I: pbuilder: network access will be disabled during build I: Current time: Sat Jun 10 03:17:07 +14 2023 I: pbuilder-time-stamp: 1686316627 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-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_3.1.3-3.dsc] I: copying [./relion_3.1.3.orig.tar.gz] I: copying [./relion_3.1.3-3.debian.tar.xz] I: Extracting source gpgv: Signature made Wed Dec 7 01:51:10 2022 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./relion_3.1.3-3.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_3.1.3-3.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/29454/tmp/hooks/D01_modify_environment starting debug: Running on jtx1a. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Jun 10 03:17 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/29454/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/29454/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") BASH_VERSION='5.2.15(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=armhf DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' DIRSTACK=() DISTRIBUTION=bookworm EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=arm HOST_ARCH=armhf IFS=' ' INVOCATION_ID=42950684cc0245fead75437ef15b60b4 LANG=C LANGUAGE=it_CH:it LC_ALL=C MACHTYPE=arm-unknown-linux-gnueabihf MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnueabihf PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=29454 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.BuJ5alNF/pbuilderrc_gpXf --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.BuJ5alNF/b2 --logfile b2/build.log --extrapackages usrmerge relion_3.1.3-3.dsc' SUDO_GID=114 SUDO_UID=108 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://10.0.0.15:3142/ I: uname -a Linux i-capture-the-hostname 5.10.0-23-arm64 #1 SMP Debian 5.10.179-1 (2023-05-12) aarch64 GNU/Linux I: ls -l /bin total 5072 -rwxr-xr-x 1 root root 838488 Apr 24 11:24 bash -rwxr-xr-x 3 root root 67144 Sep 19 2022 bunzip2 -rwxr-xr-x 3 root root 67144 Sep 19 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep -rwxr-xr-x 3 root root 67144 Sep 19 2022 bzip2 -rwxr-xr-x 1 root root 67112 Sep 19 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore -rwxr-xr-x 1 root root 67632 Sep 21 2022 cat -rwxr-xr-x 1 root root 67676 Sep 21 2022 chgrp -rwxr-xr-x 1 root root 67644 Sep 21 2022 chmod -rwxr-xr-x 1 root root 67684 Sep 21 2022 chown -rwxr-xr-x 1 root root 133532 Sep 21 2022 cp -rwxr-xr-x 1 root root 132868 Jan 6 03:20 dash -rwxr-xr-x 1 root root 133220 Sep 21 2022 date -rwxr-xr-x 1 root root 67732 Sep 21 2022 dd -rwxr-xr-x 1 root root 68104 Sep 21 2022 df -rwxr-xr-x 1 root root 133632 Sep 21 2022 dir -rwxr-xr-x 1 root root 59128 Mar 23 23:02 dmesg lrwxrwxrwx 1 root root 8 Dec 20 03:33 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 20 03:33 domainname -> hostname -rwxr-xr-x 1 root root 67560 Sep 21 2022 echo -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep -rwxr-xr-x 1 root root 67548 Sep 21 2022 false -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep -rwxr-xr-x 1 root root 55748 Mar 23 23:02 findmnt -rwsr-xr-x 1 root root 26208 Mar 23 22:15 fusermount -rwxr-xr-x 1 root root 128608 Jan 25 04:43 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 64220 Apr 10 2022 gzip -rwxr-xr-x 1 root root 67032 Dec 20 03:33 hostname -rwxr-xr-x 1 root root 67720 Sep 21 2022 ln -rwxr-xr-x 1 root root 35132 Mar 23 23:51 login -rwxr-xr-x 1 root root 133632 Sep 21 2022 ls -rwxr-xr-x 1 root root 136808 Mar 23 23:02 lsblk -rwxr-xr-x 1 root root 67800 Sep 21 2022 mkdir -rwxr-xr-x 1 root root 67764 Sep 21 2022 mknod -rwxr-xr-x 1 root root 67596 Sep 21 2022 mktemp -rwxr-xr-x 1 root root 38504 Mar 23 23:02 more -rwsr-xr-x 1 root root 38496 Mar 23 23:02 mount -rwxr-xr-x 1 root root 9824 Mar 23 23:02 mountpoint -rwxr-xr-x 1 root root 133532 Sep 21 2022 mv lrwxrwxrwx 1 root root 8 Dec 20 03:33 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 67608 Sep 21 2022 pwd lrwxrwxrwx 1 root root 4 Apr 24 11:24 rbash -> bash -rwxr-xr-x 1 root root 67600 Sep 21 2022 readlink -rwxr-xr-x 1 root root 67672 Sep 21 2022 rm -rwxr-xr-x 1 root root 67600 Sep 21 2022 rmdir -rwxr-xr-x 1 root root 67400 Nov 3 2022 run-parts -rwxr-xr-x 1 root root 133372 Jan 6 09:55 sed lrwxrwxrwx 1 root root 9 Jun 10 03:17 sh -> /bin/bash -rwxr-xr-x 1 root root 67584 Sep 21 2022 sleep -rwxr-xr-x 1 root root 67644 Sep 21 2022 stty -rwsr-xr-x 1 root root 50800 Mar 23 23:02 su -rwxr-xr-x 1 root root 67584 Sep 21 2022 sync -rwxr-xr-x 1 root root 336764 Apr 7 04:25 tar -rwxr-xr-x 1 root root 67144 Nov 3 2022 tempfile -rwxr-xr-x 1 root root 133224 Sep 21 2022 touch -rwxr-xr-x 1 root root 67548 Sep 21 2022 true -rwxr-xr-x 1 root root 9768 Mar 23 22:15 ulockmgr_server -rwsr-xr-x 1 root root 22108 Mar 23 23:02 umount -rwxr-xr-x 1 root root 67572 Sep 21 2022 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 133632 Sep 21 2022 vdir -rwxr-xr-x 1 root root 42608 Mar 23 23:02 wdctl lrwxrwxrwx 1 root root 8 Dec 20 03:33 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/29454/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: armhf 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, libopenmpi-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 ... 19324 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 libopenmpi-dev; however: Package libopenmpi-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} gettext{a} gettext-base{a} gfortran-12{a} groff-base{a} ibverbs-providers{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13{a} libbrotli1{a} libbsd0{a} libcairo2{a} libcbor0.8{a} libcurl4{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-nouveau2{a} libdrm-radeon1{a} libdrm2{a} libedit2{a} libelf1{a} libevent-2.1-7{a} libevent-core-2.1-7{a} libevent-dev{a} libevent-extra-2.1-7{a} libevent-openssl-2.1-7{a} libevent-pthreads-2.1-7{a} libexpat1{a} libfabric1{a} libfftw3-bin{a} libfftw3-dev{a} libfftw3-double3{a} libfftw3-single3{a} libfido2-1{a} libfile-stripnondeterminism-perl{a} libfltk-cairo1.3{a} libfltk-forms1.3{a} libfltk-gl1.3{a} libfltk-images1.3{a} libfltk1.3{a} libfltk1.3-dev{a} libfontconfig1{a} libfreetype6{a} libgfortran-12-dev{a} libgfortran5{a} libgl1{a} libgl1-mesa-dri{a} libglapi-mesa{a} libglvnd0{a} libglx-mesa0{a} libglx0{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc15{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} libjsoncpp25{a} libldap-2.5-0{a} liblerc-dev{a} liblerc4{a} libllvm15{a} libltdl-dev{a} libltdl7{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{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} libopenmpi3{a} libpciaccess0{a} libpipeline1{a} libpixman-1-0{a} libpmix-dev{a} libpmix2{a} libpng16-16{a} libproc2-0{a} libpsl5{a} libpthread-stubs0-dev{a} librdmacm1{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsensors-config{a} libsensors5{a} libssh2-1{a} libsub-override-perl{a} libtiff-dev{a} libtiff6{a} libtiffxx6{a} libtool{a} libuchardet0{a} libuv1{a} libwebp-dev{a} libwebp7{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} 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 libarchive-cpio-perl libcoarrays-openmpi-dev libgl-dev libglu1-mesa-dev libldap-common libmail-sendmail-perl libsasl2-modules lynx psmisc publicsuffix wget xauth 0 packages upgraded, 173 newly installed, 0 to remove and 0 not upgraded. Need to get 92.6 MB of archives. After unpacking 336 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main armhf libproc2-0 armhf 2:4.0.2-3 [54.2 kB] Get: 2 http://deb.debian.org/debian bookworm/main armhf procps armhf 2:4.0.2-3 [695 kB] Get: 3 http://deb.debian.org/debian bookworm/main armhf sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 4 http://deb.debian.org/debian bookworm/main armhf libmagic-mgc armhf 1:5.44-3 [305 kB] Get: 5 http://deb.debian.org/debian bookworm/main armhf libmagic1 armhf 1:5.44-3 [96.5 kB] Get: 6 http://deb.debian.org/debian bookworm/main armhf file armhf 1:5.44-3 [41.6 kB] Get: 7 http://deb.debian.org/debian bookworm/main armhf gettext-base armhf 0.21-12 [157 kB] Get: 8 http://deb.debian.org/debian bookworm/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB] Get: 9 http://deb.debian.org/debian bookworm/main armhf groff-base armhf 1.22.4-10 [825 kB] Get: 10 http://deb.debian.org/debian bookworm/main armhf bsdextrautils armhf 2.38.1-5+b1 [78.6 kB] Get: 11 http://deb.debian.org/debian bookworm/main armhf libpipeline1 armhf 1.5.7-1 [33.6 kB] Get: 12 http://deb.debian.org/debian bookworm/main armhf man-db armhf 2.11.2-2 [1351 kB] Get: 13 http://deb.debian.org/debian bookworm/main armhf libbsd0 armhf 0.11.7-2 [113 kB] Get: 14 http://deb.debian.org/debian bookworm/main armhf libedit2 armhf 3.1-20221030-2 [77.0 kB] Get: 15 http://deb.debian.org/debian bookworm/main armhf libcbor0.8 armhf 0.8.0-2+b1 [23.1 kB] Get: 16 http://deb.debian.org/debian bookworm/main armhf libfido2-1 armhf 1.12.0-2+b1 [69.3 kB] Get: 17 http://deb.debian.org/debian bookworm/main armhf openssh-client armhf 1:9.2p1-2 [893 kB] Get: 18 http://deb.debian.org/debian bookworm/main armhf m4 armhf 1.4.19-3 [265 kB] Get: 19 http://deb.debian.org/debian bookworm/main armhf autoconf all 2.71-3 [332 kB] Get: 20 http://deb.debian.org/debian bookworm/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 21 http://deb.debian.org/debian bookworm/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 22 http://deb.debian.org/debian bookworm/main armhf autopoint all 0.21-12 [495 kB] Get: 23 http://deb.debian.org/debian bookworm/main armhf libicu72 armhf 72.1-3 [9048 kB] Get: 24 http://deb.debian.org/debian bookworm/main armhf libxml2 armhf 2.9.14+dfsg-1.2 [591 kB] Get: 25 http://deb.debian.org/debian bookworm/main armhf libarchive13 armhf 3.6.2-1 [299 kB] Get: 26 http://deb.debian.org/debian bookworm/main armhf libbrotli1 armhf 1.0.9-2+b6 [271 kB] Get: 27 http://deb.debian.org/debian bookworm/main armhf libsasl2-modules-db armhf 2.1.28+dfsg-10 [19.0 kB] Get: 28 http://deb.debian.org/debian bookworm/main armhf libsasl2-2 armhf 2.1.28+dfsg-10 [52.3 kB] Get: 29 http://deb.debian.org/debian bookworm/main armhf libldap-2.5-0 armhf 2.5.13+dfsg-5 [158 kB] Get: 30 http://deb.debian.org/debian bookworm/main armhf libnghttp2-14 armhf 1.52.0-1 [60.8 kB] Get: 31 http://deb.debian.org/debian bookworm/main armhf libpsl5 armhf 0.21.2-1 [57.5 kB] Get: 32 http://deb.debian.org/debian bookworm/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [55.2 kB] Get: 33 http://deb.debian.org/debian bookworm/main armhf libssh2-1 armhf 1.10.0-3+b1 [163 kB] Get: 34 http://deb.debian.org/debian bookworm/main armhf libcurl4 armhf 7.88.1-10 [347 kB] Get: 35 http://deb.debian.org/debian bookworm/main armhf libexpat1 armhf 2.5.0-1 [79.9 kB] Get: 36 http://deb.debian.org/debian bookworm/main armhf libjsoncpp25 armhf 1.9.5-4 [68.6 kB] Get: 37 http://deb.debian.org/debian bookworm/main armhf librhash0 armhf 1.4.3-3 [146 kB] Get: 38 http://deb.debian.org/debian bookworm/main armhf libuv1 armhf 1.44.2-1 [126 kB] Get: 39 http://deb.debian.org/debian bookworm/main armhf cmake-data all 3.25.1-1 [2026 kB] Get: 40 http://deb.debian.org/debian bookworm/main armhf cmake armhf 3.25.1-1 [4263 kB] Get: 41 http://deb.debian.org/debian bookworm/main armhf libdebhelper-perl all 13.11.4 [81.2 kB] Get: 42 http://deb.debian.org/debian bookworm/main armhf libtool all 2.4.7-5 [517 kB] Get: 43 http://deb.debian.org/debian bookworm/main armhf dh-autoreconf all 20 [17.1 kB] Get: 44 http://deb.debian.org/debian bookworm/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 45 http://deb.debian.org/debian bookworm/main armhf libsub-override-perl all 0.09-4 [9304 B] Get: 46 http://deb.debian.org/debian bookworm/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 47 http://deb.debian.org/debian bookworm/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 48 http://deb.debian.org/debian bookworm/main armhf libelf1 armhf 0.188-2.1 [170 kB] Get: 49 http://deb.debian.org/debian bookworm/main armhf dwz armhf 0.15-1 [101 kB] Get: 50 http://deb.debian.org/debian bookworm/main armhf gettext armhf 0.21-12 [1229 kB] Get: 51 http://deb.debian.org/debian bookworm/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 52 http://deb.debian.org/debian bookworm/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 53 http://deb.debian.org/debian bookworm/main armhf debhelper all 13.11.4 [942 kB] Get: 54 http://deb.debian.org/debian bookworm/main armhf libpng16-16 armhf 1.6.39-2 [260 kB] Get: 55 http://deb.debian.org/debian bookworm/main armhf libfreetype6 armhf 2.12.1+dfsg-5 [332 kB] Get: 56 http://deb.debian.org/debian bookworm/main armhf fonts-dejavu-core all 2.37-6 [1068 kB] Get: 57 http://deb.debian.org/debian bookworm/main armhf fontconfig-config armhf 2.14.1-4 [315 kB] Get: 58 http://deb.debian.org/debian bookworm/main armhf libfontconfig1 armhf 2.14.1-4 [368 kB] Get: 59 http://deb.debian.org/debian bookworm/main armhf libxau6 armhf 1:1.0.9-1 [19.0 kB] Get: 60 http://deb.debian.org/debian bookworm/main armhf libxdmcp6 armhf 1:1.1.2-3 [24.9 kB] Get: 61 http://deb.debian.org/debian bookworm/main armhf libxcb1 armhf 1.15-1 [140 kB] Get: 62 http://deb.debian.org/debian bookworm/main armhf libx11-data all 2:1.8.4-2 [292 kB] Get: 63 http://deb.debian.org/debian bookworm/main armhf libx11-6 armhf 2:1.8.4-2 [695 kB] Get: 64 http://deb.debian.org/debian bookworm/main armhf libxfixes3 armhf 1:6.0.0-2 [21.1 kB] Get: 65 http://deb.debian.org/debian bookworm/main armhf libxrender1 armhf 1:0.9.10-1.1 [30.1 kB] Get: 66 http://deb.debian.org/debian bookworm/main armhf libxcursor1 armhf 1:1.2.1-1 [37.9 kB] Get: 67 http://deb.debian.org/debian bookworm/main armhf libxext6 armhf 2:1.3.4-1+b1 [47.8 kB] Get: 68 http://deb.debian.org/debian bookworm/main armhf libxft2 armhf 2.3.6-1 [53.8 kB] Get: 69 http://deb.debian.org/debian bookworm/main armhf libxinerama1 armhf 2:1.1.4-3 [17.4 kB] Get: 70 http://deb.debian.org/debian bookworm/main armhf libfltk1.3 armhf 1.3.8-5 [505 kB] Get: 71 http://deb.debian.org/debian bookworm/main armhf libfltk-forms1.3 armhf 1.3.8-5 [51.9 kB] Get: 72 http://deb.debian.org/debian bookworm/main armhf libjpeg62-turbo armhf 1:2.1.5-2 [143 kB] Get: 73 http://deb.debian.org/debian bookworm/main armhf libfltk-images1.3 armhf 1.3.8-5 [63.4 kB] Get: 74 http://deb.debian.org/debian bookworm/main armhf fluid armhf 1.3.8-5 [214 kB] Get: 75 http://deb.debian.org/debian bookworm/main armhf libgfortran5 armhf 12.2.0-14 [246 kB] Get: 76 http://deb.debian.org/debian bookworm/main armhf libgfortran-12-dev armhf 12.2.0-14 [298 kB] Get: 77 http://deb.debian.org/debian bookworm/main armhf gfortran-12 armhf 12.2.0-14 [7633 kB] Get: 78 http://deb.debian.org/debian bookworm/main armhf libnl-3-200 armhf 3.7.0-0.2+b1 [55.8 kB] Get: 79 http://deb.debian.org/debian bookworm/main armhf libnl-route-3-200 armhf 3.7.0-0.2+b1 [156 kB] Get: 80 http://deb.debian.org/debian bookworm/main armhf libibverbs1 armhf 44.0-2 [53.6 kB] Get: 81 http://deb.debian.org/debian bookworm/main armhf ibverbs-providers armhf 44.0-2 [28.4 kB] Get: 82 http://deb.debian.org/debian bookworm/main armhf libpixman-1-0 armhf 0.42.2-1 [465 kB] Get: 83 http://deb.debian.org/debian bookworm/main armhf libxcb-render0 armhf 1.15-1 [114 kB] Get: 84 http://deb.debian.org/debian bookworm/main armhf libxcb-shm0 armhf 1.15-1 [106 kB] Get: 85 http://deb.debian.org/debian bookworm/main armhf libcairo2 armhf 1.16.0-7 [493 kB] Get: 86 http://deb.debian.org/debian bookworm/main armhf libdeflate0 armhf 1.14-1 [52.2 kB] Get: 87 http://deb.debian.org/debian bookworm/main armhf libdeflate-dev armhf 1.14-1 [48.7 kB] Get: 88 http://deb.debian.org/debian bookworm/main armhf libdrm-common all 2.4.114-1 [7112 B] Get: 89 http://deb.debian.org/debian bookworm/main armhf libdrm2 armhf 2.4.114-1+b1 [33.0 kB] Get: 90 http://deb.debian.org/debian bookworm/main armhf libdrm-amdgpu1 armhf 2.4.114-1+b1 [19.3 kB] Get: 91 http://deb.debian.org/debian bookworm/main armhf libdrm-nouveau2 armhf 2.4.114-1+b1 [16.7 kB] Get: 92 http://deb.debian.org/debian bookworm/main armhf libdrm-radeon1 armhf 2.4.114-1+b1 [19.3 kB] Get: 93 http://deb.debian.org/debian bookworm/main armhf libevent-2.1-7 armhf 2.1.12-stable-8 [161 kB] Get: 94 http://deb.debian.org/debian bookworm/main armhf libevent-core-2.1-7 armhf 2.1.12-stable-8 [120 kB] Get: 95 http://deb.debian.org/debian bookworm/main armhf libevent-extra-2.1-7 armhf 2.1.12-stable-8 [97.5 kB] Get: 96 http://deb.debian.org/debian bookworm/main armhf libevent-pthreads-2.1-7 armhf 2.1.12-stable-8 [53.2 kB] Get: 97 http://deb.debian.org/debian bookworm/main armhf libevent-openssl-2.1-7 armhf 2.1.12-stable-8 [58.3 kB] Get: 98 http://deb.debian.org/debian bookworm/main armhf libevent-dev armhf 2.1.12-stable-8 [290 kB] Get: 99 http://deb.debian.org/debian bookworm/main armhf librdmacm1 armhf 44.0-2 [60.6 kB] Get: 100 http://deb.debian.org/debian bookworm/main armhf libfabric1 armhf 1.17.0-3 [385 kB] Get: 101 http://deb.debian.org/debian bookworm/main armhf libfftw3-double3 armhf 3.3.10-1 [325 kB] Get: 102 http://deb.debian.org/debian bookworm/main armhf libfftw3-single3 armhf 3.3.10-1 [516 kB] Get: 103 http://deb.debian.org/debian bookworm/main armhf libfftw3-bin armhf 3.3.10-1 [40.8 kB] Get: 104 http://deb.debian.org/debian bookworm/main armhf libfftw3-dev armhf 3.3.10-1 [828 kB] Get: 105 http://deb.debian.org/debian bookworm/main armhf libfltk-cairo1.3 armhf 1.3.8-5 [46.5 kB] Get: 106 http://deb.debian.org/debian bookworm/main armhf libglvnd0 armhf 1.6.0-1 [51.9 kB] Get: 107 http://deb.debian.org/debian bookworm/main armhf libglapi-mesa armhf 22.3.6-1+deb12u1 [41.0 kB] Get: 108 http://deb.debian.org/debian bookworm/main armhf libx11-xcb1 armhf 2:1.8.4-2 [192 kB] Get: 109 http://deb.debian.org/debian bookworm/main armhf libxcb-dri2-0 armhf 1.15-1 [107 kB] Get: 110 http://deb.debian.org/debian bookworm/main armhf libxcb-dri3-0 armhf 1.15-1 [107 kB] Get: 111 http://deb.debian.org/debian bookworm/main armhf libxcb-glx0 armhf 1.15-1 [120 kB] Get: 112 http://deb.debian.org/debian bookworm/main armhf libxcb-present0 armhf 1.15-1 [105 kB] Get: 113 http://deb.debian.org/debian bookworm/main armhf libxcb-randr0 armhf 1.15-1 [116 kB] Get: 114 http://deb.debian.org/debian bookworm/main armhf libxcb-sync1 armhf 1.15-1 [108 kB] Get: 115 http://deb.debian.org/debian bookworm/main armhf libxcb-xfixes0 armhf 1.15-1 [110 kB] Get: 116 http://deb.debian.org/debian bookworm/main armhf libxshmfence1 armhf 1.3-1 [8592 B] Get: 117 http://deb.debian.org/debian bookworm/main armhf libxxf86vm1 armhf 1:1.1.4-1+b2 [20.2 kB] Get: 118 http://deb.debian.org/debian bookworm/main armhf libz3-4 armhf 4.8.12-3.1 [6061 kB] Get: 119 http://deb.debian.org/debian bookworm/main armhf libllvm15 armhf 1:15.0.6-4+b1 [20.5 MB] Get: 120 http://deb.debian.org/debian bookworm/main armhf libsensors-config all 1:3.6.0-7.1 [14.3 kB] Get: 121 http://deb.debian.org/debian bookworm/main armhf libsensors5 armhf 1:3.6.0-7.1 [31.6 kB] Get: 122 http://deb.debian.org/debian bookworm/main armhf libgl1-mesa-dri armhf 22.3.6-1+deb12u1 [5792 kB] Get: 123 http://deb.debian.org/debian bookworm/main armhf libglx-mesa0 armhf 22.3.6-1+deb12u1 [126 kB] Get: 124 http://deb.debian.org/debian bookworm/main armhf libglx0 armhf 1.6.0-1 [32.0 kB] Get: 125 http://deb.debian.org/debian bookworm/main armhf libgl1 armhf 1.6.0-1 [90.6 kB] Get: 126 http://deb.debian.org/debian bookworm/main armhf libfltk-gl1.3 armhf 1.3.8-5 [73.1 kB] Get: 127 http://deb.debian.org/debian bookworm/main armhf xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB] Get: 128 http://deb.debian.org/debian bookworm/main armhf x11proto-dev all 2022.1-1 [599 kB] Get: 129 http://deb.debian.org/debian bookworm/main armhf libxau-dev armhf 1:1.0.9-1 [22.4 kB] Get: 130 http://deb.debian.org/debian bookworm/main armhf libxdmcp-dev armhf 1:1.1.2-3 [40.7 kB] Get: 131 http://deb.debian.org/debian bookworm/main armhf xtrans-dev all 1.4.0-1 [98.7 kB] Get: 132 http://deb.debian.org/debian bookworm/main armhf libpthread-stubs0-dev armhf 0.4-1 [5344 B] Get: 133 http://deb.debian.org/debian bookworm/main armhf libxcb1-dev armhf 1.15-1 [179 kB] Get: 134 http://deb.debian.org/debian bookworm/main armhf libx11-dev armhf 2:1.8.4-2 [777 kB] Get: 135 http://deb.debian.org/debian bookworm/main armhf libfltk1.3-dev armhf 1.3.8-5 [810 kB] Get: 136 http://deb.debian.org/debian bookworm/main armhf libhwloc15 armhf 2.9.0-1 [127 kB] Get: 137 http://deb.debian.org/debian bookworm/main armhf libnuma1 armhf 2.0.16-1 [17.8 kB] Get: 138 http://deb.debian.org/debian bookworm/main armhf libnuma-dev armhf 2.0.16-1 [33.0 kB] Get: 139 http://deb.debian.org/debian bookworm/main armhf libltdl7 armhf 2.4.7-5 [390 kB] Get: 140 http://deb.debian.org/debian bookworm/main armhf libltdl-dev armhf 2.4.7-5 [162 kB] Get: 141 http://deb.debian.org/debian bookworm/main armhf libhwloc-dev armhf 2.9.0-1 [214 kB] Get: 142 http://deb.debian.org/debian bookworm/main armhf libpciaccess0 armhf 0.17-2 [48.7 kB] Get: 143 http://deb.debian.org/debian bookworm/main armhf libxnvctrl0 armhf 525.85.05-1 [12.2 kB] Get: 144 http://deb.debian.org/debian bookworm/main armhf ocl-icd-libopencl1 armhf 2.3.1-1 [40.1 kB] Get: 145 http://deb.debian.org/debian bookworm/main armhf libhwloc-plugins armhf 2.9.0-1 [15.9 kB] Get: 146 http://deb.debian.org/debian bookworm/main armhf libnl-3-dev armhf 3.7.0-0.2+b1 [98.4 kB] Get: 147 http://deb.debian.org/debian bookworm/main armhf libnl-route-3-dev armhf 3.7.0-0.2+b1 [183 kB] Get: 148 http://deb.debian.org/debian bookworm/main armhf libibverbs-dev armhf 44.0-2 [195 kB] Get: 149 http://deb.debian.org/debian bookworm/main armhf libjbig0 armhf 2.1-6.1 [27.1 kB] Get: 150 http://deb.debian.org/debian bookworm/main armhf libjbig-dev armhf 2.1-6.1 [27.5 kB] Get: 151 http://deb.debian.org/debian bookworm/main armhf libjpeg62-turbo-dev armhf 1:2.1.5-2 [260 kB] Get: 152 http://deb.debian.org/debian bookworm/main armhf libjpeg-dev armhf 1:2.1.5-2 [71.8 kB] Get: 153 http://deb.debian.org/debian bookworm/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 154 http://deb.debian.org/debian bookworm/main armhf libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 155 http://deb.debian.org/debian bookworm/main armhf liblerc4 armhf 4.0.0+ds-2 [137 kB] Get: 156 http://deb.debian.org/debian bookworm/main armhf liblerc-dev armhf 4.0.0+ds-2 [154 kB] Get: 157 http://deb.debian.org/debian bookworm/main armhf liblzma-dev armhf 5.4.1-0.2 [248 kB] Get: 158 http://deb.debian.org/debian bookworm/main armhf libmunge2 armhf 0.5.15-2 [15.7 kB] Get: 159 http://deb.debian.org/debian bookworm/main armhf libpmix2 armhf 4.2.2-1+b1 [553 kB] Get: 160 http://deb.debian.org/debian bookworm/main armhf libopenmpi3 armhf 4.1.4-3+b1 [1849 kB] Get: 161 http://deb.debian.org/debian bookworm/main armhf openmpi-common all 4.1.4-3 [167 kB] Get: 162 http://deb.debian.org/debian bookworm/main armhf zlib1g-dev armhf 1:1.2.13.dfsg-1 [902 kB] Get: 163 http://deb.debian.org/debian bookworm/main armhf libpmix-dev armhf 4.2.2-1+b1 [864 kB] Get: 164 http://deb.debian.org/debian bookworm/main armhf openmpi-bin armhf 4.1.4-3+b1 [194 kB] Get: 165 http://deb.debian.org/debian bookworm/main armhf libopenmpi-dev armhf 4.1.4-3+b1 [920 kB] Get: 166 http://deb.debian.org/debian bookworm/main armhf libzstd-dev armhf 1.5.4+dfsg2-5 [314 kB] Get: 167 http://deb.debian.org/debian bookworm/main armhf libwebp7 armhf 1.2.4-0.2 [242 kB] Get: 168 http://deb.debian.org/debian bookworm/main armhf libwebpmux3 armhf 1.2.4-0.2 [106 kB] Get: 169 http://deb.debian.org/debian bookworm/main armhf libwebpdemux2 armhf 1.2.4-0.2 [98.3 kB] Get: 170 http://deb.debian.org/debian bookworm/main armhf libwebp-dev armhf 1.2.4-0.2 [349 kB] Get: 171 http://deb.debian.org/debian bookworm/main armhf libtiff6 armhf 4.5.0-6 [295 kB] Get: 172 http://deb.debian.org/debian bookworm/main armhf libtiffxx6 armhf 4.5.0-6 [144 kB] Get: 173 http://deb.debian.org/debian bookworm/main armhf libtiff-dev armhf 4.5.0-6 [434 kB] Fetched 92.6 MB in 19s (5001 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libproc2-0:armhf. (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 ... 19324 files and directories currently installed.) Preparing to unpack .../000-libproc2-0_2%3a4.0.2-3_armhf.deb ... Unpacking libproc2-0:armhf (2:4.0.2-3) ... Selecting previously unselected package procps. Preparing to unpack .../001-procps_2%3a4.0.2-3_armhf.deb ... Unpacking procps (2:4.0.2-3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../002-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../003-libmagic-mgc_1%3a5.44-3_armhf.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../004-libmagic1_1%3a5.44-3_armhf.deb ... Unpacking libmagic1:armhf (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../005-file_1%3a5.44-3_armhf.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../006-gettext-base_0.21-12_armhf.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../007-libuchardet0_0.0.7-1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../008-groff-base_1.22.4-10_armhf.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../009-bsdextrautils_2.38.1-5+b1_armhf.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../010-libpipeline1_1.5.7-1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../011-man-db_2.11.2-2_armhf.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package libbsd0:armhf. Preparing to unpack .../012-libbsd0_0.11.7-2_armhf.deb ... Unpacking libbsd0:armhf (0.11.7-2) ... Selecting previously unselected package libedit2:armhf. Preparing to unpack .../013-libedit2_3.1-20221030-2_armhf.deb ... Unpacking libedit2:armhf (3.1-20221030-2) ... Selecting previously unselected package libcbor0.8:armhf. Preparing to unpack .../014-libcbor0.8_0.8.0-2+b1_armhf.deb ... Unpacking libcbor0.8:armhf (0.8.0-2+b1) ... Selecting previously unselected package libfido2-1:armhf. Preparing to unpack .../015-libfido2-1_1.12.0-2+b1_armhf.deb ... Unpacking libfido2-1:armhf (1.12.0-2+b1) ... Selecting previously unselected package openssh-client. Preparing to unpack .../016-openssh-client_1%3a9.2p1-2_armhf.deb ... Unpacking openssh-client (1:9.2p1-2) ... Selecting previously unselected package m4. Preparing to unpack .../017-m4_1.4.19-3_armhf.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../018-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../019-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../020-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 .../021-autopoint_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package libicu72:armhf. Preparing to unpack .../022-libicu72_72.1-3_armhf.deb ... Unpacking libicu72:armhf (72.1-3) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../023-libxml2_2.9.14+dfsg-1.2_armhf.deb ... Unpacking libxml2:armhf (2.9.14+dfsg-1.2) ... Selecting previously unselected package libarchive13:armhf. Preparing to unpack .../024-libarchive13_3.6.2-1_armhf.deb ... Unpacking libarchive13:armhf (3.6.2-1) ... Selecting previously unselected package libbrotli1:armhf. Preparing to unpack .../025-libbrotli1_1.0.9-2+b6_armhf.deb ... Unpacking libbrotli1:armhf (1.0.9-2+b6) ... Selecting previously unselected package libsasl2-modules-db:armhf. Preparing to unpack .../026-libsasl2-modules-db_2.1.28+dfsg-10_armhf.deb ... Unpacking libsasl2-modules-db:armhf (2.1.28+dfsg-10) ... Selecting previously unselected package libsasl2-2:armhf. Preparing to unpack .../027-libsasl2-2_2.1.28+dfsg-10_armhf.deb ... Unpacking libsasl2-2:armhf (2.1.28+dfsg-10) ... Selecting previously unselected package libldap-2.5-0:armhf. Preparing to unpack .../028-libldap-2.5-0_2.5.13+dfsg-5_armhf.deb ... Unpacking libldap-2.5-0:armhf (2.5.13+dfsg-5) ... Selecting previously unselected package libnghttp2-14:armhf. Preparing to unpack .../029-libnghttp2-14_1.52.0-1_armhf.deb ... Unpacking libnghttp2-14:armhf (1.52.0-1) ... Selecting previously unselected package libpsl5:armhf. Preparing to unpack .../030-libpsl5_0.21.2-1_armhf.deb ... Unpacking libpsl5:armhf (0.21.2-1) ... Selecting previously unselected package librtmp1:armhf. Preparing to unpack .../031-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_armhf.deb ... Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:armhf. Preparing to unpack .../032-libssh2-1_1.10.0-3+b1_armhf.deb ... Unpacking libssh2-1:armhf (1.10.0-3+b1) ... Selecting previously unselected package libcurl4:armhf. Preparing to unpack .../033-libcurl4_7.88.1-10_armhf.deb ... Unpacking libcurl4:armhf (7.88.1-10) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../034-libexpat1_2.5.0-1_armhf.deb ... Unpacking libexpat1:armhf (2.5.0-1) ... Selecting previously unselected package libjsoncpp25:armhf. Preparing to unpack .../035-libjsoncpp25_1.9.5-4_armhf.deb ... Unpacking libjsoncpp25:armhf (1.9.5-4) ... Selecting previously unselected package librhash0:armhf. Preparing to unpack .../036-librhash0_1.4.3-3_armhf.deb ... Unpacking librhash0:armhf (1.4.3-3) ... Selecting previously unselected package libuv1:armhf. Preparing to unpack .../037-libuv1_1.44.2-1_armhf.deb ... Unpacking libuv1:armhf (1.44.2-1) ... Selecting previously unselected package cmake-data. Preparing to unpack .../038-cmake-data_3.25.1-1_all.deb ... Unpacking cmake-data (3.25.1-1) ... Selecting previously unselected package cmake. Preparing to unpack .../039-cmake_3.25.1-1_armhf.deb ... Unpacking cmake (3.25.1-1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../040-libdebhelper-perl_13.11.4_all.deb ... Unpacking libdebhelper-perl (13.11.4) ... Selecting previously unselected package libtool. Preparing to unpack .../041-libtool_2.4.7-5_all.deb ... Unpacking libtool (2.4.7-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../042-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../043-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../044-libsub-override-perl_0.09-4_all.deb ... Unpacking libsub-override-perl (0.09-4) ... 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Setting up libdebhelper-perl (13.11.4) ... Setting up libbrotli1:armhf (1.0.9-2+b6) ... Setting up libsensors-config (1:3.6.0-7.1) ... Setting up libnghttp2-14:armhf (1.52.0-1) ... Setting up libmagic1:armhf (1:5.44-3) ... Setting up libdeflate0:armhf (1.14-1) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up file (1:5.44-3) ... Setting up libpthread-stubs0-dev:armhf (0.4-1) ... Setting up libjbig0:armhf (2.1-6.1) ... Setting up libsasl2-modules-db:armhf (2.1.28+dfsg-10) ... Setting up xtrans-dev (1.4.0-1) ... Setting up autotools-dev (20220109.1) ... Setting up libz3-4:armhf (4.8.12-3.1) ... Setting up libuv1:armhf (1.44.2-1) ... Setting up libmunge2 (0.5.15-2) ... Setting up libjpeg62-turbo:armhf (1:2.1.5-2) ... Setting up libx11-data (2:1.8.4-2) ... Setting up libjpeg62-turbo-dev:armhf (1:2.1.5-2) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libproc2-0:armhf (2:4.0.2-3) ... Setting up libpng16-16:armhf (1.6.39-2) ... 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Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up x11proto-dev (2022.1-1) ... Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libxdmcp6:armhf (1:1.1.2-3) ... Setting up libevent-extra-2.1-7:armhf (2.1.12-stable-8) ... Setting up libxcb1:armhf (1.15-1) ... Setting up gettext (0.21-12) ... Setting up libxcb-xfixes0:armhf (1.15-1) ... Setting up libxau-dev:armhf (1:1.0.9-1) ... Setting up libtool (2.4.7-5) ... Setting up libarchive13:armhf (3.6.2-1) ... Setting up libxcb-render0:armhf (1.15-1) ... Setting up libfftw3-bin (3.3.10-1) ... Setting up fontconfig-config (2.14.1-4) ... Setting up libxcb-glx0:armhf (1.15-1) ... Setting up libwebpdemux2:armhf (1.2.4-0.2) ... Setting up libedit2:armhf (3.1-20221030-2) ... Setting up libjpeg-dev:armhf (1:2.1.5-2) ... Setting up libjbig-dev:armhf (2.1-6.1) ... Setting up libevent-openssl-2.1-7:armhf (2.1.12-stable-8) ... 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Setting up groff-base (1.22.4-10) ... Setting up libxcb-randr0:armhf (1.15-1) ... Setting up libllvm15:armhf (1:15.0.6-4+b1) ... Setting up libcurl4:armhf (7.88.1-10) ... Setting up libx11-6:armhf (2:1.8.4-2) ... Setting up libhwloc-dev:armhf (2.9.0-1) ... Setting up libfontconfig1:armhf (2.14.1-4) ... Setting up libfftw3-dev:armhf (3.3.10-1) ... Setting up libdrm-amdgpu1:armhf (2.4.114-1+b1) ... Setting up libxcb-dri3-0:armhf (1.15-1) ... Setting up libx11-xcb1:armhf (2:1.8.4-2) ... Setting up libibverbs1:armhf (44.0-2) ... Setting up libdrm-nouveau2:armhf (2.4.114-1+b1) ... Setting up libxcb1-dev:armhf (1.15-1) ... Setting up libxrender1:armhf (1:0.9.10-1.1) ... Setting up ibverbs-providers:armhf (44.0-2) ... Setting up libdrm-radeon1:armhf (2.4.114-1+b1) ... Setting up openssh-client (1:9.2p1-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libgl1-mesa-dri:armhf (22.3.6-1+deb12u1) ... Setting up libx11-dev:armhf (2:1.8.4-2) ... Setting up libxext6:armhf (2:1.3.4-1+b1) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:armhf (1.16.0-7) ... Setting up libxxf86vm1:armhf (1:1.1.4-1+b2) ... Setting up libxnvctrl0:armhf (525.85.05-1) ... Setting up libnl-route-3-dev:armhf (3.7.0-0.2+b1) ... Setting up libxfixes3:armhf (1:6.0.0-2) ... Setting up libxinerama1:armhf (2:1.1.4-3) ... Setting up cmake (3.25.1-1) ... Setting up librdmacm1:armhf (44.0-2) ... Setting up libxft2:armhf (2.3.6-1) ... Setting up libglx-mesa0:armhf (22.3.6-1+deb12u1) ... Setting up libglx0:armhf (1.6.0-1) ... Setting up libxcursor1:armhf (1:1.2.1-1) ... Setting up debhelper (13.11.4) ... Setting up libibverbs-dev:armhf (44.0-2) ... Setting up libhwloc-plugins:armhf (2.9.0-1) ... Setting up libgl1:armhf (1.6.0-1) ... Setting up libfabric1:armhf (1.17.0-3) ... Setting up libpmix2:armhf (4.2.2-1+b1) ... Setting up libopenmpi3:armhf (4.1.4-3+b1) ... Setting up libfltk1.3:armhf (1.3.8-5) ... Setting up libfltk-gl1.3:armhf (1.3.8-5) ... Setting up libfltk-cairo1.3:armhf (1.3.8-5) ... Setting up libfltk-images1.3:armhf (1.3.8-5) ... Setting up libfltk-forms1.3:armhf (1.3.8-5) ... Setting up libpmix-dev:armhf (4.2.2-1+b1) ... Setting up openmpi-bin (4.1.4-3+b1) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up libfltk1.3-dev:armhf (1.3.8-5) ... Setting up fluid (1.3.8-5) ... Setting up libopenmpi-dev:armhf (4.1.4-3+b1) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/openmpi/include to provide /usr/include/arm-linux-gnueabihf/mpi (mpi-arm-linux-gnueabihf) in auto mode Processing triggers for libc-bin (2.36-9) ... 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 Reading package lists... Building dependency tree... Reading state information... usrmerge is already the newest version (35). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: user script /srv/workspace/pbuilder/29454/tmp/hooks/A99_set_merged_usr starting Re-configuring usrmerge... removed '/etc/unsupported-skip-usrmerge-conversion' The system has been successfully converted. I: user script /srv/workspace/pbuilder/29454/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/relion-3.1.3/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../relion_3.1.3-3_source.changes dpkg-buildpackage: info: source package relion dpkg-buildpackage: info: source version 3.1.3-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean debian/rules override_dh_clean make[1]: Entering directory '/build/relion-3.1.3' dh_clean rm -rf build make[1]: Leaving directory '/build/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/relion-3.1.3' mkdir /build/relion-3.1.3/build cd /build/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/relion-3.1.3 CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. CMake Warning (dev) at /usr/share/cmake-3.25/Modules/CMakeDetermineCompilerId.cmake:93 (if): Policy CMP0054 is not set: Only interpret if() arguments as variables or keywords when unquoted. Run "cmake --help-policy CMP0054" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Quoted variables like "CUDA" will no longer be dereferenced when the policy is set to NEW. Since the policy is not set the OLD behavior will be used. Call Stack (most recent call first): /usr/share/cmake-3.25/Modules/CMakeDetermineCCompiler.cmake:123 (CMAKE_DETERMINE_COMPILER_ID) CMakeLists.txt:6 (project) This warning is for project developers. Use -Wno-dev to suppress it. -- The C compiler identification is GNU 12.2.0 -- The CXX compiler identification is GNU 12.2.0 -- Detecting C compiler ABI info CMake Warning (dev) at /usr/share/cmake-3.25/Modules/CMakeDetermineCompilerABI.cmake:29 (if): Policy CMP0054 is not set: Only interpret if() arguments as variables or keywords when unquoted. Run "cmake --help-policy CMP0054" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Quoted variables like "CUDA" will no longer be dereferenced when the policy is set to NEW. Since the policy is not set the OLD behavior will be used. Call Stack (most recent call first): /usr/share/cmake-3.25/Modules/CMakeTestCCompiler.cmake:26 (CMAKE_DETERMINE_COMPILER_ABI) CMakeLists.txt:6 (project) This warning is for project developers. Use -Wno-dev to suppress it. -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- BUILD TYPE set to the default type: 'Release' -- Setting fallback CUDA_ARCH=35 -- ALLOW_CTF_IN_SAGD enabled - This build of RELION allows modulation of particle images by a contrast transfer function inside stochastic average gradient descent, as specified in Claim 1 of patent US10,282,513B2 -- Setting cpu precision to double -- Setting accelerated code precision to single -- Using non-cuda compilation.... -- Found MPI_C: /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") -- MPI_INCLUDE_PATH : /usr/lib/arm-linux-gnueabihf/openmpi/include;/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -- MPI_LIBRARIES : /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so;/usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -- MPI_CXX_INCLUDE_PATH : /usr/lib/arm-linux-gnueabihf/openmpi/include;/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -- MPI_CXX_LIBRARIES : /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so;/usr/lib/arm-linux-gnueabihf/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/arm-linux-gnueabihf/libX11.so -- Looking for XOpenDisplay in /usr/lib/arm-linux-gnueabihf/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/arm-linux-gnueabihf/libX11.so;/usr/lib/arm-linux-gnueabihf/libm.so -- Found FFTW -- FFTW_PATH: /usr/include -- FFTW_INCLUDES: /usr/include -- FFTW_LIBRARIES: /usr/lib/arm-linux-gnueabihf/libfftw3f.so;/usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for sincos -- Looking for sincos - found -- Looking for __sincos -- Looking for __sincos - not found -- Found TIFF: /usr/lib/arm-linux-gnueabihf/libtiff.so (found version "4.5.0") -- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.13") -- Could NOT find PNG (missing: PNG_LIBRARY PNG_PNG_INCLUDE_DIR) BUILD_SHARED_LIBS = OFF -- Building static libs (larger build size and binaries) Running apps/CMakeLists.txt... -- CMAKE_BINARY_DIR:/build/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 -- Generating done CMake Warning: Manually-specified variables were not used by the project: DoublePrec_GPU -- Build files have been written to: /build/relion-3.1.3/build make[1]: Leaving directory '/build/relion-3.1.3' debian/rules override_dh_auto_build make[1]: Entering directory '/build/relion-3.1.3' /usr/bin/make -j4 -C build make[2]: Entering directory '/build/relion-3.1.3/build' /usr/bin/cmake -S/build/relion-3.1.3 -B/build/relion-3.1.3/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/relion-3.1.3/build/CMakeFiles /build/relion-3.1.3/build//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/relion-3.1.3/build' /usr/bin/make -f CMakeFiles/copy_scripts.dir/build.make CMakeFiles/copy_scripts.dir/depend /usr/bin/make -f src/apps/CMakeFiles/relion_lib.dir/build.make src/apps/CMakeFiles/relion_lib.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3 /build/relion-3.1.3/build /build/relion-3.1.3/build /build/relion-3.1.3/build/CMakeFiles/copy_scripts.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/relion_lib.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' /usr/bin/cmake -E copy /build/relion-3.1.3/scripts/star_printtable /build/relion-3.1.3/build/bin/relion_star_printtable make[4]: Leaving directory '/build/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/relion-3.1.3/build' /usr/bin/cmake -E copy /build/relion-3.1.3/scripts/star_plottable /build/relion-3.1.3/build/bin/relion_star_plottable [ 0%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/__/macros.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/__/macros.cpp.o -MF CMakeFiles/relion_lib.dir/__/__/macros.cpp.o.d -o CMakeFiles/relion_lib.dir/__/__/macros.cpp.o -c /build/relion-3.1.3/build/macros.cpp [ 1%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/CPlot2D.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/CPlot2D.cpp.o -MF CMakeFiles/relion_lib.dir/__/CPlot2D.cpp.o.d -o CMakeFiles/relion_lib.dir/__/CPlot2D.cpp.o -c /build/relion-3.1.3/src/CPlot2D.cpp /usr/bin/cmake -E copy /build/relion-3.1.3/scripts/star_loopheader /build/relion-3.1.3/build/bin/relion_star_loopheader [ 1%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/args.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/args.cpp.o -MF CMakeFiles/relion_lib.dir/__/args.cpp.o.d -o CMakeFiles/relion_lib.dir/__/args.cpp.o -c /build/relion-3.1.3/src/args.cpp /usr/bin/cmake -E copy /build/relion-3.1.3/scripts/star_datablock_stack /build/relion-3.1.3/build/bin/relion_star_datablock_stack /usr/bin/cmake -E copy /build/relion-3.1.3/scripts/star_datablock_singlefiles /build/relion-3.1.3/build/bin/relion_star_datablock_singlefiles /usr/bin/cmake -E copy /build/relion-3.1.3/scripts/star_datablock_ctfdat /build/relion-3.1.3/build/bin/relion_star_datablock_ctfdat /usr/bin/cmake -E copy /build/relion-3.1.3/scripts/qsub.csh /build/relion-3.1.3/build/bin/relion_qsub.csh make[4]: Leaving directory '/build/relion-3.1.3/build' [ 1%] Built target copy_scripts [ 1%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/assembly.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/assembly.cpp.o -MF CMakeFiles/relion_lib.dir/__/assembly.cpp.o.d -o CMakeFiles/relion_lib.dir/__/assembly.cpp.o -c /build/relion-3.1.3/src/assembly.cpp [ 2%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/autopicker.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/autopicker.cpp.o -MF CMakeFiles/relion_lib.dir/__/autopicker.cpp.o.d -o CMakeFiles/relion_lib.dir/__/autopicker.cpp.o -c /build/relion-3.1.3/src/autopicker.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/autopicker.h:10, from /build/relion-3.1.3/src/autopicker.cpp:20: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /usr/include/c++/12/vector:70, from /build/relion-3.1.3/src/assembly.h:15, from /build/relion-3.1.3/src/assembly.cpp:8: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Atom&}; _Tp = Atom; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Atom; _Alloc = std::allocator]', inlined from 'long int Residue::addAtom(std::string, double, double, double, double, double)' at /build/relion-3.1.3/src/assembly.cpp:36:17: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:63: /usr/include/c++/12/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*]': /usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*; _Tp = Atom]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = Atom; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1617:35, inlined from 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator]' at /usr/include/c++/12/bits/vector.tcc:232:44: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from /build/relion-3.1.3/src/CPlot2D.h:30, from /build/relion-3.1.3/src/CPlot2D.cpp:27: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataPoint&}; _Tp = CDataPoint; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataSet&}; _Tp = CDataSet; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*; _Tp = Atom]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:601:31, inlined from 'Residue::Residue(const Residue&)' at /build/relion-3.1.3/src/assembly.h:73:7, inlined from 'void std::_Construct(_Tp*, _Args&& ...) [with _Tp = Residue; _Args = {const Residue&}]' at /usr/include/c++/12/bits/stl_construct.h:119:7, inlined from '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Residue*]' at /usr/include/c++/12/bits/stl_uninitialized.h:120:21, inlined from 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Residue*; bool _TrivialValueTypes = false]' at /usr/include/c++/12/bits/stl_uninitialized.h:137:32, inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Residue*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Residue*; _Tp = Residue]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Residue; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:601:31, inlined from 'Molecule::Molecule(const Molecule&)' at /build/relion-3.1.3/src/assembly.h:118:7, inlined from 'void std::_Construct(_Tp*, _Args&& ...) [with _Tp = Molecule; _Args = {const Molecule&}]' at /usr/include/c++/12/bits/stl_construct.h:119:7, inlined from '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = const Molecule*; _ForwardIterator = Molecule*]' at /usr/include/c++/12/bits/stl_uninitialized.h:120:21: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*; _Tp = Atom]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:601:31, inlined from 'Residue::Residue(const Residue&)' at /build/relion-3.1.3/src/assembly.h:73:7, inlined from 'void std::_Construct(_Tp*, _Args&& ...) [with _Tp = Residue; _Args = {const Residue&}]' at /usr/include/c++/12/bits/stl_construct.h:119:7, inlined from '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = const Residue*; _ForwardIterator = Residue*]' at /usr/include/c++/12/bits/stl_uninitialized.h:120:21: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*; _Tp = Atom]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:601:31, inlined from 'Residue::Residue(const Residue&)' at /build/relion-3.1.3/src/assembly.h:73:7, inlined from 'void std::_Construct(_Tp*, _Args&& ...) [with _Tp = Residue; _Args = {const Residue&}]' at /usr/include/c++/12/bits/stl_construct.h:119:7, inlined from '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Residue*]' at /usr/include/c++/12/bits/stl_uninitialized.h:120:21: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*; _Tp = Atom]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:601:31, inlined from 'Residue::Residue(const Residue&)' at /build/relion-3.1.3/src/assembly.h:73:7, inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = Residue; _Args = {const Residue&}; _Tp = Residue]' at /usr/include/c++/12/bits/new_allocator.h:175:4, inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = Residue; _Args = {const Residue&}; _Tp = Residue]' at /usr/include/c++/12/bits/alloc_traits.h:516:17, inlined from 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Residue&}; _Tp = Residue; _Alloc = std::allocator]' at /usr/include/c++/12/bits/vector.tcc:462:28: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator]', inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /build/relion-3.1.3/src/CPlot2D.h:168:33, inlined from 'void CPlot2D::AddDataSet(std::vector, std::vector)' at /build/relion-3.1.3/src/CPlot2D.cpp:503:29: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator]', inlined from 'void CPlot2D::AddDataSet(std::vector, std::vector)' at /build/relion-3.1.3/src/CPlot2D.cpp:505:25: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ [ 2%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o -c /build/relion-3.1.3/src/autopicker_mpi.cpp In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*; _Tp = Atom]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:601:31, inlined from 'Residue::Residue(const Residue&)' at /build/relion-3.1.3/src/assembly.h:73:7, inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = Residue; _Args = {const Residue&}; _Tp = Residue]' at /usr/include/c++/12/bits/new_allocator.h:175:4, inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = Residue; _Args = {const Residue&}; _Tp = Residue]' at /usr/include/c++/12/bits/alloc_traits.h:516:17, inlined from 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Residue; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1281:30, inlined from 'void Assembly::sortResidues()' at /build/relion-3.1.3/src/assembly.cpp:487:26: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*; _Tp = Atom]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:601:31, inlined from 'Residue::Residue(const Residue&)' at /build/relion-3.1.3/src/assembly.h:73:7, inlined from 'void std::_Construct(_Tp*, _Args&& ...) [with _Tp = Residue; _Args = {Residue&}]' at /usr/include/c++/12/bits/stl_construct.h:119:7, inlined from '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = Residue*; _ForwardIterator = Residue*]' at /usr/include/c++/12/bits/stl_uninitialized.h:120:21, inlined from 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = Residue*; _ForwardIterator = Residue*; bool _TrivialValueTypes = false]' at /usr/include/c++/12/bits/stl_uninitialized.h:137:32, inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = Residue*; _ForwardIterator = Residue*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = Residue*; _ForwardIterator = Residue*; _Tp = Residue]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = Residue; _Alloc = std::allocator]' at /usr/include/c++/12/bits/vector.tcc:251:35, inlined from 'void Assembly::sortResidues()' at /build/relion-3.1.3/src/assembly.cpp:489:30: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator]', inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /build/relion-3.1.3/src/CPlot2D.h:168:33, inlined from 'void CPlot2D::AddDataSet(int, double*, double*)' at /build/relion-3.1.3/src/CPlot2D.cpp:478:29: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator]', inlined from 'void CPlot2D::AddDataSet(int, double*, double*)' at /build/relion-3.1.3/src/CPlot2D.cpp:480:25: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator]', inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /build/relion-3.1.3/src/CPlot2D.h:168:33, inlined from 'void CPlot2D::AddDataSet(std::vector)' at /build/relion-3.1.3/src/CPlot2D.cpp:523:29: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator]', inlined from 'void CPlot2D::AddDataSet(std::vector)' at /build/relion-3.1.3/src/CPlot2D.cpp:525:25: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*; _Tp = Atom]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:601:31, inlined from 'Residue::Residue(const Residue&)' at /build/relion-3.1.3/src/assembly.h:73:7, inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = Residue; _Args = {const Residue&}; _Tp = Residue]' at /usr/include/c++/12/bits/new_allocator.h:175:4, inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = Residue; _Args = {const Residue&}; _Tp = Residue]' at /usr/include/c++/12/bits/alloc_traits.h:516:17, inlined from 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Residue; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1281:30, inlined from 'long int Molecule::addResidue(Residue&)' at /build/relion-3.1.3/src/assembly.cpp:57:20: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*; _Tp = Atom]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:601:31, inlined from 'Residue::Residue(const Residue&)' at /build/relion-3.1.3/src/assembly.h:73:7, inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = Residue; _Args = {const Residue&}; _Tp = Residue]' at /usr/include/c++/12/bits/new_allocator.h:175:4, inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = Residue; _Args = {const Residue&}; _Tp = Residue]' at /usr/include/c++/12/bits/alloc_traits.h:516:17, inlined from 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Residue; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1281:30, inlined from 'long int Molecule::addResidue(std::string, int)' at /build/relion-3.1.3/src/assembly.cpp:65:20: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/relion-3.1.3/src/CPlot2D.cpp: In member function 'void CPlot2D::ComputeLabelTickSpacing(double, double, double*, double*, double*, int, std::string)': /build/relion-3.1.3/src/CPlot2D.cpp:743:41: warning: '%d' directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] 743 | sprintf(m_cYAxisLabelFormat,"%%.%df",nfrac); | ^~ /build/relion-3.1.3/src/CPlot2D.cpp:743:37: note: directive argument in the range [0, 2147483647] 743 | sprintf(m_cYAxisLabelFormat,"%%.%df",nfrac); | ^~~~~~~~ In file included from /usr/include/stdio.h:906, from /usr/include/c++/12/cstdio:42, from /usr/include/c++/12/ext/string_conversions.h:43, from /usr/include/c++/12/bits/basic_string.h:3960, from /usr/include/c++/12/string:53, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/relion-3.1.3/src/CPlot2D.cpp:21: In function 'int sprintf(char*, const char*, ...)', inlined from 'void CPlot2D::ComputeLabelTickSpacing(double, double, double*, double*, double*, int, std::string)' at /build/relion-3.1.3/src/CPlot2D.cpp:743:16: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 14 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/relion-3.1.3/src/CPlot2D.cpp: In member function 'void CPlot2D::ComputeLabelTickSpacing(double, double, double*, double*, double*, int, std::string)': /build/relion-3.1.3/src/CPlot2D.cpp:733:41: warning: '%d' directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] 733 | sprintf(m_cXAxisLabelFormat,"%%.%df",nfrac); | ^~ /build/relion-3.1.3/src/CPlot2D.cpp:733:37: note: directive argument in the range [0, 2147483647] 733 | sprintf(m_cXAxisLabelFormat,"%%.%df",nfrac); | ^~~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'void CPlot2D::ComputeLabelTickSpacing(double, double, double*, double*, double*, int, std::string)' at /build/relion-3.1.3/src/CPlot2D.cpp:733:16: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 14 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*; _Tp = Atom]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:601:31, inlined from 'Residue::Residue(const Residue&)' at /build/relion-3.1.3/src/assembly.h:73:7, inlined from 'void std::_Construct(_Tp*, _Args&& ...) [with _Tp = Residue; _Args = {const Residue&}]' at /usr/include/c++/12/bits/stl_construct.h:119:7, inlined from '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Residue*]' at /usr/include/c++/12/bits/stl_uninitialized.h:120:21, inlined from 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Residue*; bool _TrivialValueTypes = false]' at /usr/include/c++/12/bits/stl_uninitialized.h:137:32, inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Residue*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Residue*; _Tp = Residue]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Residue; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:601:31, inlined from 'Molecule::Molecule(const Molecule&)' at /build/relion-3.1.3/src/assembly.h:118:7, inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = Molecule; _Args = {const Molecule&}; _Tp = Molecule]' at /usr/include/c++/12/bits/new_allocator.h:175:4, inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = Molecule; _Args = {const Molecule&}; _Tp = Molecule]' at /usr/include/c++/12/bits/alloc_traits.h:516:17, inlined from 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Molecule&}; _Tp = Molecule; _Alloc = std::allocator]' at /usr/include/c++/12/bits/vector.tcc:462:28: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*; _Tp = Atom]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:601:31, inlined from 'Residue::Residue(const Residue&)' at /build/relion-3.1.3/src/assembly.h:73:7, inlined from 'void std::_Construct(_Tp*, _Args&& ...) [with _Tp = Residue; _Args = {const Residue&}]' at /usr/include/c++/12/bits/stl_construct.h:119:7, inlined from '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Residue*]' at /usr/include/c++/12/bits/stl_uninitialized.h:120:21, inlined from 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Residue*; bool _TrivialValueTypes = false]' at /usr/include/c++/12/bits/stl_uninitialized.h:137:32, inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Residue*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Residue*; _Tp = Residue]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Residue; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:601:31, inlined from 'Molecule::Molecule(const Molecule&)' at /build/relion-3.1.3/src/assembly.h:118:7, inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = Molecule; _Args = {const Molecule&}; _Tp = Molecule]' at /usr/include/c++/12/bits/new_allocator.h:175:4, inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = Molecule; _Args = {const Molecule&}; _Tp = Molecule]' at /usr/include/c++/12/bits/alloc_traits.h:516:17, inlined from 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Molecule; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1281:30, inlined from 'long int Assembly::addMolecule(std::string, std::string)' at /build/relion-3.1.3/src/assembly.cpp:131:21: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/autopicker.h:10, from /build/relion-3.1.3/src/autopicker_mpi.h:12, from /build/relion-3.1.3/src/autopicker_mpi.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*; _Tp = Atom]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:601:31, inlined from 'Residue::Residue(const Residue&)' at /build/relion-3.1.3/src/assembly.h:73:7, inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = Residue; _Args = {const Residue&}; _Tp = Residue]' at /usr/include/c++/12/bits/new_allocator.h:175:4, inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = Residue; _Args = {const Residue&}; _Tp = Residue]' at /usr/include/c++/12/bits/alloc_traits.h:516:17, inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, const value_type&) [with _Tp = Residue; _Alloc = std::allocator]' at /usr/include/c++/12/bits/vector.tcc:145:30: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*; _Tp = Atom]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:601:31, inlined from 'Residue::Residue(const Residue&)' at /build/relion-3.1.3/src/assembly.h:73:7, inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = Residue; _Args = {const Residue&}; _Tp = Residue]' at /usr/include/c++/12/bits/new_allocator.h:175:4, inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = Residue; _Args = {const Residue&}; _Tp = Residue]' at /usr/include/c++/12/bits/alloc_traits.h:516:17, inlined from 'std::vector<_Tp, _Alloc>::_Temporary_value::_Temporary_value(std::vector<_Tp, _Alloc>*, _Args&& ...) [with _Args = {const Residue&}; _Tp = Residue; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1830:30, inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, const value_type&) [with _Tp = Residue; _Alloc = std::allocator]' at /usr/include/c++/12/bits/vector.tcc:156:23: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*; _Tp = Atom]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:601:31, inlined from 'Residue::Residue(const Residue&)' at /build/relion-3.1.3/src/assembly.h:73:7, inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = Residue; _Args = {Residue}; _Tp = Residue]' at /usr/include/c++/12/bits/new_allocator.h:175:4, inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = Residue; _Args = {Residue}; _Tp = Residue]' at /usr/include/c++/12/bits/alloc_traits.h:516:17, inlined from 'void std::vector<_Tp, _Alloc>::_M_insert_aux(iterator, _Arg&&) [with _Arg = Residue; _Tp = Residue; _Alloc = std::allocator]' at /usr/include/c++/12/bits/vector.tcc:417:31, inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, const value_type&) [with _Tp = Residue; _Alloc = std::allocator]' at /usr/include/c++/12/bits/vector.tcc:157:19: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*; _Tp = Atom]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:601:31, inlined from 'Residue::Residue(const Residue&)' at /build/relion-3.1.3/src/assembly.h:73:7, inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = Residue; _Args = {const Residue&}; _Tp = Residue]' at /usr/include/c++/12/bits/new_allocator.h:175:4, inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = Residue; _Args = {const Residue&}; _Tp = Residue]' at /usr/include/c++/12/bits/alloc_traits.h:516:17, inlined from 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Residue; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1281:30, inlined from 'long int Molecule::addResidue(Residue&)' at /build/relion-3.1.3/src/assembly.cpp:57:20, inlined from 'void Molecule::insertResidues(Molecule, int, int)' at /build/relion-3.1.3/src/assembly.cpp:116:14: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*; _Tp = Atom]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:601:31, inlined from 'Residue::Residue(const Residue&)' at /build/relion-3.1.3/src/assembly.h:73:7, inlined from 'void std::_Construct(_Tp*, _Args&& ...) [with _Tp = Residue; _Args = {const Residue&}]' at /usr/include/c++/12/bits/stl_construct.h:119:7, inlined from '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Residue*]' at /usr/include/c++/12/bits/stl_uninitialized.h:120:21, inlined from 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Residue*; bool _TrivialValueTypes = false]' at /usr/include/c++/12/bits/stl_uninitialized.h:137:32, inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Residue*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Residue*; _Tp = Residue]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Residue; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:601:31, inlined from 'Molecule::Molecule(const Molecule&)' at /build/relion-3.1.3/src/assembly.h:118:7, inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = Molecule; _Args = {const Molecule&}; _Tp = Molecule]' at /usr/include/c++/12/bits/new_allocator.h:175:4, inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = Molecule; _Args = {const Molecule&}; _Tp = Molecule]' at /usr/include/c++/12/bits/alloc_traits.h:516:17, inlined from 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Molecule; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1281:30, inlined from 'long int Assembly::addMolecule(Molecule&)' at /build/relion-3.1.3/src/assembly.cpp:162:21: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algo.h:60, from /usr/include/c++/12/algorithm:61, from /build/relion-3.1.3/src/funcs.h:55, from /build/relion-3.1.3/src/image.h:58: /usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = ccfPixel; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ [ 3%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/backprojector.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/backprojector.cpp.o -MF CMakeFiles/relion_lib.dir/__/backprojector.cpp.o.d -o CMakeFiles/relion_lib.dir/__/backprojector.cpp.o -c /build/relion-3.1.3/src/backprojector.cpp /usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1802 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1908 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 3%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/complex.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/complex.cpp.o -MF CMakeFiles/relion_lib.dir/__/complex.cpp.o.d -o CMakeFiles/relion_lib.dir/__/complex.cpp.o -c /build/relion-3.1.3/src/complex.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/projector.h:25, from /build/relion-3.1.3/src/backprojector.h:33, from /build/relion-3.1.3/src/backprojector.cpp:27: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 3%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctf.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/ctf.cpp.o -MF CMakeFiles/relion_lib.dir/__/ctf.cpp.o.d -o CMakeFiles/relion_lib.dir/__/ctf.cpp.o -c /build/relion-3.1.3/src/ctf.cpp /usr/include/c++/12/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_less_iter]': /usr/include/c++/12/bits/stl_algo.h:1782:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1782 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ [ 4%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner.cpp.o -MF CMakeFiles/relion_lib.dir/__/ctffind_runner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/ctffind_runner.cpp.o -c /build/relion-3.1.3/src/ctffind_runner.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-3.1.3/src/ctf.h:50, from /build/relion-3.1.3/src/ctf.cpp:45: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-3.1.3/src/ctffind_runner.cpp:20: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 4%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner_mpi.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/ctffind_runner_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/ctffind_runner_mpi.cpp.o -c /build/relion-3.1.3/src/ctffind_runner_mpi.cpp In file included from /usr/include/c++/12/vector:70, from /build/relion-3.1.3/src/funcs.h:56: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const AmyloidCoord&}; _Tp = AmyloidCoord; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = AmyloidCoord; _Alloc = std::allocator]', inlined from 'std::vector AutoPicker::findNextCandidateCoordinates(AmyloidCoord&, std::vector&, double, double, int, float, MultidimArray&, MultidimArray&)' at /build/relion-3.1.3/src/autopicker.cpp:1092:27: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = AmyloidCoord; _Alloc = std::allocator]', inlined from 'void AutoPicker::pickAmyloids(MultidimArray&, MultidimArray&, MultidimArray&, MultidimArray&, double, double, FileName&, FileName&, double, int, float)' at /build/relion-3.1.3/src/autopicker.cpp:1294:34: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = AmyloidCoord; _Alloc = std::allocator]', inlined from 'void AutoPicker::pickAmyloids(MultidimArray&, MultidimArray&, MultidimArray&, MultidimArray&, double, double, FileName&, FileName&, double, int, float)' at /build/relion-3.1.3/src/autopicker.cpp:1321:18: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, const value_type&) [with _Tp = AmyloidCoord; _Alloc = std::allocator]', inlined from 'void AutoPicker::pickAmyloids(MultidimArray&, MultidimArray&, MultidimArray&, MultidimArray&, double, double, FileName&, FileName&, double, int, float)' at /build/relion-3.1.3/src/autopicker.cpp:1338:18: /usr/include/c++/12/bits/vector.tcc:164:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 164 | _M_realloc_insert(begin() + (__position - cbegin()), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = AmyloidCoord; _Alloc = std::allocator]', inlined from 'void AutoPicker::pickAmyloids(MultidimArray&, MultidimArray&, MultidimArray&, MultidimArray&, double, double, FileName&, FileName&, double, int, float)' at /build/relion-3.1.3/src/autopicker.cpp:1350:21: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-3.1.3/src/ctffind_runner_mpi.h:25, from /build/relion-3.1.3/src/ctffind_runner_mpi.cpp:20: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const ccfPeak&}; _Tp = ccfPeak; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ccfPeak; _Alloc = std::allocator]': /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Peak&}; _Tp = Peak; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Peak; _Alloc = std::allocator]', inlined from 'void AutoPicker::prunePeakClusters(std::vector&, int, float)' at /build/relion-3.1.3/src/autopicker.cpp:3616:20: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Peak; _Alloc = std::allocator]', inlined from 'void AutoPicker::prunePeakClusters(std::vector&, int, float)' at /build/relion-3.1.3/src/autopicker.cpp:3629:23: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Peak; _Alloc = std::allocator]', inlined from 'void AutoPicker::prunePeakClusters(std::vector&, int, float)' at /build/relion-3.1.3/src/autopicker.cpp:3654:26: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Peak; _Alloc = std::allocator]', inlined from 'void AutoPicker::removeTooCloselyNeighbouringPeaks(std::vector&, int, float)' at /build/relion-3.1.3/src/autopicker.cpp:3698:26: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Peak; _Alloc = std::allocator]', inlined from 'void AutoPicker::peakSearch(const MultidimArray&, const MultidimArray&, const MultidimArray&, const MultidimArray&, int, int, std::vector&, float)' at /build/relion-3.1.3/src/autopicker.cpp:3599:20: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ [ 4%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/error.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/error.cpp.o -MF CMakeFiles/relion_lib.dir/__/error.cpp.o.d -o CMakeFiles/relion_lib.dir/__/error.cpp.o -c /build/relion-3.1.3/src/error.cpp /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {ccfPixel}; _Tp = ccfPixel; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 [ 5%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/euler.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/euler.cpp.o -MF CMakeFiles/relion_lib.dir/__/euler.cpp.o.d -o CMakeFiles/relion_lib.dir/__/euler.cpp.o -c /build/relion-3.1.3/src/euler.cpp [ 5%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/exp_model.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/exp_model.cpp.o -MF CMakeFiles/relion_lib.dir/__/exp_model.cpp.o.d -o CMakeFiles/relion_lib.dir/__/exp_model.cpp.o -c /build/relion-3.1.3/src/exp_model.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/exp_model.h:24, from /build/relion-3.1.3/src/exp_model.cpp:20: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1802 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/12/vector:63: /usr/include/c++/12/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ccfPeak*]': /usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 [ 6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/fftw.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/fftw.cpp.o -MF CMakeFiles/relion_lib.dir/__/fftw.cpp.o.d -o CMakeFiles/relion_lib.dir/__/fftw.cpp.o -c /build/relion-3.1.3/src/fftw.cpp [ 6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/filename.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/filename.cpp.o -MF CMakeFiles/relion_lib.dir/__/filename.cpp.o.d -o CMakeFiles/relion_lib.dir/__/filename.cpp.o -c /build/relion-3.1.3/src/filename.cpp In file included from /usr/include/c++/12/vector:70, from /build/relion-3.1.3/src/funcs.h:56, from /build/relion-3.1.3/src/multidim_array.h:52, from /build/relion-3.1.3/src/fftw.h:50, from /build/relion-3.1.3/src/fftw.cpp:47: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataPoint&}; _Tp = CDataPoint; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataSet&}; _Tp = CDataSet; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator]', inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /build/relion-3.1.3/src/CPlot2D.h:168:33, inlined from 'void helicalLayerLineProfile(const MultidimArray&, std::string, std::string)' at /build/relion-3.1.3/src/fftw.cpp:1725:27: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator]', inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /build/relion-3.1.3/src/CPlot2D.h:168:33, inlined from 'void helicalLayerLineProfile(const MultidimArray&, std::string, std::string)' at /build/relion-3.1.3/src/fftw.cpp:1726:27: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator]', inlined from 'void CPlot2D::AddDataSet(CDataSet)' at /build/relion-3.1.3/src/CPlot2D.h:1198:26, inlined from 'void helicalLayerLineProfile(const MultidimArray&, std::string, std::string)' at /build/relion-3.1.3/src/fftw.cpp:1741:20: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator]', inlined from 'void CPlot2D::AddDataSet(CDataSet)' at /build/relion-3.1.3/src/CPlot2D.h:1198:26, inlined from 'void helicalLayerLineProfile(const MultidimArray&, std::string, std::string)' at /build/relion-3.1.3/src/fftw.cpp:1742:20: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void AutoPicker::initialise()' at /build/relion-3.1.3/src/autopicker.cpp:319:23: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void AutoPicker::initialise()' at /build/relion-3.1.3/src/autopicker.cpp:320:22: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void AutoPicker::initialise()' at /build/relion-3.1.3/src/autopicker.cpp:321:22: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void AutoPicker::initialise()' at /build/relion-3.1.3/src/autopicker.cpp:322:22: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void AutoPicker::initialise()' at /build/relion-3.1.3/src/autopicker.cpp:324:23: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/flex_analyser.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/flex_analyser.cpp.o -MF CMakeFiles/relion_lib.dir/__/flex_analyser.cpp.o.d -o CMakeFiles/relion_lib.dir/__/flex_analyser.cpp.o -c /build/relion-3.1.3/src/flex_analyser.cpp /usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = ccfPeak; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/exp_model.h:24, from /build/relion-3.1.3/src/flex_analyser.h:24, from /build/relion-3.1.3/src/flex_analyser.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/12/bits/stl_algo.h:1625:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1625 | __heap_select(_RandomAccessIterator __first, | ^~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1625:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h:1625:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1908 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void std::__partial_sort(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1916:27: /usr/include/c++/12/bits/stl_algo.h:1900:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1900 | std::__heap_select(__first, __middle, __last, __comp); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {ccfPixel}; _Tp = ccfPixel; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = ccfPixel; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void AutoPicker::pickCCFPeaks(const MultidimArray&, const MultidimArray&, const MultidimArray&, const MultidimArray&, double, int, double, std::vector&, MultidimArray&, int, float)' at /build/relion-3.1.3/src/autopicker.cpp:1526:29: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, inlined from 'void AutoPicker::pickCCFPeaks(const MultidimArray&, const MultidimArray&, const MultidimArray&, const MultidimArray&, double, int, double, std::vector&, MultidimArray&, int, float)' at /build/relion-3.1.3/src/autopicker.cpp:1530:11: /usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1937 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1938 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1939 | __comp); | ~~~~~~~ In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1940:31, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, inlined from 'void AutoPicker::pickCCFPeaks(const MultidimArray&, const MultidimArray&, const MultidimArray&, const MultidimArray&, double, int, double, std::vector&, MultidimArray&, int, float)' at /build/relion-3.1.3/src/autopicker.cpp:1530:11: /usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {ccfPixel}; _Tp = ccfPixel; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = ccfPixel; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void AutoPicker::pickCCFPeaks(const MultidimArray&, const MultidimArray&, const MultidimArray&, const MultidimArray&, double, int, double, std::vector&, MultidimArray&, int, float)' at /build/relion-3.1.3/src/autopicker.cpp:1624:44: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ccfPeak; _Alloc = std::allocator]', inlined from 'void AutoPicker::pickCCFPeaks(const MultidimArray&, const MultidimArray&, const MultidimArray&, const MultidimArray&, double, int, double, std::vector&, MultidimArray&, int, float)' at /build/relion-3.1.3/src/autopicker.cpp:1675:27: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, inlined from 'void AutoPicker::pickCCFPeaks(const MultidimArray&, const MultidimArray&, const MultidimArray&, const MultidimArray&, double, int, double, std::vector&, MultidimArray&, int, float)' at /build/relion-3.1.3/src/autopicker.cpp:1680:11: /usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1937 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1938 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1939 | __comp); | ~~~~~~~ In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1940:31, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, inlined from 'void AutoPicker::pickCCFPeaks(const MultidimArray&, const MultidimArray&, const MultidimArray&, const MultidimArray&, double, int, double, std::vector&, MultidimArray&, int, float)' at /build/relion-3.1.3/src/autopicker.cpp:1680:11: /usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ccfPeak; _Alloc = std::allocator]', inlined from 'void AutoPicker::pickCCFPeaks(const MultidimArray&, const MultidimArray&, const MultidimArray&, const MultidimArray&, double, int, double, std::vector&, MultidimArray&, int, float)' at /build/relion-3.1.3/src/autopicker.cpp:1738:31: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ccfPeak*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ccfPeak*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ccfPeak*; _Tp = ccfPeak]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = ccfPeak; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1617:35, inlined from 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = ccfPeak; _Alloc = std::allocator]' at /usr/include/c++/12/bits/vector.tcc:232:44, inlined from 'void AutoPicker::pickCCFPeaks(const MultidimArray&, const MultidimArray&, const MultidimArray&, const MultidimArray&, double, int, double, std::vector&, MultidimArray&, int, float)' at /build/relion-3.1.3/src/autopicker.cpp:1741:18: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 7%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/funcs.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/funcs.cpp.o -MF CMakeFiles/relion_lib.dir/__/funcs.cpp.o.d -o CMakeFiles/relion_lib.dir/__/funcs.cpp.o -c /build/relion-3.1.3/src/funcs.cpp In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, inlined from 'void AutoPicker::extractHelicalTubes(std::vector&, std::vector >&, std::vector >&, std::vector >&, double, double, double, double, float)' at /build/relion-3.1.3/src/autopicker.cpp:1809:11: /usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1937 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1938 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1939 | __comp); | ~~~~~~~ In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1940:31, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, inlined from 'void AutoPicker::extractHelicalTubes(std::vector&, std::vector >&, std::vector >&, std::vector >&, double, double, double, double, float)' at /build/relion-3.1.3/src/autopicker.cpp:1809:11: /usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ccfPeak; _Alloc = std::allocator]', inlined from 'void AutoPicker::extractHelicalTubes(std::vector&, std::vector >&, std::vector >&, std::vector >&, double, double, double, double, float)' at /build/relion-3.1.3/src/autopicker.cpp:1856:29: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ccfPeak; _Alloc = std::allocator]', inlined from 'void AutoPicker::extractHelicalTubes(std::vector&, std::vector >&, std::vector >&, std::vector >&, double, double, double, double, float)' at /build/relion-3.1.3/src/autopicker.cpp:1924:34: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ccfPeak; _Alloc = std::allocator]', inlined from 'void AutoPicker::extractHelicalTubes(std::vector&, std::vector >&, std::vector >&, std::vector >&, double, double, double, double, float)' at /build/relion-3.1.3/src/autopicker.cpp:1929:34: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ccfPeak; _Alloc = std::allocator]', inlined from 'void AutoPicker::extractHelicalTubes(std::vector&, std::vector >&, std::vector >&, std::vector >&, double, double, double, double, float)' at /build/relion-3.1.3/src/autopicker.cpp:1964:33: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ccfPeak; _Alloc = std::allocator]', inlined from 'void AutoPicker::extractHelicalTubes(std::vector&, std::vector >&, std::vector >&, std::vector >&, double, double, double, double, float)' at /build/relion-3.1.3/src/autopicker.cpp:2035:36: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ccfPeak; _Alloc = std::allocator]', inlined from 'void AutoPicker::extractHelicalTubes(std::vector&, std::vector >&, std::vector >&, std::vector >&, double, double, double, double, float)' at /build/relion-3.1.3/src/autopicker.cpp:2104:33: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ccfPeak; _Alloc = std::allocator]', inlined from 'void AutoPicker::extractHelicalTubes(std::vector&, std::vector >&, std::vector >&, std::vector >&, double, double, double, double, float)' at /build/relion-3.1.3/src/autopicker.cpp:2174:36: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ccfPeak; _Alloc = std::allocator]', inlined from 'void AutoPicker::extractHelicalTubes(std::vector&, std::vector >&, std::vector >&, std::vector >&, double, double, double, double, float)' at /build/relion-3.1.3/src/autopicker.cpp:2218:27: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ccfPeak; _Alloc = std::allocator]', inlined from 'void AutoPicker::extractHelicalTubes(std::vector&, std::vector >&, std::vector >&, std::vector >&, double, double, double, double, float)' at /build/relion-3.1.3/src/autopicker.cpp:2219:26: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ccfPeak; _Alloc = std::allocator]', inlined from 'void AutoPicker::extractHelicalTubes(std::vector&, std::vector >&, std::vector >&, std::vector >&, double, double, double, double, float)' at /build/relion-3.1.3/src/autopicker.cpp:2221:27: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ccfPeak; _Alloc = std::allocator]', inlined from 'void AutoPicker::extractHelicalTubes(std::vector&, std::vector >&, std::vector >&, std::vector >&, double, double, double, double, float)' at /build/relion-3.1.3/src/autopicker.cpp:2275:33: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void AutoPicker::extractHelicalTubes(std::vector&, std::vector >&, std::vector >&, std::vector >&, double, double, double, double, float)' at /build/relion-3.1.3/src/autopicker.cpp:2293:27: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algo.h:60, from /usr/include/c++/12/algorithm:61, from /build/relion-3.1.3/src/funcs.h:55, from /build/relion-3.1.3/src/matrix1d.h:48, from /build/relion-3.1.3/src/matrix2d.h:50, from /build/relion-3.1.3/src/exp_model.h:23: /usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator > >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1802 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1908 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 7%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/healpix_sampling.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/healpix_sampling.cpp.o -MF CMakeFiles/relion_lib.dir/__/healpix_sampling.cpp.o.d -o CMakeFiles/relion_lib.dir/__/healpix_sampling.cpp.o -c /build/relion-3.1.3/src/healpix_sampling.cpp In file included from /usr/include/c++/12/vector:70, from /build/relion-3.1.3/src/funcs.h:56: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataPoint&}; _Tp = CDataPoint; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataSet&}; _Tp = CDataSet; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/helix.h:30, from /build/relion-3.1.3/src/healpix_sampling.h:31, from /build/relion-3.1.3/src/healpix_sampling.cpp:20: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 [ 7%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/helix.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/helix.cpp.o -MF CMakeFiles/relion_lib.dir/__/helix.cpp.o.d -o CMakeFiles/relion_lib.dir/__/helix.cpp.o -c /build/relion-3.1.3/src/helix.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/helix.h:30, from /build/relion-3.1.3/src/helix.cpp:22: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /usr/include/c++/12/vector:70, from /build/relion-3.1.3/src/Healpix_2.15a/healpix_base.h:35, from /build/relion-3.1.3/src/healpix_sampling.h:24: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: /usr/include/c++/12/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void HealpixSampling::setTranslations(double, double, bool, bool, double, double, double)' at /build/relion-3.1.3/src/healpix_sampling.cpp:417:31: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void HealpixSampling::setTranslations(double, double, bool, bool, double, double, double)' at /build/relion-3.1.3/src/healpix_sampling.cpp:420:32: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void HealpixSampling::setTranslations(double, double, bool, bool, double, double, double)' at /build/relion-3.1.3/src/healpix_sampling.cpp:421:32: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void HealpixSampling::setTranslations(double, double, bool, bool, double, double, double)' at /build/relion-3.1.3/src/healpix_sampling.cpp:425:32: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void HealpixSampling::setTranslations(double, double, bool, bool, double, double, double)' at /build/relion-3.1.3/src/healpix_sampling.cpp:426:32: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void HealpixSampling::setTranslations(double, double, bool, bool, double, double, double)' at /build/relion-3.1.3/src/healpix_sampling.cpp:436:30: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void HealpixSampling::setTranslations(double, double, bool, bool, double, double, double)' at /build/relion-3.1.3/src/healpix_sampling.cpp:437:30: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void HealpixSampling::addOneTranslation(double, double, double, bool, bool, double, double, double)' at /build/relion-3.1.3/src/healpix_sampling.cpp:469:26: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void HealpixSampling::addOneTranslation(double, double, double, bool, bool, double, double, double)' at /build/relion-3.1.3/src/healpix_sampling.cpp:470:26: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void HealpixSampling::addOneTranslation(double, double, double, bool, bool, double, double, double)' at /build/relion-3.1.3/src/healpix_sampling.cpp:472:27: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void HealpixSampling::pushbackOversampledPsiAngles(long int, int, double, double, std::vector&, std::vector&, std::vector&)' at /build/relion-3.1.3/src/healpix_sampling.cpp:1923:28: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void HealpixSampling::pushbackOversampledPsiAngles(long int, int, double, double, std::vector&, std::vector&, std::vector&)' at /build/relion-3.1.3/src/healpix_sampling.cpp:1924:29: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void HealpixSampling::pushbackOversampledPsiAngles(long int, int, double, double, std::vector&, std::vector&, std::vector&)' at /build/relion-3.1.3/src/healpix_sampling.cpp:1925:28: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void HealpixSampling::pushbackOversampledPsiAngles(long int, int, double, double, std::vector&, std::vector&, std::vector&)' at /build/relion-3.1.3/src/healpix_sampling.cpp:1933:29: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void HealpixSampling::pushbackOversampledPsiAngles(long int, int, double, double, std::vector&, std::vector&, std::vector&)' at /build/relion-3.1.3/src/healpix_sampling.cpp:1934:30: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void HealpixSampling::pushbackOversampledPsiAngles(long int, int, double, double, std::vector&, std::vector&, std::vector&)' at /build/relion-3.1.3/src/healpix_sampling.cpp:1937:50: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void HealpixSampling::getOrientations(long int, long int, int, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&)' at /build/relion-3.1.3/src/healpix_sampling.cpp:1844:19: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void HealpixSampling::getOrientations(long int, long int, int, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&)' at /build/relion-3.1.3/src/healpix_sampling.cpp:1845:20: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void HealpixSampling::getOrientations(long int, long int, int, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&)' at /build/relion-3.1.3/src/healpix_sampling.cpp:1846:19: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void HealpixSampling::findSymmetryMate(long int, double, std::vector&, std::vector&, std::vector&)' at /build/relion-3.1.3/src/healpix_sampling.cpp:1096:29: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void HealpixSampling::removePointsOutsideLimitedTiltAngles()' at /build/relion-3.1.3/src/healpix_sampling.cpp:2101:32: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void HealpixSampling::removePointsOutsideLimitedTiltAngles()' at /build/relion-3.1.3/src/healpix_sampling.cpp:2102:33: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void HealpixSampling::getTranslationsInPixel(long int, int, double, std::vector&, std::vector&, std::vector&, bool)' at /build/relion-3.1.3/src/healpix_sampling.cpp:1758:34: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void HealpixSampling::getTranslationsInPixel(long int, int, double, std::vector&, std::vector&, std::vector&, bool)' at /build/relion-3.1.3/src/healpix_sampling.cpp:1759:34: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void HealpixSampling::getTranslationsInPixel(long int, int, double, std::vector&, std::vector&, std::vector&, bool)' at /build/relion-3.1.3/src/healpix_sampling.cpp:1760:34: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void HealpixSampling::getTranslationsInPixel(long int, int, double, std::vector&, std::vector&, std::vector&, bool)' at /build/relion-3.1.3/src/healpix_sampling.cpp:1765:33: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void HealpixSampling::getTranslationsInPixel(long int, int, double, std::vector&, std::vector&, std::vector&, bool)' at /build/relion-3.1.3/src/healpix_sampling.cpp:1766:33: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void HealpixSampling::addOneOrientation(double, double, double, bool)' at /build/relion-3.1.3/src/healpix_sampling.cpp:572:23: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void HealpixSampling::addOneOrientation(double, double, double, bool)' at /build/relion-3.1.3/src/healpix_sampling.cpp:573:24: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void HealpixSampling::addOneOrientation(double, double, double, bool)' at /build/relion-3.1.3/src/healpix_sampling.cpp:578:23: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void HealpixSampling::addOneOrientation(double, double, double, bool)' at /build/relion-3.1.3/src/healpix_sampling.cpp:579:24: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void HealpixSampling::addOneOrientation(double, double, double, bool)' at /build/relion-3.1.3/src/healpix_sampling.cpp:584:22: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void HealpixSampling::selectOrientationsWithNonZeroPriorProbabilityFor3DHelicalReconstruction(double, double, double, double, double, double, std::vector&, std::vector&, std::vector&, std::vector&, bool, double, double, double)' at /build/relion-3.1.3/src/healpix_sampling.cpp:1365:31: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void HealpixSampling::selectOrientationsWithNonZeroPriorProbabilityFor3DHelicalReconstruction(double, double, double, double, double, double, std::vector&, std::vector&, std::vector&, std::vector&, bool, double, double, double)' at /build/relion-3.1.3/src/healpix_sampling.cpp:1381:30: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void HealpixSampling::selectOrientationsWithNonZeroPriorProbabilityFor3DHelicalReconstruction(double, double, double, double, double, double, std::vector&, std::vector&, std::vector&, std::vector&, bool, double, double, double)' at /build/relion-3.1.3/src/healpix_sampling.cpp:1397:29: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void HealpixSampling::selectOrientationsWithNonZeroPriorProbabilityFor3DHelicalReconstruction(double, double, double, double, double, double, std::vector&, std::vector&, std::vector&, std::vector&, bool, double, double, double)' at /build/relion-3.1.3/src/healpix_sampling.cpp:1436:24: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void HealpixSampling::selectOrientationsWithNonZeroPriorProbabilityFor3DHelicalReconstruction(double, double, double, double, double, double, std::vector&, std::vector&, std::vector&, std::vector&, bool, double, double, double)' at /build/relion-3.1.3/src/healpix_sampling.cpp:1469:23: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 8%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/helix_inimodel2d.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/helix_inimodel2d.cpp.o -MF CMakeFiles/relion_lib.dir/__/helix_inimodel2d.cpp.o.d -o CMakeFiles/relion_lib.dir/__/helix_inimodel2d.cpp.o -c /build/relion-3.1.3/src/helix_inimodel2d.cpp In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void HealpixSampling::selectOrientationsWithNonZeroPriorProbability(double, double, double, double, double, double, std::vector&, std::vector&, std::vector&, std::vector&, bool, double, double, double)' at /build/relion-3.1.3/src/healpix_sampling.cpp:846:31: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void HealpixSampling::selectOrientationsWithNonZeroPriorProbability(double, double, double, double, double, double, std::vector&, std::vector&, std::vector&, std::vector&, bool, double, double, double)' at /build/relion-3.1.3/src/healpix_sampling.cpp:922:31: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void HealpixSampling::selectOrientationsWithNonZeroPriorProbability(double, double, double, double, double, double, std::vector&, std::vector&, std::vector&, std::vector&, bool, double, double, double)' at /build/relion-3.1.3/src/healpix_sampling.cpp:938:29: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void HealpixSampling::selectOrientationsWithNonZeroPriorProbability(double, double, double, double, double, double, std::vector&, std::vector&, std::vector&, std::vector&, bool, double, double, double)' at /build/relion-3.1.3/src/healpix_sampling.cpp:968:24: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void HealpixSampling::selectOrientationsWithNonZeroPriorProbability(double, double, double, double, double, double, std::vector&, std::vector&, std::vector&, std::vector&, bool, double, double, double)' at /build/relion-3.1.3/src/healpix_sampling.cpp:992:23: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/algorithm:61, from /build/relion-3.1.3/src/funcs.h:55, from /build/relion-3.1.3/src/multidim_array.h:52, from /build/relion-3.1.3/src/helix.h:26: /usr/include/c++/12/bits/stl_algo.h: In function '_RandomAccessIterator std::_V2::__rotate(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, std::random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >]': /usr/include/c++/12/bits/stl_algo.h:1281:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1281 | __rotate(_RandomAccessIterator __first, | ^~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1281:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h:1281:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/helix_inimodel2d.h:29, from /build/relion-3.1.3/src/helix_inimodel2d.cpp:22: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void FlexAnalyser::make3DModelsAlongPrincipalComponents(std::vector > >&, std::vector > >&, std::vector >&)' at /build/relion-3.1.3/src/flex_analyser.cpp:564:21: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator > >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, inlined from 'void FlexAnalyser::make3DModelsAlongPrincipalComponents(std::vector > >&, std::vector > >&, std::vector >&)' at /build/relion-3.1.3/src/flex_analyser.cpp:567:13: /usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1937 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1938 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1939 | __comp); | ~~~~~~~ In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1940:31, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator > >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, inlined from 'void FlexAnalyser::make3DModelsAlongPrincipalComponents(std::vector > >&, std::vector > >&, std::vector >&)' at /build/relion-3.1.3/src/flex_analyser.cpp:567:13: /usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator]', inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /build/relion-3.1.3/src/CPlot2D.h:168:33, inlined from 'void FlexAnalyser::makePCAhistograms(std::vector > >&, std::vector >&, std::vector >&)' at /build/relion-3.1.3/src/flex_analyser.cpp:471:23: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator]', inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /build/relion-3.1.3/src/CPlot2D.h:168:33, inlined from 'void FlexAnalyser::makePCAhistograms(std::vector > >&, std::vector >&, std::vector >&)' at /build/relion-3.1.3/src/flex_analyser.cpp:472:23: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator]', inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /build/relion-3.1.3/src/CPlot2D.h:168:33, inlined from 'void FlexAnalyser::makePCAhistograms(std::vector > >&, std::vector >&, std::vector >&)' at /build/relion-3.1.3/src/flex_analyser.cpp:473:23: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator]', inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /build/relion-3.1.3/src/CPlot2D.h:168:33, inlined from 'void FlexAnalyser::makePCAhistograms(std::vector > >&, std::vector >&, std::vector >&)' at /build/relion-3.1.3/src/flex_analyser.cpp:474:23: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator]', inlined from 'void CPlot2D::AddDataSet(CDataSet)' at /build/relion-3.1.3/src/CPlot2D.h:1198:26, inlined from 'void FlexAnalyser::makePCAhistograms(std::vector > >&, std::vector >&, std::vector >&)' at /build/relion-3.1.3/src/flex_analyser.cpp:476:20: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void FlexAnalyser::makePCAhistograms(std::vector > >&, std::vector >&, std::vector >&)' at /build/relion-3.1.3/src/flex_analyser.cpp:509:21: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator > >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, inlined from 'void FlexAnalyser::makePCAhistograms(std::vector > >&, std::vector >&, std::vector >&)' at /build/relion-3.1.3/src/flex_analyser.cpp:512:13: /usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1937 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1938 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1939 | __comp); | ~~~~~~~ In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1940:31, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator > >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, inlined from 'void FlexAnalyser::makePCAhistograms(std::vector > >&, std::vector >&, std::vector >&)' at /build/relion-3.1.3/src/flex_analyser.cpp:512:13: /usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator]', inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /build/relion-3.1.3/src/CPlot2D.h:168:33, inlined from 'void FlexAnalyser::makePCAhistograms(std::vector > >&, std::vector >&, std::vector >&)' at /build/relion-3.1.3/src/flex_analyser.cpp:535:25: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator]', inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /build/relion-3.1.3/src/CPlot2D.h:168:33, inlined from 'void FlexAnalyser::makePCAhistograms(std::vector > >&, std::vector >&, std::vector >&)' at /build/relion-3.1.3/src/flex_analyser.cpp:536:25: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator]', inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /build/relion-3.1.3/src/CPlot2D.h:168:33, inlined from 'void FlexAnalyser::makePCAhistograms(std::vector > >&, std::vector >&, std::vector >&)' at /build/relion-3.1.3/src/flex_analyser.cpp:537:25: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator]', inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /build/relion-3.1.3/src/CPlot2D.h:168:33, inlined from 'void FlexAnalyser::makePCAhistograms(std::vector > >&, std::vector >&, std::vector >&)' at /build/relion-3.1.3/src/flex_analyser.cpp:538:25: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator]', inlined from 'void CPlot2D::AddDataSet(CDataSet)' at /build/relion-3.1.3/src/CPlot2D.h:1198:26, inlined from 'void FlexAnalyser::makePCAhistograms(std::vector > >&, std::vector >&, std::vector >&)' at /build/relion-3.1.3/src/flex_analyser.cpp:544:21: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function '_OutputIterator std::__move_merge(_InputIterator, _InputIterator, _InputIterator, _InputIterator, _OutputIterator, _Compare) [with _InputIterator = HelicalSegmentPriorInfoEntry*; _OutputIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/12/bits/stl_algo.h:2615:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2615 | __move_merge(_InputIterator __first1, _InputIterator __last1, | ^~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function '_OutputIterator std::__move_merge(_InputIterator, _InputIterator, _InputIterator, _InputIterator, _OutputIterator, _Compare) [with _InputIterator = __gnu_cxx::__normal_iterator >; _OutputIterator = HelicalSegmentPriorInfoEntry*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/12/bits/stl_algo.h:2615:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h:2615:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h:2615:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h:2615:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void HealpixSampling::removeSymmetryEquivalentPoints(double)' at /build/relion-3.1.3/src/healpix_sampling.cpp:2205:38: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void HealpixSampling::removeSymmetryEquivalentPoints(double)' at /build/relion-3.1.3/src/healpix_sampling.cpp:2206:39: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1802 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h: In function 'void std::__merge_sort_with_buffer(_RandomAccessIterator, _RandomAccessIterator, _Pointer, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Pointer = HelicalSegmentPriorInfoEntry*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/12/bits/stl_algo.h:2682:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2682 | __merge_sort_with_buffer(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:2682:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In function 'void std::__chunk_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Distance, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__merge_sort_with_buffer(_RandomAccessIterator, _RandomAccessIterator, _Pointer, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Pointer = HelicalSegmentPriorInfoEntry*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2693:34: /usr/include/c++/12/bits/stl_algo.h:2672:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2672 | std::__insertion_sort(__first, __first + __chunk_size, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:2675:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2675 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:2675:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In function 'void std::__merge_sort_loop(_RandomAccessIterator1, _RandomAccessIterator1, _RandomAccessIterator2, _Distance, _Compare) [with _RandomAccessIterator1 = __gnu_cxx::__normal_iterator >; _RandomAccessIterator2 = HelicalSegmentPriorInfoEntry*; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__merge_sort_with_buffer(_RandomAccessIterator, _RandomAccessIterator, _Pointer, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Pointer = HelicalSegmentPriorInfoEntry*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2697:26: /usr/include/c++/12/bits/stl_algo.h:2650:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2650 | __result = std::__move_merge(__first, __first + __step_size, | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2651 | __first + __step_size, | ~~~~~~~~~~~~~~~~~~~~~~ 2652 | __first + __two_step, | ~~~~~~~~~~~~~~~~~~~~~ 2653 | __result, __comp); | ~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:2650:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h:2658:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2658 | std::__move_merge(__first, __first + __step_size, | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2659 | __first + __step_size, __last, __result, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:2658:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In function 'void std::__merge_sort_loop(_RandomAccessIterator1, _RandomAccessIterator1, _RandomAccessIterator2, _Distance, _Compare) [with _RandomAccessIterator1 = HelicalSegmentPriorInfoEntry*; _RandomAccessIterator2 = __gnu_cxx::__normal_iterator >; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__merge_sort_with_buffer(_RandomAccessIterator, _RandomAccessIterator, _Pointer, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Pointer = HelicalSegmentPriorInfoEntry*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2700:26: /usr/include/c++/12/bits/stl_algo.h:2650:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2650 | __result = std::__move_merge(__first, __first + __step_size, | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2651 | __first + __step_size, | ~~~~~~~~~~~~~~~~~~~~~~ 2652 | __first + __two_step, | ~~~~~~~~~~~~~~~~~~~~~ 2653 | __result, __comp); | ~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:2658:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2658 | std::__move_merge(__first, __first + __step_size, | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2659 | __first + __step_size, __last, __result, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void HealpixSampling::setOrientations(int, double)' at /build/relion-3.1.3/src/healpix_sampling.cpp:501:24: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void HealpixSampling::setOrientations(int, double)' at /build/relion-3.1.3/src/healpix_sampling.cpp:502:25: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void HealpixSampling::setOrientations(int, double)' at /build/relion-3.1.3/src/healpix_sampling.cpp:531:23: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void HealpixSampling::setOrientations(int, double)' at /build/relion-3.1.3/src/healpix_sampling.cpp:532:24: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void HealpixSampling::setOrientations(int, double)' at /build/relion-3.1.3/src/healpix_sampling.cpp:548:23: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from /build/relion-3.1.3/src/time.h:31, from /build/relion-3.1.3/src/helix_inimodel2d.h:26: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: /usr/include/c++/12/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ [ 8%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/image.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/image.cpp.o -MF CMakeFiles/relion_lib.dir/__/image.cpp.o.d -o CMakeFiles/relion_lib.dir/__/image.cpp.o -c /build/relion-3.1.3/src/image.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/image.cpp:20: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /usr/include/c++/12/vector:70, from /build/relion-3.1.3/src/funcs.h:56, from /build/relion-3.1.3/src/image.h:58: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const fit_point3D&}; _Tp = fit_point3D; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ [ 9%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/local_symmetry.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/local_symmetry.cpp.o -MF CMakeFiles/relion_lib.dir/__/local_symmetry.cpp.o.d -o CMakeFiles/relion_lib.dir/__/local_symmetry.cpp.o -c /build/relion-3.1.3/src/local_symmetry.cpp In file included from /usr/include/c++/12/vector:70, from /build/relion-3.1.3/src/funcs.h:56: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void HelixAligner::readImages()' at /build/relion-3.1.3/src/helix_inimodel2d.cpp:337:21: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void HelixAligner::readImages()' at /build/relion-3.1.3/src/helix_inimodel2d.cpp:338:22: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void HelixAligner::readImages()' at /build/relion-3.1.3/src/helix_inimodel2d.cpp:363:33: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void HelixAligner::readImages()' at /build/relion-3.1.3/src/helix_inimodel2d.cpp:372:34: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = fit_point3D; _Alloc = std::allocator]', inlined from 'void subtractBackgroundRamp(Image&, int, bool, double, double, double)' at /build/relion-3.1.3/src/image.cpp:307:24: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = fit_point3D; _Alloc = std::allocator]', inlined from 'void subtractBackgroundRamp(Image&, int, bool, double, double, double)' at /build/relion-3.1.3/src/image.cpp:323:24: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void HermiteInterpolateOne3DHelicalFilament(MetaDataTable&, MetaDataTable&, int&, int, double, double, double, int, double, double, double, bool)' at /build/relion-3.1.3/src/helix.cpp:4957:21: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void HermiteInterpolateOne3DHelicalFilament(MetaDataTable&, MetaDataTable&, int&, int, double, double, double, int, double, double, double, bool)' at /build/relion-3.1.3/src/helix.cpp:4958:21: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void HermiteInterpolateOne3DHelicalFilament(MetaDataTable&, MetaDataTable&, int&, int, double, double, double, int, double, double, double, bool)' at /build/relion-3.1.3/src/helix.cpp:4959:21: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void HelixAlignerModel::initialise(int, int, int)' at /build/relion-3.1.3/src/helix_inimodel2d.cpp:37:16: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void combineParticlePriorsWithKaiLocalCTF(FileName&, FileName&, FileName&)' at /build/relion-3.1.3/src/helix.cpp:2051:61: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void combineParticlePriorsWithKaiLocalCTF(FileName&, FileName&, FileName&)' at /build/relion-3.1.3/src/helix.cpp:2052:61: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void combineParticlePriorsWithKaiLocalCTF(FileName&, FileName&, FileName&)' at /build/relion-3.1.3/src/helix.cpp:2053:62: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void combineParticlePriorsWithKaiLocalCTF(FileName&, FileName&, FileName&)' at /build/relion-3.1.3/src/helix.cpp:2054:62: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void combineParticlePriorsWithKaiLocalCTF(FileName&, FileName&, FileName&)' at /build/relion-3.1.3/src/helix.cpp:2055:71: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void combineParticlePriorsWithKaiLocalCTF(FileName&, FileName&, FileName&)' at /build/relion-3.1.3/src/helix.cpp:2056:56: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void combineParticlePriorsWithKaiLocalCTF(FileName&, FileName&, FileName&)' at /build/relion-3.1.3/src/helix.cpp:2057:75: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void combineParticlePriorsWithKaiLocalCTF(FileName&, FileName&, FileName&)' at /build/relion-3.1.3/src/helix.cpp:2058:69: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void combineParticlePriorsWithKaiLocalCTF(FileName&, FileName&, FileName&)' at /build/relion-3.1.3/src/helix.cpp:2059:56: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void combineParticlePriorsWithKaiLocalCTF(FileName&, FileName&, FileName&)' at /build/relion-3.1.3/src/helix.cpp:2060:65: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void combineParticlePriorsWithKaiLocalCTF(FileName&, FileName&, FileName&)' at /build/relion-3.1.3/src/helix.cpp:2062:60: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void combineParticlePriorsWithKaiLocalCTF(FileName&, FileName&, FileName&)' at /build/relion-3.1.3/src/helix.cpp:2064:69: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void combineParticlePriorsWithKaiLocalCTF(FileName&, FileName&, FileName&)' at /build/relion-3.1.3/src/helix.cpp:2066:66: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void combineParticlePriorsWithKaiLocalCTF(FileName&, FileName&, FileName&)' at /build/relion-3.1.3/src/helix.cpp:2068:70: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void combineParticlePriorsWithKaiLocalCTF(FileName&, FileName&, FileName&)' at /build/relion-3.1.3/src/helix.cpp:2070:71: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-3.1.3/src/local_symmetry.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void convertHelicalTubeCoordsToMetaDataTable(FileName&, MetaDataTable&, int&, int&, int, double, double, double, double, double, bool, bool)' at /build/relion-3.1.3/src/helix.cpp:1867:30: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void convertHelicalTubeCoordsToMetaDataTable(FileName&, MetaDataTable&, int&, int&, int, double, double, double, double, double, bool, bool)' at /build/relion-3.1.3/src/helix.cpp:1868:30: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void convertHelicalTubeCoordsToMetaDataTable(FileName&, MetaDataTable&, int&, int&, int, double, double, double, double, double, bool, bool)' at /build/relion-3.1.3/src/helix.cpp:1877:28: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void convertHelicalTubeCoordsToMetaDataTable(FileName&, MetaDataTable&, int&, int&, int, double, double, double, double, double, bool, bool)' at /build/relion-3.1.3/src/helix.cpp:1882:30: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void convertHelicalTubeCoordsToMetaDataTable(FileName&, MetaDataTable&, int&, int&, int, double, double, double, double, double, bool, bool)' at /build/relion-3.1.3/src/helix.cpp:1883:30: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ [ 9%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/local_symmetry_mpi.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/local_symmetry_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/local_symmetry_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/local_symmetry_mpi.cpp.o -c /build/relion-3.1.3/src/local_symmetry_mpi.cpp /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {HelicalSymmetryItem}; _Tp = HelicalSymmetryItem; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {HelicalSymmetryItem}; _Tp = HelicalSymmetryItem; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = HelicalSymmetryItem; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void makeHelicalSymmetryList(std::vector&, double, double, double, bool, double, double, double, bool)' at /build/relion-3.1.3/src/helix.cpp:69:22: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-3.1.3/src/local_symmetry_mpi.h:5, from /build/relion-3.1.3/src/local_symmetry_mpi.cpp:1: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /usr/include/c++/12/bits/stl_algo.h:61: /usr/include/c++/12/bits/stl_tempbuf.h: In constructor 'std::_Temporary_buffer<_ForwardIterator, _Tp>::_Temporary_buffer(_ForwardIterator, size_type) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = HelicalSegmentPriorInfoEntry]': /usr/include/c++/12/bits/stl_tempbuf.h:258:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 258 | _Temporary_buffer<_ForwardIterator, _Tp>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 9%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/mask.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/mask.cpp.o -MF CMakeFiles/relion_lib.dir/__/mask.cpp.o.d -o CMakeFiles/relion_lib.dir/__/mask.cpp.o -c /build/relion-3.1.3/src/mask.cpp [ 10%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/matrix1d.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/matrix1d.cpp.o -MF CMakeFiles/relion_lib.dir/__/matrix1d.cpp.o.d -o CMakeFiles/relion_lib.dir/__/matrix1d.cpp.o -c /build/relion-3.1.3/src/matrix1d.cpp In file included from /usr/include/c++/12/vector:70, from /build/relion-3.1.3/src/args.h:52, from /build/relion-3.1.3/src/local_symmetry.h:24: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ [ 10%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/matrix2d.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/matrix2d.cpp.o -MF CMakeFiles/relion_lib.dir/__/matrix2d.cpp.o.d -o CMakeFiles/relion_lib.dir/__/matrix2d.cpp.o -c /build/relion-3.1.3/src/matrix2d.cpp In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void Interpolate3DCurves(FileName&, FileName&, int, double, double, double, int, bool)' at /build/relion-3.1.3/src/helix.cpp:5283:20: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void Interpolate3DCurves(FileName&, FileName&, int, double, double, double, int, bool)' at /build/relion-3.1.3/src/helix.cpp:5293:21: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void Interpolate3DCurves(FileName&, FileName&, int, double, double, double, int, bool)' at /build/relion-3.1.3/src/helix.cpp:5295:21: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void Interpolate3DCurves(FileName&, FileName&, int, double, double, double, int, bool)' at /build/relion-3.1.3/src/helix.cpp:5305:21: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void Interpolate3DCurves(FileName&, FileName&, int, double, double, double, int, bool)' at /build/relion-3.1.3/src/helix.cpp:5307:21: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void Interpolate3DCurves(FileName&, FileName&, int, double, double, double, int, bool)' at /build/relion-3.1.3/src/helix.cpp:5334:20: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void Interpolate3DCurves(FileName&, FileName&, int, double, double, double, int, bool)' at /build/relion-3.1.3/src/helix.cpp:5335:20: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void Interpolate3DCurves(FileName&, FileName&, int, double, double, double, int, bool)' at /build/relion-3.1.3/src/helix.cpp:5336:20: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 [ 11%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/memory.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/memory.cpp.o -MF CMakeFiles/relion_lib.dir/__/memory.cpp.o.d -o CMakeFiles/relion_lib.dir/__/memory.cpp.o -c /build/relion-3.1.3/src/memory.cpp [ 11%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/metadata_container.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/metadata_container.cpp.o -MF CMakeFiles/relion_lib.dir/__/metadata_container.cpp.o.d -o CMakeFiles/relion_lib.dir/__/metadata_container.cpp.o -c /build/relion-3.1.3/src/metadata_container.cpp /usr/include/c++/12/bits/stl_algo.h: In function '_BidirectionalIterator1 std::__rotate_adaptive(_BidirectionalIterator1, _BidirectionalIterator1, _BidirectionalIterator1, _Distance, _Distance, _BidirectionalIterator2, _Distance) [with _BidirectionalIterator1 = __gnu_cxx::__normal_iterator >; _BidirectionalIterator2 = HelicalSegmentPriorInfoEntry*; _Distance = int]': /usr/include/c++/12/bits/stl_algo.h:2352:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2352 | __rotate_adaptive(_BidirectionalIterator1 __first, | ^~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:2352:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h:2352:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In function '_FIter std::_V2::rotate(_FIter, _FIter, _FIter) [with _FIter = __gnu_cxx::__normal_iterator >]', inlined from '_BidirectionalIterator1 std::__rotate_adaptive(_BidirectionalIterator1, _BidirectionalIterator1, _BidirectionalIterator1, _Distance, _Distance, _BidirectionalIterator2, _Distance) [with _BidirectionalIterator1 = __gnu_cxx::__normal_iterator >; _BidirectionalIterator2 = HelicalSegmentPriorInfoEntry*; _Distance = int]' at /usr/include/c++/12/bits/stl_algo.h:2383:20: /usr/include/c++/12/bits/stl_algo.h:1397:27: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1397 | return std::__rotate(__first, __middle, __last, | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 1398 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function 'void std::__merge_adaptive(_BidirectionalIterator, _BidirectionalIterator, _BidirectionalIterator, _Distance, _Distance, _Pointer, _Distance, _Compare) [with _BidirectionalIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Pointer = HelicalSegmentPriorInfoEntry*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/12/bits/stl_algo.h:2390:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2390 | __merge_adaptive(_BidirectionalIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:2390:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h:2390:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h:2435:37: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2435 | = std::__rotate_adaptive(__first_cut, __middle, __second_cut, | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2436 | __len1 - __len11, __len22, __buffer, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2437 | __buffer_size); | ~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:2438:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2438 | std::__merge_adaptive(__first, __first_cut, __new_middle, __len11, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2439 | __len22, __buffer, __buffer_size, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:2440:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2440 | std::__merge_adaptive(__new_middle, __second_cut, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2441 | __len1 - __len11, | ~~~~~~~~~~~~~~~~~ 2442 | __len2 - __len22, __buffer, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2443 | __buffer_size, __comp); | ~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function 'void std::__stable_sort_adaptive(_RandomAccessIterator, _RandomAccessIterator, _Pointer, _Distance, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Pointer = HelicalSegmentPriorInfoEntry*; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/12/bits/stl_algo.h:2709:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2709 | __stable_sort_adaptive(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:2709:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h:2718:38: note: parameter passing for argument of type 'const __gnu_cxx::__normal_iterator >' changed in GCC 7.1 2718 | std::__stable_sort_adaptive(__first, __middle, __buffer, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2719 | __buffer_size, __comp); | ~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:2720:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2720 | std::__stable_sort_adaptive(__middle, __last, __buffer, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2721 | __buffer_size, __comp); | ~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:2725:40: note: parameter passing for argument of type 'const __gnu_cxx::__normal_iterator >' changed in GCC 7.1 2725 | std::__merge_sort_with_buffer(__first, __middle, __buffer, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:2726:40: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2726 | std::__merge_sort_with_buffer(__middle, __last, __buffer, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:2729:28: note: parameter passing for argument of type 'const __gnu_cxx::__normal_iterator >' changed in GCC 7.1 2729 | std::__merge_adaptive(__first, __middle, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2730 | _Distance(__middle - __first), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2731 | _Distance(__last - __middle), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2732 | __buffer, __buffer_size, | ~~~~~~~~~~~~~~~~~~~~~~~~ 2733 | __comp); | ~~~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function 'void std::__merge_without_buffer(_BidirectionalIterator, _BidirectionalIterator, _BidirectionalIterator, _Distance, _Distance, _Compare) [with _BidirectionalIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/12/bits/stl_algo.h:2451:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2451 | __merge_without_buffer(_BidirectionalIterator __first, | ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:2451:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h:2451:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In function '_FIter std::_V2::rotate(_FIter, _FIter, _FIter) [with _FIter = __gnu_cxx::__normal_iterator >]', inlined from 'void std::__merge_without_buffer(_BidirectionalIterator, _BidirectionalIterator, _BidirectionalIterator, _Distance, _Distance, _Compare) [with _BidirectionalIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2491:15: /usr/include/c++/12/bits/stl_algo.h:1397:27: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1397 | return std::__rotate(__first, __middle, __last, | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 1398 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function 'void std::__merge_without_buffer(_BidirectionalIterator, _BidirectionalIterator, _BidirectionalIterator, _Distance, _Distance, _Compare) [with _BidirectionalIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/12/bits/stl_algo.h:2492:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2492 | std::__merge_without_buffer(__first, __first_cut, __new_middle, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2493 | __len11, __len22, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:2494:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2494 | std::__merge_without_buffer(__new_middle, __second_cut, __last, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2495 | __len1 - __len11, __len2 - __len22, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/12/bits/stl_algo.h:2739:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2739 | __inplace_stable_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:2739:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h:2744:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2744 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2748:33: /usr/include/c++/12/bits/stl_algo.h:2744:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2744 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2748:33, inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2748:33: /usr/include/c++/12/bits/stl_algo.h:2744:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2744 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2748:33, inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2748:33, inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2748:33: /usr/include/c++/12/bits/stl_algo.h:2744:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2744 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:2748:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2748 | std::__inplace_stable_sort(__first, __middle, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:2749:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2749 | std::__inplace_stable_sort(__middle, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:2750:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2750 | std::__merge_without_buffer(__first, __middle, __last, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2751 | __middle - __first, | ~~~~~~~~~~~~~~~~~~~ 2752 | __last - __middle, | ~~~~~~~~~~~~~~~~~~ 2753 | __comp); | ~~~~~~~ In function 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2749:33, inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2748:33, inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2748:33: /usr/include/c++/12/bits/stl_algo.h:2744:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2744 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:2748:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2748 | std::__inplace_stable_sort(__first, __middle, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2749:33, inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2749:33, inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2748:33, inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2748:33: /usr/include/c++/12/bits/stl_algo.h:2744:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2744 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:2748:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2748 | std::__inplace_stable_sort(__first, __middle, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:2749:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2749 | std::__inplace_stable_sort(__middle, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:2750:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2750 | std::__merge_without_buffer(__first, __middle, __last, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2751 | __middle - __first, | ~~~~~~~~~~~~~~~~~~~ 2752 | __last - __middle, | ~~~~~~~~~~~~~~~~~~ 2753 | __comp); | ~~~~~~~ In function 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2749:33, inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2748:33, inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2748:33: /usr/include/c++/12/bits/stl_algo.h:2750:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2750 | std::__merge_without_buffer(__first, __middle, __last, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2751 | __middle - __first, | ~~~~~~~~~~~~~~~~~~~ 2752 | __last - __middle, | ~~~~~~~~~~~~~~~~~~ 2753 | __comp); | ~~~~~~~ In function 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2748:33, inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2748:33: /usr/include/c++/12/bits/stl_algo.h:2750:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2750 | std::__merge_without_buffer(__first, __middle, __last, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2751 | __middle - __first, | ~~~~~~~~~~~~~~~~~~~ 2752 | __last - __middle, | ~~~~~~~~~~~~~~~~~~ 2753 | __comp); | ~~~~~~~ In function 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2749:33, inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2748:33: /usr/include/c++/12/bits/stl_algo.h:2744:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2744 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2748:33, inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2749:33, inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2748:33: /usr/include/c++/12/bits/stl_algo.h:2744:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2744 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:2748:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2748 | std::__inplace_stable_sort(__first, __middle, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:2749:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2749 | std::__inplace_stable_sort(__middle, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:2750:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2750 | std::__merge_without_buffer(__first, __middle, __last, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2751 | __middle - __first, | ~~~~~~~~~~~~~~~~~~~ 2752 | __last - __middle, | ~~~~~~~~~~~~~~~~~~ 2753 | __comp); | ~~~~~~~ In function 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2749:33, inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2749:33, inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2748:33: /usr/include/c++/12/bits/stl_algo.h:2744:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2744 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:2748:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2748 | std::__inplace_stable_sort(__first, __middle, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:2749:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2749 | std::__inplace_stable_sort(__middle, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:2750:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2750 | std::__merge_without_buffer(__first, __middle, __last, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2751 | __middle - __first, | ~~~~~~~~~~~~~~~~~~~ 2752 | __last - __middle, | ~~~~~~~~~~~~~~~~~~ 2753 | __comp); | ~~~~~~~ In function 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2749:33, inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2748:33: /usr/include/c++/12/bits/stl_algo.h:2750:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2750 | std::__merge_without_buffer(__first, __middle, __last, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2751 | __middle - __first, | ~~~~~~~~~~~~~~~~~~~ 2752 | __last - __middle, | ~~~~~~~~~~~~~~~~~~ 2753 | __comp); | ~~~~~~~ In function 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2748:33: /usr/include/c++/12/bits/stl_algo.h:2750:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2750 | std::__merge_without_buffer(__first, __middle, __last, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2751 | __middle - __first, | ~~~~~~~~~~~~~~~~~~~ 2752 | __last - __middle, | ~~~~~~~~~~~~~~~~~~ 2753 | __comp); | ~~~~~~~ In function 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2749:33: /usr/include/c++/12/bits/stl_algo.h:2744:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2744 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2748:33, inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2749:33: /usr/include/c++/12/bits/stl_algo.h:2744:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2744 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2748:33, inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2748:33, inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2749:33: /usr/include/c++/12/bits/stl_algo.h:2744:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2744 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:2748:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2748 | std::__inplace_stable_sort(__first, __middle, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:2749:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2749 | std::__inplace_stable_sort(__middle, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:2750:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2750 | std::__merge_without_buffer(__first, __middle, __last, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2751 | __middle - __first, | ~~~~~~~~~~~~~~~~~~~ 2752 | __last - __middle, | ~~~~~~~~~~~~~~~~~~ 2753 | __comp); | ~~~~~~~ In function 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2749:33, inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2748:33, inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2749:33: /usr/include/c++/12/bits/stl_algo.h:2744:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2744 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:2748:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2748 | std::__inplace_stable_sort(__first, __middle, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:2749:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2749 | std::__inplace_stable_sort(__middle, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:2750:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2750 | std::__merge_without_buffer(__first, __middle, __last, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2751 | __middle - __first, | ~~~~~~~~~~~~~~~~~~~ 2752 | __last - __middle, | ~~~~~~~~~~~~~~~~~~ 2753 | __comp); | ~~~~~~~ In function 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2748:33, inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2749:33: /usr/include/c++/12/bits/stl_algo.h:2750:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2750 | std::__merge_without_buffer(__first, __middle, __last, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2751 | __middle - __first, | ~~~~~~~~~~~~~~~~~~~ 2752 | __last - __middle, | ~~~~~~~~~~~~~~~~~~ 2753 | __comp); | ~~~~~~~ In function 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2749:33, inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2749:33: /usr/include/c++/12/bits/stl_algo.h:2744:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2744 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2748:33, inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2749:33, inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2749:33: /usr/include/c++/12/bits/stl_algo.h:2744:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2744 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:2748:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2748 | std::__inplace_stable_sort(__first, __middle, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:2749:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2749 | std::__inplace_stable_sort(__middle, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:2750:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2750 | std::__merge_without_buffer(__first, __middle, __last, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2751 | __middle - __first, | ~~~~~~~~~~~~~~~~~~~ 2752 | __last - __middle, | ~~~~~~~~~~~~~~~~~~ 2753 | __comp); | ~~~~~~~ In function 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2749:33, inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2749:33, inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2749:33: /usr/include/c++/12/bits/stl_algo.h:2744:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2744 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:2748:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2748 | std::__inplace_stable_sort(__first, __middle, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:2749:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2749 | std::__inplace_stable_sort(__middle, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:2750:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2750 | std::__merge_without_buffer(__first, __middle, __last, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2751 | __middle - __first, | ~~~~~~~~~~~~~~~~~~~ 2752 | __last - __middle, | ~~~~~~~~~~~~~~~~~~ 2753 | __comp); | ~~~~~~~ In function 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2749:33, inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2749:33: /usr/include/c++/12/bits/stl_algo.h:2750:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2750 | std::__merge_without_buffer(__first, __middle, __last, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2751 | __middle - __first, | ~~~~~~~~~~~~~~~~~~~ 2752 | __last - __middle, | ~~~~~~~~~~~~~~~~~~ 2753 | __comp); | ~~~~~~~ In function 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:2749:33: /usr/include/c++/12/bits/stl_algo.h:2750:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2750 | std::__merge_without_buffer(__first, __middle, __last, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2751 | __middle - __first, | ~~~~~~~~~~~~~~~~~~~ 2752 | __last - __middle, | ~~~~~~~~~~~~~~~~~~ 2753 | __comp); | ~~~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/12/bits/stl_algo.h:2750:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2750 | std::__merge_without_buffer(__first, __middle, __last, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2751 | __middle - __first, | ~~~~~~~~~~~~~~~~~~~ 2752 | __last - __middle, | ~~~~~~~~~~~~~~~~~~ 2753 | __comp); | ~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const HelicalSegmentPriorInfoEntry&}; _Tp = HelicalSegmentPriorInfoEntry; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = HelicalSegmentPriorInfoEntry; _Alloc = std::allocator]', inlined from 'void updatePriorsForHelicalReconstruction(MetaDataTable&, double, std::vector >, std::vector >, int, bool, bool, double, double, double, double, bool, int)' at /build/relion-3.1.3/src/helix.cpp:4475:17: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In function 'void std::__stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::stable_sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/12/bits/stl_algo.h:5034:36, inlined from 'void updatePriorsForHelicalReconstruction(MetaDataTable&, double, std::vector >, std::vector >, int, bool, bool, double, double, double, double, bool, int)' at /build/relion-3.1.3/src/helix.cpp:4479:18: /usr/include/c++/12/bits/stl_algo.h:4996:15: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 4996 | _TmpBuf __buf(__first, (__last - __first + 1) / 2); | ^~~~~ /usr/include/c++/12/bits/stl_algo.h:4999:35: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 4999 | std::__inplace_stable_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:5001:36: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 5001 | std::__stable_sort_adaptive(__first, __last, __buf.begin(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5002 | _DistanceType(__buf.size()), __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 11%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/metadata_label.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/metadata_label.cpp.o -MF CMakeFiles/relion_lib.dir/__/metadata_label.cpp.o.d -o CMakeFiles/relion_lib.dir/__/metadata_label.cpp.o -c /build/relion-3.1.3/src/metadata_label.cpp [ 12%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/metadata_table.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/metadata_table.cpp.o -MF CMakeFiles/relion_lib.dir/__/metadata_table.cpp.o.d -o CMakeFiles/relion_lib.dir/__/metadata_table.cpp.o -c /build/relion-3.1.3/src/metadata_table.cpp In file included from /usr/include/c++/12/vector:63: /usr/include/c++/12/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*]': /usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*; _Tp = Atom]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = Atom; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1617:35, inlined from 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator]' at /usr/include/c++/12/bits/vector.tcc:232:44: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*; _Tp = Atom]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:601:31, inlined from 'Residue::Residue(const Residue&)' at /build/relion-3.1.3/src/assembly.h:73:7, inlined from 'void std::_Construct(_Tp*, _Args&& ...) [with _Tp = Residue; _Args = {const Residue&}]' at /usr/include/c++/12/bits/stl_construct.h:119:7, inlined from '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Residue*]' at /usr/include/c++/12/bits/stl_uninitialized.h:120:21: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Atom*; _Tp = Atom]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Atom; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:601:31, inlined from 'Residue::Residue(const Residue&)' at /build/relion-3.1.3/src/assembly.h:73:7, inlined from 'void std::_Construct(_Tp*, _Args&& ...) [with _Tp = Residue; _Args = {Residue&}]' at /usr/include/c++/12/bits/stl_construct.h:119:7, inlined from '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = Residue*; _ForwardIterator = Residue*]' at /usr/include/c++/12/bits/stl_uninitialized.h:120:21, inlined from 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = Residue*; _ForwardIterator = Residue*; bool _TrivialValueTypes = false]' at /usr/include/c++/12/bits/stl_uninitialized.h:137:32, inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = Residue*; _ForwardIterator = Residue*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = Residue*; _ForwardIterator = Residue*; _Tp = Residue]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = Residue; _Alloc = std::allocator]' at /usr/include/c++/12/bits/vector.tcc:251:35: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algo.h:60, from /usr/include/c++/12/algorithm:61, from /build/relion-3.1.3/src/funcs.h:55, from /build/relion-3.1.3/src/metadata_table.h:43, from /build/relion-3.1.3/src/metadata_table.cpp:45: /usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Distance = int; _Tp = pair; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1802 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1908 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1908 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1802 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 [ 12%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/micrograph_model.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/micrograph_model.cpp.o -MF CMakeFiles/relion_lib.dir/__/micrograph_model.cpp.o.d -o CMakeFiles/relion_lib.dir/__/micrograph_model.cpp.o -c /build/relion-3.1.3/src/micrograph_model.cpp In file included from /usr/include/c++/12/vector:70, from /build/relion-3.1.3/src/metadata_table.h:33: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataPoint&}; _Tp = CDataPoint; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataSet&}; _Tp = CDataSet; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator]', inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /build/relion-3.1.3/src/CPlot2D.h:168:33, inlined from 'void MetaDataTable::addToCPlot2D(CPlot2D*, EMDLabel, EMDLabel, double, double, double, double, std::string)' at /build/relion-3.1.3/src/metadata_table.cpp:1528:23: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator]', inlined from 'void CPlot2D::AddDataSet(CDataSet)' at /build/relion-3.1.3/src/CPlot2D.h:1198:26, inlined from 'void MetaDataTable::addToCPlot2D(CPlot2D*, EMDLabel, EMDLabel, double, double, double, double, std::string)' at /build/relion-3.1.3/src/metadata_table.cpp:1532:20: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void getLocalSearchOperatorSamplings(const Matrix1D&, const Matrix1D&, std::vector >&, double, double, bool, bool)' at /build/relion-3.1.3/src/local_symmetry.cpp:1550:18: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void getLocalSearchOperatorSamplings(const Matrix1D&, const Matrix1D&, std::vector >&, double, double, bool, bool)' at /build/relion-3.1.3/src/local_symmetry.cpp:1553:17: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void getLocalSearchOperatorSamplings(const Matrix1D&, const Matrix1D&, std::vector >&, double, double, bool, bool)' at /build/relion-3.1.3/src/local_symmetry.cpp:1557:18: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void getLocalSearchOperatorSamplings(const Matrix1D&, const Matrix1D&, std::vector >&, double, double, bool, bool)' at /build/relion-3.1.3/src/local_symmetry.cpp:1560:17: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void getLocalSearchOperatorSamplings(const Matrix1D&, const Matrix1D&, std::vector >&, double, double, bool, bool)' at /build/relion-3.1.3/src/local_symmetry.cpp:1564:18: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void getLocalSearchOperatorSamplings(const Matrix1D&, const Matrix1D&, std::vector >&, double, double, bool, bool)' at /build/relion-3.1.3/src/local_symmetry.cpp:1567:17: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void getLocalSearchOperatorSamplings(const Matrix1D&, const Matrix1D&, std::vector >&, double, double, bool, bool)' at /build/relion-3.1.3/src/local_symmetry.cpp:1577:17: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void getLocalSearchOperatorSamplings(const Matrix1D&, const Matrix1D&, std::vector >&, double, double, bool, bool)' at /build/relion-3.1.3/src/local_symmetry.cpp:1580:16: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void getLocalSearchOperatorSamplings(const Matrix1D&, const Matrix1D&, std::vector >&, double, double, bool, bool)' at /build/relion-3.1.3/src/local_symmetry.cpp:1585:17: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void getLocalSearchOperatorSamplings(const Matrix1D&, const Matrix1D&, std::vector >&, double, double, bool, bool)' at /build/relion-3.1.3/src/local_symmetry.cpp:1588:16: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void getLocalSearchOperatorSamplings(const Matrix1D&, const Matrix1D&, std::vector >&, double, double, bool, bool)' at /build/relion-3.1.3/src/local_symmetry.cpp:1593:17: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void getLocalSearchOperatorSamplings(const Matrix1D&, const Matrix1D&, std::vector >&, double, double, bool, bool)' at /build/relion-3.1.3/src/local_symmetry.cpp:1596:16: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/micrograph_model.cpp:23: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 523 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, inlined from 'static void MetaDataTable::histogram(std::vector&, std::vector&, std::vector&, int, std::string, CPlot2D*, long int, double, double, bool, bool)' at /build/relion-3.1.3/src/metadata_table.cpp:1363:11: /usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1937 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1938 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1939 | __comp); | ~~~~~~~ In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1940:31, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, inlined from 'static void MetaDataTable::histogram(std::vector&, std::vector&, std::vector&, int, std::string, CPlot2D*, long int, double, double, bool, bool)' at /build/relion-3.1.3/src/metadata_table.cpp:1363:11: /usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'static void MetaDataTable::histogram(std::vector&, std::vector&, std::vector&, int, std::string, CPlot2D*, long int, double, double, bool, bool)' at /build/relion-3.1.3/src/metadata_table.cpp:1407:14: /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'static void MetaDataTable::histogram(std::vector&, std::vector&, std::vector&, int, std::string, CPlot2D*, long int, double, double, bool, bool)' at /build/relion-3.1.3/src/metadata_table.cpp:1408:14: /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, inlined from 'static void MetaDataTable::histogram(std::vector&, std::vector&, std::vector&, int, std::string, CPlot2D*, long int, double, double, bool, bool)' at /build/relion-3.1.3/src/metadata_table.cpp:1363:11: /usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1937 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1938 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1939 | __comp); | ~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void MetaDataTable::columnHistogram(EMDLabel, std::vector&, std::vector&, int, CPlot2D*, long int, double, double, bool, bool)' at /build/relion-3.1.3/src/metadata_table.cpp:1341:19: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::pair; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void MetaDataTable::sort(EMDLabel, bool, bool, bool)' at /build/relion-3.1.3/src/metadata_table.cpp:508:15: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator*, vector > >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, inlined from 'void MetaDataTable::sort(EMDLabel, bool, bool, bool)' at /build/relion-3.1.3/src/metadata_table.cpp:512:11: /usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1937 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1938 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1939 | __comp); | ~~~~~~~ In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1940:31, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator*, vector > >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, inlined from 'void MetaDataTable::sort(EMDLabel, bool, bool, bool)' at /build/relion-3.1.3/src/metadata_table.cpp:512:11: /usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'bool MetaDataTable::setValueFromString(EMDLabel, const std::string&, long int)' at /build/relion-3.1.3/src/metadata_table.cpp:385:16: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from /build/relion-3.1.3/src/micrograph_model.h:23, from /build/relion-3.1.3/src/micrograph_model.cpp:21: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 523 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void Micrograph::read(FileName, bool)' at /build/relion-3.1.3/src/micrograph_model.cpp:454:21: /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void Micrograph::read(FileName, bool)' at /build/relion-3.1.3/src/micrograph_model.cpp:455:21: /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'MetaDataTable removeDuplicatedParticles(MetaDataTable&, EMDLabel, double, double, FileName, bool)' at /build/relion-3.1.3/src/metadata_table.cpp:1885:19: /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void Micrograph::setMovie(FileName, FileName, double)' at /build/relion-3.1.3/src/micrograph_model.cpp:575:21: /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void Micrograph::setMovie(FileName, FileName, double)' at /build/relion-3.1.3/src/micrograph_model.cpp:576:21: /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 12%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ml_model.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/ml_model.cpp.o -MF CMakeFiles/relion_lib.dir/__/ml_model.cpp.o.d -o CMakeFiles/relion_lib.dir/__/ml_model.cpp.o -c /build/relion-3.1.3/src/ml_model.cpp [ 13%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ml_optimiser.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/ml_optimiser.cpp.o -MF CMakeFiles/relion_lib.dir/__/ml_optimiser.cpp.o.d -o CMakeFiles/relion_lib.dir/__/ml_optimiser.cpp.o -c /build/relion-3.1.3/src/ml_optimiser.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/projector.h:25, from /build/relion-3.1.3/src/ml_model.h:23, from /build/relion-3.1.3/src/ml_model.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/projector.h:25, from /build/relion-3.1.3/src/ml_model.h:23, from /build/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-3.1.3/src/ml_optimiser.cpp:44: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/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/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/ml_optimiser_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/ml_optimiser_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/ml_optimiser_mpi.cpp.o -c /build/relion-3.1.3/src/ml_optimiser_mpi.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/projector.h:25, from /build/relion-3.1.3/src/ml_model.h:23, from /build/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-3.1.3/src/ml_optimiser_mpi.h:24, from /build/relion-3.1.3/src/ml_optimiser_mpi.cpp:20: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /usr/include/c++/12/vector:70, from /build/relion-3.1.3/src/funcs.h:56, from /build/relion-3.1.3/src/multidim_array.h:52, from /build/relion-3.1.3/src/fftw.h:50, from /build/relion-3.1.3/src/projector.h:23: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 523 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: /usr/include/c++/12/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algo.h:60, from /usr/include/c++/12/algorithm:61, from /build/relion-3.1.3/src/funcs.h:55, from /build/relion-3.1.3/src/multidim_array.h:52, from /build/relion-3.1.3/src/fftw.h:50, from /build/relion-3.1.3/src/projector.h:23: /usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator > >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1802 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1908 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:63: /usr/include/c++/12/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = move_iterator; _ForwardIterator = BackProjector*]': /usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void MlModel::initialiseBodies(FileName, FileName, bool, int)' at /build/relion-3.1.3/src/ml_model.cpp:1085:21: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void MlModel::initialiseBodies(FileName, FileName, bool, int)' at /build/relion-3.1.3/src/ml_model.cpp:1086:23: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void MlModel::initialiseBodies(FileName, FileName, bool, int)' at /build/relion-3.1.3/src/ml_model.cpp:1087:34: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void MlModel::initialiseBodies(FileName, FileName, bool, int)' at /build/relion-3.1.3/src/ml_model.cpp:1088:36: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from /build/relion-3.1.3/src/ml_optimiser.h:33: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 523 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: /usr/include/c++/12/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void MlModel::initialise(bool)' at /build/relion-3.1.3/src/ml_model.cpp:45:26: /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void MlModel::read(FileName)' at /build/relion-3.1.3/src/ml_model.cpp:341:19: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator > >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, inlined from 'void MlOptimiser::maximizationOtherParameters()' at /build/relion-3.1.3/src/ml_optimiser.cpp:4255:12: /usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1937 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1938 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1939 | __comp); | ~~~~~~~ In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1940:31, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator > >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, inlined from 'void MlOptimiser::maximizationOtherParameters()' at /build/relion-3.1.3/src/ml_optimiser.cpp:4255:12: /usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = BackProjector; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 523 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = BackProjector*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = move_iterator; _ForwardIterator = BackProjector*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = move_iterator; _ForwardIterator = BackProjector*; _Tp = BackProjector]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from '_ForwardIterator std::__uninitialized_move_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = BackProjector*; _ForwardIterator = BackProjector*; _Allocator = allocator]' at /usr/include/c++/12/bits/stl_uninitialized.h:382:41, inlined from 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = BackProjector; _Alloc = std::allocator]' at /usr/include/c++/12/bits/vector.tcc:542:32: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = BackProjector*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = move_iterator; _ForwardIterator = BackProjector*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = move_iterator; _ForwardIterator = BackProjector*; _Tp = BackProjector]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from '_ForwardIterator std::__uninitialized_move_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = BackProjector*; _ForwardIterator = BackProjector*; _Allocator = allocator]' at /usr/include/c++/12/bits/stl_uninitialized.h:382:41, inlined from 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = BackProjector; _Alloc = std::allocator]' at /usr/include/c++/12/bits/vector.tcc:562:32: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = BackProjector; _Alloc = std::allocator]', inlined from 'void MlWsumModel::initialise(MlModel&, FileName, bool, bool)' at /build/relion-3.1.3/src/ml_model.cpp:1503:14: /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 14%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/motioncorr_runner.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/motioncorr_runner.cpp.o -MF CMakeFiles/relion_lib.dir/__/motioncorr_runner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/motioncorr_runner.cpp.o -c /build/relion-3.1.3/src/motioncorr_runner.cpp [ 14%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/motioncorr_runner_mpi.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/motioncorr_runner_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/motioncorr_runner_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/motioncorr_runner_mpi.cpp.o -c /build/relion-3.1.3/src/motioncorr_runner_mpi.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-3.1.3/src/motioncorr_runner.cpp:22: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-3.1.3/src/motioncorr_runner_mpi.h:25, from /build/relion-3.1.3/src/motioncorr_runner_mpi.cpp:20: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/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/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/mpi.cpp.o -c /build/relion-3.1.3/src/mpi.cpp [ 15%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/multidim_array.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/multidim_array.cpp.o -MF CMakeFiles/relion_lib.dir/__/multidim_array.cpp.o.d -o CMakeFiles/relion_lib.dir/__/multidim_array.cpp.o -c /build/relion-3.1.3/src/multidim_array.cpp [ 15%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/numerical_recipes.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/numerical_recipes.cpp.o -MF CMakeFiles/relion_lib.dir/__/numerical_recipes.cpp.o.d -o CMakeFiles/relion_lib.dir/__/numerical_recipes.cpp.o -c /build/relion-3.1.3/src/numerical_recipes.cpp In file included from /build/relion-3.1.3/src/numerical_recipes.h:48, from /build/relion-3.1.3/src/numerical_recipes.cpp:49: In function 'void free_Tvector(T*&, int, int) [with T = double]', inlined from 'double brent(double, double, double, double (*)(double*, void*), void*, double, double*, int, double*, double*)' at /build/relion-3.1.3/src/numerical_recipes.cpp:594:25: /build/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/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/relion-3.1.3/src/numerical_recipes.cpp:579:13: note: declared here 579 | RFLOAT *xt=NULL; | ^~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void MlOptimiser::initialiseGeneral(int)' at /build/relion-3.1.3/src/ml_optimiser.cpp:1933:33: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void MlOptimiser::initialiseGeneral(int)' at /build/relion-3.1.3/src/ml_optimiser.cpp:1934:34: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void MlOptimiser::initialiseGeneral(int)' at /build/relion-3.1.3/src/ml_optimiser.cpp:1938:32: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 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/relion-3.1.3/src/numerical_recipes.cpp:767:25: /build/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/relion-3.1.3/src/numerical_recipes.cpp: In function 'void powell(double*, double*, int, double, int&, double&, double (*)(double*, void*), void*, bool)': /build/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/relion-3.1.3/src/numerical_recipes.cpp:768:25: /build/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/relion-3.1.3/src/numerical_recipes.cpp: In function 'void powell(double*, double*, int, double, int&, double&, double (*)(double*, void*), void*, bool)': /build/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/relion-3.1.3/src/numerical_recipes.cpp:769:25: /build/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/relion-3.1.3/src/numerical_recipes.cpp: In function 'void powell(double*, double*, int, double, int&, double&, double (*)(double*, void*), void*, bool)': /build/relion-3.1.3/src/numerical_recipes.cpp:703:13: note: declared here 703 | RFLOAT *pt, *ptt, *xit; | ^~ [ 15%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/parallel.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/parallel.cpp.o -MF CMakeFiles/relion_lib.dir/__/parallel.cpp.o.d -o CMakeFiles/relion_lib.dir/__/parallel.cpp.o -c /build/relion-3.1.3/src/parallel.cpp In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void MlOptimiser::convertAllSquaredDifferencesToWeights(long int, int, int, int, int, int, int, int, int, int, int, int, int, MultidimArray&, MultidimArray&, std::vector >&, std::vector >&, std::vector >&, std::vector >&, std::vector >&, std::vector&, std::vector&, std::vector >&, std::vector >&)' at /build/relion-3.1.3/src/ml_optimiser.cpp:6682:23: /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void MlOptimiser::convertAllSquaredDifferencesToWeights(long int, int, int, int, int, int, int, int, int, int, int, int, int, MultidimArray&, MultidimArray&, std::vector >&, std::vector >&, std::vector >&, std::vector >&, std::vector >&, std::vector&, std::vector&, std::vector >&, std::vector >&)' at /build/relion-3.1.3/src/ml_optimiser.cpp:7049:31: /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 16%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/particle_subtractor.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/particle_subtractor.cpp.o -MF CMakeFiles/relion_lib.dir/__/particle_subtractor.cpp.o.d -o CMakeFiles/relion_lib.dir/__/particle_subtractor.cpp.o -c /build/relion-3.1.3/src/particle_subtractor.cpp In file included from /usr/include/c++/12/vector:70, from /build/relion-3.1.3/src/motioncorr_runner.h:25: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataPoint&}; _Tp = CDataPoint; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataSet&}; _Tp = CDataSet; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/projector.h:25, from /build/relion-3.1.3/src/ml_model.h:23, from /build/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-3.1.3/src/particle_subtractor.h:24, from /build/relion-3.1.3/src/particle_subtractor.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator]', inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /build/relion-3.1.3/src/CPlot2D.h:168:33, inlined from 'void MotioncorrRunner::plotShifts(FileName, Micrograph&)' at /build/relion-3.1.3/src/motioncorr_runner.cpp:737:24: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator]', inlined from 'void CPlot2D::AddDataSet(CDataSet)' at /build/relion-3.1.3/src/CPlot2D.h:1198:26, inlined from 'void MotioncorrRunner::plotShifts(FileName, Micrograph&)' at /build/relion-3.1.3/src/motioncorr_runner.cpp:740:20: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator]', inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /build/relion-3.1.3/src/CPlot2D.h:168:33, inlined from 'void MotioncorrRunner::plotShifts(FileName, Micrograph&)' at /build/relion-3.1.3/src/motioncorr_runner.cpp:749:28: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator]', inlined from 'void CPlot2D::AddDataSet(CDataSet)' at /build/relion-3.1.3/src/CPlot2D.h:1198:26, inlined from 'void MotioncorrRunner::plotShifts(FileName, Micrograph&)' at /build/relion-3.1.3/src/motioncorr_runner.cpp:750:21: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator]', inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /build/relion-3.1.3/src/CPlot2D.h:168:33, inlined from 'void MotioncorrRunner::plotShifts(FileName, Micrograph&)' at /build/relion-3.1.3/src/motioncorr_runner.cpp:776:20: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator]', inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /build/relion-3.1.3/src/CPlot2D.h:168:33, inlined from 'void MotioncorrRunner::plotShifts(FileName, Micrograph&)' at /build/relion-3.1.3/src/motioncorr_runner.cpp:778:20: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator]', inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /build/relion-3.1.3/src/CPlot2D.h:168:33, inlined from 'void MotioncorrRunner::plotShifts(FileName, Micrograph&)' at /build/relion-3.1.3/src/motioncorr_runner.cpp:779:44: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator]', inlined from 'void CPlot2D::AddDataSet(CDataSet)' at /build/relion-3.1.3/src/CPlot2D.h:1198:26, inlined from 'void MotioncorrRunner::plotShifts(FileName, Micrograph&)' at /build/relion-3.1.3/src/motioncorr_runner.cpp:782:21: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator]', inlined from 'void CPlot2D::AddDataSet(CDataSet)' at /build/relion-3.1.3/src/CPlot2D.h:1198:26, inlined from 'void MotioncorrRunner::plotShifts(FileName, Micrograph&)' at /build/relion-3.1.3/src/motioncorr_runner.cpp:783:21: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator]', inlined from 'void CPlot2D::AddDataSet(CDataSet)' at /build/relion-3.1.3/src/CPlot2D.h:1198:26, inlined from 'void MotioncorrRunner::plotShifts(FileName, Micrograph&)' at /build/relion-3.1.3/src/motioncorr_runner.cpp:785:21: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ [ 16%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/pipeline_control.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/pipeline_control.cpp.o -MF CMakeFiles/relion_lib.dir/__/pipeline_control.cpp.o.d -o CMakeFiles/relion_lib.dir/__/pipeline_control.cpp.o -c /build/relion-3.1.3/src/pipeline_control.cpp [ 17%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/pipeline_jobs.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/pipeline_jobs.cpp.o -MF CMakeFiles/relion_lib.dir/__/pipeline_jobs.cpp.o.d -o CMakeFiles/relion_lib.dir/__/pipeline_jobs.cpp.o -c /build/relion-3.1.3/src/pipeline_jobs.cpp In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void MlOptimiser::expectationSomeParticles(long int, long int)' at /build/relion-3.1.3/src/ml_optimiser.cpp:3402:33: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void MlOptimiser::getAllSquaredDifferences(long int, int, int, int, int, int, int, int, int, int, int, int, int, std::vector >&, std::vector >&, std::vector > >&, std::vector >&, MultidimArray&, MultidimArray&, std::vector&, std::vector&, std::vector >&, std::vector >&, std::vector > > >&, std::vector >&, std::vector >&, std::vector >&)' at /build/relion-3.1.3/src/ml_optimiser.cpp:6108:22: /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void MlOptimiser::storeWeightedSums(long int, int, int, int, int, int, int, int, int, int, int, int, std::vector >&, std::vector >&, std::vector > >&, std::vector > >&, std::vector >&, std::vector >&, std::vector >&, std::vector >&, MultidimArray&, MultidimArray&, std::vector >&, std::vector >&, std::vector >&, std::vector&, std::vector&, std::vector >&, std::vector >&, std::vector > > >&, std::vector > > >&, std::vector >&, std::vector >&, std::vector >&)' at /build/relion-3.1.3/src/ml_optimiser.cpp:7233:23: /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void MlOptimiser::storeWeightedSums(long int, int, int, int, int, int, int, int, int, int, int, int, std::vector >&, std::vector >&, std::vector > >&, std::vector > >&, std::vector >&, std::vector >&, std::vector >&, std::vector >&, MultidimArray&, MultidimArray&, std::vector >&, std::vector >&, std::vector >&, std::vector&, std::vector&, std::vector >&, std::vector >&, std::vector > > >&, std::vector > > >&, std::vector >&, std::vector >&, std::vector >&)' at /build/relion-3.1.3/src/ml_optimiser.cpp:7315:23: /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void MlOptimiser::storeWeightedSums(long int, int, int, int, int, int, int, int, int, int, int, int, std::vector >&, std::vector >&, std::vector > >&, std::vector > >&, std::vector >&, std::vector >&, std::vector >&, std::vector >&, MultidimArray&, MultidimArray&, std::vector >&, std::vector >&, std::vector >&, std::vector&, std::vector&, std::vector >&, std::vector >&, std::vector > > >&, std::vector > > >&, std::vector >&, std::vector >&, std::vector >&)' at /build/relion-3.1.3/src/ml_optimiser.cpp:7317:27: /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'bool MotioncorrRunner::executeOwnMotionCorrection(Micrograph&)' at /build/relion-3.1.3/src/motioncorr_runner.cpp:1442:30: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'bool MotioncorrRunner::executeOwnMotionCorrection(Micrograph&)' at /build/relion-3.1.3/src/motioncorr_runner.cpp:1443:30: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'bool MotioncorrRunner::executeOwnMotionCorrection(Micrograph&)' at /build/relion-3.1.3/src/motioncorr_runner.cpp:1453:29: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ [ 17%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/pipeliner.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/pipeliner.cpp.o -MF CMakeFiles/relion_lib.dir/__/pipeliner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/pipeliner.cpp.o -c /build/relion-3.1.3/src/pipeliner.cpp In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void MlOptimiser::expectationOneParticle(long int, int)' at /build/relion-3.1.3/src/ml_optimiser.cpp:3741:32: /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 17%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/postprocessing.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/postprocessing.cpp.o -MF CMakeFiles/relion_lib.dir/__/postprocessing.cpp.o.d -o CMakeFiles/relion_lib.dir/__/postprocessing.cpp.o -c /build/relion-3.1.3/src/postprocessing.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/postprocessing.h:24, from /build/relion-3.1.3/src/postprocessing.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /usr/include/c++/12/vector:70, from /build/relion-3.1.3/src/funcs.h:56, from /build/relion-3.1.3/src/image.h:58: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const fit_point2D&}; _Tp = fit_point2D; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = fit_point2D; _Alloc = std::allocator]', inlined from 'void Postprocessing::makeGuinierPlot(MultidimArray >&, std::vector&)' at /build/relion-3.1.3/src/postprocessing.cpp:652:21: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ [ 18%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/preprocessing.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/preprocessing.cpp.o -MF CMakeFiles/relion_lib.dir/__/preprocessing.cpp.o.d -o CMakeFiles/relion_lib.dir/__/preprocessing.cpp.o -c /build/relion-3.1.3/src/preprocessing.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/preprocessing.h:29, from /build/relion-3.1.3/src/preprocessing.cpp:20: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void Postprocessing::run_locres(int, int)' at /build/relion-3.1.3/src/postprocessing.cpp:1139:22: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ [ 18%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/preprocessing_mpi.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/preprocessing_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/preprocessing_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/preprocessing_mpi.cpp.o -c /build/relion-3.1.3/src/preprocessing_mpi.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/preprocessing.h:29, from /build/relion-3.1.3/src/preprocessing_mpi.h:24, from /build/relion-3.1.3/src/preprocessing_mpi.cpp:20: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 18%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/projector.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/projector.cpp.o -MF CMakeFiles/relion_lib.dir/__/projector.cpp.o.d -o CMakeFiles/relion_lib.dir/__/projector.cpp.o -c /build/relion-3.1.3/src/projector.cpp [ 19%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/reconstructor.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/reconstructor.cpp.o -MF CMakeFiles/relion_lib.dir/__/reconstructor.cpp.o.d -o CMakeFiles/relion_lib.dir/__/reconstructor.cpp.o -c /build/relion-3.1.3/src/reconstructor.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/projector.h:25, from /build/relion-3.1.3/src/projector.cpp:20: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/projector.h:25, from /build/relion-3.1.3/src/backprojector.h:33, from /build/relion-3.1.3/src/reconstructor.h:23, from /build/relion-3.1.3/src/reconstructor.cpp:20: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/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/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/reconstructor_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/reconstructor_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/reconstructor_mpi.cpp.o -c /build/relion-3.1.3/src/reconstructor_mpi.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/projector.h:25, from /build/relion-3.1.3/src/backprojector.h:33, from /build/relion-3.1.3/src/reconstructor.h:23, from /build/relion-3.1.3/src/reconstructor_mpi.h:25, from /build/relion-3.1.3/src/reconstructor_mpi.cpp:20: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/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/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/renderEER.cpp.o -MF CMakeFiles/relion_lib.dir/__/renderEER.cpp.o.d -o CMakeFiles/relion_lib.dir/__/renderEER.cpp.o -c /build/relion-3.1.3/src/renderEER.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/renderEER.cpp:10: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/renderEER.cpp: In member function 'void EERRenderer::readLegacy(FILE*)': /build/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); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from /build/relion-3.1.3/src/renderEER.cpp:4: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator]', inlined from 'void EERRenderer::readLegacy(FILE*)' at /build/relion-3.1.3/src/renderEER.cpp:205:26: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator]', inlined from 'void EERRenderer::readLegacy(FILE*)' at /build/relion-3.1.3/src/renderEER.cpp:206:25: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = long long int; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 523 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = long long int; _Alloc = std::allocator]', inlined from 'void EERRenderer::lazyReadFrames()' at /build/relion-3.1.3/src/renderEER.cpp:230:23: /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = long long int; _Alloc = std::allocator]', inlined from 'void EERRenderer::lazyReadFrames()' at /build/relion-3.1.3/src/renderEER.cpp:231:22: /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 20%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/scheduler.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/scheduler.cpp.o -MF CMakeFiles/relion_lib.dir/__/scheduler.cpp.o.d -o CMakeFiles/relion_lib.dir/__/scheduler.cpp.o -c /build/relion-3.1.3/src/scheduler.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-3.1.3/src/scheduler.h:26, from /build/relion-3.1.3/src/scheduler.cpp:20: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /usr/include/c++/12/bits/stl_algo.h:60, from /usr/include/c++/12/algorithm:61, from /build/relion-3.1.3/src/funcs.h:55, from /build/relion-3.1.3/src/metadata_table.h:43, from /build/relion-3.1.3/src/pipeliner.h:30, from /build/relion-3.1.3/src/scheduler.h:25: /usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector, allocator > > >; _Distance = int; _Tp = pair; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector, allocator > > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 1908 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector, allocator > > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 1802 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 [ 20%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/strings.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/strings.cpp.o -MF CMakeFiles/relion_lib.dir/__/strings.cpp.o.d -o CMakeFiles/relion_lib.dir/__/strings.cpp.o -c /build/relion-3.1.3/src/strings.cpp [ 21%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/symmetries.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/symmetries.cpp.o -MF CMakeFiles/relion_lib.dir/__/symmetries.cpp.o.d -o CMakeFiles/relion_lib.dir/__/symmetries.cpp.o -c /build/relion-3.1.3/src/symmetries.cpp [ 21%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/tabfuncs.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/tabfuncs.cpp.o -MF CMakeFiles/relion_lib.dir/__/tabfuncs.cpp.o.d -o CMakeFiles/relion_lib.dir/__/tabfuncs.cpp.o -c /build/relion-3.1.3/src/tabfuncs.cpp [ 21%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/tiff_converter.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/tiff_converter.cpp.o -MF CMakeFiles/relion_lib.dir/__/tiff_converter.cpp.o.d -o CMakeFiles/relion_lib.dir/__/tiff_converter.cpp.o -c /build/relion-3.1.3/src/tiff_converter.cpp In file included from /usr/include/c++/12/map:60, from /build/relion-3.1.3/src/metadata_table.h:32: /usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::allocator >&>, std::tuple<>}; _Key = std::__cxx11::basic_string; _Val = std::pair, SchedulerFloatVariable>; _KeyOfValue = std::_Select1st, SchedulerFloatVariable> >; _Compare = std::less >; _Alloc = std::allocator, SchedulerFloatVariable> >]': /usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, SchedulerFloatVariable>, std::_Select1st, SchedulerFloatVariable> >, std::less >, std::allocator, SchedulerFloatVariable> > >::const_iterator' changed in GCC 7.1 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/map:61: /usr/include/c++/12/bits/stl_map.h: In function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = SchedulerFloatVariable; _Compare = std::less >; _Alloc = std::allocator, SchedulerFloatVariable> >]': /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, SchedulerFloatVariable>, std::_Select1st, SchedulerFloatVariable> >, std::less >, std::allocator, SchedulerFloatVariable> > >::const_iterator' changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = SchedulerFloatVariable; _Compare = std::less >; _Alloc = std::allocator, SchedulerFloatVariable> >]', inlined from 'float Schedule::getFloatVariableValue(std::string)' at /build/relion-3.1.3/src/scheduler.cpp:1080:37: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, SchedulerFloatVariable>, std::_Select1st, SchedulerFloatVariable> >, std::less >, std::allocator, SchedulerFloatVariable> > >::const_iterator' changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = SchedulerFloatVariable; _Compare = std::less >; _Alloc = std::allocator, SchedulerFloatVariable> >]', inlined from 'float Schedule::getFloatOriginalVariableValue(std::string)' at /build/relion-3.1.3/src/scheduler.cpp:1087:37: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, SchedulerFloatVariable>, std::_Select1st, SchedulerFloatVariable> >, std::less >, std::allocator, SchedulerFloatVariable> > >::const_iterator' changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = SchedulerFloatVariable; _Compare = std::less >; _Alloc = std::allocator, SchedulerFloatVariable> >]', inlined from 'void Schedule::setFloatOriginalVariableValue(std::string, double)' at /build/relion-3.1.3/src/scheduler.cpp:1102:30: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, SchedulerFloatVariable>, std::_Select1st, SchedulerFloatVariable> >, std::less >, std::allocator, SchedulerFloatVariable> > >::const_iterator' changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = SchedulerFloatVariable; _Compare = std::less >; _Alloc = std::allocator, SchedulerFloatVariable> >]', inlined from 'void Schedule::addFloatVariable(std::string, double)' at /build/relion-3.1.3/src/scheduler.cpp:1055:30: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, SchedulerFloatVariable>, std::_Select1st, SchedulerFloatVariable> >, std::less >, std::allocator, SchedulerFloatVariable> > >::const_iterator' changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = SchedulerFloatVariable; _Compare = std::less >; _Alloc = std::allocator, SchedulerFloatVariable> >]', inlined from 'void Schedule::setFloatVariableValue(std::string, double)' at /build/relion-3.1.3/src/scheduler.cpp:1094:30: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, SchedulerFloatVariable>, std::_Select1st, SchedulerFloatVariable> >, std::less >, std::allocator, SchedulerFloatVariable> > >::const_iterator' changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = SchedulerFloatVariable; _Compare = std::less >; _Alloc = std::allocator, SchedulerFloatVariable> >]', inlined from 'void Schedule::setFloatVariableValue(std::string, double)' at /build/relion-3.1.3/src/scheduler.cpp:1095:30: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, SchedulerFloatVariable>, std::_Select1st, SchedulerFloatVariable> >, std::less >, std::allocator, SchedulerFloatVariable> > >::const_iterator' changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/tiff_converter.cpp:24: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/tiff_converter.cpp: In member function 'void TIFFConverter::estimate(FileName)': /build/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/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 /build/relion-3.1.3/src/tiff_converter.cpp: In member function 'int TIFFConverter::checkMRCtype(FileName)': /build/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/relion-3.1.3/src/tiff_converter.cpp: In member function 'void TIFFConverter::initialise(int, int)': /build/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()); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from /build/relion-3.1.3/src/time.h:31, from /build/relion-3.1.3/src/scheduler.h:24: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector, std::allocator > >::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /build/relion-3.1.3/src/tiff_converter.cpp: In member function 'void TIFFConverter::run()': /build/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()); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::pair; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void MultidimArray::sorted_index(MultidimArray&) const [with T = double]' at /build/relion-3.1.3/src/multidim_array.h:3618:22: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector, allocator > > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator*, vector, allocator > > >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, inlined from 'void MultidimArray::sorted_index(MultidimArray&) const [with T = double]' at /build/relion-3.1.3/src/multidim_array.h:3621:18: /usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 1937 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1938 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1939 | __comp); | ~~~~~~~ In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector, allocator > > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector, allocator > > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1940:31, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator*, vector, allocator > > >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, inlined from 'void MultidimArray::sorted_index(MultidimArray&) const [with T = double]' at /build/relion-3.1.3/src/multidim_array.h:3621:18: /usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ [ 22%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/time.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/time.cpp.o -MF CMakeFiles/relion_lib.dir/__/time.cpp.o.d -o CMakeFiles/relion_lib.dir/__/time.cpp.o -c /build/relion-3.1.3/src/time.cpp In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = SchedulerFloatVariable; _Compare = std::less >; _Alloc = std::allocator, SchedulerFloatVariable> >]', inlined from 'void Schedule::read(bool, FileName)' at /build/relion-3.1.3/src/scheduler.cpp:684:33: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, SchedulerFloatVariable>, std::_Select1st, SchedulerFloatVariable> >, std::less >, std::allocator, SchedulerFloatVariable> > >::const_iterator' changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ [ 22%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/transformations.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/transformations.cpp.o -MF CMakeFiles/relion_lib.dir/__/transformations.cpp.o.d -o CMakeFiles/relion_lib.dir/__/transformations.cpp.o -c /build/relion-3.1.3/src/transformations.cpp In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = SchedulerFloatVariable; _Compare = std::less >; _Alloc = std::allocator, SchedulerFloatVariable> >]', inlined from 'void Schedule::setVariablesInJob(RelionJob&, FileName, bool&)' at /build/relion-3.1.3/src/scheduler.cpp:1628:59: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, SchedulerFloatVariable>, std::_Select1st, SchedulerFloatVariable> >, std::less >, std::allocator, SchedulerFloatVariable> > >::const_iterator' changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ [ 23%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/Healpix_2.15a/cxxutils.cc.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/Healpix_2.15a/cxxutils.cc.o -MF CMakeFiles/relion_lib.dir/__/Healpix_2.15a/cxxutils.cc.o.d -o CMakeFiles/relion_lib.dir/__/Healpix_2.15a/cxxutils.cc.o -c /build/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/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/Healpix_2.15a/healpix_base.cc.o -MF CMakeFiles/relion_lib.dir/__/Healpix_2.15a/healpix_base.cc.o.d -o CMakeFiles/relion_lib.dir/__/Healpix_2.15a/healpix_base.cc.o -c /build/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/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/Fourier_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/Fourier_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/Fourier_helper.cpp.o -c /build/relion-3.1.3/src/jaz/Fourier_helper.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/Fourier_helper.h:24, from /build/relion-3.1.3/src/jaz/Fourier_helper.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 24%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/Gaussian_pyramid.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/Gaussian_pyramid.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/Gaussian_pyramid.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/Gaussian_pyramid.cpp.o -c /build/relion-3.1.3/src/jaz/Gaussian_pyramid.cpp [ 24%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/aberration_fit.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/aberration_fit.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/aberration_fit.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/aberration_fit.cpp.o -c /build/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/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/complex_io.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/complex_io.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/complex_io.cpp.o -c /build/relion-3.1.3/src/jaz/complex_io.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/aberration_fit.h:24, from /build/relion-3.1.3/src/jaz/aberration_fit.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/complex_io.h:24, from /build/relion-3.1.3/src/jaz/complex_io.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 25%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/convolution_helper.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/convolution_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/convolution_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/convolution_helper.cpp.o -c /build/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/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf_helper.cpp.o -c /build/relion-3.1.3/src/jaz/ctf_helper.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/convolution_helper.h:24, from /build/relion-3.1.3/src/jaz/convolution_helper.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/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/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/damage_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/damage_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/damage_helper.cpp.o -c /build/relion-3.1.3/src/jaz/damage_helper.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-3.1.3/src/ctf.h:50, from /build/relion-3.1.3/src/jaz/ctf_helper.h:24, from /build/relion-3.1.3/src/jaz/ctf_helper.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-3.1.3/src/ctf.h:50, from /build/relion-3.1.3/src/jaz/fsc_helper.h:24, from /build/relion-3.1.3/src/jaz/damage_helper.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/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/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/distribution_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/distribution_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/distribution_helper.cpp.o -c /build/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/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/fftw_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/fftw_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/fftw_helper.cpp.o -c /build/relion-3.1.3/src/jaz/fftw_helper.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/distribution_helper.h:25, from /build/relion-3.1.3/src/jaz/distribution_helper.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 27%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/fsc_helper.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/fsc_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/fsc_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/fsc_helper.cpp.o -c /build/relion-3.1.3/src/jaz/fsc_helper.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-3.1.3/src/ctf.h:50, from /build/relion-3.1.3/src/jaz/fsc_helper.h:24, from /build/relion-3.1.3/src/jaz/fsc_helper.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 27%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/image_log.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/image_log.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/image_log.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/image_log.cpp.o -c /build/relion-3.1.3/src/jaz/image_log.cpp [ 28%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/interpolation.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/interpolation.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/interpolation.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/interpolation.cpp.o -c /build/relion-3.1.3/src/jaz/interpolation.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/image_log.h:24, from /build/relion-3.1.3/src/jaz/image_log.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/interpolation.h:24, from /build/relion-3.1.3/src/jaz/interpolation.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 28%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/jaz_config.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/jaz_config.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/jaz_config.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/jaz_config.cpp.o -c /build/relion-3.1.3/src/jaz/jaz_config.cpp [ 28%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/legacy_obs_model.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/legacy_obs_model.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/legacy_obs_model.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/legacy_obs_model.cpp.o -c /build/relion-3.1.3/src/jaz/legacy_obs_model.cpp [ 29%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/local_motion_fit.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/local_motion_fit.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/local_motion_fit.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/local_motion_fit.cpp.o -c /build/relion-3.1.3/src/jaz/local_motion_fit.cpp [ 29%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/micrograph_handler.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/micrograph_handler.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/micrograph_handler.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/micrograph_handler.cpp.o -c /build/relion-3.1.3/src/jaz/micrograph_handler.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/legacy_obs_model.h:4, from /build/relion-3.1.3/src/jaz/legacy_obs_model.cpp:1: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/local_motion_fit.h:24, from /build/relion-3.1.3/src/jaz/local_motion_fit.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/micrograph_handler.h:31, from /build/relion-3.1.3/src/jaz/micrograph_handler.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/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/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/new_ft.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/new_ft.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/new_ft.cpp.o -c /build/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/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/noise_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/noise_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/noise_helper.cpp.o -c /build/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/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/obs_model.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/obs_model.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/obs_model.cpp.o -c /build/relion-3.1.3/src/jaz/obs_model.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/projector.h:25, from /build/relion-3.1.3/src/jaz/noise_helper.h:25, from /build/relion-3.1.3/src/jaz/noise_helper.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-3.1.3/src/jaz/obs_model.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 31%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/parallel_ft.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/parallel_ft.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/parallel_ft.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/parallel_ft.cpp.o -c /build/relion-3.1.3/src/jaz/parallel_ft.cpp In file included from /usr/include/c++/12/vector:70, from /build/relion-3.1.3/src/jaz/noise_helper.h:24: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ [ 31%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/reference_map.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/reference_map.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/reference_map.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/reference_map.cpp.o -c /build/relion-3.1.3/src/jaz/reference_map.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/reference_map.h:24, from /build/relion-3.1.3/src/jaz/reference_map.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 31%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/refinement_helper.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/refinement_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/refinement_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/refinement_helper.cpp.o -c /build/relion-3.1.3/src/jaz/refinement_helper.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-3.1.3/src/ctf.h:50, from /build/relion-3.1.3/src/jaz/refinement_helper.h:24, from /build/relion-3.1.3/src/jaz/refinement_helper.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'static Image NoiseHelper::predictCCNoise(Projector&, double, double, int, int, Image&, CTF, double, double, double, int)' at /build/relion-3.1.3/src/jaz/noise_helper.cpp:134:40: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ [ 32%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/resampling_helper.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/resampling_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/resampling_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/resampling_helper.cpp.o -c /build/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/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/slice_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/slice_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/slice_helper.cpp.o -c /build/relion-3.1.3/src/jaz/slice_helper.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/slice_helper.h:24, from /build/relion-3.1.3/src/jaz/slice_helper.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/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/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/spectral_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/spectral_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/spectral_helper.cpp.o -c /build/relion-3.1.3/src/jaz/spectral_helper.cpp [ 33%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/stack_helper.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/stack_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/stack_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/stack_helper.cpp.o -c /build/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/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/structure_tensor.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/structure_tensor.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/structure_tensor.cpp.o -c /build/relion-3.1.3/src/jaz/structure_tensor.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/spectral_helper.h:24, from /build/relion-3.1.3/src/jaz/spectral_helper.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-3.1.3/src/ctf.h:50, from /build/relion-3.1.3/src/jaz/stack_helper.h:24, from /build/relion-3.1.3/src/jaz/stack_helper.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/img_proc/filter_helper.h:24, from /build/relion-3.1.3/src/jaz/structure_tensor.cpp:22: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/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/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/svd_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/svd_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/svd_helper.cpp.o -c /build/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/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/t_complex.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/t_complex.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/t_complex.cpp.o -c /build/relion-3.1.3/src/jaz/t_complex.cpp [ 34%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/volume_converter.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/volume_converter.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/volume_converter.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/volume_converter.cpp.o -c /build/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/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/volume_integration.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/volume_integration.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/volume_integration.cpp.o -c /build/relion-3.1.3/src/jaz/volume_integration.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/volume_converter.h:25, from /build/relion-3.1.3/src/jaz/volume_converter.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/volume_integration.h:26, from /build/relion-3.1.3/src/jaz/volume_integration.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/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/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/vtk_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/vtk_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/vtk_helper.cpp.o -c /build/relion-3.1.3/src/jaz/vtk_helper.cpp [ 36%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/gradient_descent.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/gradient_descent.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/optimization/gradient_descent.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/optimization/gradient_descent.cpp.o -c /build/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/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/lbfgs.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/optimization/lbfgs.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/optimization/lbfgs.cpp.o -c /build/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/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/nelder_mead.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/optimization/nelder_mead.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/optimization/nelder_mead.cpp.o -c /build/relion-3.1.3/src/jaz/optimization/nelder_mead.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/vtk_helper.h:24, from /build/relion-3.1.3/src/jaz/vtk_helper.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/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/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/optimization.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/optimization/optimization.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/optimization/optimization.cpp.o -c /build/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/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/aberration_estimator.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/aberration_estimator.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/aberration_estimator.cpp.o -c /build/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/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/bfactor_refiner.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/bfactor_refiner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/bfactor_refiner.cpp.o -c /build/relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/ctf/aberration_estimator.h:4, from /build/relion-3.1.3/src/jaz/ctf/aberration_estimator.cpp:1: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/ctf/bfactor_refiner.h:4, from /build/relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:1: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 38%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner.cpp.o -c /build/relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /usr/include/c++/12/vector:70, from /build/relion-3.1.3/src/funcs.h:56, from /build/relion-3.1.3/src/image.h:58: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataPoint&}; _Tp = CDataPoint; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataSet&}; _Tp = CDataSet; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator]', inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /build/relion-3.1.3/src/CPlot2D.h:168:33, inlined from 'void BFactorRefiner::writePerParticleEPS(const MetaDataTable&)' at /build/relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:474:23: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator]', inlined from 'void CPlot2D::AddDataSet(CDataSet)' at /build/relion-3.1.3/src/CPlot2D.h:1198:26, inlined from 'void BFactorRefiner::writePerParticleEPS(const MetaDataTable&)' at /build/relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:476:20: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator]', inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /build/relion-3.1.3/src/CPlot2D.h:168:33, inlined from 'void BFactorRefiner::writePerParticleDiagEPS(const MetaDataTable&, gravis::d2Vector, const std::vector >&, const std::vector >&, int)' at /build/relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:405:21: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator]', inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /build/relion-3.1.3/src/CPlot2D.h:168:33, inlined from 'void BFactorRefiner::writePerParticleDiagEPS(const MetaDataTable&, gravis::d2Vector, const std::vector >&, const std::vector >&, int)' at /build/relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:419:24: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator]', inlined from 'void CPlot2D::AddDataSet(CDataSet)' at /build/relion-3.1.3/src/CPlot2D.h:1198:26, inlined from 'void BFactorRefiner::writePerParticleDiagEPS(const MetaDataTable&, gravis::d2Vector, const std::vector >&, const std::vector >&, int)' at /build/relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:421:21: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator]', inlined from 'void CPlot2D::AddDataSet(CDataSet)' at /build/relion-3.1.3/src/CPlot2D.h:1198:26, inlined from 'void BFactorRefiner::writePerParticleDiagEPS(const MetaDataTable&, gravis::d2Vector, const std::vector >&, const std::vector >&, int)' at /build/relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:425:19: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator]', inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /build/relion-3.1.3/src/CPlot2D.h:168:33, inlined from 'void BFactorRefiner::writePerMicrographEPS(const MetaDataTable&, const std::vector >&, const std::vector >&, int)' at /build/relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:339:21: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator]', inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /build/relion-3.1.3/src/CPlot2D.h:168:33, inlined from 'void BFactorRefiner::writePerMicrographEPS(const MetaDataTable&, const std::vector >&, const std::vector >&, int)' at /build/relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:353:24: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator]', inlined from 'void CPlot2D::AddDataSet(CDataSet)' at /build/relion-3.1.3/src/CPlot2D.h:1198:26, inlined from 'void BFactorRefiner::writePerMicrographEPS(const MetaDataTable&, const std::vector >&, const std::vector >&, int)' at /build/relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:355:21: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator]', inlined from 'void CPlot2D::AddDataSet(CDataSet)' at /build/relion-3.1.3/src/CPlot2D.h:1198:26, inlined from 'void BFactorRefiner::writePerMicrographEPS(const MetaDataTable&, const std::vector >&, const std::vector >&, int)' at /build/relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:359:19: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from /build/relion-3.1.3/src/funcs.h:56, from /build/relion-3.1.3/src/image.h:58: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::pair >}; _Tp = std::pair >; _Alloc = std::allocator > >]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector > >::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair >}; _Tp = std::pair >; _Alloc = std::allocator > >]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::pair >; _Alloc = std::allocator > >]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from '_ZN14BFactorRefiner17processMicrographElR13MetaDataTableRKSt6vectorI5ImageI8tComplexIdEESaIS6_EESA_b._omp_fn.1' at /build/relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:237:36: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 38%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner_mpi.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner_mpi.cpp.o -c /build/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.h:26, from /build/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 39%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_estimator.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_estimator.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_estimator.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_estimator.cpp.o -c /build/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/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_helper.cpp.o -c /build/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/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/delocalisation_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/delocalisation_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/delocalisation_helper.cpp.o -c /build/relion-3.1.3/src/jaz/ctf/delocalisation_helper.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/ctf/defocus_estimator.h:24, from /build/relion-3.1.3/src/jaz/ctf/defocus_estimator.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-3.1.3/src/ctf.h:50, from /build/relion-3.1.3/src/jaz/ctf/delocalisation_helper.h:4, from /build/relion-3.1.3/src/jaz/ctf/delocalisation_helper.cpp:1: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-3.1.3/src/ctf.h:50, from /build/relion-3.1.3/src/jaz/ctf/defocus_helper.h:24, from /build/relion-3.1.3/src/jaz/ctf/defocus_helper.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from '_ZN19AberrationEstimator13parametricFitERKSt6vectorI13MetaDataTableSaIS1_EERS1_RS0_I8FileNameSaIS7_EE._omp_fn.0' at /build/relion-3.1.3/src/jaz/ctf/aberration_estimator.cpp:303:19: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from '_ZN19AberrationEstimator13parametricFitERKSt6vectorI13MetaDataTableSaIS1_EERS1_RS0_I8FileNameSaIS7_EE._omp_fn.0' at /build/relion-3.1.3/src/jaz/ctf/aberration_estimator.cpp:306:19: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from '_ZN19AberrationEstimator13parametricFitERKSt6vectorI13MetaDataTableSaIS1_EERS1_RS0_I8FileNameSaIS7_EE._omp_fn.0' at /build/relion-3.1.3/src/jaz/ctf/aberration_estimator.cpp:341:20: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from '_ZN19AberrationEstimator13parametricFitERKSt6vectorI13MetaDataTableSaIS1_EERS1_RS0_I8FileNameSaIS7_EE._omp_fn.0' at /build/relion-3.1.3/src/jaz/ctf/aberration_estimator.cpp:344:20: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 40%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/equation2x2.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/equation2x2.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/equation2x2.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/equation2x2.cpp.o -c /build/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/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_estimator.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_estimator.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_estimator.cpp.o -c /build/relion-3.1.3/src/jaz/ctf/magnification_estimator.cpp In file included from /usr/include/c++/12/vector:70, from /build/relion-3.1.3/src/funcs.h:56, from /build/relion-3.1.3/src/image.h:58: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataPoint&}; _Tp = CDataPoint; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataSet&}; _Tp = CDataSet; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator]', inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /build/relion-3.1.3/src/CPlot2D.h:168:33, inlined from 'void DefocusEstimator::writeEPS(const MetaDataTable&)' at /build/relion-3.1.3/src/jaz/ctf/defocus_estimator.cpp:218:23: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator]', inlined from 'void CPlot2D::AddDataSet(CDataSet)' at /build/relion-3.1.3/src/CPlot2D.h:1198:26, inlined from 'void DefocusEstimator::writeEPS(const MetaDataTable&)' at /build/relion-3.1.3/src/jaz/ctf/defocus_estimator.cpp:220:20: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/ctf/magnification_estimator.h:28, from /build/relion-3.1.3/src/jaz/ctf/magnification_estimator.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/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/magnification_helper.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_helper.cpp.o -c /build/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/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/modular_ctf_optimisation.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/modular_ctf_optimisation.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/modular_ctf_optimisation.cpp.o -c /build/relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.cpp In file included from /usr/include/c++/12/vector:70, from /build/relion-3.1.3/src/jaz/ctf/magnification_estimator.h:24: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-3.1.3/src/ctf.h:50, from /build/relion-3.1.3/src/jaz/ctf/magnification_helper.h:24, from /build/relion-3.1.3/src/jaz/ctf/magnification_helper.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/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/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_estimator.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_estimator.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_estimator.cpp.o -c /build/relion-3.1.3/src/jaz/ctf/tilt_estimator.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.h:5, from /build/relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.cpp:1: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from '_ZN22MagnificationEstimator13parametricFitERSt6vectorI13MetaDataTableSaIS1_EERS1_RS0_I8FileNameSaIS6_EE._omp_fn.0' at /build/relion-3.1.3/src/jaz/ctf/magnification_estimator.cpp:219:19: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from '_ZN22MagnificationEstimator13parametricFitERSt6vectorI13MetaDataTableSaIS1_EERS1_RS0_I8FileNameSaIS6_EE._omp_fn.0' at /build/relion-3.1.3/src/jaz/ctf/magnification_estimator.cpp:223:19: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from '_ZN22MagnificationEstimator13parametricFitERSt6vectorI13MetaDataTableSaIS1_EERS1_RS0_I8FileNameSaIS6_EE._omp_fn.0' at /build/relion-3.1.3/src/jaz/ctf/magnification_estimator.cpp:239:19: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from '_ZN22MagnificationEstimator13parametricFitERSt6vectorI13MetaDataTableSaIS1_EERS1_RS0_I8FileNameSaIS6_EE._omp_fn.0' at /build/relion-3.1.3/src/jaz/ctf/magnification_estimator.cpp:243:19: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/ctf/tilt_estimator.h:24, from /build/relion-3.1.3/src/jaz/ctf/tilt_estimator.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/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/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_helper.cpp.o -c /build/relion-3.1.3/src/jaz/ctf/tilt_helper.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-3.1.3/src/ctf.h:50, from /build/relion-3.1.3/src/jaz/ctf/tilt_helper.h:24, from /build/relion-3.1.3/src/jaz/ctf/tilt_helper.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 42%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/alignment_set.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/alignment_set.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/alignment_set.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/alignment_set.cpp.o -c /build/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/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/frame_recombiner.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/frame_recombiner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/frame_recombiner.cpp.o -c /build/relion-3.1.3/src/jaz/motion/frame_recombiner.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/motion/frame_recombiner.h:24, from /build/relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /usr/include/c++/12/vector:70, from /build/relion-3.1.3/src/funcs.h:56, from /build/relion-3.1.3/src/image.h:58: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 43%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/gp_motion_fit.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/gp_motion_fit.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/gp_motion_fit.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/gp_motion_fit.cpp.o -c /build/relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp In file included from /usr/include/c++/12/vector:70, from /build/relion-3.1.3/src/funcs.h:56, from /build/relion-3.1.3/src/multidim_array.h:52, from /build/relion-3.1.3/src/ctf.h:48: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 523 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'static void TiltHelper::extractTilt(std::vector >&, double&, double&, double, double)' at /build/relion-3.1.3/src/jaz/ctf/tilt_helper.cpp:536:26: /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'static void TiltHelper::insertTilt(std::vector >&, double, double, double, double)' at /build/relion-3.1.3/src/jaz/ctf/tilt_helper.cpp:563:26: /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 43%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_estimator.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_estimator.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/motion_estimator.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_estimator.cpp.o -c /build/relion-3.1.3/src/jaz/motion/motion_estimator.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/motion/gp_motion_fit.h:24, from /build/relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from '_ZN13TiltEstimator13parametricFitERKSt6vectorI13MetaDataTableSaIS1_EERS1_RS0_I8FileNameSaIS7_EE._omp_fn.0' at /build/relion-3.1.3/src/jaz/ctf/tilt_estimator.cpp:276:19: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from '_ZN13TiltEstimator13parametricFitERKSt6vectorI13MetaDataTableSaIS1_EERS1_RS0_I8FileNameSaIS7_EE._omp_fn.0' at /build/relion-3.1.3/src/jaz/ctf/tilt_estimator.cpp:279:19: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from '_ZN13TiltEstimator13parametricFitERKSt6vectorI13MetaDataTableSaIS1_EERS1_RS0_I8FileNameSaIS7_EE._omp_fn.0' at /build/relion-3.1.3/src/jaz/ctf/tilt_estimator.cpp:310:20: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from '_ZN13TiltEstimator13parametricFitERKSt6vectorI13MetaDataTableSaIS1_EERS1_RS0_I8FileNameSaIS7_EE._omp_fn.0' at /build/relion-3.1.3/src/jaz/ctf/tilt_estimator.cpp:313:20: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/motion/motion_estimator.h:24, from /build/relion-3.1.3/src/jaz/motion/motion_estimator.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 43%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_helper.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/motion_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_helper.cpp.o -c /build/relion-3.1.3/src/jaz/motion/motion_helper.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-3.1.3/src/ctf.h:50, from /build/relion-3.1.3/src/jaz/motion/motion_helper.h:24, from /build/relion-3.1.3/src/jaz/motion/motion_helper.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/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/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_param_estimator.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/motion_param_estimator.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_param_estimator.cpp.o -c /build/relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, from /build/relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /usr/include/c++/12/vector:70, from /build/relion-3.1.3/src/funcs.h:56, from /build/relion-3.1.3/src/image.h:58: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataPoint&}; _Tp = CDataPoint; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataSet&}; _Tp = CDataSet; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 [ 44%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner.cpp.o -c /build/relion-3.1.3/src/jaz/motion/motion_refiner.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-3.1.3/src/ctf.h:50, from /build/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-3.1.3/src/jaz/motion/motion_refiner.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/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/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner_mpi.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner_mpi.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner_mpi.cpp.o -c /build/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-3.1.3/src/ctf.h:50, from /build/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.h:27, from /build/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator]', inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /build/relion-3.1.3/src/CPlot2D.h:168:33, inlined from 'void MotionEstimator::writeOutput(const std::vector > >&, double, const std::vector >&, const std::vector >&, const std::vector >&, const std::vector >&, std::string, double)' at /build/relion-3.1.3/src/jaz/motion/motion_estimator.cpp:711:23: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator]', inlined from 'void CPlot2D::AddDataSet(CDataSet)' at /build/relion-3.1.3/src/CPlot2D.h:1198:26, inlined from 'void MotionEstimator::writeOutput(const std::vector > >&, double, const std::vector >&, const std::vector >&, const std::vector >&, const std::vector >&, std::string, double)' at /build/relion-3.1.3/src/jaz/motion/motion_estimator.cpp:714:20: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator]', inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /build/relion-3.1.3/src/CPlot2D.h:168:33, inlined from 'void MotionEstimator::writeOutput(const std::vector > >&, double, const std::vector >&, const std::vector >&, const std::vector >&, const std::vector >&, std::string, double)' at /build/relion-3.1.3/src/jaz/motion/motion_estimator.cpp:724:27: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator]', inlined from 'void CPlot2D::AddDataSet(CDataSet)' at /build/relion-3.1.3/src/CPlot2D.h:1198:26, inlined from 'void MotionEstimator::writeOutput(const std::vector > >&, double, const std::vector >&, const std::vector >&, const std::vector >&, const std::vector >&, std::string, double)' at /build/relion-3.1.3/src/jaz/motion/motion_estimator.cpp:725:20: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator]', inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /build/relion-3.1.3/src/CPlot2D.h:168:33, inlined from 'void MotionEstimator::writeOutput(const std::vector > >&, double, const std::vector >&, const std::vector >&, const std::vector >&, const std::vector >&, std::string, double)' at /build/relion-3.1.3/src/jaz/motion/motion_estimator.cpp:736:27: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator]', inlined from 'void CPlot2D::AddDataSet(CDataSet)' at /build/relion-3.1.3/src/CPlot2D.h:1198:26, inlined from 'void MotionEstimator::writeOutput(const std::vector > >&, double, const std::vector >&, const std::vector >&, const std::vector >&, const std::vector >&, std::string, double)' at /build/relion-3.1.3/src/jaz/motion/motion_estimator.cpp:737:21: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator]', inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /build/relion-3.1.3/src/CPlot2D.h:168:33, inlined from 'void MotionEstimator::writeOutput(const std::vector > >&, double, const std::vector >&, const std::vector >&, const std::vector >&, const std::vector >&, std::string, double)' at /build/relion-3.1.3/src/jaz/motion/motion_estimator.cpp:751:20: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator]', inlined from 'void CPlot2D::AddDataSet(CDataSet)' at /build/relion-3.1.3/src/CPlot2D.h:1198:26, inlined from 'void MotionEstimator::writeOutput(const std::vector > >&, double, const std::vector >&, const std::vector >&, const std::vector >&, const std::vector >&, std::string, double)' at /build/relion-3.1.3/src/jaz/motion/motion_estimator.cpp:753:21: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ [ 45%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/three_hyperparameter_fit.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/three_hyperparameter_fit.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/three_hyperparameter_fit.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/three_hyperparameter_fit.cpp.o -c /build/relion-3.1.3/src/jaz/motion/three_hyperparameter_fit.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, from /build/relion-3.1.3/src/jaz/motion/three_hyperparameter_fit.cpp:22: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 45%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/two_hyperparameter_fit.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/two_hyperparameter_fit.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/motion/two_hyperparameter_fit.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/motion/two_hyperparameter_fit.cpp.o -c /build/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/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/math/Zernike.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/math/Zernike.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/math/Zernike.cpp.o -c /build/relion-3.1.3/src/jaz/math/Zernike.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/motion/alignment_set.h:24, from /build/relion-3.1.3/src/jaz/motion/motion_param_estimator.h:24, from /build/relion-3.1.3/src/jaz/motion/two_hyperparameter_fit.cpp:22: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/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/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/color_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/img_proc/color_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/img_proc/color_helper.cpp.o -c /build/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/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/filter_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/img_proc/filter_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/img_proc/filter_helper.cpp.o -c /build/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/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/image_op.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/img_proc/image_op.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/img_proc/image_op.cpp.o -c /build/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/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/backprojection_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/tomo/backprojection_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/tomo/backprojection_helper.cpp.o -c /build/relion-3.1.3/src/jaz/tomo/backprojection_helper.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/img_proc/color_helper.h:5, from /build/relion-3.1.3/src/jaz/img_proc/color_helper.cpp:1: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/img_proc/filter_helper.h:24, from /build/relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/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/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/imod_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/tomo/imod_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/tomo/imod_helper.cpp.o -c /build/relion-3.1.3/src/jaz/tomo/imod_helper.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/tomo/backprojection_helper.h:24, from /build/relion-3.1.3/src/jaz/tomo/backprojection_helper.cpp:23: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/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/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/projection_helper.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/tomo/projection_helper.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/tomo/projection_helper.cpp.o -c /build/relion-3.1.3/src/jaz/tomo/projection_helper.cpp In file included from /usr/include/c++/12/vector:70, from /build/relion-3.1.3/src/jaz/tomo/imod_helper.h:24, from /build/relion-3.1.3/src/jaz/tomo/imod_helper.cpp:21: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gravis::t4Matrix}; _Tp = gravis::t4Matrix; _Alloc = std::allocator >]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gravis::t4Matrix}; _Tp = gravis::t4Matrix; _Alloc = std::allocator >]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gravis::t4Matrix; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'static std::vector > ImodHelper::readTiltTransforms(std::string, gravis::d4Matrix, double, double)' at /build/relion-3.1.3/src/jaz/tomo/imod_helper.cpp:55:26: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 48%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/tomo_stack.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/tomo_stack.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/tomo/tomo_stack.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/tomo/tomo_stack.cpp.o -c /build/relion-3.1.3/src/jaz/tomo/tomo_stack.cpp In file included from /usr/include/c++/12/vector:70, from /build/relion-3.1.3/src/jaz/tomo/projection_helper.h:24, from /build/relion-3.1.3/src/jaz/tomo/projection_helper.cpp:21: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gravis::t4Matrix}; _Tp = gravis::t4Matrix; _Alloc = std::allocator >]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gravis::t4Matrix}; _Tp = gravis::t4Matrix; _Alloc = std::allocator >]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gravis::t4Matrix; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'static std::vector > ProjectionHelper::loadAffineTransforms(std::string, double, double, bool)' at /build/relion-3.1.3/src/jaz/tomo/projection_helper.cpp:171:25: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from /build/relion-3.1.3/src/funcs.h:56, from /build/relion-3.1.3/src/image.h:58: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'static std::vector > ProjectionHelper::loadTiltProjectionsVol(std::string, double, double, double, double, double, double)' at /build/relion-3.1.3/src/jaz/tomo/projection_helper.cpp:105:25: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gravis::t4Matrix}; _Tp = gravis::t4Matrix; _Alloc = std::allocator >]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gravis::t4Matrix; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'static std::vector > ProjectionHelper::loadTiltProjectionsVol(std::string, double, double, double, double, double, double)' at /build/relion-3.1.3/src/jaz/tomo/projection_helper.cpp:115:26: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gravis::t4Matrix}; _Tp = gravis::t4Matrix; _Alloc = std::allocator >]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'static std::vector > ProjectionHelper::loadTiltProjections(std::string, double, double)' at /build/relion-3.1.3/src/jaz/tomo/projection_helper.cpp:54:25: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gravis::t4Matrix}; _Tp = gravis::t4Matrix; _Alloc = std::allocator >]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gravis::t4Matrix; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'static std::vector > ProjectionHelper::loadTiltProjections(std::string, double, double)' at /build/relion-3.1.3/src/jaz/tomo/projection_helper.cpp:64:26: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'static void BackprojectionHelper::backprojectRaw(const Image&, std::string, Volume&, Volume&, gravis::d3Vector, double, int)' at /build/relion-3.1.3/src/jaz/tomo/backprojection_helper.cpp:75:25: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gravis::t4Matrix}; _Tp = gravis::t4Matrix; _Alloc = std::allocator >]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gravis::t4Matrix; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'static void BackprojectionHelper::backprojectRaw(const Image&, std::string, Volume&, Volume&, gravis::d3Vector, double, int)' at /build/relion-3.1.3/src/jaz/tomo/backprojection_helper.cpp:85:26: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 49%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/io/star_converter.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/io/star_converter.cpp.o -MF CMakeFiles/relion_lib.dir/__/jaz/io/star_converter.cpp.o.d -o CMakeFiles/relion_lib.dir/__/jaz/io/star_converter.cpp.o -c /build/relion-3.1.3/src/jaz/io/star_converter.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/tomo/tomo_stack.h:25, from /build/relion-3.1.3/src/jaz/tomo/tomo_stack.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-3.1.3/src/jaz/io/star_converter.cpp:1: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 49%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyev2.c.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyev2.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyev2.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyev2.c.o -c /build/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/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevc3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevc3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevc3.c.o -c /build/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/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevd3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevd3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevd3.c.o -c /build/relion-3.1.3/src/jaz/d3x3/dsyevd3.c In file included from /usr/include/c++/12/vector:70, from /build/relion-3.1.3/src/funcs.h:56, from /build/relion-3.1.3/src/image.h:58: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gravis::t2Vector}; _Tp = gravis::t2Vector; _Alloc = std::allocator >]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ [ 50%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevh3.c.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevh3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevh3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevh3.c.o -c /build/relion-3.1.3/src/jaz/d3x3/dsyevh3.c In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gravis::t2Vector}; _Tp = gravis::t2Vector; _Alloc = std::allocator >]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gravis::t2Vector; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'std::vector > > TomoStack::loadFiducials(std::string, double)' at /build/relion-3.1.3/src/jaz/tomo/tomo_stack.cpp:340:28: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gravis::t2Vector}; _Tp = gravis::t2Vector; _Alloc = std::allocator >]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gravis::t2Vector; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'std::vector > > TomoStack::loadFiducials(std::string, double)' at /build/relion-3.1.3/src/jaz/tomo/tomo_stack.cpp:361:24: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 51%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevj3.c.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevj3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevj3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevj3.c.o -c /build/relion-3.1.3/src/jaz/d3x3/dsyevj3.c [ 51%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevq3.c.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevq3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevq3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevq3.c.o -c /build/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/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevv3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevv3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevv3.c.o -c /build/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/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsytrd3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsytrd3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsytrd3.c.o -c /build/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/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/slvsec3.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/d3x3/slvsec3.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/slvsec3.c.o -c /build/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/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c99 -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_lib.dir/__/jaz/lbfgs/lbfgs.c.o -MF CMakeFiles/relion_lib.dir/__/jaz/lbfgs/lbfgs.c.o.d -o CMakeFiles/relion_lib.dir/__/jaz/lbfgs/lbfgs.c.o -c /build/relion-3.1.3/src/jaz/lbfgs/lbfgs.c In file included from /usr/include/c++/12/vector:70, from /build/relion-3.1.3/src/funcs.h:56, from /build/relion-3.1.3/src/image.h:58: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gravis::t3Vector}; _Tp = gravis::t3Vector; _Alloc = std::allocator >]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gravis::t3Vector}; _Tp = gravis::t3Vector; _Alloc = std::allocator >]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gravis::t3Vector; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'static std::vector > FilterHelper::localMinima(Image&, double)' at /build/relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:1683:26: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'static void FilterHelper::descendTV(const Image&, Image&, double)' at /build/relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:2393:36: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'static void FilterHelper::descendTV(const Image&, Image&, double)' at /build/relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:2394:36: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'static void FilterHelper::descendTV(const Image&, Image&, double)' at /build/relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:2395:36: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'static void FilterHelper::descendTV(const Image&, Image&, double)' at /build/relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:2396:36: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'static void FilterHelper::descendTV(const Image&, Image&, double)' at /build/relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:2397:36: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'static void FilterHelper::descendTV(const Image&, Image&, double)' at /build/relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:2398:36: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ [ 53%] Linking CXX static library ../../lib/librelion_lib.a cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -P CMakeFiles/relion_lib.dir/cmake_clean_target.cmake cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E 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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/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/relion_gui_lib.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/autopick.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/align_symmetry.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/autopick_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' make[4]: Leaving directory '/build/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/autopick.dir/build.make src/apps/CMakeFiles/autopick.dir/build make[4]: Leaving directory '/build/relion-3.1.3/build' make[4]: Entering directory '/build/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]: Leaving directory '/build/relion-3.1.3/build' make[4]: Entering directory '/build/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/relion-3.1.3/build' [ 53%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o -MF CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o.d -o CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o -c /build/relion-3.1.3/src/displayer.cpp [ 54%] Building CXX object src/apps/CMakeFiles/autopick.dir/autopick.cpp.o [ 54%] Building CXX object src/apps/CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o -MF CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o.d -o CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o -c /build/relion-3.1.3/src/apps/autopick_mpi.cpp cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/autopick.dir/autopick.cpp.o -MF CMakeFiles/autopick.dir/autopick.cpp.o.d -o CMakeFiles/autopick.dir/autopick.cpp.o -c /build/relion-3.1.3/src/apps/autopick.cpp [ 54%] Building CXX object src/apps/CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o -MF CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o.d -o CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o -c /build/relion-3.1.3/src/apps/align_symmetry.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/projector.h:25, from /build/relion-3.1.3/src/apps/align_symmetry.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/autopicker.h:10, from /build/relion-3.1.3/src/apps/autopick.cpp:20: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/displayer.h:40, from /build/relion-3.1.3/src/displayer.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/autopicker.h:10, from /build/relion-3.1.3/src/autopicker_mpi.h:12, from /build/relion-3.1.3/src/apps/autopick_mpi.cpp:20: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 54%] Linking CXX executable ../../bin/relion_autopick cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/autopick.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -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/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 55%] Linking CXX executable ../../bin/relion_autopick_mpi cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/autopick_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -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/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' [ 55%] Built target autopick /usr/bin/make -f src/apps/CMakeFiles/convert_star.dir/build.make src/apps/CMakeFiles/convert_star.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/convert_star.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' [ 55%] Building CXX object src/apps/CMakeFiles/convert_star.dir/convert_star.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/convert_star.dir/convert_star.cpp.o -MF CMakeFiles/convert_star.dir/convert_star.cpp.o.d -o CMakeFiles/convert_star.dir/convert_star.cpp.o -c /build/relion-3.1.3/src/apps/convert_star.cpp make[4]: Leaving directory '/build/relion-3.1.3/build' [ 55%] Built target autopick_mpi /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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/convert_to_tiff.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' [ 55%] Building CXX object src/apps/CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o -MF CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o.d -o CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o -c /build/relion-3.1.3/src/apps/convert_to_tiff.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-3.1.3/src/apps/convert_star.cpp:24: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/tiff_converter.h:24, from /build/relion-3.1.3/src/apps/convert_to_tiff.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 55%] Linking CXX executable ../../bin/relion_convert_to_tiff cd /build/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/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -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/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' [ 55%] 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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/convert_to_tiff_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' [ 56%] Building CXX object src/apps/CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o -MF CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o.d -o CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o -c /build/relion-3.1.3/src/apps/convert_to_tiff_mpi.cpp [ 57%] Linking CXX executable ../../bin/relion_convert_star cd /build/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/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -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/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' [ 57%] Built target convert_star /usr/bin/make -f src/apps/CMakeFiles/ctf_mask_test.dir/build.make src/apps/CMakeFiles/ctf_mask_test.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/ctf_mask_test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' [ 57%] Building CXX object src/apps/CMakeFiles/ctf_mask_test.dir/ctf_mask_test.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/ctf_mask_test.dir/ctf_mask_test.cpp.o -MF CMakeFiles/ctf_mask_test.dir/ctf_mask_test.cpp.o.d -o CMakeFiles/ctf_mask_test.dir/ctf_mask_test.cpp.o -c /build/relion-3.1.3/src/apps/ctf_mask_test.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/tiff_converter.h:24, from /build/relion-3.1.3/src/apps/convert_to_tiff_mpi.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/apps/ctf_mask_test.cpp:7: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/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_mpi cd /build/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/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -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/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' [ 57%] Built target convert_to_tiff_mpi /usr/bin/make -f src/apps/CMakeFiles/ctf_refine.dir/build.make src/apps/CMakeFiles/ctf_refine.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/ctf_refine.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' [ 57%] Building CXX object src/apps/CMakeFiles/ctf_refine.dir/ctf_refine.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/ctf_refine.dir/ctf_refine.cpp.o -MF CMakeFiles/ctf_refine.dir/ctf_refine.cpp.o.d -o CMakeFiles/ctf_refine.dir/ctf_refine.cpp.o -c /build/relion-3.1.3/src/apps/ctf_refine.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-3.1.3/src/apps/ctf_refine.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 57%] Linking CXX executable ../../bin/relion_align_symmetry cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/align_symmetry.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -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/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' [ 57%] Built target align_symmetry /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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/ctf_refine_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' [ 57%] Building CXX object src/apps/CMakeFiles/ctf_refine_mpi.dir/ctf_refine_mpi.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/ctf_refine_mpi.dir/ctf_refine_mpi.cpp.o -MF CMakeFiles/ctf_refine_mpi.dir/ctf_refine_mpi.cpp.o.d -o CMakeFiles/ctf_refine_mpi.dir/ctf_refine_mpi.cpp.o -c /build/relion-3.1.3/src/apps/ctf_refine_mpi.cpp [ 58%] Linking CXX executable ../../bin/relion_ctf_refine cd /build/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/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -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/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' [ 58%] Built target ctf_refine /usr/bin/make -f src/apps/CMakeFiles/ctf_toolbox.dir/build.make src/apps/CMakeFiles/ctf_toolbox.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/ctf_toolbox.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' [ 59%] Building CXX object src/apps/CMakeFiles/ctf_toolbox.dir/ctf_toolbox.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/ctf_toolbox.dir/ctf_toolbox.cpp.o -MF CMakeFiles/ctf_toolbox.dir/ctf_toolbox.cpp.o.d -o CMakeFiles/ctf_toolbox.dir/ctf_toolbox.cpp.o -c /build/relion-3.1.3/src/apps/ctf_toolbox.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-3.1.3/src/jaz/ctf/ctf_refiner.h:24, from /build/relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.h:26, from /build/relion-3.1.3/src/apps/ctf_refine_mpi.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/apps/ctf_toolbox.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 59%] Linking CXX executable ../../bin/relion_ctf_refine_mpi cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/ctf_refine_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -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/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 60%] Linking CXX executable ../../bin/relion_ctf_mask_test cd /build/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/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -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/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' [ 60%] Built target ctf_mask_test /usr/bin/make -f src/apps/CMakeFiles/demodulate.dir/build.make src/apps/CMakeFiles/demodulate.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/demodulate.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.3/build' [ 60%] Built target ctf_refine_mpi /usr/bin/make -f src/apps/CMakeFiles/estimate_gain.dir/build.make src/apps/CMakeFiles/estimate_gain.dir/depend make[4]: Leaving directory '/build/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/relion-3.1.3/build' make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/estimate_gain.dir/DependInfo.cmake --color= [ 60%] Building CXX object src/apps/CMakeFiles/demodulate.dir/demodulate.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/demodulate.dir/demodulate.cpp.o -MF CMakeFiles/demodulate.dir/demodulate.cpp.o.d -o CMakeFiles/demodulate.dir/demodulate.cpp.o -c /build/relion-3.1.3/src/apps/demodulate.cpp make[4]: Leaving directory '/build/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/relion-3.1.3/build' [ 60%] Building CXX object src/apps/CMakeFiles/estimate_gain.dir/estimate_gain.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/estimate_gain.dir/estimate_gain.cpp.o -MF CMakeFiles/estimate_gain.dir/estimate_gain.cpp.o.d -o CMakeFiles/estimate_gain.dir/estimate_gain.cpp.o -c /build/relion-3.1.3/src/apps/estimate_gain.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/vtk_helper.h:24, from /build/relion-3.1.3/src/apps/demodulate.cpp:1: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/apps/estimate_gain.cpp:27: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 60%] Linking CXX executable ../../bin/relion_ctf_toolbox cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/ctf_toolbox.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -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/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' [ 60%] Built target ctf_toolbox /usr/bin/make -f src/apps/CMakeFiles/external_reconstruct.dir/build.make src/apps/CMakeFiles/external_reconstruct.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/external_reconstruct.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' [ 61%] Building CXX object src/apps/CMakeFiles/external_reconstruct.dir/external_reconstruct.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/external_reconstruct.dir/external_reconstruct.cpp.o -MF CMakeFiles/external_reconstruct.dir/external_reconstruct.cpp.o.d -o CMakeFiles/external_reconstruct.dir/external_reconstruct.cpp.o -c /build/relion-3.1.3/src/apps/external_reconstruct.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/apps/external_reconstruct.cpp:24: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 62%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o -MF CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o.d -o CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o -c /build/relion-3.1.3/src/gui_entries.cpp [ 62%] Linking CXX executable ../../bin/relion_estimate_gain cd /build/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/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -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/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' [ 62%] Built target estimate_gain /usr/bin/make -f src/apps/CMakeFiles/find_tiltpairs.dir/build.make src/apps/CMakeFiles/find_tiltpairs.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/find_tiltpairs.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' [ 62%] Building CXX object src/apps/CMakeFiles/find_tiltpairs.dir/find_tiltpairs.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/find_tiltpairs.dir/find_tiltpairs.cpp.o -MF CMakeFiles/find_tiltpairs.dir/find_tiltpairs.cpp.o.d -o CMakeFiles/find_tiltpairs.dir/find_tiltpairs.cpp.o -c /build/relion-3.1.3/src/apps/find_tiltpairs.cpp [ 62%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o -MF CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o.d -o CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o -c /build/relion-3.1.3/src/gui_jobwindow.cpp [ 63%] Linking CXX executable ../../bin/relion_demodulate cd /build/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/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -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/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' [ 63%] Built target demodulate /usr/bin/make -f src/apps/CMakeFiles/flex_analyse.dir/build.make src/apps/CMakeFiles/flex_analyse.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/flex_analyse.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' [ 63%] Building CXX object src/apps/CMakeFiles/flex_analyse.dir/flex_analyse.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/flex_analyse.dir/flex_analyse.cpp.o -MF CMakeFiles/flex_analyse.dir/flex_analyse.cpp.o.d -o CMakeFiles/flex_analyse.dir/flex_analyse.cpp.o -c /build/relion-3.1.3/src/apps/flex_analyse.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/exp_model.h:24, from /build/relion-3.1.3/src/apps/../flex_analyser.h:24, from /build/relion-3.1.3/src/apps/flex_analyse.cpp:22: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 63%] Linking CXX executable ../../bin/relion_external_reconstruct cd /build/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/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -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/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 64%] Linking CXX executable ../../bin/relion_find_tiltpairs cd /build/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/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -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/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' [ 64%] Built target find_tiltpairs /usr/bin/make -f src/apps/CMakeFiles/flex_analyse_mpi.dir/build.make src/apps/CMakeFiles/flex_analyse_mpi.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/flex_analyse_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' make[4]: Leaving directory '/build/relion-3.1.3/build' [ 64%] Building CXX object src/apps/CMakeFiles/flex_analyse_mpi.dir/flex_analyse_mpi.cpp.o [ 64%] Built target external_reconstruct cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/flex_analyse_mpi.dir/flex_analyse_mpi.cpp.o -MF CMakeFiles/flex_analyse_mpi.dir/flex_analyse_mpi.cpp.o.d -o CMakeFiles/flex_analyse_mpi.dir/flex_analyse_mpi.cpp.o -c /build/relion-3.1.3/src/apps/flex_analyse_mpi.cpp /usr/bin/make -f src/apps/CMakeFiles/helix_inimodel2d.dir/build.make src/apps/CMakeFiles/helix_inimodel2d.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/helix_inimodel2d.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' [ 65%] Building CXX object src/apps/CMakeFiles/helix_inimodel2d.dir/helix_inimodel2d.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/helix_inimodel2d.dir/helix_inimodel2d.cpp.o -MF CMakeFiles/helix_inimodel2d.dir/helix_inimodel2d.cpp.o.d -o CMakeFiles/helix_inimodel2d.dir/helix_inimodel2d.cpp.o -c /build/relion-3.1.3/src/apps/helix_inimodel2d.cpp [ 66%] Linking CXX executable ../../bin/relion_flex_analyse cd /build/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/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -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/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/exp_model.h:24, from /build/relion-3.1.3/src/apps/../flex_analyser.h:24, from /build/relion-3.1.3/src/apps/flex_analyse_mpi.cpp:22: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/apps/../helix_inimodel2d.h:29, from /build/relion-3.1.3/src/apps/helix_inimodel2d.cpp:22: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/build/relion-3.1.3/build' [ 66%] Built target flex_analyse /usr/bin/make -f src/apps/CMakeFiles/helix_toolbox.dir/build.make src/apps/CMakeFiles/helix_toolbox.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/helix_toolbox.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' [ 67%] Building CXX object src/apps/CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o -MF CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o.d -o CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o -c /build/relion-3.1.3/src/apps/helix_toolbox.cpp [ 67%] Linking CXX executable ../../bin/relion_helix_inimodel2d cd /build/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/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -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/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' [ 67%] Built target helix_inimodel2d /usr/bin/make -f src/apps/CMakeFiles/image_handler.dir/build.make src/apps/CMakeFiles/image_handler.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/image_handler.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' [ 67%] Building CXX object src/apps/CMakeFiles/image_handler.dir/image_handler.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/image_handler.dir/image_handler.cpp.o -MF CMakeFiles/image_handler.dir/image_handler.cpp.o.d -o CMakeFiles/image_handler.dir/image_handler.cpp.o -c /build/relion-3.1.3/src/apps/image_handler.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/helix.h:30, from /build/relion-3.1.3/src/apps/helix_toolbox.cpp:22: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/apps/image_handler.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 67%] Linking CXX executable ../../bin/relion_flex_analyse_mpi cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/flex_analyse_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -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/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 67%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o -MF CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o.d -o CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o -c /build/relion-3.1.3/src/gui_mainwindow.cpp make[4]: Leaving directory '/build/relion-3.1.3/build' [ 67%] Built target flex_analyse_mpi /usr/bin/make -f src/apps/CMakeFiles/import.dir/build.make src/apps/CMakeFiles/import.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/import.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' [ 67%] Building CXX object src/apps/CMakeFiles/import.dir/import.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/import.dir/import.cpp.o -MF CMakeFiles/import.dir/import.cpp.o.d -o CMakeFiles/import.dir/import.cpp.o -c /build/relion-3.1.3/src/apps/import.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-3.1.3/src/scheduler.h:26, from /build/relion-3.1.3/src/gui_mainwindow.h:28, from /build/relion-3.1.3/src/gui_mainwindow.cpp:22: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-3.1.3/src/apps/import.cpp:22: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 67%] Linking CXX executable ../../bin/relion_import cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/import.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -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/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' [ 67%] 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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/localsym.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' [ 68%] Building CXX object src/apps/CMakeFiles/localsym.dir/localsym.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/localsym.dir/localsym.cpp.o -MF CMakeFiles/localsym.dir/localsym.cpp.o.d -o CMakeFiles/localsym.dir/localsym.cpp.o -c /build/relion-3.1.3/src/apps/localsym.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-3.1.3/src/apps/localsym.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 68%] Linking CXX executable ../../bin/relion_localsym cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/localsym.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -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/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' [ 68%] 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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/localsym_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' [ 69%] Building CXX object src/apps/CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o -MF CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o.d -o CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o -c /build/relion-3.1.3/src/apps/localsym_mpi.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/local_symmetry.h:30, from /build/relion-3.1.3/src/local_symmetry_mpi.h:5, from /build/relion-3.1.3/src/apps/localsym_mpi.cpp:1: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 69%] Linking CXX executable ../../bin/relion_localsym_mpi cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/localsym_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -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/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' [ 69%] Built target localsym_mpi /usr/bin/make -f src/apps/CMakeFiles/mask_create.dir/build.make src/apps/CMakeFiles/mask_create.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/mask_create.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' [ 69%] Building CXX object src/apps/CMakeFiles/mask_create.dir/mask_create.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/mask_create.dir/mask_create.cpp.o -MF CMakeFiles/mask_create.dir/mask_create.cpp.o.d -o CMakeFiles/mask_create.dir/mask_create.cpp.o -c /build/relion-3.1.3/src/apps/mask_create.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/apps/mask_create.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 69%] Linking CXX executable ../../bin/relion_helix_toolbox cd /build/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/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -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/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 70%] Linking CXX executable ../../bin/relion_image_handler cd /build/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/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -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/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 71%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/manualpicker.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/manualpicker.cpp.o -MF CMakeFiles/relion_gui_lib.dir/__/manualpicker.cpp.o.d -o CMakeFiles/relion_gui_lib.dir/__/manualpicker.cpp.o -c /build/relion-3.1.3/src/manualpicker.cpp make[4]: Leaving directory '/build/relion-3.1.3/build' [ 71%] Built target helix_toolbox /usr/bin/make -f src/apps/CMakeFiles/merge_particles.dir/build.make src/apps/CMakeFiles/merge_particles.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/merge_particles.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' [ 72%] Building CXX object src/apps/CMakeFiles/merge_particles.dir/merge_particles.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/merge_particles.dir/merge_particles.cpp.o -MF CMakeFiles/merge_particles.dir/merge_particles.cpp.o.d -o CMakeFiles/merge_particles.dir/merge_particles.cpp.o -c /build/relion-3.1.3/src/apps/merge_particles.cpp make[4]: Leaving directory '/build/relion-3.1.3/build' [ 72%] Built target image_handler /usr/bin/make -f src/apps/CMakeFiles/motion_refine.dir/build.make src/apps/CMakeFiles/motion_refine.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/motion_refine.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' [ 73%] Building CXX object src/apps/CMakeFiles/motion_refine.dir/motion_refine.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/motion_refine.dir/motion_refine.cpp.o -MF CMakeFiles/motion_refine.dir/motion_refine.cpp.o.d -o CMakeFiles/motion_refine.dir/motion_refine.cpp.o -c /build/relion-3.1.3/src/apps/motion_refine.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-3.1.3/src/manualpicker.h:43, from /build/relion-3.1.3/src/manualpicker.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/io/star_converter.h:5, from /build/relion-3.1.3/src/apps/merge_particles.cpp:2: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-3.1.3/src/ctf.h:50, from /build/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-3.1.3/src/apps/motion_refine.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/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/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/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -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/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' [ 73%] Built target merge_particles /usr/bin/make -f src/apps/CMakeFiles/motion_refine_mpi.dir/build.make src/apps/CMakeFiles/motion_refine_mpi.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/motion_refine_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' [ 73%] Building CXX object src/apps/CMakeFiles/motion_refine_mpi.dir/motion_refine_mpi.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/motion_refine_mpi.dir/motion_refine_mpi.cpp.o -MF CMakeFiles/motion_refine_mpi.dir/motion_refine_mpi.cpp.o.d -o CMakeFiles/motion_refine_mpi.dir/motion_refine_mpi.cpp.o -c /build/relion-3.1.3/src/apps/motion_refine_mpi.cpp [ 73%] Linking CXX executable ../../bin/relion_motion_refine cd /build/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/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -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/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-3.1.3/src/ctf.h:50, from /build/relion-3.1.3/src/jaz/motion/motion_refiner.h:25, from /build/relion-3.1.3/src/jaz/motion/motion_refiner_mpi.h:27, from /build/relion-3.1.3/src/apps/motion_refine_mpi.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/build/relion-3.1.3/build' [ 73%] Built target motion_refine /usr/bin/make -f src/apps/CMakeFiles/mrc2vtk.dir/build.make src/apps/CMakeFiles/mrc2vtk.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/mrc2vtk.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' [ 73%] Building CXX object src/apps/CMakeFiles/mrc2vtk.dir/mrc2vtk.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/mrc2vtk.dir/mrc2vtk.cpp.o -MF CMakeFiles/mrc2vtk.dir/mrc2vtk.cpp.o.d -o CMakeFiles/mrc2vtk.dir/mrc2vtk.cpp.o -c /build/relion-3.1.3/src/apps/mrc2vtk.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/apps/mrc2vtk.cpp:1: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 73%] Linking CXX executable ../../bin/relion_mask_create cd /build/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/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -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/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 74%] Linking CXX executable ../../bin/relion_motion_refine_mpi cd /build/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/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -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/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' [ 74%] Built target mask_create /usr/bin/make -f src/apps/CMakeFiles/particle_FCC.dir/build.make src/apps/CMakeFiles/particle_FCC.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/particle_FCC.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' [ 75%] Building CXX object src/apps/CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o -MF CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o.d -o CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o -c /build/relion-3.1.3/src/apps/particle_FCC.cpp make[4]: Leaving directory '/build/relion-3.1.3/build' [ 75%] Built target motion_refine_mpi /usr/bin/make -f src/apps/CMakeFiles/particle_reposition.dir/build.make src/apps/CMakeFiles/particle_reposition.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/particle_reposition.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' [ 76%] Building CXX object src/apps/CMakeFiles/particle_reposition.dir/particle_reposition.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/particle_reposition.dir/particle_reposition.cpp.o -MF CMakeFiles/particle_reposition.dir/particle_reposition.cpp.o.d -o CMakeFiles/particle_reposition.dir/particle_reposition.cpp.o -c /build/relion-3.1.3/src/apps/particle_reposition.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/apps/particle_FCC.cpp:7: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/projector.h:25, from /build/relion-3.1.3/src/ml_model.h:23, from /build/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-3.1.3/src/apps/particle_reposition.cpp:22: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 76%] Linking CXX executable ../../bin/relion_particle_FCC cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_FCC.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -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/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 76%] Linking CXX executable ../../bin/relion_mrc2vtk cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/mrc2vtk.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -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/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' [ 76%] Built target mrc2vtk /usr/bin/make -f src/apps/CMakeFiles/particle_select.dir/build.make src/apps/CMakeFiles/particle_select.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/particle_select.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' make[4]: Leaving directory '/build/relion-3.1.3/build' [ 76%] Building CXX object src/apps/CMakeFiles/particle_select.dir/particle_select.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/particle_select.dir/particle_select.cpp.o -MF CMakeFiles/particle_select.dir/particle_select.cpp.o.d -o CMakeFiles/particle_select.dir/particle_select.cpp.o -c /build/relion-3.1.3/src/apps/particle_select.cpp [ 76%] Built target particle_FCC /usr/bin/make -f src/apps/CMakeFiles/particle_subtract.dir/build.make src/apps/CMakeFiles/particle_subtract.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/particle_subtract.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' [ 76%] Building CXX object src/apps/CMakeFiles/particle_subtract.dir/particle_subtract.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/particle_subtract.dir/particle_subtract.cpp.o -MF CMakeFiles/particle_subtract.dir/particle_subtract.cpp.o.d -o CMakeFiles/particle_subtract.dir/particle_subtract.cpp.o -c /build/relion-3.1.3/src/apps/particle_subtract.cpp [ 76%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/cxxutils.cc.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/cxxutils.cc.o -MF CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/cxxutils.cc.o.d -o CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/cxxutils.cc.o -c /build/relion-3.1.3/src/Healpix_2.15a/cxxutils.cc In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-3.1.3/src/ctf.h:50, from /build/relion-3.1.3/src/jaz/stack_helper.h:24, from /build/relion-3.1.3/src/apps/particle_select.cpp:1: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/projector.h:25, from /build/relion-3.1.3/src/ml_model.h:23, from /build/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-3.1.3/src/apps/../particle_subtractor.h:24, from /build/relion-3.1.3/src/apps/particle_subtract.cpp:22: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 77%] Linking CXX executable ../../bin/relion_particle_select cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_select.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -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/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' [ 77%] Built target particle_select /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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/particle_subtract_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' [ 77%] Building CXX object src/apps/CMakeFiles/particle_subtract_mpi.dir/particle_subtract_mpi.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/particle_subtract_mpi.dir/particle_subtract_mpi.cpp.o -MF CMakeFiles/particle_subtract_mpi.dir/particle_subtract_mpi.cpp.o.d -o CMakeFiles/particle_subtract_mpi.dir/particle_subtract_mpi.cpp.o -c /build/relion-3.1.3/src/apps/particle_subtract_mpi.cpp [ 78%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o -MF CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o.d -o CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o -c /build/relion-3.1.3/src/Healpix_2.15a/healpix_base.cc [ 79%] Linking CXX executable ../../bin/relion_particle_subtract cd /build/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/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -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/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/projector.h:25, from /build/relion-3.1.3/src/ml_model.h:23, from /build/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-3.1.3/src/apps/../particle_subtractor.h:24, from /build/relion-3.1.3/src/apps/particle_subtract_mpi.cpp:22: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/build/relion-3.1.3/build' [ 79%] Built target particle_subtract /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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/particle_symmetry_expand.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' [ 80%] Building CXX object src/apps/CMakeFiles/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o -MF CMakeFiles/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o.d -o CMakeFiles/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o -c /build/relion-3.1.3/src/apps/particle_symmetry_expand.cpp [ 80%] Linking CXX static library ../../lib/librelion_gui_lib.a cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -P CMakeFiles/relion_gui_lib.dir/cmake_clean_target.cmake cd /build/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 /usr/bin/ranlib ../../lib/librelion_gui_lib.a In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-3.1.3/src/apps/particle_symmetry_expand.cpp:26: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/build/relion-3.1.3/build' [ 80%] Built target relion_gui_lib /usr/bin/make -f src/apps/CMakeFiles/pipeliner.dir/build.make src/apps/CMakeFiles/pipeliner.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/pipeliner.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' [ 80%] Building CXX object src/apps/CMakeFiles/pipeliner.dir/pipeliner.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/pipeliner.dir/pipeliner.cpp.o -MF CMakeFiles/pipeliner.dir/pipeliner.cpp.o.d -o CMakeFiles/pipeliner.dir/pipeliner.cpp.o -c /build/relion-3.1.3/src/apps/pipeliner.cpp [ 80%] Linking CXX executable ../../bin/relion_particle_symmetry_expand cd /build/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/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -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/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 80%] Linking CXX executable ../../bin/relion_particle_subtract_mpi cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_subtract_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -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/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' [ 80%] Built target particle_symmetry_expand /usr/bin/make -f src/apps/CMakeFiles/plot_delocalisation.dir/build.make src/apps/CMakeFiles/plot_delocalisation.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/plot_delocalisation.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' [ 80%] Building CXX object src/apps/CMakeFiles/plot_delocalisation.dir/plot_delocalisation.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/plot_delocalisation.dir/plot_delocalisation.cpp.o -MF CMakeFiles/plot_delocalisation.dir/plot_delocalisation.cpp.o.d -o CMakeFiles/plot_delocalisation.dir/plot_delocalisation.cpp.o -c /build/relion-3.1.3/src/apps/plot_delocalisation.cpp [ 80%] Linking CXX executable ../../bin/relion_particle_reposition cd /build/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/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -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/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/apps/plot_delocalisation.cpp:7: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/build/relion-3.1.3/build' [ 80%] Built target particle_subtract_mpi /usr/bin/make -f src/apps/CMakeFiles/postprocess.dir/build.make src/apps/CMakeFiles/postprocess.dir/depend make[4]: Leaving directory '/build/relion-3.1.3/build' make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/postprocess.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' In file included from /usr/include/c++/12/vector:70, from /build/relion-3.1.3/src/args.h:52, from /build/relion-3.1.3/src/apps/plot_delocalisation.cpp:6: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataPoint&}; _Tp = CDataPoint; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ [ 80%] Building CXX object src/apps/CMakeFiles/postprocess.dir/postprocess.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/postprocess.dir/postprocess.cpp.o -MF CMakeFiles/postprocess.dir/postprocess.cpp.o.d -o CMakeFiles/postprocess.dir/postprocess.cpp.o -c /build/relion-3.1.3/src/apps/postprocess.cpp /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CDataSet&}; _Tp = CDataSet; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 [ 80%] Built target particle_reposition /usr/bin/make -f src/apps/CMakeFiles/postprocess_mpi.dir/build.make src/apps/CMakeFiles/postprocess_mpi.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/postprocess_mpi.dir/DependInfo.cmake --color= In file included from /usr/include/c++/12/vector:64: /usr/include/c++/12/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataSet; _Alloc = std::allocator]': /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ make[4]: Leaving directory '/build/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/relion-3.1.3/build' [ 81%] Building CXX object src/apps/CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o -MF CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o.d -o CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o -c /build/relion-3.1.3/src/apps/postprocess_mpi.cpp In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator]', inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /build/relion-3.1.3/src/CPlot2D.h:168:33, inlined from 'int main(int, char**)' at /build/relion-3.1.3/src/apps/plot_delocalisation.cpp:207:23: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CDataPoint; _Alloc = std::allocator]', inlined from 'void CDataSet::AddDataPoint(CDataPoint)' at /build/relion-3.1.3/src/CPlot2D.h:168:33, inlined from 'int main(int, char**)' at /build/relion-3.1.3/src/apps/plot_delocalisation.cpp:213:21: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/postprocessing.h:24, from /build/relion-3.1.3/src/apps/postprocess.cpp:20: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/postprocessing.h:24, from /build/relion-3.1.3/src/apps/postprocess_mpi.cpp:20: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 82%] Linking CXX executable ../../bin/relion_pipeliner cd /build/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/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -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/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 82%] Linking CXX executable ../../bin/relion_postprocess cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/postprocess.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -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/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 82%] Linking CXX executable ../../bin/relion_postprocess_mpi cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/postprocess_mpi.dir/link.txt --verbose=1 [ 83%] Linking CXX executable ../../bin/relion_plot_delocalisation cd /build/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/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -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/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -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/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' [ 83%] Built target pipeliner /usr/bin/make -f src/apps/CMakeFiles/prepare_subtomo.dir/build.make src/apps/CMakeFiles/prepare_subtomo.dir/depend make[4]: Leaving directory '/build/relion-3.1.3/build' make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/prepare_subtomo.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.3/build' make[4]: Leaving directory '/build/relion-3.1.3/build' [ 83%] Built target plot_delocalisation /usr/bin/make -f src/apps/CMakeFiles/prepare_subtomo.dir/build.make src/apps/CMakeFiles/prepare_subtomo.dir/build make[4]: Entering directory '/build/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/preprocess.dir/build.make src/apps/CMakeFiles/preprocess.dir/depend [ 83%] Built target postprocess_mpi /usr/bin/make -f src/apps/CMakeFiles/preprocess_mpi.dir/build.make src/apps/CMakeFiles/preprocess_mpi.dir/depend [ 83%] Building CXX object src/apps/CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/preprocess.dir/DependInfo.cmake --color= cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o -MF CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o.d -o CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o -c /build/relion-3.1.3/src/apps/prepare_subtomo.cpp make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/preprocess_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.3/build' make[4]: Leaving directory '/build/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/relion-3.1.3/build' [ 83%] Built target postprocess /usr/bin/make -f src/apps/CMakeFiles/project.dir/build.make src/apps/CMakeFiles/project.dir/depend make[4]: Leaving directory '/build/relion-3.1.3/build' /usr/bin/make -f src/apps/CMakeFiles/preprocess_mpi.dir/build.make src/apps/CMakeFiles/preprocess_mpi.dir/build [ 83%] Building CXX object src/apps/CMakeFiles/preprocess.dir/preprocess.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/preprocess.dir/preprocess.cpp.o -MF CMakeFiles/preprocess.dir/preprocess.cpp.o.d -o CMakeFiles/preprocess.dir/preprocess.cpp.o -c /build/relion-3.1.3/src/apps/preprocess.cpp make[4]: Entering directory '/build/relion-3.1.3/build' make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/project.dir/DependInfo.cmake --color= [ 83%] Building CXX object src/apps/CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o -MF CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o.d -o CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o -c /build/relion-3.1.3/src/apps/preprocess_mpi.cpp make[4]: Leaving directory '/build/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/relion-3.1.3/build' [ 84%] Building CXX object src/apps/CMakeFiles/project.dir/project.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/project.dir/project.cpp.o -MF CMakeFiles/project.dir/project.cpp.o.d -o CMakeFiles/project.dir/project.cpp.o -c /build/relion-3.1.3/src/apps/project.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/preprocessing.h:29, from /build/relion-3.1.3/src/apps/preprocess.cpp:20: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/helix.h:30, from /build/relion-3.1.3/src/apps/prepare_subtomo.cpp:22: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/projector.h:25, from /build/relion-3.1.3/src/apps/project.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/preprocessing.h:29, from /build/relion-3.1.3/src/preprocessing_mpi.h:24, from /build/relion-3.1.3/src/apps/preprocess_mpi.cpp:20: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 85%] Linking CXX executable ../../bin/relion_preprocess cd /build/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/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -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/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 85%] Linking CXX executable ../../bin/relion_preprocess_mpi cd /build/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/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -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/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' [ 85%] Built target preprocess /usr/bin/make -f src/apps/CMakeFiles/reconstruct.dir/build.make src/apps/CMakeFiles/reconstruct.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/reconstruct.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' [ 85%] Building CXX object src/apps/CMakeFiles/reconstruct.dir/reconstruct.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/reconstruct.dir/reconstruct.cpp.o -MF CMakeFiles/reconstruct.dir/reconstruct.cpp.o.d -o CMakeFiles/reconstruct.dir/reconstruct.cpp.o -c /build/relion-3.1.3/src/apps/reconstruct.cpp make[4]: Leaving directory '/build/relion-3.1.3/build' [ 85%] Built target preprocess_mpi /usr/bin/make -f src/apps/CMakeFiles/reconstruct_mpi.dir/build.make src/apps/CMakeFiles/reconstruct_mpi.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/reconstruct_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' [ 85%] Building CXX object src/apps/CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o -MF CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o.d -o CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o -c /build/relion-3.1.3/src/apps/reconstruct_mpi.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/projector.h:25, from /build/relion-3.1.3/src/backprojector.h:33, from /build/relion-3.1.3/src/reconstructor.h:23, from /build/relion-3.1.3/src/apps/reconstruct.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/projector.h:25, from /build/relion-3.1.3/src/backprojector.h:33, from /build/relion-3.1.3/src/reconstructor.h:23, from /build/relion-3.1.3/src/reconstructor_mpi.h:25, from /build/relion-3.1.3/src/apps/reconstruct_mpi.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /usr/include/c++/12/vector:70, from /build/relion-3.1.3/src/args.h:52, from /build/relion-3.1.3/src/apps/prepare_subtomo.cpp:21: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 [ 86%] Linking CXX executable ../../bin/relion_reconstruct cd /build/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/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -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/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 87%] Linking CXX executable ../../bin/relion_reconstruct_mpi cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/reconstruct_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -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/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' [ 87%] Built target reconstruct /usr/bin/make -f src/apps/CMakeFiles/refine.dir/build.make src/apps/CMakeFiles/refine.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/refine.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' [ 87%] Building CXX object src/apps/CMakeFiles/refine.dir/refine.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/refine.dir/refine.cpp.o -MF CMakeFiles/refine.dir/refine.cpp.o.d -o CMakeFiles/refine.dir/refine.cpp.o -c /build/relion-3.1.3/src/apps/refine.cpp make[4]: Leaving directory '/build/relion-3.1.3/build' [ 87%] Built target reconstruct_mpi /usr/bin/make -f src/apps/CMakeFiles/refine_mpi.dir/build.make src/apps/CMakeFiles/refine_mpi.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/refine_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' [ 88%] Building CXX object src/apps/CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o -MF CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o.d -o CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o -c /build/relion-3.1.3/src/apps/refine_mpi.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/projector.h:25, from /build/relion-3.1.3/src/ml_model.h:23, from /build/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-3.1.3/src/apps/refine.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void prepare_subtomo::run()' at /build/relion-3.1.3/src/apps/prepare_subtomo.cpp:634:20: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void prepare_subtomo::run()' at /build/relion-3.1.3/src/apps/prepare_subtomo.cpp:652:27: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void prepare_subtomo::run()' at /build/relion-3.1.3/src/apps/prepare_subtomo.cpp:801:26: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void prepare_subtomo::run()' at /build/relion-3.1.3/src/apps/prepare_subtomo.cpp:802:24: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void prepare_subtomo::run()' at /build/relion-3.1.3/src/apps/prepare_subtomo.cpp:816:25: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void prepare_subtomo::run()' at /build/relion-3.1.3/src/apps/prepare_subtomo.cpp:833:23: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/projector.h:25, from /build/relion-3.1.3/src/ml_model.h:23, from /build/relion-3.1.3/src/ml_optimiser.h:35, from /build/relion-3.1.3/src/ml_optimiser_mpi.h:24, from /build/relion-3.1.3/src/apps/refine_mpi.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 88%] Linking CXX executable ../../bin/relion_refine cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/refine.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -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/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 88%] Linking CXX executable ../../bin/relion_project cd /build/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/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -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/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' [ 88%] Built target refine /usr/bin/make -f src/apps/CMakeFiles/reposition.dir/build.make src/apps/CMakeFiles/reposition.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/reposition.dir/DependInfo.cmake --color= [ 88%] Linking CXX executable ../../bin/relion_refine_mpi cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/refine_mpi.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/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/relion-3.1.3/build' /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -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/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 88%] Building CXX object src/apps/CMakeFiles/reposition.dir/reposition.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/reposition.dir/reposition.cpp.o -MF CMakeFiles/reposition.dir/reposition.cpp.o.d -o CMakeFiles/reposition.dir/reposition.cpp.o -c /build/relion-3.1.3/src/apps/reposition.cpp make[4]: Leaving directory '/build/relion-3.1.3/build' [ 88%] Built target project /usr/bin/make -f src/apps/CMakeFiles/run_ctffind.dir/build.make src/apps/CMakeFiles/run_ctffind.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/run_ctffind.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' [ 88%] Building CXX object src/apps/CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o -MF CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o.d -o CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o -c /build/relion-3.1.3/src/apps/run_ctffind.cpp make[4]: Leaving directory '/build/relion-3.1.3/build' [ 88%] Built target refine_mpi /usr/bin/make -f src/apps/CMakeFiles/run_ctffind_mpi.dir/build.make src/apps/CMakeFiles/run_ctffind_mpi.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/run_ctffind_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' [ 89%] Building CXX object src/apps/CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o -MF CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o.d -o CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o -c /build/relion-3.1.3/src/apps/run_ctffind_mpi.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-3.1.3/src/apps/reposition.cpp:1: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-3.1.3/src/apps/run_ctffind.cpp:20: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/ctffind_runner.h:31, from /build/relion-3.1.3/src/ctffind_runner_mpi.h:25, from /build/relion-3.1.3/src/apps/run_ctffind_mpi.cpp:20: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 89%] Linking CXX executable ../../bin/relion_run_ctffind cd /build/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/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -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/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' [ 89%] Linking CXX executable ../../bin/relion_run_ctffind_mpi cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/run_ctffind_mpi.dir/link.txt --verbose=1 [ 89%] Built target run_ctffind /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -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/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff /usr/bin/make -f src/apps/CMakeFiles/run_motioncorr.dir/build.make src/apps/CMakeFiles/run_motioncorr.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/run_motioncorr.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' [ 90%] Building CXX object src/apps/CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o -MF CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o.d -o CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o -c /build/relion-3.1.3/src/apps/run_motioncorr.cpp make[4]: Leaving directory '/build/relion-3.1.3/build' [ 90%] Built target run_ctffind_mpi /usr/bin/make -f src/apps/CMakeFiles/run_motioncorr_mpi.dir/build.make src/apps/CMakeFiles/run_motioncorr_mpi.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/run_motioncorr_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' [ 90%] Building CXX object src/apps/CMakeFiles/run_motioncorr_mpi.dir/run_motioncorr_mpi.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/run_motioncorr_mpi.dir/run_motioncorr_mpi.cpp.o -MF CMakeFiles/run_motioncorr_mpi.dir/run_motioncorr_mpi.cpp.o.d -o CMakeFiles/run_motioncorr_mpi.dir/run_motioncorr_mpi.cpp.o -c /build/relion-3.1.3/src/apps/run_motioncorr_mpi.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-3.1.3/src/apps/run_motioncorr.cpp:20: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/motioncorr_runner.h:32, from /build/relion-3.1.3/src/motioncorr_runner_mpi.h:25, from /build/relion-3.1.3/src/apps/run_motioncorr_mpi.cpp:20: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 91%] Linking CXX executable ../../bin/relion_reposition cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/reposition.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -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/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 91%] Linking CXX executable ../../bin/relion_run_motioncorr cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/run_motioncorr.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -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/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' [ 91%] Built target reposition /usr/bin/make -f src/apps/CMakeFiles/scheduler.dir/build.make src/apps/CMakeFiles/scheduler.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/scheduler.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' [ 91%] Building CXX object src/apps/CMakeFiles/scheduler.dir/scheduler.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/scheduler.dir/scheduler.cpp.o -MF CMakeFiles/scheduler.dir/scheduler.cpp.o.d -o CMakeFiles/scheduler.dir/scheduler.cpp.o -c /build/relion-3.1.3/src/apps/scheduler.cpp make[4]: Leaving directory '/build/relion-3.1.3/build' [ 91%] Built target run_motioncorr /usr/bin/make -f src/apps/CMakeFiles/stack_create.dir/build.make src/apps/CMakeFiles/stack_create.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/stack_create.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' [ 92%] Building CXX object src/apps/CMakeFiles/stack_create.dir/stack_create.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/stack_create.dir/stack_create.cpp.o -MF CMakeFiles/stack_create.dir/stack_create.cpp.o.d -o CMakeFiles/stack_create.dir/stack_create.cpp.o -c /build/relion-3.1.3/src/apps/stack_create.cpp [ 93%] Linking CXX executable ../../bin/relion_run_motioncorr_mpi cd /build/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/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -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/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' [ 93%] Built target run_motioncorr_mpi /usr/bin/make -f src/apps/CMakeFiles/star_handler.dir/build.make src/apps/CMakeFiles/star_handler.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/star_handler.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' [ 94%] Building CXX object src/apps/CMakeFiles/star_handler.dir/star_handler.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/star_handler.dir/star_handler.cpp.o -MF CMakeFiles/star_handler.dir/star_handler.cpp.o.d -o CMakeFiles/star_handler.dir/star_handler.cpp.o -c /build/relion-3.1.3/src/apps/star_handler.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/apps/stack_create.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-3.1.3/src/scheduler.h:26, from /build/relion-3.1.3/src/apps/scheduler.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 95%] Linking CXX executable ../../bin/relion_prepare_subtomo cd /build/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/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -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/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' [ 95%] Built target prepare_subtomo /usr/bin/make -f src/apps/CMakeFiles/tiltpair_plot.dir/build.make src/apps/CMakeFiles/tiltpair_plot.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/tiltpair_plot.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/apps/star_handler.cpp:21: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 95%] Building CXX object src/apps/CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o -MF CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o.d -o CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o -c /build/relion-3.1.3/src/apps/tiltpair_plot.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/apps/tiltpair_plot.cpp:25: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 96%] Linking CXX executable ../../bin/relion_tiltpair_plot cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiltpair_plot.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -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/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' [ 96%] 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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/tomo_test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' [ 96%] Building CXX object src/apps/CMakeFiles/tomo_test.dir/tomo_test.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/tomo_test.dir/tomo_test.cpp.o -MF CMakeFiles/tomo_test.dir/tomo_test.cpp.o.d -o CMakeFiles/tomo_test.dir/tomo_test.cpp.o -c /build/relion-3.1.3/src/apps/tomo_test.cpp [ 96%] Linking CXX executable ../../bin/relion_scheduler cd /build/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/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -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/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/tomo/tomo_stack.h:25, from /build/relion-3.1.3/src/apps/tomo_test.cpp:2: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /usr/include/c++/12/vector:70, from /build/relion-3.1.3/src/funcs.h:56, from /build/relion-3.1.3/src/image.h:58: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from /build/relion-3.1.3/src/funcs.h:56, from /build/relion-3.1.3/src/image.h:58: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gravis::t3Vector&}; _Tp = gravis::t3Vector; _Alloc = std::allocator >]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/relion-3.1.3/build' [ 96%] Built target scheduler /usr/bin/make -f src/apps/CMakeFiles/display.dir/build.make src/apps/CMakeFiles/display.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/display.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' [ 96%] Building CXX object src/apps/CMakeFiles/display.dir/display.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/display.dir/display.cpp.o -MF CMakeFiles/display.dir/display.cpp.o.d -o CMakeFiles/display.dir/display.cpp.o -c /build/relion-3.1.3/src/apps/display.cpp [ 96%] Linking CXX executable ../../bin/relion_stack_create cd /build/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/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -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/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' [ 96%] Built target stack_create /usr/bin/make -f src/apps/CMakeFiles/relion.dir/build.make src/apps/CMakeFiles/relion.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/relion.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' [ 96%] Building CXX object src/apps/CMakeFiles/relion.dir/maingui.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/relion.dir/maingui.cpp.o -MF CMakeFiles/relion.dir/maingui.cpp.o.d -o CMakeFiles/relion.dir/maingui.cpp.o -c /build/relion-3.1.3/src/apps/maingui.cpp In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/apps/display.cpp:25: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void star_handler_parameters::discard_on_image_stats()' at /build/relion-3.1.3/src/apps/star_handler.cpp:292:18: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void star_handler_parameters::discard_on_image_stats()' at /build/relion-3.1.3/src/apps/star_handler.cpp:293:21: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/jaz/obs_model.h:24, from /build/relion-3.1.3/src/scheduler.h:26, from /build/relion-3.1.3/src/gui_mainwindow.h:28, from /build/relion-3.1.3/src/apps/maingui.cpp:23: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gravis::t3Vector; _Alloc = std::allocator >]', inlined from 'int main(int, char**)' at /build/relion-3.1.3/src/apps/tomo_test.cpp:107:17: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ [ 97%] Linking CXX executable ../../bin/relion_display cd /build/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/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -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/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gui_lib.a /usr/lib/arm-linux-gnueabihf/libfltk_images.so /usr/lib/arm-linux-gnueabihf/libfltk_forms.so /usr/lib/arm-linux-gnueabihf/libfltk.so -lX11 -lm -ltiff ../../lib/librelion_lib.a -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' [ 97%] Built target display /usr/bin/make -f src/apps/CMakeFiles/manualpick.dir/build.make src/apps/CMakeFiles/manualpick.dir/depend make[4]: Entering directory '/build/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/manualpick.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' [ 97%] Building CXX object src/apps/CMakeFiles/manualpick.dir/manualpick.cpp.o cd /build/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/relion-3.1.3/src/ -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/build/relion-3.1.3 -I/usr/lib/fltk -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -MD -MT src/apps/CMakeFiles/manualpick.dir/manualpick.cpp.o -MF CMakeFiles/manualpick.dir/manualpick.cpp.o.d -o CMakeFiles/manualpick.dir/manualpick.cpp.o -c /build/relion-3.1.3/src/apps/manualpick.cpp [ 98%] Linking CXX executable ../../bin/relion_tomo_test cd /build/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/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -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/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 99%] Linking CXX executable ../../bin/relion cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/relion.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -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/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gui_lib.a /usr/lib/arm-linux-gnueabihf/libfltk_images.so /usr/lib/arm-linux-gnueabihf/libfltk_forms.so /usr/lib/arm-linux-gnueabihf/libfltk.so -lX11 -lm -ltiff ../../lib/librelion_lib.a -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' [ 99%] Built target tomo_test In file included from /build/relion-3.1.3/src/image.h:455, from /build/relion-3.1.3/src/apps/manualpick.cpp:25: /build/relion-3.1.3/src/rwTIFF.h: In member function 'int Image::readTIFF(TIFF*, long int, bool, bool, const FileName&)': /build/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/arm-linux-gnueabihf/tiffio.h:31, from /build/relion-3.1.3/src/image.h:57: /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:16: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:44:45: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 44 | uint16 sampleFormat, bitsPerSample, resolutionUnit; | ^~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:185:43: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 185 | uint32 cur_width, cur_length; | ^~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/relion-3.1.3/src/rwTIFF.h:186:50: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 186 | uint16 cur_sampleFormat, cur_bitsPerSample; | ^~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ make[4]: Leaving directory '/build/relion-3.1.3/build' [ 99%] Built target relion [100%] Linking CXX executable ../../bin/relion_manualpick cd /build/relion-3.1.3/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/manualpick.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -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/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gui_lib.a /usr/lib/arm-linux-gnueabihf/libfltk_images.so /usr/lib/arm-linux-gnueabihf/libfltk_forms.so /usr/lib/arm-linux-gnueabihf/libfltk.so -lX11 -lm -ltiff ../../lib/librelion_lib.a -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' [100%] Built target manualpick [100%] Linking CXX executable ../../bin/relion_star_handler cd /build/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 -ffile-prefix-map=/build/relion-3.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/star_handler.dir/star_handler.cpp.o -o ../../bin/relion_star_handler ../../lib/librelion_lib.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.3/build' [100%] Built target star_handler make[3]: Leaving directory '/build/relion-3.1.3/build' /usr/bin/cmake -E cmake_progress_start /build/relion-3.1.3/build/CMakeFiles 0 make[2]: Leaving directory '/build/relion-3.1.3/build' make[1]: Leaving directory '/build/relion-3.1.3' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/relion-3.1.3' /usr/bin/make -C build install DESTDIR=/build/relion-3.1.3/debian/tmp/cli make[2]: Entering directory '/build/relion-3.1.3/build' /usr/bin/cmake -S/build/relion-3.1.3 -B/build/relion-3.1.3/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/relion-3.1.3/build/CMakeFiles /build/relion-3.1.3/build//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3 /build/relion-3.1.3/build /build/relion-3.1.3/build /build/relion-3.1.3/build/CMakeFiles/copy_scripts.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' /usr/bin/cmake -E copy /build/relion-3.1.3/scripts/star_printtable /build/relion-3.1.3/build/bin/relion_star_printtable /usr/bin/cmake -E copy /build/relion-3.1.3/scripts/star_plottable /build/relion-3.1.3/build/bin/relion_star_plottable /usr/bin/cmake -E copy /build/relion-3.1.3/scripts/star_loopheader /build/relion-3.1.3/build/bin/relion_star_loopheader /usr/bin/cmake -E copy /build/relion-3.1.3/scripts/star_datablock_stack /build/relion-3.1.3/build/bin/relion_star_datablock_stack /usr/bin/cmake -E copy /build/relion-3.1.3/scripts/star_datablock_singlefiles /build/relion-3.1.3/build/bin/relion_star_datablock_singlefiles /usr/bin/cmake -E copy /build/relion-3.1.3/scripts/star_datablock_ctfdat /build/relion-3.1.3/build/bin/relion_star_datablock_ctfdat /usr/bin/cmake -E copy /build/relion-3.1.3/scripts/qsub.csh /build/relion-3.1.3/build/bin/relion_qsub.csh make[4]: Leaving directory '/build/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/relion_lib.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/relion_lib.dir/build'. make[4]: Leaving directory '/build/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/relion_gui_lib.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/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/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/align_symmetry.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/align_symmetry.dir/build'. make[4]: Leaving directory '/build/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/autopick.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/autopick.dir/build'. make[4]: Leaving directory '/build/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/autopick_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/autopick_mpi.dir/build'. make[4]: Leaving directory '/build/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/convert_star.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/convert_star.dir/build'. make[4]: Leaving directory '/build/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/convert_to_tiff.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/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/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/convert_to_tiff_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/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/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/ctf_mask_test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/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/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/ctf_refine.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/ctf_refine.dir/build'. make[4]: Leaving directory '/build/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/ctf_refine_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/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/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/ctf_toolbox.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/ctf_toolbox.dir/build'. make[4]: Leaving directory '/build/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/demodulate.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/demodulate.dir/build'. make[4]: Leaving directory '/build/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/display.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/display.dir/build'. make[4]: Leaving directory '/build/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/estimate_gain.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/estimate_gain.dir/build'. make[4]: Leaving directory '/build/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/external_reconstruct.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/external_reconstruct.dir/build'. make[4]: Leaving directory '/build/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/find_tiltpairs.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/find_tiltpairs.dir/build'. make[4]: Leaving directory '/build/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/flex_analyse.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/flex_analyse.dir/build'. make[4]: Leaving directory '/build/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/flex_analyse_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/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/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/helix_inimodel2d.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/helix_inimodel2d.dir/build'. make[4]: Leaving directory '/build/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/helix_toolbox.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/helix_toolbox.dir/build'. make[4]: Leaving directory '/build/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/image_handler.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/image_handler.dir/build'. make[4]: Leaving directory '/build/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/import.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/import.dir/build'. make[4]: Leaving directory '/build/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/localsym.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/localsym.dir/build'. make[4]: Leaving directory '/build/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/localsym_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/localsym_mpi.dir/build'. make[4]: Leaving directory '/build/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/relion.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/relion.dir/build'. make[4]: Leaving directory '/build/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/manualpick.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/manualpick.dir/build'. make[4]: Leaving directory '/build/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/mask_create.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/mask_create.dir/build'. make[4]: Leaving directory '/build/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/merge_particles.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/merge_particles.dir/build'. make[4]: Leaving directory '/build/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/motion_refine.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/motion_refine.dir/build'. make[4]: Leaving directory '/build/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/motion_refine_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/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/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/mrc2vtk.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/mrc2vtk.dir/build'. make[4]: Leaving directory '/build/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/particle_FCC.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/particle_FCC.dir/build'. make[4]: Leaving directory '/build/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/particle_reposition.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/particle_reposition.dir/build'. make[4]: Leaving directory '/build/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/particle_select.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/particle_select.dir/build'. make[4]: Leaving directory '/build/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/particle_subtract.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/particle_subtract.dir/build'. make[4]: Leaving directory '/build/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/particle_subtract_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/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/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/particle_symmetry_expand.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/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/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/pipeliner.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/pipeliner.dir/build'. make[4]: Leaving directory '/build/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/plot_delocalisation.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/plot_delocalisation.dir/build'. make[4]: Leaving directory '/build/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/postprocess.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/postprocess.dir/build'. make[4]: Leaving directory '/build/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/postprocess_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/postprocess_mpi.dir/build'. make[4]: Leaving directory '/build/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/prepare_subtomo.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/prepare_subtomo.dir/build'. make[4]: Leaving directory '/build/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/preprocess.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/preprocess.dir/build'. make[4]: Leaving directory '/build/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/preprocess_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/preprocess_mpi.dir/build'. make[4]: Leaving directory '/build/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/project.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/project.dir/build'. make[4]: Leaving directory '/build/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/reconstruct.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/reconstruct.dir/build'. make[4]: Leaving directory '/build/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/reconstruct_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/reconstruct_mpi.dir/build'. make[4]: Leaving directory '/build/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/refine.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/refine.dir/build'. make[4]: Leaving directory '/build/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/refine_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/refine_mpi.dir/build'. make[4]: Leaving directory '/build/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/reposition.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/reposition.dir/build'. make[4]: Leaving directory '/build/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/run_ctffind.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/run_ctffind.dir/build'. make[4]: Leaving directory '/build/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/run_ctffind_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/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/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/run_motioncorr.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/run_motioncorr.dir/build'. make[4]: Leaving directory '/build/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/run_motioncorr_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/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/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/scheduler.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/scheduler.dir/build'. make[4]: Leaving directory '/build/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/stack_create.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/stack_create.dir/build'. make[4]: Leaving directory '/build/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/star_handler.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/star_handler.dir/build'. make[4]: Leaving directory '/build/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/tiltpair_plot.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/tiltpair_plot.dir/build'. make[4]: Leaving directory '/build/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/relion-3.1.3/build' cd /build/relion-3.1.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.3 /build/relion-3.1.3/src/apps /build/relion-3.1.3/build /build/relion-3.1.3/build/src/apps /build/relion-3.1.3/build/src/apps/CMakeFiles/tomo_test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/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/relion-3.1.3/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/tomo_test.dir/build'. make[4]: Leaving directory '/build/relion-3.1.3/build' [100%] Built target tomo_test make[3]: Leaving directory '/build/relion-3.1.3/build' /usr/bin/cmake -E cmake_progress_start /build/relion-3.1.3/build/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/relion-3.1.3/build' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/relion-3.1.3/build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_demodulate -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_tomo_test -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_tiltpair_plot -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_manualpick -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_star_loopheader -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_convert_to_tiff_mpi -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_plot_delocalisation -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_helix_inimodel2d -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_mask_create -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_stack_create -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_image_handler -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_estimate_gain -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_align_symmetry -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_run_motioncorr_mpi -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_flex_analyse_mpi -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_subtract -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_scheduler -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_display -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_symmetry_expand -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_run_ctffind -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_mrc2vtk -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_preprocess_mpi -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_postprocess_mpi -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_ctf_mask_test -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_reconstruct -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_helix_toolbox -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_star_plottable -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_autopick -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_select -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_localsym -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_star_handler -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_star_datablock_ctfdat -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_localsym_mpi -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_reposition -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_subtract_mpi -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_star_datablock_singlefiles -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_ctf_toolbox -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_motion_refine_mpi -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_autopick_mpi -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_run_ctffind_mpi -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_ctf_refine_mpi -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_external_reconstruct -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_reposition -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_preprocess -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_qsub.csh -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_flex_analyse -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_project -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_prepare_subtomo -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_refine -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_run_motioncorr -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_ctf_refine -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_star_datablock_stack -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_find_tiltpairs -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_reconstruct_mpi -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_refine_mpi -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_convert_star -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_convert_to_tiff -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_motion_refine -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_FCC -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_postprocess -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_import -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_merge_particles -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_pipeliner -- Installing: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_star_printtable -- Up-to-date: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_align_symmetry -- Up-to-date: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_autopick -- Up-to-date: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_autopick_mpi -- Up-to-date: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_convert_star -- Up-to-date: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_convert_to_tiff -- Up-to-date: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_convert_to_tiff_mpi -- Up-to-date: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_ctf_mask_test -- Up-to-date: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_ctf_refine -- Up-to-date: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_ctf_refine_mpi -- Up-to-date: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_ctf_toolbox -- Up-to-date: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_demodulate -- Up-to-date: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_display -- Up-to-date: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_estimate_gain -- Up-to-date: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_external_reconstruct -- Up-to-date: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_find_tiltpairs -- Up-to-date: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_flex_analyse -- Up-to-date: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_flex_analyse_mpi -- Up-to-date: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_helix_inimodel2d -- Up-to-date: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_helix_toolbox -- Up-to-date: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_image_handler -- Up-to-date: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_import -- Up-to-date: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_localsym -- Up-to-date: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_localsym_mpi -- Up-to-date: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion -- Up-to-date: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_manualpick -- Up-to-date: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_mask_create -- Up-to-date: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_merge_particles -- Up-to-date: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_motion_refine -- Up-to-date: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_motion_refine_mpi -- Up-to-date: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_mrc2vtk -- Up-to-date: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_FCC -- Up-to-date: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_reposition -- Up-to-date: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_select -- Up-to-date: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_subtract -- Up-to-date: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_subtract_mpi -- Up-to-date: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_particle_symmetry_expand -- Up-to-date: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_pipeliner -- Up-to-date: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_plot_delocalisation -- Up-to-date: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_postprocess -- Up-to-date: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_postprocess_mpi -- Up-to-date: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_prepare_subtomo -- Up-to-date: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_preprocess -- Up-to-date: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_preprocess_mpi -- Up-to-date: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_project -- Up-to-date: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_reconstruct -- Up-to-date: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_reconstruct_mpi -- Up-to-date: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_refine -- Up-to-date: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_refine_mpi -- Up-to-date: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_reposition -- Up-to-date: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_run_ctffind -- Up-to-date: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_run_ctffind_mpi -- Up-to-date: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_run_motioncorr -- Up-to-date: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_run_motioncorr_mpi -- Up-to-date: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_scheduler -- Up-to-date: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_stack_create -- Up-to-date: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_star_handler -- Up-to-date: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_tiltpair_plot -- Up-to-date: /build/relion-3.1.3/debian/tmp/cli/usr/bin/relion_tomo_test make[2]: Leaving directory '/build/relion-3.1.3/build' mkdir -p /build/relion-3.1.3/debian/tmp/gui/usr/bin rm /build/relion-3.1.3/debian/tmp/cli/usr/bin/*.csh # Useless ... set -e; for prog in relion relion_display relion_manualpick; do \ mv /build/relion-3.1.3/debian/tmp/cli/usr/bin/$prog \ /build/relion-3.1.3/debian/tmp/gui/usr/bin; done make[1]: Leaving directory '/build/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 dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_reposition contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_prepare_subtomo contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion-gui/usr/bin/relion_display contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_demodulate contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_run_ctffind contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion-gui/usr/bin/relion_manualpick contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion-gui/usr/bin/relion contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_flex_analyse_mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_postprocess_mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_autopick contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_find_tiltpairs contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_convert_to_tiff_mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_star_handler contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_refine contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_ctf_mask_test contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_helix_inimodel2d contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_ctf_refine_mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_preprocess_mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_reconstruct contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_run_motioncorr contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_project contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_particle_select contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_estimate_gain contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_tomo_test contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_ctf_refine contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_particle_subtract_mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_ctf_toolbox contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_image_handler contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_preprocess contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_helix_toolbox contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_merge_particles contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_flex_analyse contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_convert_star contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_particle_subtract contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_convert_to_tiff contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_mrc2vtk contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_autopick_mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_particle_FCC contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_tiltpair_plot contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_import contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_reconstruct_mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_align_symmetry contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_postprocess contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_stack_create contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_pipeliner contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_particle_reposition contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_particle_symmetry_expand contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_localsym contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_external_reconstruct contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_scheduler contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_mask_create contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_motion_refine contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_run_ctffind_mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_plot_delocalisation contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_motion_refine_mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_run_motioncorr_mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_refine_mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/relion/usr/bin/relion_localsym_mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'relion' in '../relion_3.1.3-3_armhf.deb'. dpkg-deb: building package 'relion-gui-dbgsym' in '../relion-gui-dbgsym_3.1.3-3_armhf.deb'. dpkg-deb: building package 'relion-gui' in '../relion-gui_3.1.3-3_armhf.deb'. dpkg-deb: building package 'relion-dbgsym' in '../relion-dbgsym_3.1.3-3_armhf.deb'. dpkg-genbuildinfo --build=binary -O../relion_3.1.3-3_armhf.buildinfo dpkg-genchanges --build=binary -O../relion_3.1.3-3_armhf.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: user script /srv/workspace/pbuilder/29454/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/29454/tmp/hooks/B01_cleanup finished 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/29454 and its subdirectories I: Current time: Sat Jun 10 04:07:23 +14 2023 I: pbuilder-time-stamp: 1686319643