipeliner /usr/bin/make -f src/apps/CMakeFiles/prepare_subtomo.dir/build.make src/apps/CMakeFiles/prepare_subtomo.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/prepare_subtomo.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' [ 80%] Building CXX object src/apps/CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/apps/prepare_subtomo.cpp make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 80%] Linking CXX executable ../../bin/relion_postprocess cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/postprocess.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 80%] Built target particle_symmetry_expand /usr/bin/make -f src/apps/CMakeFiles/preprocess.dir/build.make src/apps/CMakeFiles/preprocess.dir/depend /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/postprocess.dir/postprocess.cpp.o -o ../../bin/relion_postprocess ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/preprocess.dir/DependInfo.cmake "--color=" [ 80%] 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/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/preprocess_mpi.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/preprocess.dir/build.make src/apps/CMakeFiles/preprocess.dir/build make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' [ 80%] Building CXX object src/apps/CMakeFiles/preprocess.dir/preprocess.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/apps/preprocess.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, from /build/reproducible-path/relion-3.1.3/src/manualpicker.h:43, from /build/reproducible-path/relion-3.1.3/src/manualpicker.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 43 | uint32 width, length; // apparent dimensions in the file | ^~~~~ [ 80%] Building CXX object src/apps/CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31, from /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/apps/preprocess_mpi.cpp /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 80%] Built target postprocess /usr/bin/make -f src/apps/CMakeFiles/project.dir/build.make src/apps/CMakeFiles/project.dir/depend In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/helix.h:30, from /build/reproducible-path/relion-3.1.3/src/apps/prepare_subtomo.cpp:22: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/project.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/project.dir/build.make src/apps/CMakeFiles/project.dir/build make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' [ 80%] Linking CXX executable ../../bin/relion_postprocess_mpi cd /build/reproducible-path/relion-3.1.3/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=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o -o ../../bin/relion_postprocess_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 81%] Building CXX object src/apps/CMakeFiles/project.dir/project.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/apps/project.cpp [ 82%] Linking CXX executable ../../bin/relion_particle_subtract cd /build/reproducible-path/relion-3.1.3/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=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/particle_subtract.dir/particle_subtract.cpp.o -o ../../bin/relion_particle_subtract ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/projector.h:25, from /build/reproducible-path/relion-3.1.3/src/apps/project.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 82%] Built target postprocess_mpi /usr/bin/make -f src/apps/CMakeFiles/reconstruct.dir/build.make src/apps/CMakeFiles/reconstruct.dir/depend In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/preprocessing.h:29, from /build/reproducible-path/relion-3.1.3/src/preprocessing_mpi.h:24, from /build/reproducible-path/relion-3.1.3/src/apps/preprocess_mpi.cpp:20: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/reconstruct.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/reconstruct.dir/build.make src/apps/CMakeFiles/reconstruct.dir/build In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/preprocessing.h:29, from /build/reproducible-path/relion-3.1.3/src/apps/preprocess.cpp:20: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 82%] Building CXX object src/apps/CMakeFiles/reconstruct.dir/reconstruct.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/apps/reconstruct.cpp make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 82%] Built target particle_subtract /usr/bin/make -f src/apps/CMakeFiles/reconstruct_mpi.dir/build.make src/apps/CMakeFiles/reconstruct_mpi.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/reconstruct_mpi.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' [ 82%] Building CXX object src/apps/CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/apps/reconstruct_mpi.cpp [ 82%] Linking CXX executable ../../bin/relion_preprocess_mpi cd /build/reproducible-path/relion-3.1.3/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=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o -o ../../bin/relion_preprocess_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/projector.h:25, from /build/reproducible-path/relion-3.1.3/src/backprojector.h:33, from /build/reproducible-path/relion-3.1.3/src/reconstructor.h:23, from /build/reproducible-path/relion-3.1.3/src/apps/reconstruct.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 82%] Linking CXX executable ../../bin/relion_particle_subtract_mpi cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_subtract_mpi.dir/link.txt --verbose=1 [ 83%] Linking CXX executable ../../bin/relion_preprocess cd /build/reproducible-path/relion-3.1.3/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=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/particle_subtract_mpi.dir/particle_subtract_mpi.cpp.o -o ../../bin/relion_particle_subtract_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/preprocess.dir/preprocess.cpp.o -o ../../bin/relion_preprocess ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/projector.h:25, from /build/reproducible-path/relion-3.1.3/src/backprojector.h:33, from /build/reproducible-path/relion-3.1.3/src/reconstructor.h:23, from /build/reproducible-path/relion-3.1.3/src/reconstructor_mpi.h:25, from /build/reproducible-path/relion-3.1.3/src/apps/reconstruct_mpi.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 83%] Built target preprocess_mpi /usr/bin/make -f src/apps/CMakeFiles/refine.dir/build.make src/apps/CMakeFiles/refine.dir/depend make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/refine.dir/DependInfo.cmake "--color=" [ 83%] Built target preprocess /usr/bin/make -f src/apps/CMakeFiles/refine_mpi.dir/build.make src/apps/CMakeFiles/refine_mpi.dir/depend make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/refine.dir/build.make src/apps/CMakeFiles/refine.dir/build make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/refine_mpi.dir/DependInfo.cmake "--color=" [ 83%] Building CXX object src/apps/CMakeFiles/refine.dir/refine.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/apps/refine.cpp make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' [ 84%] Building CXX object src/apps/CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/apps/refine_mpi.cpp [ 84%] Linking CXX executable ../../bin/relion_particle_reposition cd /build/reproducible-path/relion-3.1.3/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=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/particle_reposition.dir/particle_reposition.cpp.o -o ../../bin/relion_particle_reposition ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 84%] Linking CXX executable ../../bin/relion_helix_toolbox cd /build/reproducible-path/relion-3.1.3/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=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o -o ../../bin/relion_helix_toolbox ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 85%] Linking CXX executable ../../bin/relion_image_handler [ 85%] Built target particle_subtract_mpi /usr/bin/make -f src/apps/CMakeFiles/reposition.dir/build.make src/apps/CMakeFiles/reposition.dir/depend cd /build/reproducible-path/relion-3.1.3/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=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/image_handler.dir/image_handler.cpp.o -o ../../bin/relion_image_handler ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/reposition.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/reposition.dir/build.make src/apps/CMakeFiles/reposition.dir/build make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' [ 85%] Building CXX object src/apps/CMakeFiles/reposition.dir/reposition.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/apps/reposition.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/projector.h:25, from /build/reproducible-path/relion-3.1.3/src/ml_model.h:23, from /build/reproducible-path/relion-3.1.3/src/ml_optimiser.h:35, from /build/reproducible-path/relion-3.1.3/src/apps/refine.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 85%] Built target helix_toolbox /usr/bin/make -f src/apps/CMakeFiles/run_ctffind.dir/build.make src/apps/CMakeFiles/run_ctffind.dir/depend make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/run_ctffind.dir/DependInfo.cmake "--color=" [ 85%] Built target image_handler /usr/bin/make -f src/apps/CMakeFiles/run_ctffind_mpi.dir/build.make src/apps/CMakeFiles/run_ctffind_mpi.dir/depend make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 85%] Built target particle_reposition /usr/bin/make -f src/apps/CMakeFiles/run_ctffind.dir/build.make src/apps/CMakeFiles/run_ctffind.dir/build make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/run_ctffind_mpi.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/run_motioncorr.dir/build.make src/apps/CMakeFiles/run_motioncorr.dir/depend make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' [ 85%] Building CXX object src/apps/CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/apps/run_ctffind.cpp make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/run_motioncorr.dir/DependInfo.cmake "--color=" [ 86%] Building CXX object src/apps/CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/apps/run_ctffind_mpi.cpp make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' [ 87%] Building CXX object src/apps/CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/apps/run_motioncorr.cpp In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/projector.h:25, from /build/reproducible-path/relion-3.1.3/src/ml_model.h:23, from /build/reproducible-path/relion-3.1.3/src/ml_optimiser.h:35, from /build/reproducible-path/relion-3.1.3/src/ml_optimiser_mpi.h:24, from /build/reproducible-path/relion-3.1.3/src/apps/refine_mpi.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, from /build/reproducible-path/relion-3.1.3/src/apps/reposition.cpp:1: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 88%] Linking CXX executable ../../bin/relion_reconstruct cd /build/reproducible-path/relion-3.1.3/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=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/reconstruct.dir/reconstruct.cpp.o -o ../../bin/relion_reconstruct ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/ctffind_runner.h:31, from /build/reproducible-path/relion-3.1.3/src/ctffind_runner_mpi.h:25, from /build/reproducible-path/relion-3.1.3/src/apps/run_ctffind_mpi.cpp:20: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/ctffind_runner.h:31, from /build/reproducible-path/relion-3.1.3/src/apps/run_ctffind.cpp:20: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/motioncorr_runner.h:32, from /build/reproducible-path/relion-3.1.3/src/apps/run_motioncorr.cpp:20: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 89%] Linking CXX executable ../../bin/relion_reconstruct_mpi cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/reconstruct_mpi.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o -o ../../bin/relion_reconstruct_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 89%] Built target reconstruct /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/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/run_motioncorr_mpi.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' [ 89%] Building CXX object src/apps/CMakeFiles/run_motioncorr_mpi.dir/run_motioncorr_mpi.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/apps/run_motioncorr_mpi.cpp [ 89%] Linking CXX executable ../../bin/relion_run_ctffind_mpi cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/run_ctffind_mpi.dir/link.txt --verbose=1 [ 89%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/cxxutils.cc.o /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o -o ../../bin/relion_run_ctffind_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/Healpix_2.15a/cxxutils.cc make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 89%] Built target reconstruct_mpi /usr/bin/make -f src/apps/CMakeFiles/scheduler.dir/build.make src/apps/CMakeFiles/scheduler.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/scheduler.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/scheduler.dir/build.make src/apps/CMakeFiles/scheduler.dir/build make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' [ 89%] Building CXX object src/apps/CMakeFiles/scheduler.dir/scheduler.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/apps/scheduler.cpp [ 89%] Linking CXX executable ../../bin/relion_run_motioncorr cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/run_motioncorr.dir/link.txt --verbose=1 [ 89%] Linking CXX executable ../../bin/relion_run_ctffind cd /build/reproducible-path/relion-3.1.3/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=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o -o ../../bin/relion_run_motioncorr ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o -o ../../bin/relion_run_ctffind ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/motioncorr_runner.h:32, from /build/reproducible-path/relion-3.1.3/src/motioncorr_runner_mpi.h:25, from /build/reproducible-path/relion-3.1.3/src/apps/run_motioncorr_mpi.cpp:20: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 89%] Linking CXX executable ../../bin/relion_refine make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/refine.dir/link.txt --verbose=1 [ 89%] Built target run_ctffind_mpi /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/refine.dir/refine.cpp.o -o ../../bin/relion_refine ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff /usr/bin/make -f src/apps/CMakeFiles/stack_create.dir/build.make src/apps/CMakeFiles/stack_create.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/stack_create.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' [ 90%] Building CXX object src/apps/CMakeFiles/stack_create.dir/stack_create.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/apps/stack_create.cpp make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 90%] Built target run_ctffind /usr/bin/make -f src/apps/CMakeFiles/star_handler.dir/build.make src/apps/CMakeFiles/star_handler.dir/depend In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, from /build/reproducible-path/relion-3.1.3/src/scheduler.h:26, from /build/reproducible-path/relion-3.1.3/src/apps/scheduler.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/star_handler.dir/DependInfo.cmake "--color=" /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 90%] Built target run_motioncorr /usr/bin/make -f src/apps/CMakeFiles/tiltpair_plot.dir/build.make src/apps/CMakeFiles/tiltpair_plot.dir/depend make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/tiltpair_plot.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' [ 91%] Building CXX object src/apps/CMakeFiles/star_handler.dir/star_handler.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/apps/star_handler.cpp [ 91%] Building CXX object src/apps/CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/apps/tiltpair_plot.cpp make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 91%] Built target refine /usr/bin/make -f src/apps/CMakeFiles/tomo_test.dir/build.make src/apps/CMakeFiles/tomo_test.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/tomo_test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/tomo_test.dir/build.make src/apps/CMakeFiles/tomo_test.dir/build [ 92%] Linking CXX executable ../../bin/relion_reposition cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/reposition.dir/link.txt --verbose=1 make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/apps/stack_create.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 92%] Building CXX object src/apps/CMakeFiles/tomo_test.dir/tomo_test.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/apps/tomo_test.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/reposition.dir/reposition.cpp.o -o ../../bin/relion_reposition ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 93%] Linking CXX executable ../../bin/relion_run_motioncorr_mpi cd /build/reproducible-path/relion-3.1.3/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=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/run_motioncorr_mpi.dir/run_motioncorr_mpi.cpp.o -o ../../bin/relion_run_motioncorr_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 93%] Linking CXX executable ../../bin/relion_refine_mpi cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/refine_mpi.dir/link.txt --verbose=1 In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/apps/tiltpair_plot.cpp:25: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 94%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/Healpix_2.15a/healpix_base.cc /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o -o ../../bin/relion_refine_mpi ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 94%] Built target run_motioncorr_mpi In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/apps/star_handler.cpp:21: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/tomo/tomo_stack.h:25, from /build/reproducible-path/relion-3.1.3/src/apps/tomo_test.cpp:2: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 94%] Built target reposition make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 94%] Built target refine_mpi [ 94%] Linking CXX static library ../../lib/librelion_gui_lib.a cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -P CMakeFiles/relion_gui_lib.dir/cmake_clean_target.cmake cd /build/reproducible-path/relion-3.1.3/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 [ 94%] Linking CXX executable ../../bin/relion_scheduler cd /build/reproducible-path/relion-3.1.3/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=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/scheduler.dir/scheduler.cpp.o -o ../../bin/relion_scheduler ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff /usr/bin/ranlib ../../lib/librelion_gui_lib.a make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 95%] Linking CXX executable ../../bin/relion_tiltpair_plot cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiltpair_plot.dir/link.txt --verbose=1 [ 95%] Built target scheduler /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o -o ../../bin/relion_tiltpair_plot ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 95%] Linking CXX executable ../../bin/relion_project cd /build/reproducible-path/relion-3.1.3/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=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/project.dir/project.cpp.o -o ../../bin/relion_project ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 95%] Built target tiltpair_plot make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 95%] Built target project [ 96%] Linking CXX executable ../../bin/relion_tomo_test cd /build/reproducible-path/relion-3.1.3/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=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/tomo_test.dir/tomo_test.cpp.o -o ../../bin/relion_tomo_test ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 96%] Built target relion_gui_lib /usr/bin/make -f src/apps/CMakeFiles/display.dir/build.make src/apps/CMakeFiles/display.dir/depend /usr/bin/make -f src/apps/CMakeFiles/relion.dir/build.make src/apps/CMakeFiles/relion.dir/depend /usr/bin/make -f src/apps/CMakeFiles/manualpick.dir/build.make src/apps/CMakeFiles/manualpick.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/display.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/relion.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/manualpick.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/relion.dir/build.make src/apps/CMakeFiles/relion.dir/build make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/display.dir/build.make src/apps/CMakeFiles/display.dir/build make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/manualpick.dir/build.make src/apps/CMakeFiles/manualpick.dir/build make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' [ 96%] Building CXX object src/apps/CMakeFiles/relion.dir/maingui.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/apps/maingui.cpp [ 96%] Building CXX object src/apps/CMakeFiles/display.dir/display.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/apps/display.cpp [ 96%] Building CXX object src/apps/CMakeFiles/manualpick.dir/manualpick.cpp.o cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/reproducible-path/relion-3.1.3/src/ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/relion-3.1.3/src/apps/manualpick.cpp make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 96%] Built target tomo_test [ 97%] Linking CXX executable ../../bin/relion_prepare_subtomo cd /build/reproducible-path/relion-3.1.3/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=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o -o ../../bin/relion_prepare_subtomo ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 97%] Built target prepare_subtomo In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/apps/manualpick.cpp:25: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/jaz/obs_model.h:24, from /build/reproducible-path/relion-3.1.3/src/scheduler.h:26, from /build/reproducible-path/relion-3.1.3/src/gui_mainwindow.h:28, from /build/reproducible-path/relion-3.1.3/src/apps/maingui.cpp:23: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/reproducible-path/relion-3.1.3/src/image.h:455, from /build/reproducible-path/relion-3.1.3/src/apps/display.cpp:25: /build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/reproducible-path/relion-3.1.3/src/rwTIFF.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 /build/reproducible-path/relion-3.1.3/src/image.h:57: /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/relion-3.1.3/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:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 98%] Linking CXX executable ../../bin/relion_manualpick cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/manualpick.dir/link.txt --verbose=1 [ 99%] Linking CXX executable ../../bin/relion_display cd /build/reproducible-path/relion-3.1.3/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=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/manualpick.dir/manualpick.cpp.o -o ../../bin/relion_manualpick ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../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 -lfftw3f -lfftw3 -ltiff /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/display.dir/display.cpp.o -o ../../bin/relion_display ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../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 -lfftw3f -lfftw3 -ltiff [100%] Linking CXX executable ../../bin/relion cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/relion.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/relion.dir/maingui.cpp.o -o ../../bin/relion ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl ../../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 -lfftw3f -lfftw3 -ltiff [100%] Built target display [100%] Built target manualpick [100%] Linking CXX executable ../../bin/relion_stack_create cd /build/reproducible-path/relion-3.1.3/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=/build/reproducible-path/relion-3.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/stack_create.dir/stack_create.cpp.o -o ../../bin/relion_stack_create ../../lib/librelion_lib.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [100%] Built target stack_create [100%] Built target relion [100%] Linking CXX executable ../../bin/relion_star_handler cd /build/reproducible-path/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/star_handler.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 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'/build/reproducible-path/relion-3.1.3' /usr/bin/make -C build install DESTDIR=/build/reproducible-path/relion-3.1.3/debian/tmp/cli make[2]: Entering directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/cmake -S/build/reproducible-path/relion-3.1.3 -B/build/reproducible-path/relion-3.1.3/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/relion-3.1.3/build/CMakeFiles /build/reproducible-path/relion-3.1.3/build//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/make -f CMakeFiles/copy_scripts.dir/build.make CMakeFiles/copy_scripts.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/CMakeFiles/copy_scripts.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/make -f CMakeFiles/copy_scripts.dir/build.make CMakeFiles/copy_scripts.dir/build make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/cmake -E copy /build/reproducible-path/relion-3.1.3/scripts/star_printtable /build/reproducible-path/relion-3.1.3/build/bin/relion_star_printtable /usr/bin/cmake -E copy /build/reproducible-path/relion-3.1.3/scripts/star_plottable /build/reproducible-path/relion-3.1.3/build/bin/relion_star_plottable /usr/bin/cmake -E copy /build/reproducible-path/relion-3.1.3/scripts/star_loopheader /build/reproducible-path/relion-3.1.3/build/bin/relion_star_loopheader /usr/bin/cmake -E copy /build/reproducible-path/relion-3.1.3/scripts/star_datablock_stack /build/reproducible-path/relion-3.1.3/build/bin/relion_star_datablock_stack /usr/bin/cmake -E copy /build/reproducible-path/relion-3.1.3/scripts/star_datablock_singlefiles /build/reproducible-path/relion-3.1.3/build/bin/relion_star_datablock_singlefiles /usr/bin/cmake -E copy /build/reproducible-path/relion-3.1.3/scripts/star_datablock_ctfdat /build/reproducible-path/relion-3.1.3/build/bin/relion_star_datablock_ctfdat /usr/bin/cmake -E copy /build/reproducible-path/relion-3.1.3/scripts/qsub.csh /build/reproducible-path/relion-3.1.3/build/bin/relion_qsub.csh make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 0%] Built target copy_scripts /usr/bin/make -f src/apps/CMakeFiles/relion_lib.dir/build.make src/apps/CMakeFiles/relion_lib.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/relion_lib.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/relion_lib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 53%] Built target relion_lib /usr/bin/make -f src/apps/CMakeFiles/relion_gui_lib.dir/build.make src/apps/CMakeFiles/relion_gui_lib.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/relion_gui_lib.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/relion_gui_lib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 56%] Built target relion_gui_lib /usr/bin/make -f src/apps/CMakeFiles/align_symmetry.dir/build.make src/apps/CMakeFiles/align_symmetry.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/align_symmetry.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/align_symmetry.dir/build.make src/apps/CMakeFiles/align_symmetry.dir/build make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/align_symmetry.dir/build'. make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 56%] Built target align_symmetry /usr/bin/make -f src/apps/CMakeFiles/autopick.dir/build.make src/apps/CMakeFiles/autopick.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/autopick.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/autopick.dir/build.make src/apps/CMakeFiles/autopick.dir/build make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/autopick.dir/build'. make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 57%] Built target autopick /usr/bin/make -f src/apps/CMakeFiles/autopick_mpi.dir/build.make src/apps/CMakeFiles/autopick_mpi.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/autopick_mpi.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/autopick_mpi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 58%] Built target autopick_mpi /usr/bin/make -f src/apps/CMakeFiles/convert_star.dir/build.make src/apps/CMakeFiles/convert_star.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/convert_star.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/convert_star.dir/build'. make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 59%] Built target convert_star /usr/bin/make -f src/apps/CMakeFiles/convert_to_tiff.dir/build.make src/apps/CMakeFiles/convert_to_tiff.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/convert_to_tiff.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/convert_to_tiff.dir/build'. make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 59%] Built target convert_to_tiff /usr/bin/make -f src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build.make src/apps/CMakeFiles/convert_to_tiff_mpi.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/convert_to_tiff_mpi.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 60%] Built target convert_to_tiff_mpi /usr/bin/make -f src/apps/CMakeFiles/ctf_mask_test.dir/build.make src/apps/CMakeFiles/ctf_mask_test.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/ctf_mask_test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/ctf_mask_test.dir/build'. make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 61%] Built target ctf_mask_test /usr/bin/make -f src/apps/CMakeFiles/ctf_refine.dir/build.make src/apps/CMakeFiles/ctf_refine.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/ctf_refine.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/ctf_refine.dir/build'. make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 62%] Built target ctf_refine /usr/bin/make -f src/apps/CMakeFiles/ctf_refine_mpi.dir/build.make src/apps/CMakeFiles/ctf_refine_mpi.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/ctf_refine_mpi.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/ctf_refine_mpi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 62%] Built target ctf_refine_mpi /usr/bin/make -f src/apps/CMakeFiles/ctf_toolbox.dir/build.make src/apps/CMakeFiles/ctf_toolbox.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/ctf_toolbox.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/ctf_toolbox.dir/build'. make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 63%] Built target ctf_toolbox /usr/bin/make -f src/apps/CMakeFiles/demodulate.dir/build.make src/apps/CMakeFiles/demodulate.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/demodulate.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/demodulate.dir/build.make src/apps/CMakeFiles/demodulate.dir/build make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/demodulate.dir/build'. make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 64%] Built target demodulate /usr/bin/make -f src/apps/CMakeFiles/display.dir/build.make src/apps/CMakeFiles/display.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/display.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/display.dir/build.make src/apps/CMakeFiles/display.dir/build make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/display.dir/build'. make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 65%] Built target display /usr/bin/make -f src/apps/CMakeFiles/estimate_gain.dir/build.make src/apps/CMakeFiles/estimate_gain.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/estimate_gain.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/estimate_gain.dir/build'. make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 65%] Built target estimate_gain /usr/bin/make -f src/apps/CMakeFiles/external_reconstruct.dir/build.make src/apps/CMakeFiles/external_reconstruct.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/external_reconstruct.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/external_reconstruct.dir/build'. make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 66%] Built target external_reconstruct /usr/bin/make -f src/apps/CMakeFiles/find_tiltpairs.dir/build.make src/apps/CMakeFiles/find_tiltpairs.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/find_tiltpairs.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/find_tiltpairs.dir/build'. make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 67%] Built target find_tiltpairs /usr/bin/make -f src/apps/CMakeFiles/flex_analyse.dir/build.make src/apps/CMakeFiles/flex_analyse.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/flex_analyse.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/flex_analyse.dir/build'. make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 68%] Built target flex_analyse /usr/bin/make -f src/apps/CMakeFiles/flex_analyse_mpi.dir/build.make src/apps/CMakeFiles/flex_analyse_mpi.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/flex_analyse_mpi.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/flex_analyse_mpi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 68%] Built target flex_analyse_mpi /usr/bin/make -f src/apps/CMakeFiles/helix_inimodel2d.dir/build.make src/apps/CMakeFiles/helix_inimodel2d.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/helix_inimodel2d.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/helix_inimodel2d.dir/build'. make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 69%] Built target helix_inimodel2d /usr/bin/make -f src/apps/CMakeFiles/helix_toolbox.dir/build.make src/apps/CMakeFiles/helix_toolbox.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/helix_toolbox.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/helix_toolbox.dir/build'. make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 70%] Built target helix_toolbox /usr/bin/make -f src/apps/CMakeFiles/image_handler.dir/build.make src/apps/CMakeFiles/image_handler.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/image_handler.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/image_handler.dir/build'. make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 71%] Built target image_handler /usr/bin/make -f src/apps/CMakeFiles/import.dir/build.make src/apps/CMakeFiles/import.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/import.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/import.dir/build.make src/apps/CMakeFiles/import.dir/build make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/import.dir/build'. make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 71%] Built target import /usr/bin/make -f src/apps/CMakeFiles/localsym.dir/build.make src/apps/CMakeFiles/localsym.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/localsym.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/localsym.dir/build.make src/apps/CMakeFiles/localsym.dir/build make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/localsym.dir/build'. make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 72%] Built target localsym /usr/bin/make -f src/apps/CMakeFiles/localsym_mpi.dir/build.make src/apps/CMakeFiles/localsym_mpi.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/localsym_mpi.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/localsym_mpi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 73%] Built target localsym_mpi /usr/bin/make -f src/apps/CMakeFiles/relion.dir/build.make src/apps/CMakeFiles/relion.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/relion.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/relion.dir/build.make src/apps/CMakeFiles/relion.dir/build make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/relion.dir/build'. make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 74%] Built target relion /usr/bin/make -f src/apps/CMakeFiles/manualpick.dir/build.make src/apps/CMakeFiles/manualpick.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/manualpick.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/manualpick.dir/build.make src/apps/CMakeFiles/manualpick.dir/build make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/manualpick.dir/build'. make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 75%] Built target manualpick /usr/bin/make -f src/apps/CMakeFiles/mask_create.dir/build.make src/apps/CMakeFiles/mask_create.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/mask_create.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/mask_create.dir/build'. make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 75%] Built target mask_create /usr/bin/make -f src/apps/CMakeFiles/merge_particles.dir/build.make src/apps/CMakeFiles/merge_particles.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/merge_particles.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/merge_particles.dir/build'. make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 76%] Built target merge_particles /usr/bin/make -f src/apps/CMakeFiles/motion_refine.dir/build.make src/apps/CMakeFiles/motion_refine.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/motion_refine.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/motion_refine.dir/build'. make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 77%] Built target motion_refine /usr/bin/make -f src/apps/CMakeFiles/motion_refine_mpi.dir/build.make src/apps/CMakeFiles/motion_refine_mpi.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/motion_refine_mpi.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/motion_refine_mpi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 78%] Built target motion_refine_mpi /usr/bin/make -f src/apps/CMakeFiles/mrc2vtk.dir/build.make src/apps/CMakeFiles/mrc2vtk.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/mrc2vtk.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/mrc2vtk.dir/build.make src/apps/CMakeFiles/mrc2vtk.dir/build make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/mrc2vtk.dir/build'. make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 78%] Built target mrc2vtk /usr/bin/make -f src/apps/CMakeFiles/particle_FCC.dir/build.make src/apps/CMakeFiles/particle_FCC.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/particle_FCC.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/particle_FCC.dir/build'. make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 79%] Built target particle_FCC /usr/bin/make -f src/apps/CMakeFiles/particle_reposition.dir/build.make src/apps/CMakeFiles/particle_reposition.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/particle_reposition.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/particle_reposition.dir/build'. make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 80%] Built target particle_reposition /usr/bin/make -f src/apps/CMakeFiles/particle_select.dir/build.make src/apps/CMakeFiles/particle_select.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/particle_select.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/particle_select.dir/build.make src/apps/CMakeFiles/particle_select.dir/build make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/particle_select.dir/build'. make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 81%] Built target particle_select /usr/bin/make -f src/apps/CMakeFiles/particle_subtract.dir/build.make src/apps/CMakeFiles/particle_subtract.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/particle_subtract.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/particle_subtract.dir/build'. make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 82%] Built target particle_subtract /usr/bin/make -f src/apps/CMakeFiles/particle_subtract_mpi.dir/build.make src/apps/CMakeFiles/particle_subtract_mpi.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/particle_subtract_mpi.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/particle_subtract_mpi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 82%] Built target particle_subtract_mpi /usr/bin/make -f src/apps/CMakeFiles/particle_symmetry_expand.dir/build.make src/apps/CMakeFiles/particle_symmetry_expand.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/particle_symmetry_expand.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/particle_symmetry_expand.dir/build'. make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/pipeliner.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/pipeliner.dir/build.make src/apps/CMakeFiles/pipeliner.dir/build make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/pipeliner.dir/build'. make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 84%] Built target pipeliner /usr/bin/make -f src/apps/CMakeFiles/plot_delocalisation.dir/build.make src/apps/CMakeFiles/plot_delocalisation.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/plot_delocalisation.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/plot_delocalisation.dir/build'. make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/postprocess.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/postprocess.dir/build.make src/apps/CMakeFiles/postprocess.dir/build make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/postprocess.dir/build'. make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 85%] Built target postprocess /usr/bin/make -f src/apps/CMakeFiles/postprocess_mpi.dir/build.make src/apps/CMakeFiles/postprocess_mpi.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/postprocess_mpi.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/postprocess_mpi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/prepare_subtomo.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/prepare_subtomo.dir/build'. make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 87%] Built target prepare_subtomo /usr/bin/make -f src/apps/CMakeFiles/preprocess.dir/build.make src/apps/CMakeFiles/preprocess.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/preprocess.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/preprocess.dir/build.make src/apps/CMakeFiles/preprocess.dir/build make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/preprocess.dir/build'. make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/preprocess_mpi.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/preprocess_mpi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/project.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/project.dir/build.make src/apps/CMakeFiles/project.dir/build make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/project.dir/build'. make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 89%] Built target project /usr/bin/make -f src/apps/CMakeFiles/reconstruct.dir/build.make src/apps/CMakeFiles/reconstruct.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/reconstruct.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/reconstruct.dir/build.make src/apps/CMakeFiles/reconstruct.dir/build make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/reconstruct.dir/build'. make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/reconstruct_mpi.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/reconstruct_mpi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 91%] Built target reconstruct_mpi /usr/bin/make -f src/apps/CMakeFiles/refine.dir/build.make src/apps/CMakeFiles/refine.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/refine.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/refine.dir/build.make src/apps/CMakeFiles/refine.dir/build make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/refine.dir/build'. make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/refine_mpi.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/refine_mpi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 92%] Built target refine_mpi /usr/bin/make -f src/apps/CMakeFiles/reposition.dir/build.make src/apps/CMakeFiles/reposition.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/reposition.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/reposition.dir/build.make src/apps/CMakeFiles/reposition.dir/build make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/reposition.dir/build'. make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 93%] Built target reposition /usr/bin/make -f src/apps/CMakeFiles/run_ctffind.dir/build.make src/apps/CMakeFiles/run_ctffind.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/run_ctffind.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/run_ctffind.dir/build'. make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 93%] Built target run_ctffind /usr/bin/make -f src/apps/CMakeFiles/run_ctffind_mpi.dir/build.make src/apps/CMakeFiles/run_ctffind_mpi.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/run_ctffind_mpi.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/run_ctffind_mpi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 94%] Built target run_ctffind_mpi /usr/bin/make -f src/apps/CMakeFiles/run_motioncorr.dir/build.make src/apps/CMakeFiles/run_motioncorr.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/run_motioncorr.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/run_motioncorr.dir/build'. make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 95%] Built target run_motioncorr /usr/bin/make -f src/apps/CMakeFiles/run_motioncorr_mpi.dir/build.make src/apps/CMakeFiles/run_motioncorr_mpi.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/run_motioncorr_mpi.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/run_motioncorr_mpi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 96%] Built target run_motioncorr_mpi /usr/bin/make -f src/apps/CMakeFiles/scheduler.dir/build.make src/apps/CMakeFiles/scheduler.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/scheduler.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/scheduler.dir/build.make src/apps/CMakeFiles/scheduler.dir/build make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/scheduler.dir/build'. make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [ 96%] Built target scheduler /usr/bin/make -f src/apps/CMakeFiles/stack_create.dir/build.make src/apps/CMakeFiles/stack_create.dir/depend make[4]: Entering directory '/build/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/stack_create.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/stack_create.dir/build'. make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/star_handler.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/star_handler.dir/build'. make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/tiltpair_plot.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/tiltpair_plot.dir/build'. make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' cd /build/reproducible-path/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/relion-3.1.3 /build/reproducible-path/relion-3.1.3/src/apps /build/reproducible-path/relion-3.1.3/build /build/reproducible-path/relion-3.1.3/build/src/apps /build/reproducible-path/relion-3.1.3/build/src/apps/CMakeFiles/tomo_test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/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/reproducible-path/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/tomo_test.dir/build'. make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' [100%] Built target tomo_test make[3]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/relion-3.1.3/build/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/reproducible-path/relion-3.1.3/build' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_run_motioncorr_mpi -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_autopick -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_subtract -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_flex_analyse -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_merge_particles -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_star_datablock_stack -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_star_datablock_ctfdat -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_refine -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_ctf_refine -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_run_motioncorr -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_prepare_subtomo -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_FCC -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_reconstruct -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_star_loopheader -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_localsym -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_star_plottable -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_helix_toolbox -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_qsub.csh -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_stack_create -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_flex_analyse_mpi -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_localsym_mpi -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_tomo_test -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_reconstruct_mpi -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_scheduler -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_star_printtable -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_motion_refine_mpi -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_ctf_refine_mpi -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_ctf_mask_test -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_ctf_toolbox -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_star_datablock_singlefiles -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_reposition -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_convert_to_tiff_mpi -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_refine_mpi -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_demodulate -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_run_ctffind_mpi -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_symmetry_expand -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_run_ctffind -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_mask_create -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_helix_inimodel2d -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_postprocess_mpi -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_estimate_gain -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_convert_to_tiff -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_align_symmetry -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_preprocess_mpi -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_reposition -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_external_reconstruct -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_subtract_mpi -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_pipeliner -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_preprocess -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_motion_refine -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_import -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_project -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_plot_delocalisation -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_autopick_mpi -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_postprocess -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_tiltpair_plot -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_mrc2vtk -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_display -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_image_handler -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_star_handler -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_find_tiltpairs -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_convert_star -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_select -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion -- Installing: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_manualpick -- Up-to-date: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_align_symmetry -- Up-to-date: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_autopick -- Up-to-date: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_autopick_mpi -- Up-to-date: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_convert_star -- Up-to-date: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_convert_to_tiff -- Up-to-date: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_convert_to_tiff_mpi -- Up-to-date: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_ctf_mask_test -- Up-to-date: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_ctf_refine -- Up-to-date: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_ctf_refine_mpi -- Up-to-date: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_ctf_toolbox -- Up-to-date: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_demodulate -- Up-to-date: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_display -- Up-to-date: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_estimate_gain -- Up-to-date: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_external_reconstruct -- Up-to-date: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_find_tiltpairs -- Up-to-date: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_flex_analyse -- Up-to-date: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_flex_analyse_mpi -- Up-to-date: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_helix_inimodel2d -- Up-to-date: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_helix_toolbox -- Up-to-date: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_image_handler -- Up-to-date: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_import -- Up-to-date: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_localsym -- Up-to-date: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_localsym_mpi -- Up-to-date: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion -- Up-to-date: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_manualpick -- Up-to-date: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_mask_create -- Up-to-date: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_merge_particles -- Up-to-date: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_motion_refine -- Up-to-date: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_motion_refine_mpi -- Up-to-date: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_mrc2vtk -- Up-to-date: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_FCC -- Up-to-date: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_reposition -- Up-to-date: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_select -- Up-to-date: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_subtract -- Up-to-date: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_subtract_mpi -- Up-to-date: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_symmetry_expand -- Up-to-date: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_pipeliner -- Up-to-date: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_plot_delocalisation -- Up-to-date: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_postprocess -- Up-to-date: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_postprocess_mpi -- Up-to-date: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_prepare_subtomo -- Up-to-date: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_preprocess -- Up-to-date: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_preprocess_mpi -- Up-to-date: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_project -- Up-to-date: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_reconstruct -- Up-to-date: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_reconstruct_mpi -- Up-to-date: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_refine -- Up-to-date: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_refine_mpi -- Up-to-date: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_reposition -- Up-to-date: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_run_ctffind -- Up-to-date: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_run_ctffind_mpi -- Up-to-date: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_run_motioncorr -- Up-to-date: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_run_motioncorr_mpi -- Up-to-date: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_scheduler -- Up-to-date: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_stack_create -- Up-to-date: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_star_handler -- Up-to-date: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_tiltpair_plot -- Up-to-date: /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/relion_tomo_test make[2]: Leaving directory '/build/reproducible-path/relion-3.1.3/build' mkdir -p /build/reproducible-path/relion-3.1.3/debian/tmp/gui/usr/bin rm /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/*.csh # Useless ... set -e; for prog in relion relion_display relion_manualpick; do \ mv /build/reproducible-path/relion-3.1.3/debian/tmp/cli/usr/bin/$prog \ /build/reproducible-path/relion-3.1.3/debian/tmp/gui/usr/bin; done make[1]: Leaving directory '/build/reproducible-path/relion-3.1.3' 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 dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'relion-gui' in '../relion-gui_3.1.3-4_amd64.deb'. dpkg-deb: building package 'relion-dbgsym' in '../relion-dbgsym_3.1.3-4_amd64.deb'. dpkg-deb: building package 'relion' in '../relion_3.1.3-4_amd64.deb'. dpkg-deb: building package 'relion-gui-dbgsym' in '../relion-gui-dbgsym_3.1.3-4_amd64.deb'. dpkg-genbuildinfo --build=binary -O../relion_3.1.3-4_amd64.buildinfo dpkg-genchanges --build=binary -O../relion_3.1.3-4_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2452736 and its subdirectories I: Current time: Sat Nov 9 15:09:11 -12 2024 I: pbuilder-time-stamp: 1731208151 Sun Nov 10 03:09:16 UTC 2024 I: 1st build successful. Starting 2nd build on remote node infom02-amd64.debian.net. Sun Nov 10 03:09:16 UTC 2024 I: Preparing to do remote build '2' on infom02-amd64.debian.net. Sun Nov 10 03:14:26 UTC 2024 I: Deleting $TMPDIR on infom02-amd64.debian.net. Sun Nov 10 03:14:26 UTC 2024 I: relion_3.1.3-4_amd64.changes: Format: 1.8 Date: Sat, 09 Nov 2024 18:14:58 +0100 Source: relion Binary: relion relion-dbgsym relion-gui relion-gui-dbgsym Architecture: amd64 Version: 3.1.3-4 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: relion - toolkit for 3D reconstructions in cryo-electron microscopy relion-gui - toolkit for 3D reconstructions in cryo-electron microscopy (gui a Closes: 1086914 Changes: relion (3.1.3-4) unstable; urgency=medium . * Team upload. * d/control: migrate to mpi-default-*. (Closes: #1086914) * d/control: declare compliance to standards version 4.7.0. Checksums-Sha1: 2d023921aebf8fbe0a8e907887a6101007038d9b 329727072 relion-dbgsym_3.1.3-4_amd64.deb f5fcea330c7c564fd0420f5b0f0c5a714d12cf83 18591124 relion-gui-dbgsym_3.1.3-4_amd64.deb 4fdb706eb17c591528ee1f445137ee76c279e5db 1160028 relion-gui_3.1.3-4_amd64.deb c5a4b9bd21d92a67f687301bad3265fc4d92da41 11236 relion_3.1.3-4_amd64.buildinfo baaa3b38808bf7170cc169fd841f04453028bee7 15638996 relion_3.1.3-4_amd64.deb Checksums-Sha256: 6b227878c260fcb1b5a5c5f847b87bf070ff4f86bfa1a49abaedb6e09f314cf7 329727072 relion-dbgsym_3.1.3-4_amd64.deb 23b13d132112ce88a59287cfe6e4f1d928516f7f781c6ce7bea5ee39fb1d8a03 18591124 relion-gui-dbgsym_3.1.3-4_amd64.deb ba18f47a1ec61dca9e7e887d9b7103647b99155fa1dae57703f89f57f3001d3c 1160028 relion-gui_3.1.3-4_amd64.deb 1f027129eb8b41d773b53e5595d6dc681ce5456532c1a0085df34dad0f83a2c0 11236 relion_3.1.3-4_amd64.buildinfo 6e6f32f67ab5e80c42c4e8c80ba078dfc432f2c5218d47cb6c4d917558835a48 15638996 relion_3.1.3-4_amd64.deb Files: c57e72ad86a2bf1db52643a744c69475 329727072 debug optional relion-dbgsym_3.1.3-4_amd64.deb f793977f6be38d10a392b27665d96659 18591124 debug optional relion-gui-dbgsym_3.1.3-4_amd64.deb 4fe00b8740803cfedbb926067e6d973f 1160028 science optional relion-gui_3.1.3-4_amd64.deb 8683ff0e2e64648d0199256036942841 11236 science optional relion_3.1.3-4_amd64.buildinfo df71e4e8f044c75cc42cb48944955114 15638996 science optional relion_3.1.3-4_amd64.deb Sun Nov 10 03:14:28 UTC 2024 I: diffoscope 283 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_37-36557.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.NsZJyNAm/relion_3.1.3-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.NsZJyNAm/relion_3.1.3-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.NsZJyNAm/relion_3.1.3-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.NsZJyNAm/b1/relion_3.1.3-4_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.NsZJyNAm/b2/relion_3.1.3-4_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 4.098s) 4.098s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 3.739s) 3.739s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 4.429s CPU time consumed: 4.429s Sun Nov 10 03:15:07 UTC 2024 I: diffoscope 283 found no differences in the changes files, and a .buildinfo file also exists. Sun Nov 10 03:15:07 UTC 2024 I: relion from unstable built successfully and reproducibly on amd64. Sun Nov 10 03:15:09 UTC 2024 I: Submitting .buildinfo files to external archives: Sun Nov 10 03:15:09 UTC 2024 I: Submitting 12K b1/relion_3.1.3-4_amd64.buildinfo.asc Sun Nov 10 03:15:10 UTC 2024 I: Submitting 12K b2/relion_3.1.3-4_amd64.buildinfo.asc Sun Nov 10 03:15:13 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun Nov 10 03:15:13 UTC 2024 I: Done submitting .buildinfo files. Sun Nov 10 03:15:13 UTC 2024 I: Removing signed relion_3.1.3-4_amd64.buildinfo.asc files: removed './b1/relion_3.1.3-4_amd64.buildinfo.asc' removed './b2/relion_3.1.3-4_amd64.buildinfo.asc'