I: pbuilder: network access will be disabled during build I: Current time: Mon Jul 25 01:13:01 -12 2022 I: pbuilder-time-stamp: 1658754781 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration 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: using eatmydata during job I: Copying source file I: copying [relion_3.1.0-4.dsc] I: copying [./relion_3.1.0.orig.tar.xz] I: copying [./relion_3.1.0-4.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.UWupU3xK/trustedkeys.kbx': General error gpgv: Signature made Wed Oct 7 02:36:44 2020 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./relion_3.1.0-4.dsc dpkg-source: info: extracting relion in relion-3.1.0 dpkg-source: info: unpacking relion_3.1.0.orig.tar.xz dpkg-source: info: unpacking relion_3.1.0-4.debian.tar.xz I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/52110/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=18' DISTRIBUTION='' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='a6d962679054447ab53e38b25a6a3024' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='52110' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.4wiMpvkHix/pbuilderrc_LqQ7 --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.4wiMpvkHix/b1 --logfile b1/build.log relion_3.1.0-4.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://85.184.249.68:3128' I: uname -a Linux ionos16-i386 4.19.0-17-amd64 #1 SMP Debian 4.19.194-1 (2021-06-10) x86_64 GNU/Linux I: ls -l /bin total 5776 -rwxr-xr-x 1 root root 1367848 Feb 24 2021 bash -rwxr-xr-x 3 root root 38280 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 17768 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 38824 Sep 22 2020 cat -rwxr-xr-x 1 root root 71624 Sep 22 2020 chgrp -rwxr-xr-x 1 root root 67528 Sep 22 2020 chmod -rwxr-xr-x 1 root root 75752 Sep 22 2020 chown -rwxr-xr-x 1 root root 157960 Sep 22 2020 cp -rwxr-xr-x 1 root root 128724 Dec 10 2020 dash -rwxr-xr-x 1 root root 124904 Sep 22 2020 date -rwxr-xr-x 1 root root 92172 Sep 22 2020 dd -rwxr-xr-x 1 root root 100752 Sep 22 2020 df -rwxr-xr-x 1 root root 153964 Sep 22 2020 dir -rwxr-xr-x 1 root root 83644 Feb 7 2021 dmesg lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname -rwxr-xr-x 1 root root 34664 Sep 22 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 34664 Sep 22 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 71928 Feb 7 2021 findmnt -rwsr-xr-x 1 root root 30112 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 210488 Nov 9 2020 grep -rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip -rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe -rwxr-xr-x 1 root root 100952 Mar 2 2021 gzip -rwxr-xr-x 1 root root 21916 Nov 6 2019 hostname -rwxr-xr-x 1 root root 83980 Sep 22 2020 ln -rwxr-xr-x 1 root root 55572 Feb 7 2020 login -rwxr-xr-x 1 root root 153964 Sep 22 2020 ls -rwxr-xr-x 1 root root 153124 Feb 7 2021 lsblk -rwxr-xr-x 1 root root 96328 Sep 22 2020 mkdir -rwxr-xr-x 1 root root 79912 Sep 22 2020 mknod -rwxr-xr-x 1 root root 47048 Sep 22 2020 mktemp -rwxr-xr-x 1 root root 58920 Feb 7 2021 more -rwsr-xr-x 1 root root 50720 Feb 7 2021 mount -rwxr-xr-x 1 root root 13856 Feb 7 2021 mountpoint -rwxr-xr-x 1 root root 157996 Sep 22 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 18 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 38824 Sep 22 2020 pwd lrwxrwxrwx 1 root root 4 Feb 24 2021 rbash -> bash -rwxr-xr-x 1 root root 46984 Sep 22 2020 readlink -rwxr-xr-x 1 root root 75720 Sep 22 2020 rm -rwxr-xr-x 1 root root 46984 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 22292 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Jul 23 03:46 sh -> dash -rwxr-xr-x 1 root root 34696 Sep 22 2020 sleep -rwxr-xr-x 1 root root 83880 Sep 22 2020 stty -rwsr-xr-x 1 root root 79396 Feb 7 2021 su -rwxr-xr-x 1 root root 34696 Sep 22 2020 sync -rwxr-xr-x 1 root root 602584 Feb 16 2021 tar -rwxr-xr-x 1 root root 13860 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 108520 Sep 22 2020 touch -rwxr-xr-x 1 root root 34664 Sep 22 2020 true -rwxr-xr-x 1 root root 17768 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 30236 Feb 7 2021 umount -rwxr-xr-x 1 root root 34664 Sep 22 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress -rwxr-xr-x 1 root root 153964 Sep 22 2020 vdir -rwxr-xr-x 1 root root 63024 Feb 7 2021 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat -rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp -rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff -rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep -rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep -rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce -rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep -rwxr-xr-x 1 root root 2206 Mar 2 2021 zless -rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore -rwxr-xr-x 1 root root 4553 Mar 2 2021 znew I: user script /srv/workspace/pbuilder/52110/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: i386 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 ... 19675 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-10{a} groff-base{a} ibverbs-providers{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13{a} libbrotli1{a} libbsd0{a} libcairo2{a} libcbor0{a} libcurl4{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-intel1{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-long3{a} libfftw3-quad3{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-10-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} libicu67{a} libjbig-dev{a} libjbig0{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libjs-jquery{a} libjs-jquery-ui{a} libjsoncpp24{a} libldap-2.4-2{a} libllvm11{a} libltdl-dev{a} libltdl7{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libmd0{a} libncurses6{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} libprocps8{a} libpsl5{a} libpsm-infinipath1{a} libpthread-stubs0-dev{a} librdmacm1{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsensors-config{a} libsensors5{a} libsigsegv2{a} libssh2-1{a} libsub-override-perl{a} libtiff-dev{a} libtiff5{a} libtiffxx5{a} libtool{a} libuchardet0{a} libuv1{a} libvulkan1{a} libwebp6{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-render0{a} libxcb-shm0{a} libxcb-sync1{a} libxcb-xfixes0{a} libxcb1{a} libxcb1-dev{a} libxcursor1{a} libxdamage1{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} 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} ucf{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 libgpm2 libldap-common libmail-sendmail-perl libsasl2-modules lynx mesa-vulkan-drivers psmisc publicsuffix wget xauth 0 packages upgraded, 175 newly installed, 0 to remove and 0 not upgraded. Need to get 108 MB of archives. After unpacking 404 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main i386 bsdextrautils i386 2.36.1-7 [148 kB] Get: 2 http://deb.debian.org/debian bullseye/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB] Get: 3 http://deb.debian.org/debian bullseye/main i386 groff-base i386 1.22.4-6 [952 kB] Get: 4 http://deb.debian.org/debian bullseye/main i386 libpipeline1 i386 1.5.3-1 [36.8 kB] Get: 5 http://deb.debian.org/debian bullseye/main i386 man-db i386 2.9.4-2 [1367 kB] Get: 6 http://deb.debian.org/debian bullseye/main i386 libncurses6 i386 6.2+20201114-2 [110 kB] Get: 7 http://deb.debian.org/debian bullseye/main i386 libprocps8 i386 2:3.3.17-5 [64.2 kB] Get: 8 http://deb.debian.org/debian bullseye/main i386 procps i386 2:3.3.17-5 [501 kB] Get: 9 http://deb.debian.org/debian bullseye/main i386 sensible-utils all 0.0.14 [14.8 kB] Get: 10 http://deb.debian.org/debian bullseye/main i386 libmagic-mgc i386 1:5.39-3 [273 kB] Get: 11 http://deb.debian.org/debian bullseye/main i386 libmagic1 i386 1:5.39-3 [133 kB] Get: 12 http://deb.debian.org/debian bullseye/main i386 file i386 1:5.39-3 [69.0 kB] Get: 13 http://deb.debian.org/debian bullseye/main i386 gettext-base i386 0.21-4 [176 kB] Get: 14 http://deb.debian.org/debian bullseye/main i386 libmd0 i386 1.0.3-3 [28.9 kB] Get: 15 http://deb.debian.org/debian bullseye/main i386 libbsd0 i386 0.11.3-1 [111 kB] Get: 16 http://deb.debian.org/debian bullseye/main i386 libedit2 i386 3.1-20191231-2+b1 [101 kB] Get: 17 http://deb.debian.org/debian bullseye/main i386 libcbor0 i386 0.5.0+dfsg-2 [26.2 kB] Get: 18 http://deb.debian.org/debian bullseye/main i386 libfido2-1 i386 1.6.0-2 [59.9 kB] Get: 19 http://deb.debian.org/debian bullseye/main i386 openssh-client i386 1:8.4p1-5 [991 kB] Get: 20 http://deb.debian.org/debian bullseye/main i386 ucf all 3.0043 [74.0 kB] Get: 21 http://deb.debian.org/debian bullseye/main i386 libsigsegv2 i386 2.13-1 [35.1 kB] Get: 22 http://deb.debian.org/debian bullseye/main i386 m4 i386 1.4.18-5 [206 kB] Get: 23 http://deb.debian.org/debian bullseye/main i386 autoconf all 2.69-14 [313 kB] Get: 24 http://deb.debian.org/debian bullseye/main i386 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 25 http://deb.debian.org/debian bullseye/main i386 automake all 1:1.16.3-2 [814 kB] Get: 26 http://deb.debian.org/debian bullseye/main i386 autopoint all 0.21-4 [510 kB] Get: 27 http://deb.debian.org/debian bullseye/main i386 cmake-data all 3.18.4-2 [1725 kB] Get: 28 http://deb.debian.org/debian bullseye/main i386 libicu67 i386 67.1-6 [8776 kB] Get: 29 http://deb.debian.org/debian bullseye/main i386 libxml2 i386 2.9.10+dfsg-6.7 [728 kB] Get: 30 http://deb.debian.org/debian bullseye/main i386 libarchive13 i386 3.4.3-2+b1 [384 kB] Get: 31 http://deb.debian.org/debian bullseye/main i386 libbrotli1 i386 1.0.9-2+b2 [286 kB] Get: 32 http://deb.debian.org/debian bullseye/main i386 libsasl2-modules-db i386 2.1.27+dfsg-2.1 [70.0 kB] Get: 33 http://deb.debian.org/debian bullseye/main i386 libsasl2-2 i386 2.1.27+dfsg-2.1 [110 kB] Get: 34 http://deb.debian.org/debian bullseye/main i386 libldap-2.4-2 i386 2.4.57+dfsg-3 [244 kB] Get: 35 http://deb.debian.org/debian bullseye/main i386 libnghttp2-14 i386 1.43.0-1 [85.7 kB] Get: 36 http://deb.debian.org/debian bullseye/main i386 libpsl5 i386 0.21.0-1.2 [57.9 kB] Get: 37 http://deb.debian.org/debian bullseye/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b2 [64.3 kB] Get: 38 http://deb.debian.org/debian bullseye/main i386 libssh2-1 i386 1.9.0-2 [164 kB] Get: 39 http://deb.debian.org/debian bullseye/main i386 libcurl4 i386 7.74.0-1.2 [372 kB] Get: 40 http://deb.debian.org/debian bullseye/main i386 libexpat1 i386 2.2.10-2 [98.8 kB] Get: 41 http://deb.debian.org/debian bullseye/main i386 libjsoncpp24 i386 1.9.4-4 [86.1 kB] Get: 42 http://deb.debian.org/debian bullseye/main i386 librhash0 i386 1.4.1-2 [144 kB] Get: 43 http://deb.debian.org/debian bullseye/main i386 libuv1 i386 1.40.0-1 [139 kB] Get: 44 http://deb.debian.org/debian bullseye/main i386 cmake i386 3.18.4-2 [7029 kB] Get: 45 http://deb.debian.org/debian bullseye/main i386 libdebhelper-perl all 13.3.4 [189 kB] Get: 46 http://deb.debian.org/debian bullseye/main i386 libtool all 2.4.6-15 [513 kB] Get: 47 http://deb.debian.org/debian bullseye/main i386 dh-autoreconf all 20 [17.1 kB] Get: 48 http://deb.debian.org/debian bullseye/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 49 http://deb.debian.org/debian bullseye/main i386 libsub-override-perl all 0.09-2 [10.2 kB] Get: 50 http://deb.debian.org/debian bullseye/main i386 libfile-stripnondeterminism-perl all 1.11.0-1 [25.6 kB] Get: 51 http://deb.debian.org/debian bullseye/main i386 dh-strip-nondeterminism all 1.11.0-1 [15.3 kB] Get: 52 http://deb.debian.org/debian bullseye/main i386 libelf1 i386 0.183-1 [171 kB] Get: 53 http://deb.debian.org/debian bullseye/main i386 dwz i386 0.13+20210201-1 [179 kB] Get: 54 http://deb.debian.org/debian bullseye/main i386 gettext i386 0.21-4 [1322 kB] Get: 55 http://deb.debian.org/debian bullseye/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 56 http://deb.debian.org/debian bullseye/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 57 http://deb.debian.org/debian bullseye/main i386 debhelper all 13.3.4 [1049 kB] Get: 58 http://deb.debian.org/debian bullseye/main i386 libpng16-16 i386 1.6.37-3 [303 kB] Get: 59 http://deb.debian.org/debian bullseye/main i386 libfreetype6 i386 2.10.4+dfsg-1 [429 kB] Get: 60 http://deb.debian.org/debian bullseye/main i386 fonts-dejavu-core all 2.37-2 [1069 kB] Get: 61 http://deb.debian.org/debian bullseye/main i386 fontconfig-config all 2.13.1-4.2 [281 kB] Get: 62 http://deb.debian.org/debian bullseye/main i386 libfontconfig1 i386 2.13.1-4.2 [358 kB] Get: 63 http://deb.debian.org/debian bullseye/main i386 libxau6 i386 1:1.0.9-1 [20.0 kB] Get: 64 http://deb.debian.org/debian bullseye/main i386 libxdmcp6 i386 1:1.1.2-3 [26.7 kB] Get: 65 http://deb.debian.org/debian bullseye/main i386 libxcb1 i386 1.14-3 [144 kB] Get: 66 http://deb.debian.org/debian bullseye/main i386 libx11-data all 2:1.7.1-1 [310 kB] Get: 67 http://deb.debian.org/debian bullseye/main i386 libx11-6 i386 2:1.7.1-1 [796 kB] Get: 68 http://deb.debian.org/debian bullseye/main i386 libxfixes3 i386 1:5.0.3-2 [22.6 kB] Get: 69 http://deb.debian.org/debian bullseye/main i386 libxrender1 i386 1:0.9.10-1 [34.1 kB] Get: 70 http://deb.debian.org/debian bullseye/main i386 libxcursor1 i386 1:1.2.0-2 [38.8 kB] Get: 71 http://deb.debian.org/debian bullseye/main i386 libxext6 i386 2:1.3.3-1.1 [55.2 kB] Get: 72 http://deb.debian.org/debian bullseye/main i386 libxft2 i386 2.3.2-2 [58.2 kB] Get: 73 http://deb.debian.org/debian bullseye/main i386 libxinerama1 i386 2:1.1.4-2 [17.9 kB] Get: 74 http://deb.debian.org/debian bullseye/main i386 libfltk1.3 i386 1.3.5-3 [593 kB] Get: 75 http://deb.debian.org/debian bullseye/main i386 libfltk-forms1.3 i386 1.3.5-3 [50.5 kB] Get: 76 http://deb.debian.org/debian bullseye/main i386 libjpeg62-turbo i386 1:2.0.6-4 [160 kB] Get: 77 http://deb.debian.org/debian bullseye/main i386 libfltk-images1.3 i386 1.3.5-3 [64.4 kB] Get: 78 http://deb.debian.org/debian bullseye/main i386 fluid i386 1.3.5-3 [239 kB] Get: 79 http://deb.debian.org/debian bullseye/main i386 libgfortran5 i386 10.2.1-6 [643 kB] Get: 80 http://deb.debian.org/debian bullseye/main i386 libgfortran-10-dev i386 10.2.1-6 [705 kB] Get: 81 http://deb.debian.org/debian bullseye/main i386 gfortran-10 i386 10.2.1-6 [9642 kB] Get: 82 http://deb.debian.org/debian bullseye/main i386 libnl-3-200 i386 3.4.0-1+b1 [66.4 kB] Get: 83 http://deb.debian.org/debian bullseye/main i386 libnl-route-3-200 i386 3.4.0-1+b1 [168 kB] Get: 84 http://deb.debian.org/debian bullseye/main i386 libibverbs1 i386 33.2-1 [64.6 kB] Get: 85 http://deb.debian.org/debian bullseye/main i386 ibverbs-providers i386 33.2-1 [275 kB] Get: 86 http://deb.debian.org/debian bullseye/main i386 libpixman-1-0 i386 0.40.0-1 [545 kB] Get: 87 http://deb.debian.org/debian bullseye/main i386 libxcb-render0 i386 1.14-3 [112 kB] Get: 88 http://deb.debian.org/debian bullseye/main i386 libxcb-shm0 i386 1.14-3 [102 kB] Get: 89 http://deb.debian.org/debian bullseye/main i386 libcairo2 i386 1.16.0-5 [746 kB] Get: 90 http://deb.debian.org/debian bullseye/main i386 libdeflate0 i386 1.7-1 [48.4 kB] Get: 91 http://deb.debian.org/debian bullseye/main i386 libdeflate-dev i386 1.7-1 [44.4 kB] Get: 92 http://deb.debian.org/debian bullseye/main i386 libdrm-common all 2.4.104-1 [14.9 kB] Get: 93 http://deb.debian.org/debian bullseye/main i386 libdrm2 i386 2.4.104-1 [44.3 kB] Get: 94 http://deb.debian.org/debian bullseye/main i386 libdrm-amdgpu1 i386 2.4.104-1 [31.5 kB] Get: 95 http://deb.debian.org/debian bullseye/main i386 libpciaccess0 i386 0.16-1 [55.7 kB] Get: 96 http://deb.debian.org/debian bullseye/main i386 libdrm-intel1 i386 2.4.104-1 [74.5 kB] Get: 97 http://deb.debian.org/debian bullseye/main i386 libdrm-nouveau2 i386 2.4.104-1 [28.5 kB] Get: 98 http://deb.debian.org/debian bullseye/main i386 libdrm-radeon1 i386 2.4.104-1 [31.4 kB] Get: 99 http://deb.debian.org/debian bullseye/main i386 libevent-2.1-7 i386 2.1.12-stable-1 [203 kB] Get: 100 http://deb.debian.org/debian bullseye/main i386 libevent-core-2.1-7 i386 2.1.12-stable-1 [148 kB] Get: 101 http://deb.debian.org/debian bullseye/main i386 libevent-extra-2.1-7 i386 2.1.12-stable-1 [116 kB] Get: 102 http://deb.debian.org/debian bullseye/main i386 libevent-pthreads-2.1-7 i386 2.1.12-stable-1 [57.3 kB] Get: 103 http://deb.debian.org/debian bullseye/main i386 libevent-openssl-2.1-7 i386 2.1.12-stable-1 [64.9 kB] Get: 104 http://deb.debian.org/debian bullseye/main i386 libevent-dev i386 2.1.12-stable-1 [332 kB] Get: 105 http://deb.debian.org/debian bullseye/main i386 libpsm-infinipath1 i386 3.3+20.604758e7-6.1 [178 kB] Get: 106 http://deb.debian.org/debian bullseye/main i386 librdmacm1 i386 33.2-1 [75.2 kB] Get: 107 http://deb.debian.org/debian bullseye/main i386 libfabric1 i386 1.11.0-2 [518 kB] Get: 108 http://deb.debian.org/debian bullseye/main i386 libfftw3-double3 i386 3.3.8-2 [640 kB] Get: 109 http://deb.debian.org/debian bullseye/main i386 libfftw3-long3 i386 3.3.8-2 [326 kB] Get: 110 http://deb.debian.org/debian bullseye/main i386 libfftw3-quad3 i386 3.3.8-2 [1762 kB] Get: 111 http://deb.debian.org/debian bullseye/main i386 libfftw3-single3 i386 3.3.8-2 [652 kB] Get: 112 http://deb.debian.org/debian bullseye/main i386 libfftw3-bin i386 3.3.8-2 [53.5 kB] Get: 113 http://deb.debian.org/debian bullseye/main i386 libfftw3-dev i386 3.3.8-2 [3170 kB] Get: 114 http://deb.debian.org/debian bullseye/main i386 libfltk-cairo1.3 i386 1.3.5-3 [43.5 kB] Get: 115 http://deb.debian.org/debian bullseye/main i386 libglvnd0 i386 1.3.2-1 [44.1 kB] Get: 116 http://deb.debian.org/debian bullseye/main i386 libglapi-mesa i386 20.3.4-1 [71.6 kB] Get: 117 http://deb.debian.org/debian bullseye/main i386 libx11-xcb1 i386 2:1.7.1-1 [203 kB] Get: 118 http://deb.debian.org/debian bullseye/main i386 libxcb-dri2-0 i386 1.14-3 [103 kB] Get: 119 http://deb.debian.org/debian bullseye/main i386 libxcb-dri3-0 i386 1.14-3 [103 kB] Get: 120 http://deb.debian.org/debian bullseye/main i386 libxcb-glx0 i386 1.14-3 [120 kB] Get: 121 http://deb.debian.org/debian bullseye/main i386 libxcb-present0 i386 1.14-3 [101 kB] Get: 122 http://deb.debian.org/debian bullseye/main i386 libxcb-sync1 i386 1.14-3 [105 kB] Get: 123 http://deb.debian.org/debian bullseye/main i386 libxcb-xfixes0 i386 1.14-3 [105 kB] Get: 124 http://deb.debian.org/debian bullseye/main i386 libxdamage1 i386 1:1.1.5-2 [15.9 kB] Get: 125 http://deb.debian.org/debian bullseye/main i386 libxshmfence1 i386 1.3-1 [8976 B] Get: 126 http://deb.debian.org/debian bullseye/main i386 libxxf86vm1 i386 1:1.1.4-1+b2 [21.7 kB] Get: 127 http://deb.debian.org/debian bullseye/main i386 libz3-4 i386 4.8.10-1 [7737 kB] Get: 128 http://deb.debian.org/debian bullseye/main i386 libllvm11 i386 1:11.0.1-2 [17.7 MB] Get: 129 http://deb.debian.org/debian bullseye/main i386 libsensors-config all 1:3.6.0-7 [32.3 kB] Get: 130 http://deb.debian.org/debian bullseye/main i386 libsensors5 i386 1:3.6.0-7 [53.2 kB] Get: 131 http://deb.debian.org/debian bullseye/main i386 libvulkan1 i386 1.2.162.0-1 [110 kB] Get: 132 http://deb.debian.org/debian bullseye/main i386 libgl1-mesa-dri i386 20.3.4-1 [9945 kB] Get: 133 http://deb.debian.org/debian bullseye/main i386 libglx-mesa0 i386 20.3.4-1 [195 kB] Get: 134 http://deb.debian.org/debian bullseye/main i386 libglx0 i386 1.3.2-1 [39.1 kB] Get: 135 http://deb.debian.org/debian bullseye/main i386 libgl1 i386 1.3.2-1 [83.6 kB] Get: 136 http://deb.debian.org/debian bullseye/main i386 libfltk-gl1.3 i386 1.3.5-3 [76.6 kB] Get: 137 http://deb.debian.org/debian bullseye/main i386 xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB] Get: 138 http://deb.debian.org/debian bullseye/main i386 x11proto-dev all 2020.1-1 [594 kB] Get: 139 http://deb.debian.org/debian bullseye/main i386 libxau-dev i386 1:1.0.9-1 [23.3 kB] Get: 140 http://deb.debian.org/debian bullseye/main i386 libxdmcp-dev i386 1:1.1.2-3 [42.7 kB] Get: 141 http://deb.debian.org/debian bullseye/main i386 xtrans-dev all 1.4.0-1 [98.7 kB] Get: 142 http://deb.debian.org/debian bullseye/main i386 libpthread-stubs0-dev i386 0.4-1 [5340 B] Get: 143 http://deb.debian.org/debian bullseye/main i386 libxcb1-dev i386 1.14-3 [181 kB] Get: 144 http://deb.debian.org/debian bullseye/main i386 libx11-dev i386 2:1.7.1-1 [875 kB] Get: 145 http://deb.debian.org/debian bullseye/main i386 libfltk1.3-dev i386 1.3.5-3 [901 kB] Get: 146 http://deb.debian.org/debian bullseye/main i386 libhwloc15 i386 2.4.1+dfsg-1 [164 kB] Get: 147 http://deb.debian.org/debian bullseye/main i386 libnuma1 i386 2.0.12-1+b1 [27.9 kB] Get: 148 http://deb.debian.org/debian bullseye/main i386 libnuma-dev i386 2.0.12-1+b1 [41.2 kB] Get: 149 http://deb.debian.org/debian bullseye/main i386 libltdl7 i386 2.4.6-15 [392 kB] Get: 150 http://deb.debian.org/debian bullseye/main i386 libltdl-dev i386 2.4.6-15 [164 kB] Get: 151 http://deb.debian.org/debian bullseye/main i386 libhwloc-dev i386 2.4.1+dfsg-1 [250 kB] Get: 152 http://deb.debian.org/debian bullseye/main i386 libxnvctrl0 i386 460.56-1 [26.8 kB] Get: 153 http://deb.debian.org/debian bullseye/main i386 ocl-icd-libopencl1 i386 2.2.14-2 [45.0 kB] Get: 154 http://deb.debian.org/debian bullseye/main i386 libhwloc-plugins i386 2.4.1+dfsg-1 [22.0 kB] Get: 155 http://deb.debian.org/debian bullseye/main i386 libnl-3-dev i386 3.4.0-1+b1 [107 kB] Get: 156 http://deb.debian.org/debian bullseye/main i386 libnl-route-3-dev i386 3.4.0-1+b1 [192 kB] Get: 157 http://deb.debian.org/debian bullseye/main i386 libibverbs-dev i386 33.2-1 [521 kB] Get: 158 http://deb.debian.org/debian bullseye/main i386 libjbig0 i386 2.1-3.1+b2 [31.5 kB] Get: 159 http://deb.debian.org/debian bullseye/main i386 libjbig-dev i386 2.1-3.1+b2 [30.8 kB] Get: 160 http://deb.debian.org/debian bullseye/main i386 libjpeg62-turbo-dev i386 1:2.0.6-4 [299 kB] Get: 161 http://deb.debian.org/debian bullseye/main i386 libjpeg-dev i386 1:2.0.6-4 [67.8 kB] Get: 162 http://deb.debian.org/debian bullseye/main i386 libjs-jquery all 3.5.1+dfsg+~3.5.5-7 [315 kB] Get: 163 http://deb.debian.org/debian bullseye/main i386 libjs-jquery-ui all 1.12.1+dfsg-8 [232 kB] Get: 164 http://deb.debian.org/debian bullseye/main i386 liblzma-dev i386 5.2.5-2 [240 kB] Get: 165 http://deb.debian.org/debian bullseye/main i386 libpmix2 i386 4.0.0-4 [582 kB] Get: 166 http://deb.debian.org/debian bullseye/main i386 libopenmpi3 i386 4.1.0-10 [2144 kB] Get: 167 http://deb.debian.org/debian bullseye/main i386 openmpi-common all 4.1.0-10 [179 kB] Get: 168 http://deb.debian.org/debian bullseye/main i386 libpmix-dev i386 4.0.0-4 [717 kB] Get: 169 http://deb.debian.org/debian bullseye/main i386 zlib1g-dev i386 1:1.2.11.dfsg-2 [194 kB] Get: 170 http://deb.debian.org/debian bullseye/main i386 openmpi-bin i386 4.1.0-10 [209 kB] Get: 171 http://deb.debian.org/debian bullseye/main i386 libopenmpi-dev i386 4.1.0-10 [1142 kB] Get: 172 http://deb.debian.org/debian bullseye/main i386 libwebp6 i386 0.6.1-2.1 [269 kB] Get: 173 http://deb.debian.org/debian bullseye/main i386 libtiff5 i386 4.2.0-1 [305 kB] Get: 174 http://deb.debian.org/debian bullseye/main i386 libtiffxx5 i386 4.2.0-1 [129 kB] Get: 175 http://deb.debian.org/debian bullseye/main i386 libtiff-dev i386 4.2.0-1 [438 kB] Fetched 108 MB in 2s (68.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19675 files and directories currently installed.) Preparing to unpack .../000-bsdextrautils_2.36.1-7_i386.deb ... Unpacking bsdextrautils (2.36.1-7) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../001-libuchardet0_0.0.7-1_i386.deb ... Unpacking libuchardet0:i386 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../002-groff-base_1.22.4-6_i386.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../003-libpipeline1_1.5.3-1_i386.deb ... Unpacking libpipeline1:i386 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../004-man-db_2.9.4-2_i386.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package libncurses6:i386. Preparing to unpack .../005-libncurses6_6.2+20201114-2_i386.deb ... Unpacking libncurses6:i386 (6.2+20201114-2) ... Selecting previously unselected package libprocps8:i386. Preparing to unpack .../006-libprocps8_2%3a3.3.17-5_i386.deb ... Unpacking libprocps8:i386 (2:3.3.17-5) ... Selecting previously unselected package procps. Preparing to unpack .../007-procps_2%3a3.3.17-5_i386.deb ... Unpacking procps (2:3.3.17-5) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../008-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../009-libmagic-mgc_1%3a5.39-3_i386.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../010-libmagic1_1%3a5.39-3_i386.deb ... Unpacking libmagic1:i386 (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../011-file_1%3a5.39-3_i386.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../012-gettext-base_0.21-4_i386.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package libmd0:i386. Preparing to unpack .../013-libmd0_1.0.3-3_i386.deb ... Unpacking libmd0:i386 (1.0.3-3) ... Selecting previously unselected package libbsd0:i386. Preparing to unpack .../014-libbsd0_0.11.3-1_i386.deb ... Unpacking libbsd0:i386 (0.11.3-1) ... Selecting previously unselected package libedit2:i386. Preparing to unpack .../015-libedit2_3.1-20191231-2+b1_i386.deb ... Unpacking libedit2:i386 (3.1-20191231-2+b1) ... Selecting previously unselected package libcbor0:i386. Preparing to unpack .../016-libcbor0_0.5.0+dfsg-2_i386.deb ... Unpacking libcbor0:i386 (0.5.0+dfsg-2) ... Selecting previously unselected package libfido2-1:i386. Preparing to unpack .../017-libfido2-1_1.6.0-2_i386.deb ... Unpacking libfido2-1:i386 (1.6.0-2) ... Selecting previously unselected package openssh-client. Preparing to unpack .../018-openssh-client_1%3a8.4p1-5_i386.deb ... Unpacking openssh-client (1:8.4p1-5) ... Selecting previously unselected package ucf. Preparing to unpack .../019-ucf_3.0043_all.deb ... Moving old data out of the way Unpacking ucf (3.0043) ... Selecting previously unselected package libsigsegv2:i386. Preparing to unpack .../020-libsigsegv2_2.13-1_i386.deb ... Unpacking libsigsegv2:i386 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../021-m4_1.4.18-5_i386.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../022-autoconf_2.69-14_all.deb ... Unpacking autoconf (2.69-14) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../023-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../024-automake_1%3a1.16.3-2_all.deb ... Unpacking automake (1:1.16.3-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../025-autopoint_0.21-4_all.deb ... Unpacking autopoint (0.21-4) ... Selecting previously unselected package cmake-data. Preparing to unpack .../026-cmake-data_3.18.4-2_all.deb ... Unpacking cmake-data (3.18.4-2) ... Selecting previously unselected package libicu67:i386. Preparing to unpack .../027-libicu67_67.1-6_i386.deb ... Unpacking libicu67:i386 (67.1-6) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../028-libxml2_2.9.10+dfsg-6.7_i386.deb ... Unpacking libxml2:i386 (2.9.10+dfsg-6.7) ... Selecting previously unselected package libarchive13:i386. Preparing to unpack .../029-libarchive13_3.4.3-2+b1_i386.deb ... Unpacking libarchive13:i386 (3.4.3-2+b1) ... Selecting previously unselected package libbrotli1:i386. Preparing to unpack .../030-libbrotli1_1.0.9-2+b2_i386.deb ... Unpacking libbrotli1:i386 (1.0.9-2+b2) ... Selecting previously unselected package libsasl2-modules-db:i386. Preparing to unpack .../031-libsasl2-modules-db_2.1.27+dfsg-2.1_i386.deb ... Unpacking libsasl2-modules-db:i386 (2.1.27+dfsg-2.1) ... Selecting previously unselected package libsasl2-2:i386. Preparing to unpack .../032-libsasl2-2_2.1.27+dfsg-2.1_i386.deb ... Unpacking libsasl2-2:i386 (2.1.27+dfsg-2.1) ... Selecting previously unselected package libldap-2.4-2:i386. Preparing to unpack .../033-libldap-2.4-2_2.4.57+dfsg-3_i386.deb ... Unpacking libldap-2.4-2:i386 (2.4.57+dfsg-3) ... Selecting previously unselected package libnghttp2-14:i386. Preparing to unpack .../034-libnghttp2-14_1.43.0-1_i386.deb ... Unpacking libnghttp2-14:i386 (1.43.0-1) ... Selecting previously unselected package libpsl5:i386. Preparing to unpack .../035-libpsl5_0.21.0-1.2_i386.deb ... Unpacking libpsl5:i386 (0.21.0-1.2) ... Selecting previously unselected package librtmp1:i386. Preparing to unpack .../036-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_i386.deb ... Unpacking librtmp1:i386 (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:i386. Preparing to unpack .../037-libssh2-1_1.9.0-2_i386.deb ... Unpacking libssh2-1:i386 (1.9.0-2) ... Selecting previously unselected package libcurl4:i386. Preparing to unpack .../038-libcurl4_7.74.0-1.2_i386.deb ... Unpacking libcurl4:i386 (7.74.0-1.2) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../039-libexpat1_2.2.10-2_i386.deb ... Unpacking libexpat1:i386 (2.2.10-2) ... Selecting previously unselected package libjsoncpp24:i386. Preparing to unpack .../040-libjsoncpp24_1.9.4-4_i386.deb ... Unpacking libjsoncpp24:i386 (1.9.4-4) ... Selecting previously unselected package librhash0:i386. Preparing to unpack .../041-librhash0_1.4.1-2_i386.deb ... Unpacking librhash0:i386 (1.4.1-2) ... Selecting previously unselected package libuv1:i386. Preparing to unpack .../042-libuv1_1.40.0-1_i386.deb ... Unpacking libuv1:i386 (1.40.0-1) ... Selecting previously unselected package cmake. Preparing to unpack .../043-cmake_3.18.4-2_i386.deb ... Unpacking cmake (3.18.4-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../044-libdebhelper-perl_13.3.4_all.deb ... Unpacking libdebhelper-perl (13.3.4) ... Selecting previously unselected package libtool. Preparing to unpack .../045-libtool_2.4.6-15_all.deb ... Unpacking libtool (2.4.6-15) ... Selecting previously unselected package dh-autoreconf. 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Setting up libpipeline1:i386 (1.5.3-1) ... Setting up libpixman-1-0:i386 (0.40.0-1) ... Setting up libpciaccess0:i386 (0.16-1) ... Setting up libxau6:i386 (1:1.0.9-1) ... Setting up libpsl5:i386 (0.21.0-1.2) ... Setting up libfftw3-single3:i386 (3.3.8-2) ... Setting up bsdextrautils (2.36.1-7) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libicu67:i386 (67.1-6) ... Setting up libmagic-mgc (1:5.39-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglvnd0:i386 (1.3.2-1) ... Setting up libdebhelper-perl (13.3.4) ... Setting up libbrotli1:i386 (1.0.9-2+b2) ... Setting up libcbor0:i386 (0.5.0+dfsg-2) ... Setting up libsensors-config (1:3.6.0-7) ... Setting up libnghttp2-14:i386 (1.43.0-1) ... Setting up libmagic1:i386 (1:5.39-3) ... Setting up libdeflate0:i386 (1.7-1) ... Setting up libfftw3-long3:i386 (3.3.8-2) ... Setting up gettext-base (0.21-4) ... Setting up file (1:5.39-3) ... Setting up libpthread-stubs0-dev:i386 (0.4-1) ... Setting up libjbig0:i386 (2.1-3.1+b2) ... Setting up libsasl2-modules-db:i386 (2.1.27+dfsg-2.1) ... Setting up xtrans-dev (1.4.0-1) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libz3-4:i386 (4.8.10-1) ... Setting up libuv1:i386 (1.40.0-1) ... Setting up libjpeg62-turbo:i386 (1:2.0.6-4) ... Setting up libx11-data (2:1.7.1-1) ... Setting up libjpeg62-turbo-dev:i386 (1:2.0.6-4) ... Setting up librtmp1:i386 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libncurses6:i386 (6.2+20201114-2) ... Setting up libsigsegv2:i386 (2.13-1) ... Setting up libfftw3-quad3:i386 (3.3.8-2) ... Setting up libpng16-16:i386 (1.6.37-3) ... Setting up libhwloc15:i386 (2.4.1+dfsg-1) ... Setting up libevent-core-2.1-7:i386 (2.1.12-stable-1) ... Setting up libevent-2.1-7:i386 (2.1.12-stable-1) ... Setting up autopoint (0.21-4) ... Setting up libwebp6:i386 (0.6.1-2.1) ... Setting up fonts-dejavu-core (2.37-2) ... Setting up libsensors5:i386 (1:3.6.0-7) ... Setting up libltdl7:i386 (2.4.6-15) ... Setting up libfftw3-double3:i386 (3.3.8-2) ... Setting up libglapi-mesa:i386 (20.3.4-1) ... Setting up libsasl2-2:i386 (2.1.27+dfsg-2.1) ... Setting up libgfortran5:i386 (10.2.1-6) ... Setting up libvulkan1:i386 (1.2.162.0-1) ... Setting up libjsoncpp24:i386 (1.9.4-4) ... Setting up liblzma-dev:i386 (5.2.5-2) ... Setting up zlib1g-dev:i386 (1:1.2.11.dfsg-2) ... Setting up libnuma1:i386 (2.0.12-1+b1) ... Setting up libmd0:i386 (1.0.3-3) ... Setting up sensible-utils (0.0.14) ... Setting up ocl-icd-libopencl1:i386 (2.2.14-2) ... Setting up libxshmfence1:i386 (1.3-1) ... Setting up librhash0:i386 (1.4.1-2) ... Setting up libuchardet0:i386 (0.0.7-1) ... Setting up libnl-3-200:i386 (3.4.0-1+b1) ... Setting up openmpi-common (4.1.0-10) ... Setting up libsub-override-perl (0.09-2) ... Setting up libgfortran-10-dev:i386 (10.2.1-6) ... Setting up libssh2-1:i386 (1.9.0-2) ... Setting up xorg-sgml-doctools (1:1.11-1.1) ... Setting up cmake-data (3.18.4-2) ... Setting up libtiff5:i386 (4.2.0-1) ... Setting up libpsm-infinipath1 (3.3+20.604758e7-6.1) ... update-alternatives: using /usr/lib/libpsm1/libpsm_infinipath.so.1.16 to provide /usr/lib/i386-linux-gnu/libpsm_infinipath.so.1 (libpsm_infinipath.so.1) in auto mode Setting up libjs-jquery (3.5.1+dfsg+~3.5.5-7) ... Setting up libfido2-1:i386 (1.6.0-2) ... Setting up libbsd0:i386 (0.11.3-1) ... Setting up libdeflate-dev:i386 (1.7-1) ... Setting up libdrm-common (2.4.104-1) ... Setting up libelf1:i386 (0.183-1) ... Setting up libxml2:i386 (2.9.10+dfsg-6.7) ... Setting up libprocps8:i386 (2:3.3.17-5) ... Setting up libtiffxx5:i386 (4.2.0-1) ... Setting up libevent-pthreads-2.1-7:i386 (2.1.12-stable-1) ... Setting up x11proto-dev (2020.1-1) ... Setting up libfile-stripnondeterminism-perl (1.11.0-1) ... Setting up libxdmcp6:i386 (1:1.1.2-3) ... Setting up libevent-extra-2.1-7:i386 (2.1.12-stable-1) ... 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Setting up libpmix-dev:i386 (4.0.0-4) ... Setting up openmpi-bin (4.1.0-10) ... 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 (1.3.5-3) ... Setting up fluid (1.3.5-3) ... Setting up libopenmpi-dev:i386 (4.1.0-10) ... update-alternatives: using /usr/lib/i386-linux-gnu/openmpi/include to provide /usr/include/i386-linux-gnu/mpi (mpi-i386-linux-gnu) in auto mode Processing triggers for libc-bin (2.31-12) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/relion-3.1.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package relion dpkg-buildpackage: info: source version 3.1.0-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean debian/rules override_dh_clean make[1]: Entering directory '/build/relion-3.1.0' dh_clean rm -rf build make[1]: Leaving directory '/build/relion-3.1.0' debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_build make[1]: Entering directory '/build/relion-3.1.0' mkdir /build/relion-3.1.0/build cd /build/relion-3.1.0/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-3.1.0;\ make -j18; DESTDIR=/build/relion-3.1.0/debian/tmp/cli make install CMake Warning (dev) at /usr/share/cmake-3.18/Modules/CMakeDetermineCompilerId.cmake:72 (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-3.18/Modules/CMakeDetermineCCompiler.cmake:116 (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 10.2.1 -- The CXX compiler identification is GNU 10.2.1 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- BUILD TYPE set to the default type: 'Release' -- Setting fallback CUDA_ARCH=35 -- ALLOW_CTF_IN_SAGD enabled - This build of RELION allows modulation of particle images by a contrast transfer function inside stochastic average gradient descent, as specified in Claim 1 of patent US10,282,513B2 -- Setting cpu precision to double -- Setting accelerated code precision to single -- Using non-cuda compilation.... -- Found MPI_C: /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/lib/i386-linux-gnu/openmpi/lib/libmpi_cxx.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") -- MPI_INCLUDE_PATH : /usr/lib/i386-linux-gnu/openmpi/include/openmpi;/usr/lib/i386-linux-gnu/openmpi/include -- MPI_LIBRARIES : /usr/lib/i386-linux-gnu/openmpi/lib/libmpi_cxx.so;/usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -- MPI_CXX_INCLUDE_PATH : /usr/lib/i386-linux-gnu/openmpi/include/openmpi;/usr/lib/i386-linux-gnu/openmpi/include -- MPI_CXX_LIBRARIES : /usr/lib/i386-linux-gnu/openmpi/lib/libmpi_cxx.so;/usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -- CMAKE_C_COMPILER : /usr/bin/gcc -- CMAKE_CXX_COMPILER : /usr/bin/g++ -- MPI_C_COMPILER : /usr/bin/mpicc -- MPI_CXX_COMPILER : /usr/bin/mpicxx -- CMAKE_CXX_COMPILER_ID : GNU -- CMAKE_C_COMPILER : /usr/bin/mpicc -- CMAKE_CXX_COMPILER : /usr/bin/mpicxx -- MPI_C_COMPILER : /usr/bin/mpicc -- MPI_CXX_COMPILER : /usr/bin/mpicxx -- Found X11: /usr/include -- Looking for XOpenDisplay in /usr/lib/i386-linux-gnu/libX11.so -- Looking for XOpenDisplay in /usr/lib/i386-linux-gnu/libX11.so - found -- Looking for gethostbyname -- Looking for gethostbyname - found -- Looking for connect -- Looking for connect - found -- Looking for remove -- Looking for remove - found -- Looking for shmat -- Looking for shmat - found -- Found FLTK: fltk_images;fltk_forms;fltk -- X11 and FLTK were found -- FLTK_LIBRARIES: fltk_images;fltk_forms;fltk;/usr/lib/i386-linux-gnu/libX11.so;/usr/lib/i386-linux-gnu/libm.so -- Found FFTW -- FFTW_PATH: /usr/include -- FFTW_INCLUDES: /usr/include -- FFTW_LIBRARIES: /usr/lib/i386-linux-gnu/libfftw3f.so;/usr/lib/i386-linux-gnu/libfftw3.so -- Looking for sincos -- Looking for sincos - found -- Looking for __sincos -- Looking for __sincos - not found -- Found TIFF: /usr/lib/i386-linux-gnu/libtiff.so (found version "4.2.0") -- Found ZLIB: /usr/lib/i386-linux-gnu/libz.so (found version "1.2.11") -- 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-3.1.0/build -- Git commit ID: GITDIR-NOTFOUND -- 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-3.1.0/build make[2]: Entering directory '/build/relion-3.1.0/build' /usr/bin/cmake -S/build/relion-3.1.0 -B/build/relion-3.1.0/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/relion-3.1.0/build/CMakeFiles /build/relion-3.1.0/build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/relion-3.1.0/build' make -f CMakeFiles/copy_scripts.dir/build.make CMakeFiles/copy_scripts.dir/depend make -f src/apps/CMakeFiles/relion_lib.dir/build.make src/apps/CMakeFiles/relion_lib.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0 /build/relion-3.1.0/build /build/relion-3.1.0/build /build/relion-3.1.0/build/CMakeFiles/copy_scripts.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/relion_lib.dir/DependInfo.cmake --color= Scanning dependencies of target copy_scripts make[4]: Leaving directory '/build/relion-3.1.0/build' make -f CMakeFiles/copy_scripts.dir/build.make CMakeFiles/copy_scripts.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' /usr/bin/cmake -E copy /build/relion-3.1.0/scripts/star_printtable /build/relion-3.1.0/build/bin/relion_star_printtable /usr/bin/cmake -E copy /build/relion-3.1.0/scripts/star_plottable /build/relion-3.1.0/build/bin/relion_star_plottable /usr/bin/cmake -E copy /build/relion-3.1.0/scripts/star_loopheader /build/relion-3.1.0/build/bin/relion_star_loopheader /usr/bin/cmake -E copy /build/relion-3.1.0/scripts/star_datablock_stack /build/relion-3.1.0/build/bin/relion_star_datablock_stack /usr/bin/cmake -E copy /build/relion-3.1.0/scripts/star_datablock_singlefiles /build/relion-3.1.0/build/bin/relion_star_datablock_singlefiles /usr/bin/cmake -E copy /build/relion-3.1.0/scripts/star_datablock_ctfdat /build/relion-3.1.0/build/bin/relion_star_datablock_ctfdat /usr/bin/cmake -E copy /build/relion-3.1.0/scripts/qsub.csh /build/relion-3.1.0/build/bin/relion_qsub.csh make[4]: Leaving directory '/build/relion-3.1.0/build' [ 0%] Built target copy_scripts Scanning dependencies of target relion_lib make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/relion_lib.dir/build.make src/apps/CMakeFiles/relion_lib.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 0%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/__/macros.cpp.o [ 1%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/CPlot2D.cpp.o [ 1%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/args.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/CPlot2D.cpp.o -c /build/relion-3.1.0/src/CPlot2D.cpp [ 2%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/autopicker.cpp.o [ 2%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/assembly.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/__/macros.cpp.o -c /build/relion-3.1.0/build/macros.cpp [ 2%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o [ 3%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/fftw.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/args.cpp.o -c /build/relion-3.1.0/src/args.cpp cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/assembly.cpp.o -c /build/relion-3.1.0/src/assembly.cpp [ 4%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/backprojector.cpp.o [ 5%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/error.cpp.o [ 5%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/complex.cpp.o [ 6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/autopicker.cpp.o -c /build/relion-3.1.0/src/autopicker.cpp [ 6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner_mpi.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o -c /build/relion-3.1.0/src/autopicker_mpi.cpp [ 6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctf.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/backprojector.cpp.o -c /build/relion-3.1.0/src/backprojector.cpp cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/complex.cpp.o -c /build/relion-3.1.0/src/complex.cpp cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/ctf.cpp.o -c /build/relion-3.1.0/src/ctf.cpp [ 6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/euler.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/ctffind_runner.cpp.o -c /build/relion-3.1.0/src/ctffind_runner.cpp [ 6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/exp_model.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/ctffind_runner_mpi.cpp.o -c /build/relion-3.1.0/src/ctffind_runner_mpi.cpp [ 6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/filename.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/error.cpp.o -c /build/relion-3.1.0/src/error.cpp cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/euler.cpp.o -c /build/relion-3.1.0/src/euler.cpp cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/exp_model.cpp.o -c /build/relion-3.1.0/src/exp_model.cpp cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/fftw.cpp.o -c /build/relion-3.1.0/src/fftw.cpp cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/filename.cpp.o -c /build/relion-3.1.0/src/filename.cpp [ 7%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/flex_analyser.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/flex_analyser.cpp.o -c /build/relion-3.1.0/src/flex_analyser.cpp [ 7%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/funcs.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/funcs.cpp.o -c /build/relion-3.1.0/src/funcs.cpp [ 7%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/healpix_sampling.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/healpix_sampling.cpp.o -c /build/relion-3.1.0/src/healpix_sampling.cpp [ 8%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/helix.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/helix.cpp.o -c /build/relion-3.1.0/src/helix.cpp [ 8%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/helix_inimodel2d.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/helix_inimodel2d.cpp.o -c /build/relion-3.1.0/src/helix_inimodel2d.cpp [ 8%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/image.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/image.cpp.o -c /build/relion-3.1.0/src/image.cpp [ 9%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/local_symmetry.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/local_symmetry.cpp.o -c /build/relion-3.1.0/src/local_symmetry.cpp [ 9%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/local_symmetry_mpi.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/local_symmetry_mpi.cpp.o -c /build/relion-3.1.0/src/local_symmetry_mpi.cpp [ 10%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/mask.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/mask.cpp.o -c /build/relion-3.1.0/src/mask.cpp [ 10%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/matrix1d.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/matrix1d.cpp.o -c /build/relion-3.1.0/src/matrix1d.cpp [ 10%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/matrix2d.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/matrix2d.cpp.o -c /build/relion-3.1.0/src/matrix2d.cpp /build/relion-3.1.0/src/CPlot2D.cpp: In member function 'void CPlot2D::ComputeLabelTickSpacing(double, double, double*, double*, double*, int, std::string)': /build/relion-3.1.0/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-3.1.0/src/CPlot2D.cpp:743:37: note: directive argument in the range [0, 2147483647] 743 | sprintf(m_cYAxisLabelFormat,"%%.%df",nfrac); | ^~~~~~~~ /build/relion-3.1.0/src/CPlot2D.cpp:743:16: note: 'sprintf' output between 5 and 14 bytes into a destination of size 10 743 | sprintf(m_cYAxisLabelFormat,"%%.%df",nfrac); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/relion-3.1.0/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-3.1.0/src/CPlot2D.cpp:733:37: note: directive argument in the range [0, 2147483647] 733 | sprintf(m_cXAxisLabelFormat,"%%.%df",nfrac); | ^~~~~~~~ /build/relion-3.1.0/src/CPlot2D.cpp:733:16: note: 'sprintf' output between 5 and 14 bytes into a destination of size 10 733 | sprintf(m_cXAxisLabelFormat,"%%.%df",nfrac); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 11%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/memory.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/memory.cpp.o -c /build/relion-3.1.0/src/memory.cpp [ 11%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/metadata_container.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/metadata_container.cpp.o -c /build/relion-3.1.0/src/metadata_container.cpp [ 11%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/metadata_label.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/metadata_label.cpp.o -c /build/relion-3.1.0/src/metadata_label.cpp [ 12%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/metadata_table.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/metadata_table.cpp.o -c /build/relion-3.1.0/src/metadata_table.cpp [ 12%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/micrograph_model.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/micrograph_model.cpp.o -c /build/relion-3.1.0/src/micrograph_model.cpp [ 13%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ml_model.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/ml_model.cpp.o -c /build/relion-3.1.0/src/ml_model.cpp [ 13%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ml_optimiser.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/ml_optimiser.cpp.o -c /build/relion-3.1.0/src/ml_optimiser.cpp [ 13%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ml_optimiser_mpi.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/ml_optimiser_mpi.cpp.o -c /build/relion-3.1.0/src/ml_optimiser_mpi.cpp [ 14%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/motioncorr_runner.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/motioncorr_runner.cpp.o -c /build/relion-3.1.0/src/motioncorr_runner.cpp [ 14%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/motioncorr_runner_mpi.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/motioncorr_runner_mpi.cpp.o -c /build/relion-3.1.0/src/motioncorr_runner_mpi.cpp [ 14%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/mpi.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/mpi.cpp.o -c /build/relion-3.1.0/src/mpi.cpp [ 15%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/multidim_array.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/multidim_array.cpp.o -c /build/relion-3.1.0/src/multidim_array.cpp [ 15%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/numerical_recipes.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/numerical_recipes.cpp.o -c /build/relion-3.1.0/src/numerical_recipes.cpp [ 16%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/parallel.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/parallel.cpp.o -c /build/relion-3.1.0/src/parallel.cpp [ 16%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/particle_subtractor.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/particle_subtractor.cpp.o -c /build/relion-3.1.0/src/particle_subtractor.cpp [ 16%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/pipeline_control.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/pipeline_control.cpp.o -c /build/relion-3.1.0/src/pipeline_control.cpp [ 17%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/pipeline_jobs.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/pipeline_jobs.cpp.o -c /build/relion-3.1.0/src/pipeline_jobs.cpp [ 17%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/pipeliner.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/pipeliner.cpp.o -c /build/relion-3.1.0/src/pipeliner.cpp [ 18%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/postprocessing.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/postprocessing.cpp.o -c /build/relion-3.1.0/src/postprocessing.cpp [ 18%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/preprocessing.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/preprocessing.cpp.o -c /build/relion-3.1.0/src/preprocessing.cpp [ 18%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/preprocessing_mpi.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/preprocessing_mpi.cpp.o -c /build/relion-3.1.0/src/preprocessing_mpi.cpp [ 19%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/projector.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/projector.cpp.o -c /build/relion-3.1.0/src/projector.cpp [ 19%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/reconstructor.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/reconstructor.cpp.o -c /build/relion-3.1.0/src/reconstructor.cpp [ 19%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/reconstructor_mpi.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/reconstructor_mpi.cpp.o -c /build/relion-3.1.0/src/reconstructor_mpi.cpp [ 20%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/scheduler.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/scheduler.cpp.o -c /build/relion-3.1.0/src/scheduler.cpp [ 20%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/strings.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/strings.cpp.o -c /build/relion-3.1.0/src/strings.cpp [ 21%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/symmetries.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/symmetries.cpp.o -c /build/relion-3.1.0/src/symmetries.cpp [ 21%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/tabfuncs.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/tabfuncs.cpp.o -c /build/relion-3.1.0/src/tabfuncs.cpp [ 21%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/tiff_converter.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/tiff_converter.cpp.o -c /build/relion-3.1.0/src/tiff_converter.cpp [ 22%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/time.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/time.cpp.o -c /build/relion-3.1.0/src/time.cpp [ 22%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/transformations.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/transformations.cpp.o -c /build/relion-3.1.0/src/transformations.cpp [ 22%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/Healpix_2.15a/cxxutils.cc.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/Healpix_2.15a/cxxutils.cc.o -c /build/relion-3.1.0/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-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/Healpix_2.15a/healpix_base.cc.o -c /build/relion-3.1.0/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-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/Fourier_helper.cpp.o -c /build/relion-3.1.0/src/jaz/Fourier_helper.cpp [ 24%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/Gaussian_pyramid.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/Gaussian_pyramid.cpp.o -c /build/relion-3.1.0/src/jaz/Gaussian_pyramid.cpp [ 24%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/aberration_fit.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/aberration_fit.cpp.o -c /build/relion-3.1.0/src/jaz/aberration_fit.cpp [ 24%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/complex_io.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/complex_io.cpp.o -c /build/relion-3.1.0/src/jaz/complex_io.cpp [ 25%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/convolution_helper.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/convolution_helper.cpp.o -c /build/relion-3.1.0/src/jaz/convolution_helper.cpp [ 25%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf_helper.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/ctf_helper.cpp.o -c /build/relion-3.1.0/src/jaz/ctf_helper.cpp [ 26%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/damage_helper.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/damage_helper.cpp.o -c /build/relion-3.1.0/src/jaz/damage_helper.cpp [ 26%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/distribution_helper.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/distribution_helper.cpp.o -c /build/relion-3.1.0/src/jaz/distribution_helper.cpp [ 26%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/fftw_helper.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/fftw_helper.cpp.o -c /build/relion-3.1.0/src/jaz/fftw_helper.cpp [ 27%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/fsc_helper.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/fsc_helper.cpp.o -c /build/relion-3.1.0/src/jaz/fsc_helper.cpp [ 27%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/image_log.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/image_log.cpp.o -c /build/relion-3.1.0/src/jaz/image_log.cpp [ 27%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/interpolation.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/interpolation.cpp.o -c /build/relion-3.1.0/src/jaz/interpolation.cpp [ 28%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/jaz_config.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/jaz_config.cpp.o -c /build/relion-3.1.0/src/jaz/jaz_config.cpp [ 28%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/legacy_obs_model.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/legacy_obs_model.cpp.o -c /build/relion-3.1.0/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-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/local_motion_fit.cpp.o -c /build/relion-3.1.0/src/jaz/local_motion_fit.cpp [ 29%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/micrograph_handler.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/micrograph_handler.cpp.o -c /build/relion-3.1.0/src/jaz/micrograph_handler.cpp [ 29%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/new_ft.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/new_ft.cpp.o -c /build/relion-3.1.0/src/jaz/new_ft.cpp [ 30%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/noise_helper.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/noise_helper.cpp.o -c /build/relion-3.1.0/src/jaz/noise_helper.cpp [ 30%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/obs_model.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/obs_model.cpp.o -c /build/relion-3.1.0/src/jaz/obs_model.cpp [ 30%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/parallel_ft.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/parallel_ft.cpp.o -c /build/relion-3.1.0/src/jaz/parallel_ft.cpp [ 31%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/reference_map.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/reference_map.cpp.o -c /build/relion-3.1.0/src/jaz/reference_map.cpp [ 31%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/refinement_helper.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/refinement_helper.cpp.o -c /build/relion-3.1.0/src/jaz/refinement_helper.cpp [ 32%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/resampling_helper.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/resampling_helper.cpp.o -c /build/relion-3.1.0/src/jaz/resampling_helper.cpp [ 32%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/slice_helper.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/slice_helper.cpp.o -c /build/relion-3.1.0/src/jaz/slice_helper.cpp [ 32%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/spectral_helper.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/spectral_helper.cpp.o -c /build/relion-3.1.0/src/jaz/spectral_helper.cpp [ 33%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/stack_helper.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/stack_helper.cpp.o -c /build/relion-3.1.0/src/jaz/stack_helper.cpp [ 33%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/structure_tensor.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/structure_tensor.cpp.o -c /build/relion-3.1.0/src/jaz/structure_tensor.cpp [ 34%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/svd_helper.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/svd_helper.cpp.o -c /build/relion-3.1.0/src/jaz/svd_helper.cpp [ 34%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/t_complex.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/t_complex.cpp.o -c /build/relion-3.1.0/src/jaz/t_complex.cpp [ 34%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/volume_converter.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/volume_converter.cpp.o -c /build/relion-3.1.0/src/jaz/volume_converter.cpp [ 35%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/volume_integration.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/volume_integration.cpp.o -c /build/relion-3.1.0/src/jaz/volume_integration.cpp [ 35%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/vtk_helper.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/vtk_helper.cpp.o -c /build/relion-3.1.0/src/jaz/vtk_helper.cpp [ 35%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/gradient_descent.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/optimization/gradient_descent.cpp.o -c /build/relion-3.1.0/src/jaz/optimization/gradient_descent.cpp [ 36%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/lbfgs.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/optimization/lbfgs.cpp.o -c /build/relion-3.1.0/src/jaz/optimization/lbfgs.cpp [ 36%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/nelder_mead.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/optimization/nelder_mead.cpp.o -c /build/relion-3.1.0/src/jaz/optimization/nelder_mead.cpp [ 36%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/aberration_estimator.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/ctf/aberration_estimator.cpp.o -c /build/relion-3.1.0/src/jaz/ctf/aberration_estimator.cpp [ 37%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/optimization/optimization.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/optimization/optimization.cpp.o -c /build/relion-3.1.0/src/jaz/optimization/optimization.cpp [ 37%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/bfactor_refiner.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/ctf/bfactor_refiner.cpp.o -c /build/relion-3.1.0/src/jaz/ctf/bfactor_refiner.cpp [ 38%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner.cpp.o -c /build/relion-3.1.0/src/jaz/ctf/ctf_refiner.cpp [ 38%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner_mpi.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/ctf/ctf_refiner_mpi.cpp.o -c /build/relion-3.1.0/src/jaz/ctf/ctf_refiner_mpi.cpp [ 38%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_estimator.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_estimator.cpp.o -c /build/relion-3.1.0/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-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/ctf/defocus_helper.cpp.o -c /build/relion-3.1.0/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-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/ctf/delocalisation_helper.cpp.o -c /build/relion-3.1.0/src/jaz/ctf/delocalisation_helper.cpp [ 40%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/equation2x2.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/ctf/equation2x2.cpp.o -c /build/relion-3.1.0/src/jaz/ctf/equation2x2.cpp [ 40%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_estimator.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_estimator.cpp.o -c /build/relion-3.1.0/src/jaz/ctf/magnification_estimator.cpp [ 40%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_helper.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/ctf/magnification_helper.cpp.o -c /build/relion-3.1.0/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-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/ctf/modular_ctf_optimisation.cpp.o -c /build/relion-3.1.0/src/jaz/ctf/modular_ctf_optimisation.cpp [ 41%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_estimator.cpp.o [ 41%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_helper.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_estimator.cpp.o -c /build/relion-3.1.0/src/jaz/ctf/tilt_estimator.cpp cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/ctf/tilt_helper.cpp.o -c /build/relion-3.1.0/src/jaz/ctf/tilt_helper.cpp [ 42%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/alignment_set.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/motion/alignment_set.cpp.o -c /build/relion-3.1.0/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-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/motion/frame_recombiner.cpp.o -c /build/relion-3.1.0/src/jaz/motion/frame_recombiner.cpp [ 43%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/gp_motion_fit.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/motion/gp_motion_fit.cpp.o -c /build/relion-3.1.0/src/jaz/motion/gp_motion_fit.cpp [ 43%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_estimator.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_estimator.cpp.o -c /build/relion-3.1.0/src/jaz/motion/motion_estimator.cpp [ 43%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_helper.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_helper.cpp.o -c /build/relion-3.1.0/src/jaz/motion/motion_helper.cpp [ 44%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_param_estimator.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_param_estimator.cpp.o -c /build/relion-3.1.0/src/jaz/motion/motion_param_estimator.cpp [ 44%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner.cpp.o -c /build/relion-3.1.0/src/jaz/motion/motion_refiner.cpp [ 45%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner_mpi.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/motion/motion_refiner_mpi.cpp.o -c /build/relion-3.1.0/src/jaz/motion/motion_refiner_mpi.cpp [ 45%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/three_hyperparameter_fit.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/motion/three_hyperparameter_fit.cpp.o -c /build/relion-3.1.0/src/jaz/motion/three_hyperparameter_fit.cpp [ 45%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/two_hyperparameter_fit.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/motion/two_hyperparameter_fit.cpp.o -c /build/relion-3.1.0/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-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/math/Zernike.cpp.o -c /build/relion-3.1.0/src/jaz/math/Zernike.cpp [ 46%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/color_helper.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/img_proc/color_helper.cpp.o -c /build/relion-3.1.0/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-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/img_proc/filter_helper.cpp.o -c /build/relion-3.1.0/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-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/img_proc/image_op.cpp.o -c /build/relion-3.1.0/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-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/tomo/backprojection_helper.cpp.o -c /build/relion-3.1.0/src/jaz/tomo/backprojection_helper.cpp [ 48%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/imod_helper.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/tomo/imod_helper.cpp.o -c /build/relion-3.1.0/src/jaz/tomo/imod_helper.cpp [ 48%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/projection_helper.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/tomo/projection_helper.cpp.o -c /build/relion-3.1.0/src/jaz/tomo/projection_helper.cpp [ 48%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomo/tomo_stack.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/tomo/tomo_stack.cpp.o -c /build/relion-3.1.0/src/jaz/tomo/tomo_stack.cpp [ 49%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/io/star_converter.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/io/star_converter.cpp.o -c /build/relion-3.1.0/src/jaz/io/star_converter.cpp [ 49%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyev2.c.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c99 -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyev2.c.o -c /build/relion-3.1.0/src/jaz/d3x3/dsyev2.c [ 49%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevc3.c.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c99 -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevc3.c.o -c /build/relion-3.1.0/src/jaz/d3x3/dsyevc3.c [ 50%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevd3.c.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c99 -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevd3.c.o -c /build/relion-3.1.0/src/jaz/d3x3/dsyevd3.c [ 50%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevh3.c.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicc 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-DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevj3.c.o -c /build/relion-3.1.0/src/jaz/d3x3/dsyevj3.c [ 51%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevq3.c.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c99 -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevq3.c.o -c /build/relion-3.1.0/src/jaz/d3x3/dsyevq3.c [ 51%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevv3.c.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c99 -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevv3.c.o -c /build/relion-3.1.0/src/jaz/d3x3/dsyevv3.c [ 52%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsytrd3.c.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c99 -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsytrd3.c.o -c /build/relion-3.1.0/src/jaz/d3x3/dsytrd3.c [ 52%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/slvsec3.c.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c99 -O3 -DNDEBUG -o CMakeFiles/relion_lib.dir/__/jaz/d3x3/slvsec3.c.o -c /build/relion-3.1.0/src/jaz/d3x3/slvsec3.c [ 53%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/lbfgs/lbfgs.c.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicc -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g 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CMakeFiles/relion_lib.dir/__/ctffind_runner.cpp.o CMakeFiles/relion_lib.dir/__/ctffind_runner_mpi.cpp.o CMakeFiles/relion_lib.dir/__/error.cpp.o CMakeFiles/relion_lib.dir/__/euler.cpp.o CMakeFiles/relion_lib.dir/__/exp_model.cpp.o CMakeFiles/relion_lib.dir/__/fftw.cpp.o CMakeFiles/relion_lib.dir/__/filename.cpp.o CMakeFiles/relion_lib.dir/__/flex_analyser.cpp.o CMakeFiles/relion_lib.dir/__/funcs.cpp.o CMakeFiles/relion_lib.dir/__/healpix_sampling.cpp.o CMakeFiles/relion_lib.dir/__/helix.cpp.o CMakeFiles/relion_lib.dir/__/helix_inimodel2d.cpp.o CMakeFiles/relion_lib.dir/__/image.cpp.o CMakeFiles/relion_lib.dir/__/local_symmetry.cpp.o CMakeFiles/relion_lib.dir/__/local_symmetry_mpi.cpp.o CMakeFiles/relion_lib.dir/__/mask.cpp.o CMakeFiles/relion_lib.dir/__/matrix1d.cpp.o CMakeFiles/relion_lib.dir/__/matrix2d.cpp.o CMakeFiles/relion_lib.dir/__/memory.cpp.o CMakeFiles/relion_lib.dir/__/metadata_container.cpp.o CMakeFiles/relion_lib.dir/__/metadata_label.cpp.o CMakeFiles/relion_lib.dir/__/metadata_table.cpp.o CMakeFiles/relion_lib.dir/__/micrograph_model.cpp.o CMakeFiles/relion_lib.dir/__/ml_model.cpp.o CMakeFiles/relion_lib.dir/__/ml_optimiser.cpp.o CMakeFiles/relion_lib.dir/__/ml_optimiser_mpi.cpp.o CMakeFiles/relion_lib.dir/__/motioncorr_runner.cpp.o CMakeFiles/relion_lib.dir/__/motioncorr_runner_mpi.cpp.o CMakeFiles/relion_lib.dir/__/mpi.cpp.o CMakeFiles/relion_lib.dir/__/multidim_array.cpp.o CMakeFiles/relion_lib.dir/__/numerical_recipes.cpp.o CMakeFiles/relion_lib.dir/__/parallel.cpp.o CMakeFiles/relion_lib.dir/__/particle_subtractor.cpp.o CMakeFiles/relion_lib.dir/__/pipeline_control.cpp.o CMakeFiles/relion_lib.dir/__/pipeline_jobs.cpp.o CMakeFiles/relion_lib.dir/__/pipeliner.cpp.o CMakeFiles/relion_lib.dir/__/postprocessing.cpp.o CMakeFiles/relion_lib.dir/__/preprocessing.cpp.o CMakeFiles/relion_lib.dir/__/preprocessing_mpi.cpp.o CMakeFiles/relion_lib.dir/__/projector.cpp.o CMakeFiles/relion_lib.dir/__/reconstructor.cpp.o 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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-3.1.0/build' [ 53%] Built target relion_lib make -f src/apps/CMakeFiles/particle_FCC.dir/build.make src/apps/CMakeFiles/particle_FCC.dir/depend make -f src/apps/CMakeFiles/image_handler.dir/build.make src/apps/CMakeFiles/image_handler.dir/depend make -f src/apps/CMakeFiles/plot_delocalisation.dir/build.make src/apps/CMakeFiles/plot_delocalisation.dir/depend make -f src/apps/CMakeFiles/postprocess_mpi.dir/build.make src/apps/CMakeFiles/postprocess_mpi.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/particle_FCC.dir/DependInfo.cmake --color= make -f src/apps/CMakeFiles/helix_toolbox.dir/build.make 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src/apps/CMakeFiles/localsym_mpi.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/localsym.dir/DependInfo.cmake --color= 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-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/relion_gui_lib.dir/DependInfo.cmake --color= make -f src/apps/CMakeFiles/prepare_subtomo.dir/build.make src/apps/CMakeFiles/prepare_subtomo.dir/depend make -f src/apps/CMakeFiles/particle_subtract_mpi.dir/build.make src/apps/CMakeFiles/particle_subtract_mpi.dir/depend make -f src/apps/CMakeFiles/external_reconstruct.dir/build.make src/apps/CMakeFiles/external_reconstruct.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/localsym_mpi.dir/DependInfo.cmake --color= make -f src/apps/CMakeFiles/import.dir/build.make src/apps/CMakeFiles/import.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/flex_analyse_mpi.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/prepare_subtomo.dir/DependInfo.cmake --color= make -f src/apps/CMakeFiles/flex_analyse.dir/build.make src/apps/CMakeFiles/flex_analyse.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/external_reconstruct.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps 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src/apps/CMakeFiles/helix_toolbox.dir/build make[4]: Leaving directory '/build/relion-3.1.0/build' make[4]: Leaving directory '/build/relion-3.1.0/build' make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/particle_FCC.dir/build.make src/apps/CMakeFiles/particle_FCC.dir/build make -f src/apps/CMakeFiles/plot_delocalisation.dir/build.make src/apps/CMakeFiles/plot_delocalisation.dir/build make -f src/apps/CMakeFiles/helix_inimodel2d.dir/build.make src/apps/CMakeFiles/helix_inimodel2d.dir/build Scanning dependencies of target image_handler make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Leaving directory '/build/relion-3.1.0/build' make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Entering directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/image_handler.dir/build.make src/apps/CMakeFiles/image_handler.dir/build Scanning dependencies of target localsym Scanning dependencies of target external_reconstruct Scanning dependencies of target prepare_subtomo make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Leaving directory '/build/relion-3.1.0/build' make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/localsym.dir/build.make src/apps/CMakeFiles/localsym.dir/build make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/prepare_subtomo.dir/build.make src/apps/CMakeFiles/prepare_subtomo.dir/build Scanning dependencies of target preprocess_mpi make -f src/apps/CMakeFiles/external_reconstruct.dir/build.make src/apps/CMakeFiles/external_reconstruct.dir/build make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/preprocess_mpi.dir/build.make src/apps/CMakeFiles/preprocess_mpi.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Entering 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'/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/flex_analyse_mpi.dir/build.make src/apps/CMakeFiles/flex_analyse_mpi.dir/build make -f src/apps/CMakeFiles/import.dir/build.make src/apps/CMakeFiles/import.dir/build make[4]: Leaving directory '/build/relion-3.1.0/build' Scanning dependencies of target flex_analyse make -f src/apps/CMakeFiles/localsym_mpi.dir/build.make src/apps/CMakeFiles/localsym_mpi.dir/build [ 55%] Building CXX object src/apps/CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o make[4]: Leaving directory '/build/relion-3.1.0/build' [ 56%] Building CXX object src/apps/CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o [ 57%] Building CXX object src/apps/CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o make -f src/apps/CMakeFiles/flex_analyse.dir/build.make src/apps/CMakeFiles/flex_analyse.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' Scanning dependencies of target autopick [ 57%] Building CXX object src/apps/CMakeFiles/plot_delocalisation.dir/plot_delocalisation.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o -c /build/relion-3.1.0/src/apps/postprocess_mpi.cpp [ 58%] Building CXX object src/apps/CMakeFiles/helix_inimodel2d.dir/helix_inimodel2d.cpp.o make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/helix_toolbox.dir/helix_toolbox.cpp.o -c /build/relion-3.1.0/src/apps/helix_toolbox.cpp make[4]: Leaving directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/particle_FCC.dir/particle_FCC.cpp.o -c /build/relion-3.1.0/src/apps/particle_FCC.cpp cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/plot_delocalisation.dir/plot_delocalisation.cpp.o -c /build/relion-3.1.0/src/apps/plot_delocalisation.cpp make -f src/apps/CMakeFiles/autopick.dir/build.make src/apps/CMakeFiles/autopick.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Entering directory '/build/relion-3.1.0/build' [ 58%] Building CXX object src/apps/CMakeFiles/image_handler.dir/image_handler.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/image_handler.dir/image_handler.cpp.o -c /build/relion-3.1.0/src/apps/image_handler.cpp cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/helix_inimodel2d.dir/helix_inimodel2d.cpp.o -c /build/relion-3.1.0/src/apps/helix_inimodel2d.cpp Scanning dependencies of target relion_gui_lib [ 59%] Building CXX object src/apps/CMakeFiles/localsym.dir/localsym.cpp.o Scanning dependencies of target particle_subtract_mpi make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/localsym.dir/localsym.cpp.o -c /build/relion-3.1.0/src/apps/localsym.cpp make[4]: Leaving directory '/build/relion-3.1.0/build' [ 59%] Building CXX object src/apps/CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o make[4]: Leaving directory '/build/relion-3.1.0/build' [ 60%] Building CXX object src/apps/CMakeFiles/external_reconstruct.dir/external_reconstruct.cpp.o [ 61%] Building CXX object src/apps/CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o -c /build/relion-3.1.0/src/apps/prepare_subtomo.cpp make -f src/apps/CMakeFiles/relion_gui_lib.dir/build.make src/apps/CMakeFiles/relion_gui_lib.dir/build cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/external_reconstruct.dir/external_reconstruct.cpp.o -c /build/relion-3.1.0/src/apps/external_reconstruct.cpp cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o -c /build/relion-3.1.0/src/apps/preprocess_mpi.cpp make[4]: Entering directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/particle_subtract_mpi.dir/build.make src/apps/CMakeFiles/particle_subtract_mpi.dir/build [ 61%] Building CXX object src/apps/CMakeFiles/import.dir/import.cpp.o [ 61%] Building CXX object src/apps/CMakeFiles/flex_analyse.dir/flex_analyse.cpp.o make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/import.dir/import.cpp.o -c /build/relion-3.1.0/src/apps/import.cpp [ 61%] Building CXX object src/apps/CMakeFiles/flex_analyse_mpi.dir/flex_analyse_mpi.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/flex_analyse.dir/flex_analyse.cpp.o -c /build/relion-3.1.0/src/apps/flex_analyse.cpp [ 62%] Building CXX object src/apps/CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o -c /build/relion-3.1.0/src/apps/localsym_mpi.cpp cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/flex_analyse_mpi.dir/flex_analyse_mpi.cpp.o -c /build/relion-3.1.0/src/apps/flex_analyse_mpi.cpp [ 63%] Building CXX object src/apps/CMakeFiles/autopick.dir/autopick.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/autopick.dir/autopick.cpp.o -c /build/relion-3.1.0/src/apps/autopick.cpp [ 63%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o [ 64%] Building CXX object src/apps/CMakeFiles/particle_subtract_mpi.dir/particle_subtract_mpi.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o -c /build/relion-3.1.0/src/displayer.cpp cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/particle_subtract_mpi.dir/particle_subtract_mpi.cpp.o -c /build/relion-3.1.0/src/apps/particle_subtract_mpi.cpp [ 64%] Linking CXX executable ../../bin/relion_localsym cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/localsym.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 64%] Linking CXX executable ../../bin/relion_helix_inimodel2d cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/helix_inimodel2d.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 64%] Linking CXX executable ../../bin/relion_autopick cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/autopick.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.0/build' [ 64%] Built target helix_inimodel2d 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-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/convert_to_tiff.dir/DependInfo.cmake --color= Scanning dependencies of target convert_to_tiff make[4]: Leaving directory '/build/relion-3.1.0/build' 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-3.1.0/build' [ 64%] Building CXX object src/apps/CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o -c /build/relion-3.1.0/src/apps/convert_to_tiff.cpp [ 64%] Linking CXX executable ../../bin/relion_localsym_mpi cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/localsym_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.0/build' [ 64%] Built target localsym 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-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/ctf_refine_mpi.dir/DependInfo.cmake --color= Scanning dependencies of target ctf_refine_mpi make[4]: Leaving directory '/build/relion-3.1.0/build' 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-3.1.0/build' [ 64%] Building CXX object src/apps/CMakeFiles/ctf_refine_mpi.dir/ctf_refine_mpi.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/ctf_refine_mpi.dir/ctf_refine_mpi.cpp.o -c /build/relion-3.1.0/src/apps/ctf_refine_mpi.cpp [ 64%] Linking CXX executable ../../bin/relion_preprocess_mpi cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/preprocess_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.0/build' [ 64%] Linking CXX executable ../../bin/relion_particle_FCC cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_FCC.dir/link.txt --verbose=1 [ 64%] Built target autopick make -f src/apps/CMakeFiles/merge_particles.dir/build.make src/apps/CMakeFiles/merge_particles.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/merge_particles.dir/DependInfo.cmake --color= /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff Scanning dependencies of target merge_particles make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/merge_particles.dir/build.make src/apps/CMakeFiles/merge_particles.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 65%] Building CXX object src/apps/CMakeFiles/merge_particles.dir/merge_particles.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/merge_particles.dir/merge_particles.cpp.o -c /build/relion-3.1.0/src/apps/merge_particles.cpp [ 65%] Linking CXX executable ../../bin/relion_postprocess_mpi cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/postprocess_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.0/build' [ 65%] Built target localsym_mpi make -f src/apps/CMakeFiles/mask_create.dir/build.make src/apps/CMakeFiles/mask_create.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/mask_create.dir/DependInfo.cmake --color= Scanning dependencies of target mask_create make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/mask_create.dir/build.make src/apps/CMakeFiles/mask_create.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 65%] Building CXX object src/apps/CMakeFiles/mask_create.dir/mask_create.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/mask_create.dir/mask_create.cpp.o -c /build/relion-3.1.0/src/apps/mask_create.cpp [ 65%] Linking CXX executable ../../bin/relion_convert_to_tiff cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/convert_to_tiff.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/relion-3.1.0/build' /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.0/build' [ 65%] Built target preprocess_mpi make -f src/apps/CMakeFiles/project.dir/build.make src/apps/CMakeFiles/project.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/project.dir/DependInfo.cmake --color= [ 65%] Linking CXX executable ../../bin/relion_plot_delocalisation cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/plot_delocalisation.dir/link.txt --verbose=1 [ 65%] Built target postprocess_mpi 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-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/ctf_mask_test.dir/DependInfo.cmake --color= /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff Scanning dependencies of target project make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/project.dir/build.make src/apps/CMakeFiles/project.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' Scanning dependencies of target ctf_mask_test make[4]: Leaving directory '/build/relion-3.1.0/build' 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-3.1.0/build' [ 66%] Building CXX object src/apps/CMakeFiles/project.dir/project.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/project.dir/project.cpp.o -c /build/relion-3.1.0/src/apps/project.cpp [ 66%] Building CXX object src/apps/CMakeFiles/ctf_mask_test.dir/ctf_mask_test.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/ctf_mask_test.dir/ctf_mask_test.cpp.o -c /build/relion-3.1.0/src/apps/ctf_mask_test.cpp make[4]: Leaving directory '/build/relion-3.1.0/build' [ 66%] Built target particle_FCC make -f src/apps/CMakeFiles/preprocess.dir/build.make src/apps/CMakeFiles/preprocess.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/preprocess.dir/DependInfo.cmake --color= Scanning dependencies of target preprocess make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/preprocess.dir/build.make src/apps/CMakeFiles/preprocess.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 66%] Building CXX object src/apps/CMakeFiles/preprocess.dir/preprocess.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/preprocess.dir/preprocess.cpp.o -c /build/relion-3.1.0/src/apps/preprocess.cpp make[4]: Leaving directory '/build/relion-3.1.0/build' [ 66%] Built target convert_to_tiff make -f src/apps/CMakeFiles/convert_star.dir/build.make src/apps/CMakeFiles/convert_star.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/convert_star.dir/DependInfo.cmake --color= Scanning dependencies of target convert_star make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/convert_star.dir/build.make src/apps/CMakeFiles/convert_star.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 66%] Building CXX object src/apps/CMakeFiles/convert_star.dir/convert_star.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/convert_star.dir/convert_star.cpp.o -c /build/relion-3.1.0/src/apps/convert_star.cpp make[4]: Leaving directory '/build/relion-3.1.0/build' [ 66%] Built target plot_delocalisation make -f src/apps/CMakeFiles/demodulate.dir/build.make src/apps/CMakeFiles/demodulate.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/demodulate.dir/DependInfo.cmake --color= Scanning dependencies of target demodulate make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/demodulate.dir/build.make src/apps/CMakeFiles/demodulate.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 66%] Building CXX object src/apps/CMakeFiles/demodulate.dir/demodulate.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/demodulate.dir/demodulate.cpp.o -c /build/relion-3.1.0/src/apps/demodulate.cpp [ 66%] Linking CXX executable ../../bin/relion_flex_analyse_mpi cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/flex_analyse_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 67%] Linking CXX executable ../../bin/relion_flex_analyse cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/flex_analyse.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 67%] Linking CXX executable ../../bin/relion_import cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/import.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 67%] Linking CXX executable ../../bin/relion_merge_particles cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/merge_particles.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 67%] Linking CXX executable ../../bin/relion_find_tiltpairs cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/find_tiltpairs.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.0/build' [ 67%] Built target find_tiltpairs make -f src/apps/CMakeFiles/motion_refine.dir/build.make src/apps/CMakeFiles/motion_refine.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/motion_refine.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' [ 67%] Built target merge_particles make -f src/apps/CMakeFiles/tomo_test.dir/build.make src/apps/CMakeFiles/tomo_test.dir/depend Scanning dependencies of target motion_refine make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/tomo_test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/motion_refine.dir/build.make src/apps/CMakeFiles/motion_refine.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 67%] Building CXX object src/apps/CMakeFiles/motion_refine.dir/motion_refine.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/motion_refine.dir/motion_refine.cpp.o -c /build/relion-3.1.0/src/apps/motion_refine.cpp Scanning dependencies of target tomo_test make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/tomo_test.dir/build.make src/apps/CMakeFiles/tomo_test.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Leaving directory '/build/relion-3.1.0/build' [ 67%] Building CXX object src/apps/CMakeFiles/tomo_test.dir/tomo_test.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/tomo_test.dir/tomo_test.cpp.o -c /build/relion-3.1.0/src/apps/tomo_test.cpp [ 67%] Linking CXX executable ../../bin/relion_ctf_refine_mpi cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/ctf_refine_mpi.dir/link.txt --verbose=1 [ 67%] Built target flex_analyse_mpi make -f src/apps/CMakeFiles/scheduler.dir/build.make src/apps/CMakeFiles/scheduler.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/scheduler.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 67%] Built target import 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-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/convert_to_tiff_mpi.dir/DependInfo.cmake --color= Scanning dependencies of target scheduler make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/scheduler.dir/build.make src/apps/CMakeFiles/scheduler.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 67%] Building CXX object src/apps/CMakeFiles/scheduler.dir/scheduler.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/scheduler.dir/scheduler.cpp.o -c /build/relion-3.1.0/src/apps/scheduler.cpp Scanning dependencies of target convert_to_tiff_mpi make[4]: Leaving directory '/build/relion-3.1.0/build' 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-3.1.0/build' [ 68%] Building CXX object src/apps/CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o -c /build/relion-3.1.0/src/apps/convert_to_tiff_mpi.cpp make[4]: Leaving directory '/build/relion-3.1.0/build' [ 68%] Built target flex_analyse 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-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/motion_refine_mpi.dir/DependInfo.cmake --color= Scanning dependencies of target motion_refine_mpi make[4]: Leaving directory '/build/relion-3.1.0/build' 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-3.1.0/build' [ 68%] Building CXX object src/apps/CMakeFiles/motion_refine_mpi.dir/motion_refine_mpi.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/motion_refine_mpi.dir/motion_refine_mpi.cpp.o -c /build/relion-3.1.0/src/apps/motion_refine_mpi.cpp [ 68%] Linking CXX executable ../../bin/relion_preprocess cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/preprocess.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 69%] Linking CXX executable ../../bin/relion_convert_star cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/convert_star.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 69%] Linking CXX executable ../../bin/relion_external_reconstruct cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/external_reconstruct.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.0/build' [ 69%] Built target preprocess make -f src/apps/CMakeFiles/mrc2vtk.dir/build.make src/apps/CMakeFiles/mrc2vtk.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/mrc2vtk.dir/DependInfo.cmake --color= Scanning dependencies of target mrc2vtk make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/mrc2vtk.dir/build.make src/apps/CMakeFiles/mrc2vtk.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 69%] Building CXX object src/apps/CMakeFiles/mrc2vtk.dir/mrc2vtk.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/mrc2vtk.dir/mrc2vtk.cpp.o -c /build/relion-3.1.0/src/apps/mrc2vtk.cpp make[4]: Leaving directory '/build/relion-3.1.0/build' make[4]: Leaving directory '/build/relion-3.1.0/build' [ 69%] Built target external_reconstruct make -f src/apps/CMakeFiles/particle_reposition.dir/build.make src/apps/CMakeFiles/particle_reposition.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/particle_reposition.dir/DependInfo.cmake --color= [ 69%] Built target convert_star make -f src/apps/CMakeFiles/particle_select.dir/build.make src/apps/CMakeFiles/particle_select.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/particle_select.dir/DependInfo.cmake --color= Scanning dependencies of target particle_reposition make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/particle_reposition.dir/build.make src/apps/CMakeFiles/particle_reposition.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' Scanning dependencies of target particle_select make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/particle_select.dir/build.make src/apps/CMakeFiles/particle_select.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 69%] Building CXX object src/apps/CMakeFiles/particle_reposition.dir/particle_reposition.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/particle_reposition.dir/particle_reposition.cpp.o -c /build/relion-3.1.0/src/apps/particle_reposition.cpp [ 69%] Building CXX object src/apps/CMakeFiles/particle_select.dir/particle_select.cpp.o make[4]: Leaving directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/particle_select.dir/particle_select.cpp.o -c /build/relion-3.1.0/src/apps/particle_select.cpp [ 69%] Built target ctf_refine_mpi make -f src/apps/CMakeFiles/particle_subtract.dir/build.make src/apps/CMakeFiles/particle_subtract.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/particle_subtract.dir/DependInfo.cmake --color= Scanning dependencies of target particle_subtract make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/particle_subtract.dir/build.make src/apps/CMakeFiles/particle_subtract.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 69%] Building CXX object src/apps/CMakeFiles/particle_subtract.dir/particle_subtract.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/particle_subtract.dir/particle_subtract.cpp.o -c /build/relion-3.1.0/src/apps/particle_subtract.cpp [ 69%] Linking CXX executable ../../bin/relion_convert_to_tiff_mpi cd /build/relion-3.1.0/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 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 69%] Linking CXX executable ../../bin/relion_particle_subtract_mpi cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_subtract_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.0/build' [ 69%] Built target convert_to_tiff_mpi make -f src/apps/CMakeFiles/ctf_refine.dir/build.make src/apps/CMakeFiles/ctf_refine.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/ctf_refine.dir/DependInfo.cmake --color= Scanning dependencies of target ctf_refine make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/ctf_refine.dir/build.make src/apps/CMakeFiles/ctf_refine.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 69%] Building CXX object src/apps/CMakeFiles/ctf_refine.dir/ctf_refine.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/ctf_refine.dir/ctf_refine.cpp.o -c /build/relion-3.1.0/src/apps/ctf_refine.cpp [ 70%] Linking CXX executable ../../bin/relion_motion_refine cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/motion_refine.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 70%] Linking CXX executable ../../bin/relion_mask_create cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/mask_create.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.0/build' [ 70%] Built target particle_subtract_mpi 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-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/particle_symmetry_expand.dir/DependInfo.cmake --color= Scanning dependencies of target particle_symmetry_expand make[4]: Leaving directory '/build/relion-3.1.0/build' 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-3.1.0/build' [ 70%] Building CXX object src/apps/CMakeFiles/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o -c /build/relion-3.1.0/src/apps/particle_symmetry_expand.cpp [ 71%] Linking CXX executable ../../bin/relion_particle_select cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_select.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 72%] Linking CXX executable ../../bin/relion_ctf_mask_test cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/ctf_mask_test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 73%] Linking CXX executable ../../bin/relion_motion_refine_mpi cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/motion_refine_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 73%] Linking CXX executable ../../bin/relion_mrc2vtk cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/mrc2vtk.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.0/build' [ 73%] Built target motion_refine make -f src/apps/CMakeFiles/postprocess.dir/build.make src/apps/CMakeFiles/postprocess.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/postprocess.dir/DependInfo.cmake --color= Scanning dependencies of target postprocess make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/postprocess.dir/build.make src/apps/CMakeFiles/postprocess.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 74%] Building CXX object src/apps/CMakeFiles/postprocess.dir/postprocess.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/postprocess.dir/postprocess.cpp.o -c /build/relion-3.1.0/src/apps/postprocess.cpp make[4]: Leaving directory '/build/relion-3.1.0/build' [ 74%] Built target mask_create make -f src/apps/CMakeFiles/reconstruct.dir/build.make src/apps/CMakeFiles/reconstruct.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/reconstruct.dir/DependInfo.cmake --color= Scanning dependencies of target reconstruct make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/reconstruct.dir/build.make src/apps/CMakeFiles/reconstruct.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 74%] Building CXX object src/apps/CMakeFiles/reconstruct.dir/reconstruct.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/reconstruct.dir/reconstruct.cpp.o -c /build/relion-3.1.0/src/apps/reconstruct.cpp make[4]: Leaving directory '/build/relion-3.1.0/build' [ 74%] Built target mrc2vtk make -f src/apps/CMakeFiles/reconstruct_mpi.dir/build.make src/apps/CMakeFiles/reconstruct_mpi.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/reconstruct_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' [ 74%] Built target particle_select make -f src/apps/CMakeFiles/ctf_toolbox.dir/build.make src/apps/CMakeFiles/ctf_toolbox.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/ctf_toolbox.dir/DependInfo.cmake --color= Scanning dependencies of target reconstruct_mpi make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/reconstruct_mpi.dir/build.make src/apps/CMakeFiles/reconstruct_mpi.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 74%] Building CXX object src/apps/CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o -c /build/relion-3.1.0/src/apps/reconstruct_mpi.cpp Scanning dependencies of target ctf_toolbox make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/ctf_toolbox.dir/build.make src/apps/CMakeFiles/ctf_toolbox.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 75%] Building CXX object src/apps/CMakeFiles/ctf_toolbox.dir/ctf_toolbox.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/ctf_toolbox.dir/ctf_toolbox.cpp.o -c /build/relion-3.1.0/src/apps/ctf_toolbox.cpp make[4]: Leaving directory '/build/relion-3.1.0/build' [ 75%] Built target ctf_mask_test make -f src/apps/CMakeFiles/refine.dir/build.make src/apps/CMakeFiles/refine.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/refine.dir/DependInfo.cmake --color= Scanning dependencies of target refine make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/refine.dir/build.make src/apps/CMakeFiles/refine.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 76%] Building CXX object src/apps/CMakeFiles/refine.dir/refine.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/refine.dir/refine.cpp.o -c /build/relion-3.1.0/src/apps/refine.cpp [ 77%] Linking CXX executable ../../bin/relion_ctf_refine cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/ctf_refine.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 78%] Linking CXX executable ../../bin/relion_demodulate cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/demodulate.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.0/build' [ 78%] Built target motion_refine_mpi make -f src/apps/CMakeFiles/refine_mpi.dir/build.make src/apps/CMakeFiles/refine_mpi.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/refine_mpi.dir/DependInfo.cmake --color= Scanning dependencies of target refine_mpi make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/refine_mpi.dir/build.make src/apps/CMakeFiles/refine_mpi.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 79%] Building CXX object src/apps/CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o -c /build/relion-3.1.0/src/apps/refine_mpi.cpp [ 79%] Linking CXX executable ../../bin/relion_scheduler cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/scheduler.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 80%] Linking CXX executable ../../bin/relion_tomo_test cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/tomo_test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.0/build' [ 80%] Built target demodulate make -f src/apps/CMakeFiles/estimate_gain.dir/build.make src/apps/CMakeFiles/estimate_gain.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/estimate_gain.dir/DependInfo.cmake --color= Scanning dependencies of target estimate_gain make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/estimate_gain.dir/build.make src/apps/CMakeFiles/estimate_gain.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 80%] Building CXX object src/apps/CMakeFiles/estimate_gain.dir/estimate_gain.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/estimate_gain.dir/estimate_gain.cpp.o -c /build/relion-3.1.0/src/apps/estimate_gain.cpp make[4]: Leaving directory '/build/relion-3.1.0/build' [ 80%] Built target ctf_refine make -f src/apps/CMakeFiles/autopick_mpi.dir/build.make src/apps/CMakeFiles/autopick_mpi.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/autopick_mpi.dir/DependInfo.cmake --color= Scanning dependencies of target autopick_mpi make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/autopick_mpi.dir/build.make src/apps/CMakeFiles/autopick_mpi.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 80%] Building CXX object src/apps/CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o -c /build/relion-3.1.0/src/apps/autopick_mpi.cpp make[4]: Leaving directory '/build/relion-3.1.0/build' [ 80%] Built target tomo_test make -f src/apps/CMakeFiles/run_motioncorr.dir/build.make src/apps/CMakeFiles/run_motioncorr.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/run_motioncorr.dir/DependInfo.cmake --color= Scanning dependencies of target run_motioncorr make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/run_motioncorr.dir/build.make src/apps/CMakeFiles/run_motioncorr.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 81%] Building CXX object src/apps/CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o -c /build/relion-3.1.0/src/apps/run_motioncorr.cpp make[4]: Leaving directory '/build/relion-3.1.0/build' [ 81%] Built target scheduler make -f src/apps/CMakeFiles/align_symmetry.dir/build.make src/apps/CMakeFiles/align_symmetry.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/align_symmetry.dir/DependInfo.cmake --color= Scanning dependencies of target align_symmetry make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/align_symmetry.dir/build.make src/apps/CMakeFiles/align_symmetry.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 81%] Building CXX object src/apps/CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o -c /build/relion-3.1.0/src/apps/align_symmetry.cpp [ 82%] Linking CXX executable ../../bin/relion_particle_symmetry_expand cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_symmetry_expand.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 82%] Linking CXX executable ../../bin/relion_postprocess cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/postprocess.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.0/build' [ 82%] Built target particle_symmetry_expand make -f src/apps/CMakeFiles/reposition.dir/build.make src/apps/CMakeFiles/reposition.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/reposition.dir/DependInfo.cmake --color= Scanning dependencies of target reposition make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/reposition.dir/build.make src/apps/CMakeFiles/reposition.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 82%] Building CXX object src/apps/CMakeFiles/reposition.dir/reposition.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/reposition.dir/reposition.cpp.o -c /build/relion-3.1.0/src/apps/reposition.cpp make[4]: Leaving directory '/build/relion-3.1.0/build' [ 83%] Linking CXX executable ../../bin/relion_reconstruct cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/reconstruct.dir/link.txt --verbose=1 [ 83%] Built target postprocess make -f src/apps/CMakeFiles/run_ctffind.dir/build.make src/apps/CMakeFiles/run_ctffind.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/run_ctffind.dir/DependInfo.cmake --color= /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff Scanning dependencies of target run_ctffind make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/run_ctffind.dir/build.make src/apps/CMakeFiles/run_ctffind.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 83%] Building CXX object src/apps/CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o -c /build/relion-3.1.0/src/apps/run_ctffind.cpp [ 83%] Linking CXX executable ../../bin/relion_particle_subtract cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_subtract.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 83%] Linking CXX executable ../../bin/relion_run_motioncorr cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/run_motioncorr.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.0/build' [ 83%] Built target reconstruct 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-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/run_ctffind_mpi.dir/DependInfo.cmake --color= Scanning dependencies of target run_ctffind_mpi make[4]: Leaving directory '/build/relion-3.1.0/build' 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-3.1.0/build' [ 84%] Building CXX object src/apps/CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o -c /build/relion-3.1.0/src/apps/run_ctffind_mpi.cpp make[4]: Leaving directory '/build/relion-3.1.0/build' [ 84%] Built target run_motioncorr [ 84%] Linking CXX executable ../../bin/relion_reconstruct_mpi make -f src/apps/CMakeFiles/run_motioncorr_mpi.dir/build.make src/apps/CMakeFiles/run_motioncorr_mpi.dir/depend cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/reconstruct_mpi.dir/link.txt --verbose=1 make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/run_motioncorr_mpi.dir/DependInfo.cmake --color= /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff Scanning dependencies of target run_motioncorr_mpi make[4]: Leaving directory '/build/relion-3.1.0/build' 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-3.1.0/build' [ 84%] Building CXX object src/apps/CMakeFiles/run_motioncorr_mpi.dir/run_motioncorr_mpi.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/run_motioncorr_mpi.dir/run_motioncorr_mpi.cpp.o -c /build/relion-3.1.0/src/apps/run_motioncorr_mpi.cpp [ 84%] Linking CXX executable ../../bin/relion_helix_toolbox cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/helix_toolbox.dir/link.txt --verbose=1 [ 84%] Linking CXX executable ../../bin/relion_project cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/project.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 85%] Linking CXX executable ../../bin/relion_autopick_mpi cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/autopick_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.0/build' [ 85%] Built target particle_subtract make -f src/apps/CMakeFiles/stack_create.dir/build.make src/apps/CMakeFiles/stack_create.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/stack_create.dir/DependInfo.cmake --color= Scanning dependencies of target stack_create make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/stack_create.dir/build.make src/apps/CMakeFiles/stack_create.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 86%] Building CXX object src/apps/CMakeFiles/stack_create.dir/stack_create.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/stack_create.dir/stack_create.cpp.o -c /build/relion-3.1.0/src/apps/stack_create.cpp [ 86%] Linking CXX executable ../../bin/relion_run_ctffind cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/run_ctffind.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.0/build' [ 86%] Built target helix_toolbox make -f src/apps/CMakeFiles/star_handler.dir/build.make src/apps/CMakeFiles/star_handler.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/star_handler.dir/DependInfo.cmake --color= Scanning dependencies of target star_handler make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/star_handler.dir/build.make src/apps/CMakeFiles/star_handler.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 87%] Building CXX object src/apps/CMakeFiles/star_handler.dir/star_handler.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/star_handler.dir/star_handler.cpp.o -c /build/relion-3.1.0/src/apps/star_handler.cpp make[4]: Leaving directory '/build/relion-3.1.0/build' [ 87%] Built target reconstruct_mpi make -f src/apps/CMakeFiles/tiltpair_plot.dir/build.make src/apps/CMakeFiles/tiltpair_plot.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/tiltpair_plot.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' [ 87%] Built target project Scanning dependencies of target tiltpair_plot make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/tiltpair_plot.dir/build.make src/apps/CMakeFiles/tiltpair_plot.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 88%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o -c /build/relion-3.1.0/src/gui_entries.cpp [ 88%] Building CXX object src/apps/CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o -c /build/relion-3.1.0/src/apps/tiltpair_plot.cpp make[4]: Leaving directory '/build/relion-3.1.0/build' [ 88%] Built target autopick_mpi [ 88%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o -c /build/relion-3.1.0/src/gui_jobwindow.cpp make[4]: Leaving directory '/build/relion-3.1.0/build' [ 88%] Built target run_ctffind [ 89%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o -c /build/relion-3.1.0/src/gui_mainwindow.cpp [ 90%] Linking CXX executable ../../bin/relion_image_handler cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/image_handler.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.0/build' [ 90%] Built target image_handler [ 90%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/manualpicker.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_gui_lib.dir/__/manualpicker.cpp.o -c /build/relion-3.1.0/src/manualpicker.cpp [ 90%] Linking CXX executable ../../bin/relion_refine cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/refine.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 90%] Linking CXX executable ../../bin/relion_run_ctffind_mpi cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/run_ctffind_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 91%] Linking CXX executable ../../bin/relion_particle_reposition cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/particle_reposition.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 91%] Linking CXX executable ../../bin/relion_ctf_toolbox cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/ctf_toolbox.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 92%] Linking CXX executable ../../bin/relion_run_motioncorr_mpi cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/run_motioncorr_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 92%] Linking CXX executable ../../bin/relion_estimate_gain cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/estimate_gain.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.0/build' make[4]: Leaving directory '/build/relion-3.1.0/build' [ 92%] Built target run_ctffind_mpi [ 92%] Built target ctf_toolbox [ 92%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/cxxutils.cc.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/cxxutils.cc.o -c /build/relion-3.1.0/src/Healpix_2.15a/cxxutils.cc [ 93%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o -c /build/relion-3.1.0/src/Healpix_2.15a/healpix_base.cc [ 94%] Linking CXX executable ../../bin/relion_reposition cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/reposition.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.0/build' [ 94%] Built target run_motioncorr_mpi make[4]: Leaving directory '/build/relion-3.1.0/build' [ 94%] Built target refine make[4]: Leaving directory '/build/relion-3.1.0/build' [ 94%] Built target estimate_gain make[4]: Leaving directory '/build/relion-3.1.0/build' [ 94%] Built target particle_reposition [ 94%] Linking CXX executable ../../bin/relion_refine_mpi cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/refine_mpi.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff [ 95%] Linking CXX executable ../../bin/relion_tiltpair_plot cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiltpair_plot.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.0/build' [ 95%] Built target reposition make[4]: Leaving directory '/build/relion-3.1.0/build' [ 95%] Built target tiltpair_plot [ 96%] Linking CXX executable ../../bin/relion_prepare_subtomo cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/prepare_subtomo.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.0/build' [ 96%] Built target prepare_subtomo make[4]: Leaving directory '/build/relion-3.1.0/build' [ 96%] Built target refine_mpi [ 96%] Linking CXX executable ../../bin/relion_align_symmetry cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/align_symmetry.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.0/build' [ 96%] Built target align_symmetry [ 96%] Linking CXX executable ../../bin/relion_stack_create cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/stack_create.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.0/build' [ 96%] Built target stack_create [ 96%] Linking CXX executable ../../bin/relion_star_handler cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/star_handler.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl -ltiff -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.0/build' [ 96%] Built target star_handler [ 96%] Linking CXX static library ../../lib/librelion_gui_lib.a cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -P CMakeFiles/relion_gui_lib.dir/cmake_clean_target.cmake cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/relion_gui_lib.dir/link.txt --verbose=1 /usr/bin/ar qc ../../lib/librelion_gui_lib.a CMakeFiles/relion_gui_lib.dir/__/displayer.cpp.o CMakeFiles/relion_gui_lib.dir/__/gui_entries.cpp.o CMakeFiles/relion_gui_lib.dir/__/gui_jobwindow.cpp.o CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o CMakeFiles/relion_gui_lib.dir/__/manualpicker.cpp.o CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/cxxutils.cc.o CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o /usr/bin/ranlib ../../lib/librelion_gui_lib.a make[4]: Leaving directory '/build/relion-3.1.0/build' [ 96%] Built target relion_gui_lib make -f src/apps/CMakeFiles/display.dir/build.make src/apps/CMakeFiles/display.dir/depend make -f src/apps/CMakeFiles/manualpick.dir/build.make src/apps/CMakeFiles/manualpick.dir/depend make -f src/apps/CMakeFiles/maingui.dir/build.make src/apps/CMakeFiles/maingui.dir/depend make -f src/apps/CMakeFiles/pipeliner.dir/build.make src/apps/CMakeFiles/pipeliner.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/display.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/manualpick.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/maingui.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/pipeliner.dir/DependInfo.cmake --color= Scanning dependencies of target manualpick Scanning dependencies of target maingui make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/manualpick.dir/build.make src/apps/CMakeFiles/manualpick.dir/build make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/maingui.dir/build.make src/apps/CMakeFiles/maingui.dir/build Scanning dependencies of target pipeliner make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/pipeliner.dir/build.make src/apps/CMakeFiles/pipeliner.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Entering directory '/build/relion-3.1.0/build' Scanning dependencies of target display make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/display.dir/build.make src/apps/CMakeFiles/display.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' [ 96%] Building CXX object src/apps/CMakeFiles/manualpick.dir/manualpick.cpp.o [ 96%] Building CXX object src/apps/CMakeFiles/maingui.dir/maingui.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/manualpick.dir/manualpick.cpp.o -c /build/relion-3.1.0/src/apps/manualpick.cpp cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/maingui.dir/maingui.cpp.o -c /build/relion-3.1.0/src/apps/maingui.cpp [ 96%] Building CXX object src/apps/CMakeFiles/pipeliner.dir/pipeliner.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/pipeliner.dir/pipeliner.cpp.o -c /build/relion-3.1.0/src/apps/pipeliner.cpp [ 96%] Building CXX object src/apps/CMakeFiles/display.dir/display.cpp.o cd /build/relion-3.1.0/build/src/apps && /usr/bin/mpicxx -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-3.1.0/src/ -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -I/usr/lib/i386-linux-gnu/openmpi/include -I/build/relion-3.1.0 -I/usr/lib/fltk -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -o CMakeFiles/display.dir/display.cpp.o -c /build/relion-3.1.0/src/apps/display.cpp [ 97%] Linking CXX executable ../../bin/relion_display cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/display.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gui_lib.a /usr/lib/i386-linux-gnu/libfltk_images.so /usr/lib/i386-linux-gnu/libfltk_forms.so /usr/lib/i386-linux-gnu/libfltk.so -lX11 -lm -ltiff ../../lib/librelion_lib.a -lfftw3f -lfftw3 -ltiff [ 98%] Linking CXX executable ../../bin/relion_manualpick cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/manualpick.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gui_lib.a /usr/lib/i386-linux-gnu/libfltk_images.so /usr/lib/i386-linux-gnu/libfltk_forms.so /usr/lib/i386-linux-gnu/libfltk.so -lX11 -lm -ltiff ../../lib/librelion_lib.a -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.0/build' [ 99%] Linking CXX executable ../../bin/relion_maingui cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/maingui.dir/link.txt --verbose=1 [ 99%] Built target display /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++0x -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/maingui.dir/maingui.cpp.o -o ../../bin/relion_maingui ../../lib/librelion_lib.a /usr/lib/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gui_lib.a /usr/lib/i386-linux-gnu/libfltk_images.so /usr/lib/i386-linux-gnu/libfltk_forms.so /usr/lib/i386-linux-gnu/libfltk.so -lX11 -lm -ltiff ../../lib/librelion_lib.a -lfftw3f -lfftw3 -ltiff make[4]: Leaving directory '/build/relion-3.1.0/build' [ 99%] Built target manualpick [100%] Linking CXX executable ../../bin/relion_pipeliner cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/pipeliner.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -fdebug-prefix-map=/build/relion-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so -ldl ../../lib/librelion_gui_lib.a /usr/lib/i386-linux-gnu/libfltk_images.so /usr/lib/i386-linux-gnu/libfltk_forms.so /usr/lib/i386-linux-gnu/libfltk.so -lX11 -lm -ltiff ../../lib/librelion_lib.a -lfftw3f -lfftw3 -ltiff cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E copy /build/relion-3.1.0/build/bin/relion_maingui /build/relion-3.1.0/build/bin/relion cd /build/relion-3.1.0/build/src/apps && /usr/bin/cmake -E copy /build/relion-3.1.0/build/bin/relion_qsub.csh /build/relion-3.1.0/build/bin/qsub.csh make[4]: Leaving directory '/build/relion-3.1.0/build' [100%] Built target maingui make[4]: Leaving directory '/build/relion-3.1.0/build' [100%] Built target pipeliner make[3]: Leaving directory '/build/relion-3.1.0/build' /usr/bin/cmake -E cmake_progress_start /build/relion-3.1.0/build/CMakeFiles 0 make[2]: Leaving directory '/build/relion-3.1.0/build' make[2]: Entering directory '/build/relion-3.1.0/build' /usr/bin/cmake -S/build/relion-3.1.0 -B/build/relion-3.1.0/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/relion-3.1.0/build/CMakeFiles /build/relion-3.1.0/build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/relion-3.1.0/build' make -f CMakeFiles/copy_scripts.dir/build.make CMakeFiles/copy_scripts.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0 /build/relion-3.1.0/build /build/relion-3.1.0/build /build/relion-3.1.0/build/CMakeFiles/copy_scripts.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f CMakeFiles/copy_scripts.dir/build.make CMakeFiles/copy_scripts.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' /usr/bin/cmake -E copy /build/relion-3.1.0/scripts/star_printtable /build/relion-3.1.0/build/bin/relion_star_printtable /usr/bin/cmake -E copy /build/relion-3.1.0/scripts/star_plottable /build/relion-3.1.0/build/bin/relion_star_plottable /usr/bin/cmake -E copy /build/relion-3.1.0/scripts/star_loopheader /build/relion-3.1.0/build/bin/relion_star_loopheader /usr/bin/cmake -E copy /build/relion-3.1.0/scripts/star_datablock_stack /build/relion-3.1.0/build/bin/relion_star_datablock_stack /usr/bin/cmake -E copy /build/relion-3.1.0/scripts/star_datablock_singlefiles /build/relion-3.1.0/build/bin/relion_star_datablock_singlefiles /usr/bin/cmake -E copy /build/relion-3.1.0/scripts/star_datablock_ctfdat /build/relion-3.1.0/build/bin/relion_star_datablock_ctfdat /usr/bin/cmake -E copy /build/relion-3.1.0/scripts/qsub.csh /build/relion-3.1.0/build/bin/relion_qsub.csh make[4]: Leaving directory '/build/relion-3.1.0/build' [ 0%] Built target copy_scripts make -f src/apps/CMakeFiles/relion_lib.dir/build.make src/apps/CMakeFiles/relion_lib.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/relion_lib.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/relion_lib.dir/build.make src/apps/CMakeFiles/relion_lib.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/relion_lib.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 53%] Built target relion_lib make -f src/apps/CMakeFiles/particle_FCC.dir/build.make src/apps/CMakeFiles/particle_FCC.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/particle_FCC.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/particle_FCC.dir/build.make src/apps/CMakeFiles/particle_FCC.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/particle_FCC.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 54%] Built target particle_FCC make -f src/apps/CMakeFiles/image_handler.dir/build.make src/apps/CMakeFiles/image_handler.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/image_handler.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/image_handler.dir/build.make src/apps/CMakeFiles/image_handler.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/image_handler.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 55%] Built target image_handler make -f src/apps/CMakeFiles/plot_delocalisation.dir/build.make src/apps/CMakeFiles/plot_delocalisation.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/plot_delocalisation.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/plot_delocalisation.dir/build.make src/apps/CMakeFiles/plot_delocalisation.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/plot_delocalisation.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 55%] Built target plot_delocalisation make -f src/apps/CMakeFiles/postprocess_mpi.dir/build.make src/apps/CMakeFiles/postprocess_mpi.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/postprocess_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/postprocess_mpi.dir/build.make src/apps/CMakeFiles/postprocess_mpi.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/postprocess_mpi.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 56%] Built target postprocess_mpi make -f src/apps/CMakeFiles/helix_toolbox.dir/build.make src/apps/CMakeFiles/helix_toolbox.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/helix_toolbox.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/helix_toolbox.dir/build.make src/apps/CMakeFiles/helix_toolbox.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/helix_toolbox.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 57%] Built target helix_toolbox make -f src/apps/CMakeFiles/preprocess_mpi.dir/build.make src/apps/CMakeFiles/preprocess_mpi.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/preprocess_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/preprocess_mpi.dir/build.make src/apps/CMakeFiles/preprocess_mpi.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/preprocess_mpi.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 58%] Built target preprocess_mpi make -f src/apps/CMakeFiles/helix_inimodel2d.dir/build.make src/apps/CMakeFiles/helix_inimodel2d.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/helix_inimodel2d.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/helix_inimodel2d.dir/build.make src/apps/CMakeFiles/helix_inimodel2d.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/helix_inimodel2d.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 59%] Built target helix_inimodel2d make -f src/apps/CMakeFiles/find_tiltpairs.dir/build.make src/apps/CMakeFiles/find_tiltpairs.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/find_tiltpairs.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/find_tiltpairs.dir/build.make src/apps/CMakeFiles/find_tiltpairs.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/find_tiltpairs.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 60%] Built target find_tiltpairs make -f src/apps/CMakeFiles/localsym.dir/build.make src/apps/CMakeFiles/localsym.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/localsym.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/localsym.dir/build.make src/apps/CMakeFiles/localsym.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/localsym.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 61%] Built target localsym 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-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/relion_gui_lib.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' 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-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/relion_gui_lib.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 64%] Built target relion_gui_lib make -f src/apps/CMakeFiles/display.dir/build.make src/apps/CMakeFiles/display.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/display.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/display.dir/build.make src/apps/CMakeFiles/display.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/display.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 65%] Built target display make -f src/apps/CMakeFiles/localsym_mpi.dir/build.make src/apps/CMakeFiles/localsym_mpi.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/localsym_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/localsym_mpi.dir/build.make src/apps/CMakeFiles/localsym_mpi.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/localsym_mpi.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 66%] Built target localsym_mpi 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-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/flex_analyse_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' 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-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/flex_analyse_mpi.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 66%] Built target flex_analyse_mpi make -f src/apps/CMakeFiles/prepare_subtomo.dir/build.make src/apps/CMakeFiles/prepare_subtomo.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/prepare_subtomo.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/prepare_subtomo.dir/build.make src/apps/CMakeFiles/prepare_subtomo.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/prepare_subtomo.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 67%] Built target prepare_subtomo 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-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/particle_subtract_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' 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-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/particle_subtract_mpi.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 68%] Built target particle_subtract_mpi make -f src/apps/CMakeFiles/external_reconstruct.dir/build.make src/apps/CMakeFiles/external_reconstruct.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/external_reconstruct.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/external_reconstruct.dir/build.make src/apps/CMakeFiles/external_reconstruct.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/external_reconstruct.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 69%] Built target external_reconstruct make -f src/apps/CMakeFiles/manualpick.dir/build.make src/apps/CMakeFiles/manualpick.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/manualpick.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/manualpick.dir/build.make src/apps/CMakeFiles/manualpick.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/manualpick.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 70%] Built target manualpick make -f src/apps/CMakeFiles/import.dir/build.make src/apps/CMakeFiles/import.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/import.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/import.dir/build.make src/apps/CMakeFiles/import.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/import.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 70%] Built target import make -f src/apps/CMakeFiles/maingui.dir/build.make src/apps/CMakeFiles/maingui.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/maingui.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/maingui.dir/build.make src/apps/CMakeFiles/maingui.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/maingui.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 71%] Built target maingui make -f src/apps/CMakeFiles/flex_analyse.dir/build.make src/apps/CMakeFiles/flex_analyse.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/flex_analyse.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/flex_analyse.dir/build.make src/apps/CMakeFiles/flex_analyse.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/flex_analyse.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 72%] Built target flex_analyse make -f src/apps/CMakeFiles/autopick.dir/build.make src/apps/CMakeFiles/autopick.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/autopick.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/autopick.dir/build.make src/apps/CMakeFiles/autopick.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/autopick.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 73%] Built target autopick 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-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/convert_to_tiff.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' 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-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/convert_to_tiff.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 73%] Built target convert_to_tiff 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-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/ctf_refine_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' 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-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/ctf_refine_mpi.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 73%] Built target ctf_refine_mpi make -f src/apps/CMakeFiles/merge_particles.dir/build.make src/apps/CMakeFiles/merge_particles.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/merge_particles.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/merge_particles.dir/build.make src/apps/CMakeFiles/merge_particles.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/merge_particles.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 74%] Built target merge_particles make -f src/apps/CMakeFiles/mask_create.dir/build.make src/apps/CMakeFiles/mask_create.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/mask_create.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/mask_create.dir/build.make src/apps/CMakeFiles/mask_create.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/mask_create.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 74%] Built target mask_create make -f src/apps/CMakeFiles/project.dir/build.make src/apps/CMakeFiles/project.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/project.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/project.dir/build.make src/apps/CMakeFiles/project.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/project.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 75%] Built target project 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-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/ctf_mask_test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' 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-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/ctf_mask_test.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 76%] Built target ctf_mask_test make -f src/apps/CMakeFiles/preprocess.dir/build.make src/apps/CMakeFiles/preprocess.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/preprocess.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/preprocess.dir/build.make src/apps/CMakeFiles/preprocess.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/preprocess.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 76%] Built target preprocess make -f src/apps/CMakeFiles/convert_star.dir/build.make src/apps/CMakeFiles/convert_star.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/convert_star.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/convert_star.dir/build.make src/apps/CMakeFiles/convert_star.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/convert_star.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 77%] Built target convert_star make -f src/apps/CMakeFiles/demodulate.dir/build.make src/apps/CMakeFiles/demodulate.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/demodulate.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/demodulate.dir/build.make src/apps/CMakeFiles/demodulate.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/demodulate.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 78%] Built target demodulate make -f src/apps/CMakeFiles/motion_refine.dir/build.make src/apps/CMakeFiles/motion_refine.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/motion_refine.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/motion_refine.dir/build.make src/apps/CMakeFiles/motion_refine.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/motion_refine.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 79%] Built target motion_refine make -f src/apps/CMakeFiles/tomo_test.dir/build.make src/apps/CMakeFiles/tomo_test.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/tomo_test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/tomo_test.dir/build.make src/apps/CMakeFiles/tomo_test.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/tomo_test.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 80%] Built target tomo_test make -f src/apps/CMakeFiles/scheduler.dir/build.make src/apps/CMakeFiles/scheduler.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/scheduler.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/scheduler.dir/build.make src/apps/CMakeFiles/scheduler.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/scheduler.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 80%] Built target scheduler 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-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/convert_to_tiff_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' 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-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/convert_to_tiff_mpi.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 81%] Built target convert_to_tiff_mpi 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-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/motion_refine_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' 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-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/motion_refine_mpi.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 82%] Built target motion_refine_mpi make -f src/apps/CMakeFiles/mrc2vtk.dir/build.make src/apps/CMakeFiles/mrc2vtk.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/mrc2vtk.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/mrc2vtk.dir/build.make src/apps/CMakeFiles/mrc2vtk.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/mrc2vtk.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 82%] Built target mrc2vtk make -f src/apps/CMakeFiles/particle_reposition.dir/build.make src/apps/CMakeFiles/particle_reposition.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/particle_reposition.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/particle_reposition.dir/build.make src/apps/CMakeFiles/particle_reposition.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/particle_reposition.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 83%] Built target particle_reposition make -f src/apps/CMakeFiles/particle_select.dir/build.make src/apps/CMakeFiles/particle_select.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/particle_select.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/particle_select.dir/build.make src/apps/CMakeFiles/particle_select.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/particle_select.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 84%] Built target particle_select make -f src/apps/CMakeFiles/particle_subtract.dir/build.make src/apps/CMakeFiles/particle_subtract.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/particle_subtract.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/particle_subtract.dir/build.make src/apps/CMakeFiles/particle_subtract.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/particle_subtract.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 84%] Built target particle_subtract make -f src/apps/CMakeFiles/ctf_refine.dir/build.make src/apps/CMakeFiles/ctf_refine.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/ctf_refine.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/ctf_refine.dir/build.make src/apps/CMakeFiles/ctf_refine.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/ctf_refine.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 85%] Built target ctf_refine 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-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/particle_symmetry_expand.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' 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-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/particle_symmetry_expand.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 86%] Built target particle_symmetry_expand make -f src/apps/CMakeFiles/postprocess.dir/build.make src/apps/CMakeFiles/postprocess.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/postprocess.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/postprocess.dir/build.make src/apps/CMakeFiles/postprocess.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/postprocess.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 87%] Built target postprocess make -f src/apps/CMakeFiles/reconstruct.dir/build.make src/apps/CMakeFiles/reconstruct.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/reconstruct.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/reconstruct.dir/build.make src/apps/CMakeFiles/reconstruct.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/reconstruct.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 88%] Built target reconstruct make -f src/apps/CMakeFiles/reconstruct_mpi.dir/build.make src/apps/CMakeFiles/reconstruct_mpi.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/reconstruct_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/reconstruct_mpi.dir/build.make src/apps/CMakeFiles/reconstruct_mpi.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/reconstruct_mpi.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 88%] Built target reconstruct_mpi make -f src/apps/CMakeFiles/ctf_toolbox.dir/build.make src/apps/CMakeFiles/ctf_toolbox.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/ctf_toolbox.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/ctf_toolbox.dir/build.make src/apps/CMakeFiles/ctf_toolbox.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/ctf_toolbox.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 89%] Built target ctf_toolbox make -f src/apps/CMakeFiles/refine.dir/build.make src/apps/CMakeFiles/refine.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/refine.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/refine.dir/build.make src/apps/CMakeFiles/refine.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/refine.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 90%] Built target refine make -f src/apps/CMakeFiles/refine_mpi.dir/build.make src/apps/CMakeFiles/refine_mpi.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/refine_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/refine_mpi.dir/build.make src/apps/CMakeFiles/refine_mpi.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/refine_mpi.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 91%] Built target refine_mpi make -f src/apps/CMakeFiles/estimate_gain.dir/build.make src/apps/CMakeFiles/estimate_gain.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/estimate_gain.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/estimate_gain.dir/build.make src/apps/CMakeFiles/estimate_gain.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/estimate_gain.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 91%] Built target estimate_gain make -f src/apps/CMakeFiles/pipeliner.dir/build.make src/apps/CMakeFiles/pipeliner.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/pipeliner.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/pipeliner.dir/build.make src/apps/CMakeFiles/pipeliner.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/pipeliner.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 92%] Built target pipeliner make -f src/apps/CMakeFiles/autopick_mpi.dir/build.make src/apps/CMakeFiles/autopick_mpi.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/autopick_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/autopick_mpi.dir/build.make src/apps/CMakeFiles/autopick_mpi.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/autopick_mpi.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 93%] Built target autopick_mpi make -f src/apps/CMakeFiles/run_motioncorr.dir/build.make src/apps/CMakeFiles/run_motioncorr.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/run_motioncorr.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/run_motioncorr.dir/build.make src/apps/CMakeFiles/run_motioncorr.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/run_motioncorr.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 94%] Built target run_motioncorr make -f src/apps/CMakeFiles/align_symmetry.dir/build.make src/apps/CMakeFiles/align_symmetry.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/align_symmetry.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/align_symmetry.dir/build.make src/apps/CMakeFiles/align_symmetry.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/align_symmetry.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 94%] Built target align_symmetry make -f src/apps/CMakeFiles/reposition.dir/build.make src/apps/CMakeFiles/reposition.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/reposition.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/reposition.dir/build.make src/apps/CMakeFiles/reposition.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/reposition.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 95%] Built target reposition make -f src/apps/CMakeFiles/run_ctffind.dir/build.make src/apps/CMakeFiles/run_ctffind.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/run_ctffind.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/run_ctffind.dir/build.make src/apps/CMakeFiles/run_ctffind.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/run_ctffind.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 95%] Built target run_ctffind 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-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/run_ctffind_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' 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-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/run_ctffind_mpi.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 96%] Built target run_ctffind_mpi 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-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/run_motioncorr_mpi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' 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-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/run_motioncorr_mpi.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 97%] Built target run_motioncorr_mpi make -f src/apps/CMakeFiles/stack_create.dir/build.make src/apps/CMakeFiles/stack_create.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/stack_create.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/stack_create.dir/build.make src/apps/CMakeFiles/stack_create.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/stack_create.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 98%] Built target stack_create make -f src/apps/CMakeFiles/star_handler.dir/build.make src/apps/CMakeFiles/star_handler.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/star_handler.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/star_handler.dir/build.make src/apps/CMakeFiles/star_handler.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/star_handler.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [ 99%] Built target star_handler make -f src/apps/CMakeFiles/tiltpair_plot.dir/build.make src/apps/CMakeFiles/tiltpair_plot.dir/depend make[4]: Entering directory '/build/relion-3.1.0/build' cd /build/relion-3.1.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/relion-3.1.0 /build/relion-3.1.0/src/apps /build/relion-3.1.0/build /build/relion-3.1.0/build/src/apps /build/relion-3.1.0/build/src/apps/CMakeFiles/tiltpair_plot.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/relion-3.1.0/build' make -f src/apps/CMakeFiles/tiltpair_plot.dir/build.make src/apps/CMakeFiles/tiltpair_plot.dir/build make[4]: Entering directory '/build/relion-3.1.0/build' make[4]: Nothing to be done for 'src/apps/CMakeFiles/tiltpair_plot.dir/build'. make[4]: Leaving directory '/build/relion-3.1.0/build' [100%] Built target tiltpair_plot make[3]: Leaving directory '/build/relion-3.1.0/build' /usr/bin/cmake -E cmake_progress_start /build/relion-3.1.0/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/relion-3.1.0/build' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/relion-3.1.0/build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_ctf_refine -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_autopick_mpi -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_plot_delocalisation -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_motion_refine -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_particle_FCC -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_ctf_refine_mpi -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_run_motioncorr_mpi -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_manualpick -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_star_handler -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_star_printtable -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_stack_create -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_star_datablock_stack -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_mrc2vtk -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_find_tiltpairs -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_pipeliner -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_particle_subtract_mpi -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_particle_subtract -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_preprocess -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_convert_to_tiff -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_refine -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_particle_reposition -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_helix_toolbox -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_convert_to_tiff_mpi -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_project -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_external_reconstruct -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_estimate_gain -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_tiltpair_plot -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_ctf_toolbox -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_prepare_subtomo -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_demodulate -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_motion_refine_mpi -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_particle_select -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_merge_particles -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_star_datablock_singlefiles -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_reposition -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_flex_analyse_mpi -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_mask_create -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_align_symmetry -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_localsym_mpi -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_star_datablock_ctfdat -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_run_motioncorr -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_star_loopheader -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_run_ctffind -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_star_plottable -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_display -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_scheduler -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_postprocess -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_autopick -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_helix_inimodel2d -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_reconstruct -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_image_handler -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_qsub.csh -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_refine_mpi -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_run_ctffind_mpi -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/qsub.csh -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_convert_star -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_import -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_postprocess_mpi -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_localsym -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_reconstruct_mpi -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_ctf_mask_test -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_particle_symmetry_expand -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_maingui -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_tomo_test -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_preprocess_mpi -- Installing: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_flex_analyse -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_align_symmetry -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_autopick -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_autopick_mpi -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_convert_star -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_convert_to_tiff -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_convert_to_tiff_mpi -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_ctf_mask_test -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_ctf_refine -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_ctf_refine_mpi -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_ctf_toolbox -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_demodulate -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_display -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_estimate_gain -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_external_reconstruct -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_find_tiltpairs -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_flex_analyse -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_flex_analyse_mpi -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_helix_inimodel2d -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_helix_toolbox -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_image_handler -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_import -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_localsym -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_localsym_mpi -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_maingui -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_manualpick -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_mask_create -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_merge_particles -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_motion_refine -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_motion_refine_mpi -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_mrc2vtk -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_particle_FCC -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_particle_reposition -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_particle_select -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_particle_subtract -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_particle_subtract_mpi -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_particle_symmetry_expand -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_pipeliner -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_plot_delocalisation -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_postprocess -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_postprocess_mpi -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_prepare_subtomo -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_preprocess -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_preprocess_mpi -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_project -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_reconstruct -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_reconstruct_mpi -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_refine -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_refine_mpi -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_reposition -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_run_ctffind -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_run_ctffind_mpi -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_run_motioncorr -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_run_motioncorr_mpi -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_scheduler -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_stack_create -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_star_handler -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_tiltpair_plot -- Up-to-date: /build/relion-3.1.0/debian/tmp/cli/usr/bin/relion_tomo_test make[2]: Leaving directory '/build/relion-3.1.0/build' mkdir -p /build/relion-3.1.0/debian/tmp/gui/usr/bin rm /build/relion-3.1.0/debian/tmp/cli/usr/bin/*.csh # Useless ... for prog in relion relion_display relion_maingui relion_manualpick; do \ mv /build/relion-3.1.0/debian/tmp/cli/usr/bin/$prog \ /build/relion-3.1.0/debian/tmp/gui/usr/bin; done make[1]: Leaving directory '/build/relion-3.1.0' create-stamp debian/debhelper-build-stamp debian/rules override_dh_prep make[1]: Entering directory '/build/relion-3.1.0' # We don't want debian/tmp to be removed again ... dh_prep -X debian/tmp make[1]: Leaving directory '/build/relion-3.1.0' debian/rules override_dh_install-arch make[1]: Entering directory '/build/relion-3.1.0' dh_install -a make[1]: Leaving directory '/build/relion-3.1.0' dh_installdocs dh_installchangelogs dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'relion' in '../relion_3.1.0-4_i386.deb'. dpkg-deb: building package 'relion-dbgsym' in '../relion-dbgsym_3.1.0-4_i386.deb'. dpkg-deb: building package 'relion-gui' in '../relion-gui_3.1.0-4_i386.deb'. dpkg-deb: building package 'relion-gui-dbgsym' in '../relion-gui-dbgsym_3.1.0-4_i386.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../relion_3.1.0-4_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/52110 and its subdirectories I: Current time: Mon Jul 25 01:19:51 -12 2022 I: pbuilder-time-stamp: 1658755191