sbuild (Debian sbuild) 0.79.1 (22 April 2020) on carme.larted.org.uk +==============================================================================+ | relion 1.4+dfsg-4 (amd64) Tue, 29 Sep 2020 18:03:35 +0000 | +==============================================================================+ Package: relion Version: 1.4+dfsg-4 Source Version: 1.4+dfsg-4 Distribution: perl-5.32-throwaway Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: full I: NOTICE: Log filtering will replace 'var/run/schroot/mount/perl-5.32-amd64-debomatic-f4e46f22-c6c3-48e4-bb60-4c24204ddffe' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup relion_1.4+dfsg-4 perl-5.32-throwaway amd64 ------------------------------------------------------------------------------------------------------------------ I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup relion_1.4+dfsg-4 perl-5.32-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: NOTICE: Log filtering will replace 'build/relion-AWNlPt/resolver-j3nq2E' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.32 InRelease [2871 B] Get:1 file:/srv/reprepro perl-5.32 InRelease [2871 B] Get:2 http://localhost:3142/debian unstable InRelease [146 kB] Get:3 http://localhost:3142/debian sid InRelease [146 kB] Get:4 http://localhost:3142/debian unstable/main amd64 Packages.diff/Index [27.9 kB] Ign:4 http://localhost:3142/debian unstable/main amd64 Packages.diff/Index Get:5 http://localhost:3142/debian unstable/main amd64 Packages [8401 kB] Get:6 http://localhost:3142/debian sid/main Sources.diff/Index [27.9 kB] Ign:6 http://localhost:3142/debian sid/main Sources.diff/Index Get:7 http://localhost:3142/debian sid/main Sources [8869 kB] Fetched 17.6 MB in 4s (4804 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/relion_1.4+dfsg-4.dsc exists in /srv/debomatic/incoming; copying to chroot I: NOTICE: Log filtering will replace 'build/relion-AWNlPt/relion-1.4+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/relion-AWNlPt' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper (>= 11~), dh-exec, libfltk1.3-dev, libfftw3-dev, libopenmpi-dev, build-essential, fakeroot Filtered Build-Depends: debhelper (>= 11~), dh-exec, libfltk1.3-dev, libfftw3-dev, libopenmpi-dev, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [397 B] Get:5 copy:/<>/apt_archive ./ Packages [480 B] Fetched 1834 B in 0s (155 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper dh-autoreconf dh-exec dh-strip-nondeterminism dwz fakeroot file fontconfig-config fonts-dejavu-core gettext gettext-base gfortran-9 groff-base ibverbs-providers intltool-debian libarchive-zip-perl libbrotli1 libbsd0 libcairo2 libcbor0 libcroco3 libdebhelper-perl libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libdrm2 libedit2 libelf1 libevent-2.1-7 libevent-core-2.1-7 libevent-dev libevent-extra-2.1-7 libevent-openssl-2.1-7 libevent-pthreads-2.1-7 libexpat1 libfabric1 libfakeroot libfftw3-bin libfftw3-dev libfftw3-double3 libfftw3-long3 libfftw3-quad3 libfftw3-single3 libfido2-1 libfile-stripnondeterminism-perl libfltk-cairo1.3 libfltk-forms1.3 libfltk-gl1.3 libfltk-images1.3 libfltk1.3 libfltk1.3-dev libfontconfig1 libfreetype6 libgfortran-9-dev libgfortran5 libgl1 libgl1-mesa-dri libglapi-mesa libglib2.0-0 libglvnd0 libglx-mesa0 libglx0 libgssapi-krb5-2 libhwloc-dev libhwloc-plugins libhwloc15 libibverbs-dev libibverbs1 libicu67 libjpeg62-turbo libjs-jquery libjs-jquery-ui libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libllvm10 libltdl-dev libltdl7 libmagic-mgc libmagic1 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi3 libpciaccess0 libpipeline1 libpixman-1-0 libpmix-dev libpmix2 libpng16-16 libpsm-infinipath1 libpsm2-2 libpthread-stubs0-dev librdmacm1 libsensors-config libsensors5 libsigsegv2 libssl1.1 libsub-override-perl libtool libuchardet0 libucx0 libvulkan1 libx11-6 libx11-data libx11-dev libx11-xcb1 libxau-dev libxau6 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb1 libxcb1-dev libxcursor1 libxdamage1 libxdmcp-dev libxdmcp6 libxext6 libxfixes3 libxft2 libxinerama1 libxml2 libxnvctrl0 libxrender1 libxshmfence1 libxxf86vm1 libz3-4 m4 man-db node-jquery ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client po-debconf sensible-utils ucf x11proto-core-dev x11proto-dev xorg-sgml-doctools xtrans-dev zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev gfortran-9-multilib gfortran-9-doc libcoarrays-dev groff libfftw3-doc fltk1.3-doc libcairo2-dev libjpeg-dev libpng-dev libxext-dev libxft-dev libxinerama-dev krb5-doc krb5-user libhwloc-contrib-plugins libjs-jquery-ui-docs libtool-doc openmpi-doc pciutils lm-sensors gcj-jdk libx11-doc libxcb-doc m4-doc apparmor less www-browser opencl-icd gfortran | fortran-compiler keychain libpam-ssh monkeysphere ssh-askpass libmail-box-perl Recommended packages: curl | wget | lynx libarchive-cpio-perl fluid libgl-dev libglu1-mesa-dev | libglu-dev libglib2.0-data shared-mime-info xdg-user-dirs javascript-common krb5-locales libcoarrays-openmpi-dev mesa-vulkan-drivers | vulkan-icd xauth libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper dh-autoreconf dh-exec dh-strip-nondeterminism dwz fakeroot file fontconfig-config fonts-dejavu-core gettext gettext-base gfortran-9 groff-base ibverbs-providers intltool-debian libarchive-zip-perl libbrotli1 libbsd0 libcairo2 libcbor0 libcroco3 libdebhelper-perl libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libdrm2 libedit2 libelf1 libevent-2.1-7 libevent-core-2.1-7 libevent-dev libevent-extra-2.1-7 libevent-openssl-2.1-7 libevent-pthreads-2.1-7 libexpat1 libfabric1 libfakeroot libfftw3-bin libfftw3-dev libfftw3-double3 libfftw3-long3 libfftw3-quad3 libfftw3-single3 libfido2-1 libfile-stripnondeterminism-perl libfltk-cairo1.3 libfltk-forms1.3 libfltk-gl1.3 libfltk-images1.3 libfltk1.3 libfltk1.3-dev libfontconfig1 libfreetype6 libgfortran-9-dev libgfortran5 libgl1 libgl1-mesa-dri libglapi-mesa libglib2.0-0 libglvnd0 libglx-mesa0 libglx0 libgssapi-krb5-2 libhwloc-dev libhwloc-plugins libhwloc15 libibverbs-dev libibverbs1 libicu67 libjpeg62-turbo libjs-jquery libjs-jquery-ui libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libllvm10 libltdl-dev libltdl7 libmagic-mgc libmagic1 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi3 libpciaccess0 libpipeline1 libpixman-1-0 libpmix-dev libpmix2 libpng16-16 libpsm-infinipath1 libpsm2-2 libpthread-stubs0-dev librdmacm1 libsensors-config libsensors5 libsigsegv2 libssl1.1 libsub-override-perl libtool libuchardet0 libucx0 libvulkan1 libx11-6 libx11-data libx11-dev libx11-xcb1 libxau-dev libxau6 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb1 libxcb1-dev libxcursor1 libxdamage1 libxdmcp-dev libxdmcp6 libxext6 libxfixes3 libxft2 libxinerama1 libxml2 libxnvctrl0 libxrender1 libxshmfence1 libxxf86vm1 libz3-4 m4 man-db node-jquery ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client po-debconf sbuild-build-depends-main-dummy sensible-utils ucf x11proto-core-dev x11proto-dev xorg-sgml-doctools xtrans-dev zlib1g-dev 0 upgraded, 160 newly installed, 0 to remove and 0 not upgraded. Need to get 93.5 MB of archives. After this operation, 358 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [904 B] Get:2 http://localhost:3142/debian unstable/main amd64 bsdextrautils amd64 2.36-3+b1 [140 kB] Get:3 http://localhost:3142/debian unstable/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get:4 http://localhost:3142/debian unstable/main amd64 groff-base amd64 1.22.4-5 [920 kB] Get:5 http://localhost:3142/debian unstable/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get:6 http://localhost:3142/debian unstable/main amd64 man-db amd64 2.9.3-2 [1314 kB] Get:7 http://localhost:3142/debian unstable/main amd64 sensible-utils all 0.0.12+nmu1 [16.0 kB] Get:8 http://localhost:3142/debian unstable/main amd64 libmagic-mgc amd64 1:5.38-5 [262 kB] Get:9 http://localhost:3142/debian unstable/main amd64 libmagic1 amd64 1:5.38-5 [120 kB] Get:10 http://localhost:3142/debian unstable/main amd64 file amd64 1:5.38-5 [67.9 kB] Get:11 http://localhost:3142/debian unstable/main amd64 gettext-base amd64 0.19.8.1-10 [123 kB] Get:12 http://localhost:3142/debian unstable/main amd64 libbsd0 amd64 0.10.0-1 [107 kB] Get:13 http://localhost:3142/debian unstable/main amd64 libedit2 amd64 3.1-20191231-1 [95.4 kB] Get:14 http://localhost:3142/debian unstable/main amd64 libcbor0 amd64 0.5.0+dfsg-2 [24.0 kB] Get:15 http://localhost:3142/debian unstable/main amd64 libssl1.1 amd64 1.1.1g-1 [1543 kB] Get:16 http://localhost:3142/debian unstable/main amd64 libfido2-1 amd64 1.5.0-2 [52.3 kB] Get:17 http://localhost:3142/debian unstable/main amd64 libkrb5support0 amd64 1.17-10 [64.6 kB] Get:18 http://localhost:3142/debian unstable/main amd64 libk5crypto3 amd64 1.17-10 [115 kB] Get:19 http://localhost:3142/debian unstable/main amd64 libkeyutils1 amd64 1.6.1-2 [15.4 kB] Get:20 http://localhost:3142/debian unstable/main amd64 libkrb5-3 amd64 1.17-10 [366 kB] Get:21 http://localhost:3142/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.17-10 [156 kB] Get:22 http://localhost:3142/debian unstable/main amd64 openssh-client amd64 1:8.3p1-1 [910 kB] Get:23 http://localhost:3142/debian unstable/main amd64 ucf all 3.0043 [74.0 kB] Get:24 http://localhost:3142/debian unstable/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get:25 http://localhost:3142/debian unstable/main amd64 m4 amd64 1.4.18-4 [203 kB] Get:26 http://localhost:3142/debian unstable/main amd64 autoconf all 2.69-11.1 [341 kB] Get:27 http://localhost:3142/debian unstable/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get:28 http://localhost:3142/debian unstable/main amd64 automake all 1:1.16.2-4 [801 kB] Get:29 http://localhost:3142/debian unstable/main amd64 autopoint all 0.19.8.1-10 [435 kB] Get:30 http://localhost:3142/debian unstable/main amd64 libtool all 2.4.6-14 [513 kB] Get:31 http://localhost:3142/debian unstable/main amd64 dh-autoreconf all 19 [16.9 kB] Get:32 http://localhost:3142/debian unstable/main amd64 libdebhelper-perl all 13.2.1 [188 kB] Get:33 http://localhost:3142/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:34 http://localhost:3142/debian unstable/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get:35 http://localhost:3142/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.9.0-1 [25.5 kB] Get:36 http://localhost:3142/debian unstable/main amd64 dh-strip-nondeterminism all 1.9.0-1 [15.2 kB] Get:37 http://localhost:3142/debian unstable/main amd64 libelf1 amd64 0.181-1 [164 kB] Get:38 http://localhost:3142/debian unstable/main amd64 dwz amd64 0.13-5 [151 kB] Get:39 http://localhost:3142/debian unstable/main amd64 libglib2.0-0 amd64 2.66.0-2 [1361 kB] Get:40 http://localhost:3142/debian unstable/main amd64 libicu67 amd64 67.1-4 [8624 kB] Get:41 http://localhost:3142/debian unstable/main amd64 libxml2 amd64 2.9.10+dfsg-6 [692 kB] Get:42 http://localhost:3142/debian unstable/main amd64 libcroco3 amd64 0.6.13-1 [146 kB] Get:43 http://localhost:3142/debian unstable/main amd64 gettext amd64 0.19.8.1-10 [1303 kB] Get:44 http://localhost:3142/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:45 http://localhost:3142/debian unstable/main amd64 po-debconf all 1.0.21 [248 kB] Get:46 http://localhost:3142/debian unstable/main amd64 debhelper all 13.2.1 [1007 kB] Get:47 http://localhost:3142/debian unstable/main amd64 dh-exec amd64 0.23.2 [26.6 kB] Get:48 http://localhost:3142/debian unstable/main amd64 libfakeroot amd64 1.25.1-1 [46.8 kB] Get:49 http://localhost:3142/debian unstable/main amd64 fakeroot amd64 1.25.1-1 [86.8 kB] Get:50 http://localhost:3142/debian unstable/main amd64 fonts-dejavu-core all 2.37-2 [1069 kB] Get:51 http://localhost:3142/debian unstable/main amd64 fontconfig-config all 2.13.1-4.2 [281 kB] Get:52 http://localhost:3142/debian unstable/main amd64 libgfortran5 amd64 10.2.0-11 [728 kB] Get:53 http://localhost:3142/debian unstable/main amd64 libgfortran-9-dev amd64 9.3.0-18 [675 kB] Get:54 http://localhost:3142/debian unstable/main amd64 gfortran-9 amd64 9.3.0-18 [10.4 MB] Get:55 http://localhost:3142/debian unstable/main amd64 libnl-3-200 amd64 3.4.0-1+b1 [63.6 kB] Get:56 http://localhost:3142/debian unstable/main amd64 libnl-route-3-200 amd64 3.4.0-1+b1 [161 kB] Get:57 http://localhost:3142/debian unstable/main amd64 libibverbs1 amd64 31.0-1 [57.2 kB] Get:58 http://localhost:3142/debian unstable/main amd64 ibverbs-providers amd64 31.0-1 [239 kB] Get:59 http://localhost:3142/debian unstable/main amd64 libbrotli1 amd64 1.0.9-2 [287 kB] Get:60 http://localhost:3142/debian unstable/main amd64 libexpat1 amd64 2.2.9-1 [94.3 kB] Get:61 http://localhost:3142/debian unstable/main amd64 libpng16-16 amd64 1.6.37-3 [294 kB] Get:62 http://localhost:3142/debian unstable/main amd64 libfreetype6 amd64 2.10.2+dfsg-3 [409 kB] Get:63 http://localhost:3142/debian unstable/main amd64 libfontconfig1 amd64 2.13.1-4.2 [347 kB] Get:64 http://localhost:3142/debian unstable/main amd64 libpixman-1-0 amd64 0.36.0-1 [537 kB] Get:65 http://localhost:3142/debian unstable/main amd64 libxau6 amd64 1:1.0.8-1+b2 [19.9 kB] Get:66 http://localhost:3142/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:67 http://localhost:3142/debian unstable/main amd64 libxcb1 amd64 1.14-2 [139 kB] Get:68 http://localhost:3142/debian unstable/main amd64 libx11-data all 2:1.6.12-1 [311 kB] Get:69 http://localhost:3142/debian unstable/main amd64 libx11-6 amd64 2:1.6.12-1 [770 kB] Get:70 http://localhost:3142/debian unstable/main amd64 libxcb-render0 amd64 1.14-2 [111 kB] Get:71 http://localhost:3142/debian unstable/main amd64 libxcb-shm0 amd64 1.14-2 [101 kB] Get:72 http://localhost:3142/debian unstable/main amd64 libxext6 amd64 2:1.3.3-1+b2 [52.5 kB] Get:73 http://localhost:3142/debian unstable/main amd64 libxrender1 amd64 1:0.9.10-1 [33.0 kB] Get:74 http://localhost:3142/debian unstable/main amd64 libcairo2 amd64 1.16.0-4 [689 kB] Get:75 http://localhost:3142/debian unstable/main amd64 libdrm-common all 2.4.102-1 [14.5 kB] Get:76 http://localhost:3142/debian unstable/main amd64 libdrm2 amd64 2.4.102-1 [41.5 kB] Get:77 http://localhost:3142/debian unstable/main amd64 libdrm-amdgpu1 amd64 2.4.102-1 [28.2 kB] Get:78 http://localhost:3142/debian unstable/main amd64 libpciaccess0 amd64 0.16-1 [53.6 kB] Get:79 http://localhost:3142/debian unstable/main amd64 libdrm-intel1 amd64 2.4.102-1 [70.4 kB] Get:80 http://localhost:3142/debian unstable/main amd64 libdrm-nouveau2 amd64 2.4.102-1 [26.5 kB] Get:81 http://localhost:3142/debian unstable/main amd64 libdrm-radeon1 amd64 2.4.102-1 [29.7 kB] Get:82 http://localhost:3142/debian unstable/main amd64 libevent-2.1-7 amd64 2.1.12-stable-1 [188 kB] Get:83 http://localhost:3142/debian unstable/main amd64 libevent-core-2.1-7 amd64 2.1.12-stable-1 [139 kB] Get:84 http://localhost:3142/debian unstable/main amd64 libevent-extra-2.1-7 amd64 2.1.12-stable-1 [110 kB] Get:85 http://localhost:3142/debian unstable/main amd64 libevent-pthreads-2.1-7 amd64 2.1.12-stable-1 [57.1 kB] Get:86 http://localhost:3142/debian unstable/main amd64 libevent-openssl-2.1-7 amd64 2.1.12-stable-1 [64.1 kB] Get:87 http://localhost:3142/debian unstable/main amd64 libevent-dev amd64 2.1.12-stable-1 [311 kB] Get:88 http://localhost:3142/debian unstable/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6+b1 [169 kB] Get:89 http://localhost:3142/debian unstable/main amd64 libnuma1 amd64 2.0.12-1+b1 [26.3 kB] Get:90 http://localhost:3142/debian unstable/main amd64 libpsm2-2 amd64 11.2.185-1 [181 kB] Get:91 http://localhost:3142/debian unstable/main amd64 librdmacm1 amd64 31.0-1 [68.1 kB] Get:92 http://localhost:3142/debian unstable/main amd64 libfabric1 amd64 1.11.0-2 [521 kB] Get:93 http://localhost:3142/debian unstable/main amd64 libfftw3-double3 amd64 3.3.8-2 [733 kB] Get:94 http://localhost:3142/debian unstable/main amd64 libfftw3-long3 amd64 3.3.8-2 [319 kB] Get:95 http://localhost:3142/debian unstable/main amd64 libfftw3-quad3 amd64 3.3.8-2 [558 kB] Get:96 http://localhost:3142/debian unstable/main amd64 libfftw3-single3 amd64 3.3.8-2 [762 kB] Get:97 http://localhost:3142/debian unstable/main amd64 libfftw3-bin amd64 3.3.8-2 [50.7 kB] Get:98 http://localhost:3142/debian unstable/main amd64 libfftw3-dev amd64 3.3.8-2 [2106 kB] Get:99 http://localhost:3142/debian unstable/main amd64 libxfixes3 amd64 1:5.0.3-2 [22.1 kB] Get:100 http://localhost:3142/debian unstable/main amd64 libxcursor1 amd64 1:1.2.0-2 [37.3 kB] Get:101 http://localhost:3142/debian unstable/main amd64 libxft2 amd64 2.3.2-2 [57.2 kB] Get:102 http://localhost:3142/debian unstable/main amd64 libxinerama1 amd64 2:1.1.4-2 [17.7 kB] Get:103 http://localhost:3142/debian unstable/main amd64 libfltk1.3 amd64 1.3.5-1 [562 kB] Get:104 http://localhost:3142/debian unstable/main amd64 libfltk-cairo1.3 amd64 1.3.5-1 [43.0 kB] Get:105 http://localhost:3142/debian unstable/main amd64 libfltk-forms1.3 amd64 1.3.5-1 [49.7 kB] Get:106 http://localhost:3142/debian unstable/main amd64 libglvnd0 amd64 1.3.2-1 [53.6 kB] Get:107 http://localhost:3142/debian unstable/main amd64 libglapi-mesa amd64 20.1.8-1 [70.4 kB] Get:108 http://localhost:3142/debian unstable/main amd64 libx11-xcb1 amd64 2:1.6.12-1 [203 kB] Get:109 http://localhost:3142/debian unstable/main amd64 libxcb-dri2-0 amd64 1.14-2 [103 kB] Get:110 http://localhost:3142/debian unstable/main amd64 libxcb-dri3-0 amd64 1.14-2 [102 kB] Get:111 http://localhost:3142/debian unstable/main amd64 libxcb-glx0 amd64 1.14-2 [118 kB] Get:112 http://localhost:3142/debian unstable/main amd64 libxcb-present0 amd64 1.14-2 [101 kB] Get:113 http://localhost:3142/debian unstable/main amd64 libxcb-sync1 amd64 1.14-2 [105 kB] Get:114 http://localhost:3142/debian unstable/main amd64 libxdamage1 amd64 1:1.1.5-2 [15.7 kB] Get:115 http://localhost:3142/debian unstable/main amd64 libxshmfence1 amd64 1.3-1 [8820 B] Get:116 http://localhost:3142/debian unstable/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b2 [20.8 kB] Get:117 http://localhost:3142/debian unstable/main amd64 libz3-4 amd64 4.8.9-1 [6783 kB] Get:118 http://localhost:3142/debian unstable/main amd64 libllvm10 amd64 1:10.0.1-6 [16.6 MB] Get:119 http://localhost:3142/debian unstable/main amd64 libsensors-config all 1:3.6.0-2 [32.0 kB] Get:120 http://localhost:3142/debian unstable/main amd64 libsensors5 amd64 1:3.6.0-2 [53.1 kB] Get:121 http://localhost:3142/debian unstable/main amd64 libvulkan1 amd64 1.2.148.1-1 [102 kB] Get:122 http://localhost:3142/debian unstable/main amd64 libgl1-mesa-dri amd64 20.1.8-1 [9539 kB] Get:123 http://localhost:3142/debian unstable/main amd64 libglx-mesa0 amd64 20.1.8-1 [187 kB] Get:124 http://localhost:3142/debian unstable/main amd64 libglx0 amd64 1.3.2-1 [35.7 kB] Get:125 http://localhost:3142/debian unstable/main amd64 libgl1 amd64 1.3.2-1 [89.5 kB] Get:126 http://localhost:3142/debian unstable/main amd64 libfltk-gl1.3 amd64 1.3.5-1 [75.7 kB] Get:127 http://localhost:3142/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.0.5-1.1 [149 kB] Get:128 http://localhost:3142/debian unstable/main amd64 libfltk-images1.3 amd64 1.3.5-1 [62.7 kB] Get:129 http://localhost:3142/debian unstable/main amd64 xorg-sgml-doctools all 1:1.11-1 [21.9 kB] Get:130 http://localhost:3142/debian unstable/main amd64 x11proto-dev all 2020.1-1 [594 kB] Get:131 http://localhost:3142/debian unstable/main amd64 x11proto-core-dev all 2020.1-1 [3404 B] Get:132 http://localhost:3142/debian unstable/main amd64 libxau-dev amd64 1:1.0.8-1+b2 [23.1 kB] Get:133 http://localhost:3142/debian unstable/main amd64 libxdmcp-dev amd64 1:1.1.2-3 [42.2 kB] Get:134 http://localhost:3142/debian unstable/main amd64 xtrans-dev all 1.4.0-1 [98.7 kB] Get:135 http://localhost:3142/debian unstable/main amd64 libpthread-stubs0-dev amd64 0.4-1 [5344 B] Get:136 http://localhost:3142/debian unstable/main amd64 libxcb1-dev amd64 1.14-2 [176 kB] Get:137 http://localhost:3142/debian unstable/main amd64 libx11-dev amd64 2:1.6.12-1 [842 kB] Get:138 http://localhost:3142/debian unstable/main amd64 libfltk1.3-dev amd64 1.3.5-1 [853 kB] Get:139 http://localhost:3142/debian unstable/main amd64 libhwloc15 amd64 2.2.0+dfsg-4 [138 kB] Get:140 http://localhost:3142/debian unstable/main amd64 libnuma-dev amd64 2.0.12-1+b1 [39.3 kB] Get:141 http://localhost:3142/debian unstable/main amd64 libltdl7 amd64 2.4.6-14 [390 kB] Get:142 http://localhost:3142/debian unstable/main amd64 libltdl-dev amd64 2.4.6-14 [162 kB] Get:143 http://localhost:3142/debian unstable/main amd64 libhwloc-dev amd64 2.2.0+dfsg-4 [212 kB] Get:144 http://localhost:3142/debian unstable/main amd64 libxnvctrl0 amd64 450.66-1 [26.5 kB] Get:145 http://localhost:3142/debian unstable/main amd64 ocl-icd-libopencl1 amd64 2.2.12-4 [37.8 kB] Get:146 http://localhost:3142/debian unstable/main amd64 libhwloc-plugins amd64 2.2.0+dfsg-4 [20.5 kB] Get:147 http://localhost:3142/debian unstable/main amd64 libnl-3-dev amd64 3.4.0-1+b1 [102 kB] Get:148 http://localhost:3142/debian unstable/main amd64 libnl-route-3-dev amd64 3.4.0-1+b1 [176 kB] Get:149 http://localhost:3142/debian unstable/main amd64 libibverbs-dev amd64 31.0-1 [534 kB] Get:150 http://localhost:3142/debian unstable/main amd64 node-jquery all 3.5.1+dfsg-4 [309 kB] Get:151 http://localhost:3142/debian unstable/main amd64 libjs-jquery all 3.5.1+dfsg-4 [3612 B] Get:152 http://localhost:3142/debian unstable/main amd64 libjs-jquery-ui all 1.12.1+dfsg-7 [232 kB] Get:153 http://localhost:3142/debian unstable/main amd64 libpmix2 amd64 3.2.0~rc1-4 [448 kB] Get:154 http://localhost:3142/debian unstable/main amd64 libucx0 amd64 1.9.0~rc1-2 [660 kB] Get:155 http://localhost:3142/debian unstable/main amd64 libopenmpi3 amd64 4.0.5-5 [2166 kB] Get:156 http://localhost:3142/debian unstable/main amd64 openmpi-common all 4.0.5-5 [73.6 kB] Get:157 http://localhost:3142/debian unstable/main amd64 libpmix-dev amd64 3.2.0~rc1-4 [551 kB] Get:158 http://localhost:3142/debian unstable/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2 [190 kB] Get:159 http://localhost:3142/debian unstable/main amd64 openmpi-bin amd64 4.0.5-5 [127 kB] Get:160 http://localhost:3142/debian unstable/main amd64 libopenmpi-dev amd64 4.0.5-5 [1090 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 93.5 MB in 1s (150 MB/s) Selecting previously unselected package bsdextrautils. 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Setting up dh-strip-nondeterminism (1.9.0-1) ... Setting up libdrm2:amd64 (2.4.102-1) ... Setting up dwz (0.13-5) ... Setting up libnl-3-dev:amd64 (3.4.0-1+b1) ... Setting up groff-base (1.22.4-5) ... Setting up libx11-6:amd64 (2:1.6.12-1) ... Setting up libjs-jquery (3.5.1+dfsg-4) ... Setting up libfftw3-dev:amd64 (3.3.8-2) ... Setting up libdrm-amdgpu1:amd64 (2.4.102-1) ... Setting up automake (1:1.16.2-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libxcb-dri3-0:amd64 (1.14-2) ... Setting up libibverbs1:amd64 (31.0-1) ... Setting up libdrm-nouveau2:amd64 (2.4.102-1) ... Setting up gettext (0.19.8.1-10) ... Setting up libxdamage1:amd64 (1:1.1.5-2) ... Setting up libxcb1-dev:amd64 (1.14-2) ... Setting up libxrender1:amd64 (1:0.9.10-1) ... Setting up gfortran-9 (9.3.0-18) ... Setting up ibverbs-providers:amd64 (31.0-1) ... Setting up libdrm-radeon1:amd64 (2.4.102-1) ... Setting up fontconfig-config (2.13.1-4.2) ... Setting up openssh-client (1:8.3p1-1) ... Setting up libdrm-intel1:amd64 (2.4.102-1) ... Setting up libgl1-mesa-dri:amd64 (20.1.8-1) ... Setting up libx11-dev:amd64 (2:1.6.12-1) ... Setting up libxext6:amd64 (2:1.3.3-1+b2) ... Setting up man-db (2.9.3-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libxxf86vm1:amd64 (1:1.1.4-1+b2) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libxnvctrl0:amd64 (450.66-1) ... Setting up libnl-route-3-dev:amd64 (3.4.0-1+b1) ... Setting up libltdl-dev:amd64 (2.4.6-14) ... Setting up libjs-jquery-ui (1.12.1+dfsg-7) ... Setting up libxfixes3:amd64 (1:5.0.3-2) ... Setting up libxinerama1:amd64 (2:1.1.4-2) ... Setting up libhwloc-dev:amd64 (2.2.0+dfsg-4) ... Setting up libfontconfig1:amd64 (2.13.1-4.2) ... Setting up librdmacm1:amd64 (31.0-1) ... Setting up libucx0:amd64 (1.9.0~rc1-2) ... Setting up libxft2:amd64 (2.3.2-2) ... Setting up libglx-mesa0:amd64 (20.1.8-1) ... Setting up libglx0:amd64 (1.3.2-1) ... Setting up po-debconf (1.0.21) ... Setting up libxcursor1:amd64 (1:1.2.0-2) ... Setting up libibverbs-dev:amd64 (31.0-1) ... Setting up libhwloc-plugins:amd64 (2.2.0+dfsg-4) ... Setting up libcairo2:amd64 (1.16.0-4) ... Setting up libgl1:amd64 (1.3.2-1) ... Setting up libfabric1 (1.11.0-2) ... Setting up libpmix2:amd64 (3.2.0~rc1-4) ... Setting up libopenmpi3:amd64 (4.0.5-5) ... Setting up libfltk1.3:amd64 (1.3.5-1) ... Setting up libfltk-gl1.3:amd64 (1.3.5-1) ... Setting up libfltk-cairo1.3:amd64 (1.3.5-1) ... Setting up libfltk-images1.3:amd64 (1.3.5-1) ... Setting up libfltk-forms1.3:amd64 (1.3.5-1) ... Setting up libpmix-dev:amd64 (3.2.0~rc1-4) ... Setting up openmpi-bin (4.0.5-5) ... 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 (1.3.5-1) ... Setting up libopenmpi-dev:amd64 (4.0.5-5) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openmpi/include to provide /usr/include/x86_64-linux-gnu/mpi (mpi-x86_64-linux-gnu) in auto mode Setting up debhelper (13.2.1) ... Setting up dh-exec (0.23.2) ... Setting up dh-autoreconf (19) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.31-3) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in amd64 i386 all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.7.0-2-amd64 #1 SMP Debian 5.7.10-1 (2020-07-26) amd64 (x86_64) Toolchain package versions: binutils_2.35.1-1 dpkg-dev_1.20.5 g++-10_10.2.0-11 g++-9_9.3.0-18 gcc-10_10.2.0-11 gcc-9_9.3.0-18 libc6-dev_2.31-3 libstdc++-10-dev_10.2.0-11 libstdc++-9-dev_9.3.0-18 libstdc++6_10.2.0-11 linux-libc-dev_5.8.10-1 Package versions: adduser_3.118 apt_2.1.10 autoconf_2.69-11.1 automake_1:1.16.2-4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11 base-passwd_3.5.47 bash_5.0-7 binutils_2.35.1-1 binutils-common_2.35.1-1 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mount_2.36-3+b1 ncurses-base_6.2+20200918-1 ncurses-bin_6.2+20200918-1 node-jquery_3.5.1+dfsg-4 ocl-icd-libopencl1_2.2.12-4 openmpi-bin_4.0.5-5 openmpi-common_4.0.5-5 openssh-client_1:8.3p1-1 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.32.0-3 perl-base_5.32.0-3 perl-modules-5.30_5.30.3-4 perl-modules-5.32_5.32.0-3 pinentry-curses_1.1.0-4 po-debconf_1.0.21 readline-common_8.0-4 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-5 tar_1.30+dfsg-7 tzdata_2020a-1 ucf_3.0043 util-linux_2.36-3+b1 x11proto-core-dev_2020.1-1 x11proto-dev_2020.1-1 xorg-sgml-doctools_1:1.11-1 xtrans-dev_1.4.0-1 xz-utils_5.2.4-1+b1 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: relion Binary: relion-bin, relion-bin+mpi, relion-bin+gui, relion-bin+mpi+gui, librelion-dev-common, librelion-dev, librelion+mpi-dev, librelion+gui-dev, librelion+mpi+gui-dev, librelion-1.4-1, librelion+mpi-1.4-1, librelion+gui-1.4-1, librelion+mpi+gui-1.4-1 Architecture: amd64 i386 all Version: 1.4+dfsg-4 Maintainer: Debian Med Packaging Team Uploaders: Roland Fehrenbacher , Navid Fehrenbacher , Goswin von Brederlow , Andreas Tille Homepage: http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page Standards-Version: 4.1.4 Vcs-Browser: https://salsa.debian.org/med-team/relion Vcs-Git: https://salsa.debian.org/med-team/relion.git Build-Depends: debhelper (>= 11~), dh-exec, libfltk1.3-dev, libfftw3-dev, libopenmpi-dev Package-List: librelion+gui-1.4-1 deb libs optional arch=amd64,i386 librelion+gui-dev deb libdevel optional arch=amd64,i386 librelion+mpi+gui-1.4-1 deb libs optional arch=i386,amd64 librelion+mpi+gui-dev deb libdevel optional arch=amd64,i386 librelion+mpi-1.4-1 deb libs optional arch=amd64,i386 librelion+mpi-dev deb libdevel optional arch=amd64,i386 librelion-1.4-1 deb libs optional arch=amd64,i386 librelion-dev deb libdevel optional arch=amd64,i386 librelion-dev-common deb libdevel optional arch=all relion-bin deb science optional arch=amd64,i386 relion-bin+gui deb science optional arch=amd64,i386 relion-bin+mpi deb science optional arch=amd64,i386 relion-bin+mpi+gui deb science optional arch=amd64,i386 Checksums-Sha1: 9196d1f0ad262df05e955f9bd20a36be5d21c1b0 548208 relion_1.4+dfsg.orig.tar.xz 0401cfbd908ca0e20ac329b54dc89064f8769ebe 8344 relion_1.4+dfsg-4.debian.tar.xz Checksums-Sha256: 3866f1e69f825ab946c9782f484ff4a64f63fbd2152fc1f63a62373d61c37c1e 548208 relion_1.4+dfsg.orig.tar.xz decc35ec3a44ab14455e97c3bdc64a8dfa8131f9e6bb431eec126e26e488842e 8344 relion_1.4+dfsg-4.debian.tar.xz Files: e570e18a1484a37c6cdcba64583aae90 548208 relion_1.4+dfsg.orig.tar.xz 6dbbdab7bdca852823bca0b27b403eda 8344 relion_1.4+dfsg-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAlsiX80RHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtGUBRAAgBpEWxU2WP9/ct1GvxumN6cPABMcy+no 6C0FaDvqlD5zB5hJ4BfcbajDZ2xzDQaonB9bzh8kn2MaMYsWfzeIM7IIxMIKjTVs rZZVQVdOTjii49Bgmp4uu6zM2qgViaZxfizaOE98OVCMqpoWqQ4RAUQAnK35i2O7 R4njShRkmCF+biLtmiz8VmaUqflws4G5HQiLlGKwO4rtPECcl/GL5b11AhFUmqub xuQzrf1UljiUNYnaQzcofVfw1oKgM31NRgcFkUVttPwMnh+GtCuwyzm/FEVE/Ogr y02wJJBQBDEyoo04lbXCrf9YfnSyyIKa5zTBVJV4OH45xY+xUEdAik/0vSGwUrtC xRHr8RfY8FvEZzG0nVZb2FmujPJoq0fS6C4XG6/a5IVs9VcdydX6uS7al8xRCz2u JdaqDC5eP2CWcF6R2EhYo9i1v58FGevhIAGK24EvWbo2t+kWg6tO5YQ9mmYFZhjp 71c8Za5mNBAQialXoOfimasIANLIO/WqHvJ1S5ud+fsgldIg6zEb4kRXQ34NGSpd QvtigmDoWZQXVJntPOud9O82pUcN3nDRh1/VSe7yhwtQ9FBWmFpUYFX7xdRePQDQ FxptxQkDhxzZuzZUf+azEFncZQyHBTCe9EO2ss5QYXXhrDkiJUQHhbSK7KLskoDo RQZt6l9OJlM= =Xtkv -----END PGP SIGNATURE----- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.qr6d6nNP/trustedkeys.kbx': General error gpgv: Signature made Thu Jun 14 12:30:05 2018 UTC 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_1.4+dfsg-4.dsc dpkg-source: info: extracting relion in /<> dpkg-source: info: unpacking relion_1.4+dfsg.orig.tar.xz dpkg-source: info: unpacking relion_1.4+dfsg-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 0001-Fix-fltk-config-path-in-configure.patch dpkg-source: info: applying 0002-Add-ml_optimiser_mpi.cpp-length_fn_ctf-patch.patch dpkg-source: info: applying 0003-Add-enable-gui-flag-to-configure.patch dpkg-source: info: applying 0004-Fix-fltk-header-includes.patch dpkg-source: info: applying 0005-gcc-6.patch dpkg-source: info: applying 0006-correct-copy-overflow.patch Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network relion_1.4+dfsg-4 perl-5.32-throwaway amd64 ------------------------------------------------------------------------------------------------------------------ I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network relion_1.4+dfsg-4 perl-5.32-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/1001/bus HOME=/sbuild-nonexistent LANG=C LC_ALL=C.UTF-8 LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so LOGNAME=debomatic PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games PWD=/<> SCHROOT_ALIAS_NAME=perl-5.32-throwaway-amd64-debomatic SCHROOT_CHROOT_NAME=perl-5.32-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=112 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=perl-5.32-amd64-debomatic-f4e46f22-c6c3-48e4-bb60-4c24204ddffe SCHROOT_UID=1001 SCHROOT_USER=debomatic SHELL=/bin/sh USER=debomatic XDG_RUNTIME_DIR=/run/user/1001 XDG_SESSION_CLASS=background XDG_SESSION_ID=c3093249 XDG_SESSION_TYPE=unspecified dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -rfakeroot -Zxz dpkg-buildpackage: info: source package relion dpkg-buildpackage: info: source version 1.4+dfsg-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 dpkg-source: info: using options from relion-1.4+dfsg/debian/source/options: --compression=xz fakeroot debian/rules clean Relion API Version = 1.4 Relion most recent (current) lib interface = 1 dh clean dh_clean dpkg-source -Zxz -b . dpkg-source: info: using options from relion-1.4+dfsg/debian/source/options: --compression=xz dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building relion using existing ./relion_1.4+dfsg.orig.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: building relion in relion_1.4+dfsg-4.debian.tar.xz dpkg-source: info: building relion in relion_1.4+dfsg-4.dsc debian/rules build Relion API Version = 1.4 Relion most recent (current) lib interface = 1 dh build dh_update_autotools_config dh_autoreconf libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: Consider adding 'AC_CONFIG_MACRO_DIRS([m4])' to configure.ac, libtoolize: and rerunning libtoolize and aclocal. libtoolize: Consider adding '-I m4' to ACLOCAL_AMFLAGS in Makefile.am. configure.ac:16: installing './compile' configure.ac:4: installing './missing' /usr/share/automake-1.16/am/ltlibrary.am: warning: 'librelion-@RELION_API_VERSION@.la': linking libtool libraries using a non-POSIX /usr/share/automake-1.16/am/ltlibrary.am: archiver requires 'AM_PROG_AR' in 'configure.ac' Makefile.am:44: while processing Libtool library 'librelion-@RELION_API_VERSION@.la' Makefile.am: installing './depcomp' debian/rules override_dh_auto_build make[1]: Entering directory '/<>' Relion API Version = 1.4 Relion most recent (current) lib interface = 1 # We need to build 4 different versions for the 4 different binary # packages. This is necessary because unfortunately the binaries work # only with the exact same librelion they were built with. # First no MPI, no GUI (for relion-bin) ... dh_auto_configure -- --libdir=\${prefix}/lib/x86_64-linux-gnu --disable-gui ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --libexecdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --libdir=\${prefix}/lib/x86_64-linux-gnu --disable-gui checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of gcc... none checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... none checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking how to run the C preprocessor... gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for fftw3.h... yes checking for main in -lfftw3... yes checking for fftw_plan_with_nthreads in -lfftw3_threads... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating relion-1.4.pc config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands make -j4; make install prefix=/<>/debian/tmp/simple/usr make[2]: Entering directory '/<>' make all-am make[3]: Entering directory '/<>' g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/apps/reconstruct.o src/apps/reconstruct.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/apps/refine.o src/apps/refine.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/apps/preprocess.o src/apps/preprocess.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/apps/postprocess.o src/apps/postprocess.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/apps/autopick.o src/apps/autopick.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/apps/particle_polish.o src/apps/particle_polish.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/apps/particle_sort.o src/apps/particle_sort.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/apps/run_ctffind.o src/apps/run_ctffind.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/apps/star_compare.o src/apps/star_compare.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/apps/find_tiltpairs.o src/apps/find_tiltpairs.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/apps/tiltpair_plot.o src/apps/tiltpair_plot.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/apps/mask_create.o src/apps/mask_create.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/apps/stack_create.o src/apps/stack_create.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/apps/image_handler.o src/apps/image_handler.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/apps/project.o src/apps/project.cpp /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/args.lo src/args.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c src/args.cpp -fPIC -DPIC -o src/.libs/args.o src/args.cpp: In member function ‘IOParser& IOParser::operator=(const IOParser&)’: src/args.cpp:104:1: warning: no return statement in function returning non-void [-Wreturn-type] 103 | copy(in); +++ |+ return *this; 104 | } | ^ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c src/args.cpp -o src/args.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/assembly.lo src/assembly.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c src/assembly.cpp -fPIC -DPIC -o src/.libs/assembly.o /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/autopicker.lo src/autopicker.cpp /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/backprojector.lo src/backprojector.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c src/autopicker.cpp -fPIC -DPIC -o src/.libs/autopicker.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c src/backprojector.cpp -fPIC -DPIC -o src/.libs/backprojector.o src/assembly.cpp: In member function ‘void Assembly::writePDB(std::string)’: src/assembly.cpp:355:28: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=] 355 | fprintf(file, "ATOM %5d %-4s %3s %1c%4d %8.3f%8.3f%8.3f%6.2f%6.2f %4s\n", | ~~^ | | | int | %5ld 356 | atomnum, molecules[imol].residues[ires].atoms[iatom].name.c_str(), molecules[imol].residues[ires].name.c_str(), | ~~~~~~~ | | | long int /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/complex.lo src/complex.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c src/complex.cpp -fPIC -DPIC -o src/.libs/complex.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat 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src/ctffind_runner.cpp: In member function ‘void CtffindRunner::executeCtffind(FileName)’: src/ctffind_runner.cpp:237:9: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 237 | system ( fn_cmnd.c_str() ); | ~~~~~~~^~~~~~~~~~~~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c src/euler.cpp -o src/euler.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/exp_model.lo src/exp_model.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c src/exp_model.cpp -fPIC -DPIC -o src/.libs/exp_model.o /bin/bash ./libtool 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/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/Healpix_2.15a/healpix_base.lo src/Healpix_2.15a/healpix_base.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c src/Healpix_2.15a/healpix_base.cc -fPIC -DPIC -o src/Healpix_2.15a/.libs/healpix_base.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c src/Healpix_2.15a/healpix_base.cc -o src/Healpix_2.15a/healpix_base.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c src/Healpix_2.15a/cxxutils.cc -o src/Healpix_2.15a/cxxutils.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 1:4:0 -Wl,-z,relro -Wl,-z,now -o librelion-1.4.la -rpath /usr/lib/x86_64-linux-gnu src/args.lo src/assembly.lo src/autopicker.lo src/backprojector.lo src/complex.lo src/ctf.lo src/ctffind_runner.lo src/error.lo src/euler.lo src/exp_model.lo src/fftw.lo src/filename.lo src/funcs.lo src/healpix_sampling.lo src/image.lo src/mask.lo src/matrix1d.lo src/matrix2d.lo src/memory.lo src/metadata_container.lo src/metadata_label.lo src/metadata_table.lo src/ml_model.lo src/ml_optimiser.lo src/multidim_array.lo src/numerical_recipes.lo src/parallel.lo src/particle_polisher.lo src/particle_sorter.lo src/postprocessing.lo src/preprocessing.lo src/projector.lo src/strings.lo src/symmetries.lo src/tabfuncs.lo src/time.lo src/transformations.lo src/Healpix_2.15a/cxxutils.lo src/Healpix_2.15a/healpix_base.lo -lfftw3_threads -lfftw3 libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/10/crtbeginS.o src/.libs/args.o src/.libs/assembly.o src/.libs/autopicker.o src/.libs/backprojector.o src/.libs/complex.o src/.libs/ctf.o src/.libs/ctffind_runner.o src/.libs/error.o src/.libs/euler.o src/.libs/exp_model.o src/.libs/fftw.o src/.libs/filename.o src/.libs/funcs.o src/.libs/healpix_sampling.o src/.libs/image.o src/.libs/mask.o src/.libs/matrix1d.o src/.libs/matrix2d.o src/.libs/memory.o src/.libs/metadata_container.o src/.libs/metadata_label.o src/.libs/metadata_table.o src/.libs/ml_model.o src/.libs/ml_optimiser.o src/.libs/multidim_array.o src/.libs/numerical_recipes.o src/.libs/parallel.o src/.libs/particle_polisher.o src/.libs/particle_sorter.o src/.libs/postprocessing.o src/.libs/preprocessing.o src/.libs/projector.o src/.libs/strings.o src/.libs/symmetries.o src/.libs/tabfuncs.o src/.libs/time.o src/.libs/transformations.o src/Healpix_2.15a/.libs/cxxutils.o src/Healpix_2.15a/.libs/healpix_base.o -lfftw3_threads -lfftw3 -L/usr/lib/gcc/x86_64-linux-gnu/10 -L/usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/10/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/10/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/10/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/crtn.o -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,librelion-1.4.so.1 -o .libs/librelion-1.4.so.1.0.4 libtool: link: (cd ".libs" && rm -f "librelion-1.4.so.1" && ln -s "librelion-1.4.so.1.0.4" "librelion-1.4.so.1") libtool: link: (cd ".libs" && rm -f "librelion-1.4.so" && ln -s "librelion-1.4.so.1.0.4" "librelion-1.4.so") libtool: link: ar cr .libs/librelion-1.4.a src/args.o src/assembly.o src/autopicker.o src/backprojector.o src/complex.o src/ctf.o src/ctffind_runner.o src/error.o src/euler.o src/exp_model.o src/fftw.o src/filename.o src/funcs.o src/healpix_sampling.o src/image.o src/mask.o src/matrix1d.o src/matrix2d.o src/memory.o src/metadata_container.o src/metadata_label.o src/metadata_table.o src/ml_model.o src/ml_optimiser.o src/multidim_array.o src/numerical_recipes.o src/parallel.o src/particle_polisher.o src/particle_sorter.o src/postprocessing.o src/preprocessing.o src/projector.o src/strings.o src/symmetries.o src/tabfuncs.o src/time.o src/transformations.o src/Healpix_2.15a/cxxutils.o src/Healpix_2.15a/healpix_base.o libtool: link: ranlib .libs/librelion-1.4.a libtool: link: ( cd ".libs" && rm -f "librelion-1.4.la" && ln -s "../librelion-1.4.la" "librelion-1.4.la" ) /bin/bash ./libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o project src/apps/project.o librelion-1.4.la -lfftw3_threads -lfftw3 /bin/bash ./libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o reconstruct src/apps/reconstruct.o librelion-1.4.la -lfftw3_threads -lfftw3 /bin/bash ./libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o refine src/apps/refine.o librelion-1.4.la -lfftw3_threads -lfftw3 /bin/bash ./libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o preprocess src/apps/preprocess.o librelion-1.4.la -lfftw3_threads -lfftw3 libtool: link: g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/project src/apps/project.o ./.libs/librelion-1.4.so -lfftw3_threads -lfftw3 libtool: link: g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/reconstruct src/apps/reconstruct.o ./.libs/librelion-1.4.so -lfftw3_threads -lfftw3 /bin/bash ./libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o postprocess src/apps/postprocess.o librelion-1.4.la -lfftw3_threads -lfftw3 /bin/bash ./libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o autopick src/apps/autopick.o librelion-1.4.la -lfftw3_threads -lfftw3 libtool: link: g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/preprocess src/apps/preprocess.o ./.libs/librelion-1.4.so -lfftw3_threads -lfftw3 libtool: link: g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/refine src/apps/refine.o ./.libs/librelion-1.4.so -lfftw3_threads -lfftw3 /bin/bash ./libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o particle_polish src/apps/particle_polish.o librelion-1.4.la -lfftw3_threads -lfftw3 libtool: link: g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/postprocess src/apps/postprocess.o ./.libs/librelion-1.4.so -lfftw3_threads -lfftw3 /bin/bash ./libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o particle_sort src/apps/particle_sort.o librelion-1.4.la -lfftw3_threads -lfftw3 /bin/bash ./libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o run_ctffind src/apps/run_ctffind.o librelion-1.4.la -lfftw3_threads -lfftw3 libtool: link: g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/autopick src/apps/autopick.o ./.libs/librelion-1.4.so -lfftw3_threads -lfftw3 /bin/bash ./libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o star_compare src/apps/star_compare.o librelion-1.4.la -lfftw3_threads -lfftw3 libtool: link: g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/particle_polish src/apps/particle_polish.o ./.libs/librelion-1.4.so -lfftw3_threads -lfftw3 /bin/bash ./libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o find_tiltpairs src/apps/find_tiltpairs.o librelion-1.4.la -lfftw3_threads -lfftw3 libtool: link: g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/run_ctffind src/apps/run_ctffind.o ./.libs/librelion-1.4.so -lfftw3_threads -lfftw3 libtool: link: g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/particle_sort src/apps/particle_sort.o ./.libs/librelion-1.4.so -lfftw3_threads -lfftw3 /bin/bash ./libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o tiltpair_plot src/apps/tiltpair_plot.o librelion-1.4.la -lfftw3_threads -lfftw3 /bin/bash ./libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o mask_create src/apps/mask_create.o librelion-1.4.la -lfftw3_threads -lfftw3 libtool: link: g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/star_compare src/apps/star_compare.o ./.libs/librelion-1.4.so -lfftw3_threads -lfftw3 /bin/bash ./libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o stack_create src/apps/stack_create.o librelion-1.4.la -lfftw3_threads -lfftw3 libtool: link: g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/find_tiltpairs src/apps/find_tiltpairs.o ./.libs/librelion-1.4.so -lfftw3_threads -lfftw3 libtool: link: g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/tiltpair_plot src/apps/tiltpair_plot.o ./.libs/librelion-1.4.so -lfftw3_threads -lfftw3 libtool: link: g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/mask_create src/apps/mask_create.o ./.libs/librelion-1.4.so -lfftw3_threads -lfftw3 /bin/bash ./libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o image_handler src/apps/image_handler.o librelion-1.4.la -lfftw3_threads -lfftw3 libtool: link: g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/stack_create src/apps/stack_create.o ./.libs/librelion-1.4.so -lfftw3_threads -lfftw3 libtool: link: g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/image_handler src/apps/image_handler.o ./.libs/librelion-1.4.so -lfftw3_threads -lfftw3 make[3]: Leaving directory '/<>' make[2]: Leaving directory '/<>' make[2]: Entering directory '/<>' make[3]: Entering directory '/<>' /bin/mkdir -p '/<>/debian/tmp/simple/usr/lib/x86_64-linux-gnu' /bin/bash ./libtool --mode=install /usr/bin/install -c librelion-1.4.la '/<>/debian/tmp/simple/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/librelion-1.4.so.1.0.4 /<>/debian/tmp/simple/usr/lib/x86_64-linux-gnu/librelion-1.4.so.1.0.4 libtool: install: (cd /<>/debian/tmp/simple/usr/lib/x86_64-linux-gnu && { ln -s -f librelion-1.4.so.1.0.4 librelion-1.4.so.1 || { rm -f librelion-1.4.so.1 && ln -s librelion-1.4.so.1.0.4 librelion-1.4.so.1; }; }) libtool: install: (cd /<>/debian/tmp/simple/usr/lib/x86_64-linux-gnu && { ln -s -f librelion-1.4.so.1.0.4 librelion-1.4.so || { rm -f librelion-1.4.so && ln -s librelion-1.4.so.1.0.4 librelion-1.4.so; }; }) libtool: install: /usr/bin/install -c .libs/librelion-1.4.lai /<>/debian/tmp/simple/usr/lib/x86_64-linux-gnu/librelion-1.4.la libtool: install: /usr/bin/install -c .libs/librelion-1.4.a /<>/debian/tmp/simple/usr/lib/x86_64-linux-gnu/librelion-1.4.a libtool: install: chmod 644 /<>/debian/tmp/simple/usr/lib/x86_64-linux-gnu/librelion-1.4.a libtool: install: ranlib /<>/debian/tmp/simple/usr/lib/x86_64-linux-gnu/librelion-1.4.a libtool: warning: remember to run 'libtool --finish /usr/lib/x86_64-linux-gnu' /bin/mkdir -p '/<>/debian/tmp/simple/usr/bin' /bin/bash ./libtool --mode=install /usr/bin/install -c project '/<>/debian/tmp/simple/usr/bin/./relion_project' libtool: warning: 'librelion-1.4.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/project /<>/debian/tmp/simple/usr/bin/./relion_project /bin/bash ./libtool --mode=install /usr/bin/install -c reconstruct '/<>/debian/tmp/simple/usr/bin/./relion_reconstruct' libtool: warning: 'librelion-1.4.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/reconstruct /<>/debian/tmp/simple/usr/bin/./relion_reconstruct /bin/bash ./libtool --mode=install /usr/bin/install -c refine '/<>/debian/tmp/simple/usr/bin/./relion_refine' libtool: warning: 'librelion-1.4.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/refine /<>/debian/tmp/simple/usr/bin/./relion_refine /bin/bash ./libtool --mode=install /usr/bin/install -c preprocess '/<>/debian/tmp/simple/usr/bin/./relion_preprocess' libtool: warning: 'librelion-1.4.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/preprocess /<>/debian/tmp/simple/usr/bin/./relion_preprocess /bin/bash ./libtool --mode=install /usr/bin/install -c postprocess '/<>/debian/tmp/simple/usr/bin/./relion_postprocess' libtool: warning: 'librelion-1.4.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/postprocess /<>/debian/tmp/simple/usr/bin/./relion_postprocess /bin/bash ./libtool --mode=install /usr/bin/install -c autopick '/<>/debian/tmp/simple/usr/bin/./relion_autopick' libtool: warning: 'librelion-1.4.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/autopick /<>/debian/tmp/simple/usr/bin/./relion_autopick /bin/bash ./libtool --mode=install /usr/bin/install -c particle_polish '/<>/debian/tmp/simple/usr/bin/./relion_particle_polish' libtool: warning: 'librelion-1.4.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/particle_polish /<>/debian/tmp/simple/usr/bin/./relion_particle_polish /bin/bash ./libtool --mode=install /usr/bin/install -c particle_sort '/<>/debian/tmp/simple/usr/bin/./relion_particle_sort' libtool: warning: 'librelion-1.4.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/particle_sort /<>/debian/tmp/simple/usr/bin/./relion_particle_sort /bin/bash ./libtool --mode=install /usr/bin/install -c run_ctffind '/<>/debian/tmp/simple/usr/bin/./relion_run_ctffind' libtool: warning: 'librelion-1.4.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/run_ctffind /<>/debian/tmp/simple/usr/bin/./relion_run_ctffind /bin/bash ./libtool --mode=install /usr/bin/install -c star_compare '/<>/debian/tmp/simple/usr/bin/./relion_star_compare' libtool: warning: 'librelion-1.4.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/star_compare /<>/debian/tmp/simple/usr/bin/./relion_star_compare /bin/bash ./libtool --mode=install /usr/bin/install -c find_tiltpairs '/<>/debian/tmp/simple/usr/bin/./relion_find_tiltpairs' libtool: warning: 'librelion-1.4.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/find_tiltpairs /<>/debian/tmp/simple/usr/bin/./relion_find_tiltpairs /bin/bash ./libtool --mode=install /usr/bin/install -c tiltpair_plot '/<>/debian/tmp/simple/usr/bin/./relion_tiltpair_plot' libtool: warning: 'librelion-1.4.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/tiltpair_plot /<>/debian/tmp/simple/usr/bin/./relion_tiltpair_plot /bin/bash ./libtool --mode=install /usr/bin/install -c mask_create '/<>/debian/tmp/simple/usr/bin/./relion_mask_create' libtool: warning: 'librelion-1.4.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/mask_create /<>/debian/tmp/simple/usr/bin/./relion_mask_create /bin/bash ./libtool --mode=install /usr/bin/install -c stack_create '/<>/debian/tmp/simple/usr/bin/./relion_stack_create' libtool: warning: 'librelion-1.4.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/stack_create /<>/debian/tmp/simple/usr/bin/./relion_stack_create /bin/bash ./libtool --mode=install /usr/bin/install -c image_handler '/<>/debian/tmp/simple/usr/bin/./relion_image_handler' libtool: warning: 'librelion-1.4.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/image_handler /<>/debian/tmp/simple/usr/bin/./relion_image_handler /bin/bash ./libtool --mode=install /usr/bin/install -c find_tiltpairs '/<>/debian/tmp/simple/usr/bin/./relion_find_tiltpairs' libtool: warning: 'librelion-1.4.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/find_tiltpairs /<>/debian/tmp/simple/usr/bin/./relion_find_tiltpairs /bin/bash ./libtool --mode=install /usr/bin/install -c tiltpair_plot '/<>/debian/tmp/simple/usr/bin/./relion_tiltpair_plot' libtool: warning: 'librelion-1.4.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/tiltpair_plot /<>/debian/tmp/simple/usr/bin/./relion_tiltpair_plot /bin/mkdir -p '/<>/debian/tmp/simple/usr/bin' /usr/bin/install -c scripts/star_datablock_ctfdat '/<>/debian/tmp/simple/usr/bin/./relion_star_datablock_ctfdat' /usr/bin/install -c scripts/star_datablock_stack '/<>/debian/tmp/simple/usr/bin/./relion_star_datablock_stack' /usr/bin/install -c scripts/star_datablock_singlefiles '/<>/debian/tmp/simple/usr/bin/./relion_star_datablock_singlefiles' /usr/bin/install -c scripts/star_loopheader '/<>/debian/tmp/simple/usr/bin/./relion_star_loopheader' /usr/bin/install -c scripts/star_plottable '/<>/debian/tmp/simple/usr/bin/./relion_star_plottable' /usr/bin/install -c scripts/star_printtable '/<>/debian/tmp/simple/usr/bin/./relion_star_printtable' /usr/bin/install -c scripts/qsub.csh '/<>/debian/tmp/simple/usr/bin/./relion_qsub.csh' /bin/mkdir -p '/<>/debian/tmp/simple/usr/include/relion-1.4' /bin/mkdir -p '/<>/debian/tmp/simple/usr/include/relion-1.4/src' /usr/bin/install -c -m 644 src/args.h src/assembly.h src/autopicker.h src/backprojector.h src/complex.h src/ctf.h src/ctffind_runner.h src/displayer.h src/error.h src/euler.h src/exp_model.h src/fftw.h src/filename.h src/funcs.h src/gcc_version.h src/gui_entries.h src/gui_jobwindow.h src/gui_mainwindow.h src/healpix_sampling.h src/image.h src/macros.h src/mask.h src/matrix1d.h src/matrix2d.h src/memory.h src/metadata_container.h src/metadata_label.h src/metadata_table.h src/ml_model.h src/ml_optimiser.h src/multidim_array.h src/numerical_recipes.h src/parallel.h src/particle_polisher.h src/particle_sorter.h src/postprocessing.h src/preprocessing.h src/projector.h src/rwIMAGIC.h src/rwMRC.h '/<>/debian/tmp/simple/usr/include/relion-1.4/src' /bin/mkdir -p '/<>/debian/tmp/simple/usr/include/relion-1.4/src' /usr/bin/install -c -m 644 src/rwSPIDER.h src/strings.h src/symmetries.h src/tabfuncs.h src/time.h src/transformations.h '/<>/debian/tmp/simple/usr/include/relion-1.4/src' /bin/mkdir -p '/<>/debian/tmp/simple/usr/include/relion-1.4/src/Healpix_2.15a' /usr/bin/install -c -m 644 src/Healpix_2.15a/arr.h src/Healpix_2.15a/cxxutils.h src/Healpix_2.15a/datatypes.h src/Healpix_2.15a/geom_utils.h src/Healpix_2.15a/lsconstants.h src/Healpix_2.15a/message_error.h src/Healpix_2.15a/openmp_support.h src/Healpix_2.15a/pointing.h src/Healpix_2.15a/vec3.h src/Healpix_2.15a/healpix_base.h '/<>/debian/tmp/simple/usr/include/relion-1.4/src/Healpix_2.15a' /usr/bin/install -c -m 644 relion.h '/<>/debian/tmp/simple/usr/include/relion-1.4/.' /bin/mkdir -p '/<>/debian/tmp/simple/usr/lib/x86_64-linux-gnu/pkgconfig' /usr/bin/install -c -m 644 relion-1.4.pc '/<>/debian/tmp/simple/usr/lib/x86_64-linux-gnu/pkgconfig' make[3]: Leaving directory '/<>' make[2]: Leaving directory '/<>' make clean make[2]: Entering directory '/<>' rm -f project reconstruct refine preprocess postprocess autopick particle_polish particle_sort run_ctffind star_compare find_tiltpairs tiltpair_plot mask_create stack_create image_handler find_tiltpairs tiltpair_plot test -z "librelion-1.4.la" || rm -f librelion-1.4.la rm -f ./so_locations rm -rf .libs _libs rm -rf src/.libs src/_libs rm -rf src/Healpix_2.15a/.libs src/Healpix_2.15a/_libs rm -f *.o rm -f src/*.o rm -f src/*.lo rm -f src/Healpix_2.15a/*.o rm -f src/Healpix_2.15a/*.lo rm -f src/apps/*.o rm -f *.lo make[2]: Leaving directory '/<>' # ... then add MPI (for relion-bin+mpi) ... MPICXX=mpicxx.openmpi dh_auto_configure -- --libdir=\${prefix}/lib/x86_64-linux-gnu --enable-mpi --disable-gui ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --libexecdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --libdir=\${prefix}/lib/x86_64-linux-gnu --enable-mpi --disable-gui checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of gcc... none checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... none checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking how to run the C preprocessor... gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for mpic++... mpicxx.openmpi checking for fftw3.h... yes checking for main in -lfftw3... yes checking for fftw_plan_with_nthreads in -lfftw3_threads... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating relion-1.4.pc config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands make -j4; make install prefix=/<>/debian/tmp/mpi/usr make[2]: Entering directory '/<>' make all-am make[3]: Entering directory '/<>' mpicxx.openmpi -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/apps/project.o src/apps/project.cpp /bin/bash ./libtool --tag=CXX --mode=compile mpicxx.openmpi -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/args.lo src/args.cpp /bin/bash ./libtool --tag=CXX --mode=compile mpicxx.openmpi -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/assembly.lo src/assembly.cpp /bin/bash ./libtool --tag=CXX --mode=compile mpicxx.openmpi -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/autopicker.lo src/autopicker.cpp libtool: compile: mpicxx.openmpi -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c src/args.cpp -fPIC -DPIC -o src/.libs/args.o libtool: compile: mpicxx.openmpi -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c src/autopicker.cpp -fPIC -DPIC -o src/.libs/autopicker.o libtool: compile: mpicxx.openmpi -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c src/assembly.cpp -fPIC -DPIC -o src/.libs/assembly.o src/assembly.cpp: In member function ‘void Assembly::writePDB(std::string)’: src/assembly.cpp:355:28: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=] 355 | fprintf(file, "ATOM %5d %-4s %3s %1c%4d %8.3f%8.3f%8.3f%6.2f%6.2f %4s\n", | ~~^ | | | int | %5ld 356 | atomnum, molecules[imol].residues[ires].atoms[iatom].name.c_str(), molecules[imol].residues[ires].name.c_str(), | ~~~~~~~ | | | long int src/args.cpp: In member function ‘IOParser& IOParser::operator=(const IOParser&)’: src/args.cpp:104:1: warning: no return statement in function returning non-void [-Wreturn-type] 103 | copy(in); +++ |+ return *this; 104 | } | ^ libtool: compile: mpicxx.openmpi -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c src/args.cpp -o src/args.o >/dev/null 2>&1 libtool: compile: mpicxx.openmpi -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c src/assembly.cpp -o src/assembly.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile mpicxx.openmpi -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/backprojector.lo src/backprojector.cpp libtool: compile: mpicxx.openmpi -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c src/backprojector.cpp -fPIC -DPIC -o src/.libs/backprojector.o /bin/bash ./libtool --tag=CXX --mode=compile mpicxx.openmpi -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/complex.lo src/complex.cpp libtool: compile: mpicxx.openmpi -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c src/complex.cpp -fPIC -DPIC -o src/.libs/complex.o libtool: compile: mpicxx.openmpi -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c src/complex.cpp -o src/complex.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile mpicxx.openmpi -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/ctf.lo src/ctf.cpp libtool: compile: mpicxx.openmpi -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c src/ctf.cpp -fPIC -DPIC -o src/.libs/ctf.o libtool: compile: mpicxx.openmpi -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c src/autopicker.cpp -o src/autopicker.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile mpicxx.openmpi -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/ctffind_runner.lo src/ctffind_runner.cpp libtool: compile: mpicxx.openmpi -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c src/ctffind_runner.cpp -fPIC -DPIC -o src/.libs/ctffind_runner.o libtool: compile: mpicxx.openmpi -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c src/ctf.cpp -o src/ctf.o >/dev/null 2>&1 libtool: compile: mpicxx.openmpi -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c src/backprojector.cpp -o src/backprojector.o >/dev/null 2>&1 src/ctffind_runner.cpp: In member function ‘void CtffindRunner::executeCtffind(FileName)’: src/ctffind_runner.cpp:237:9: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 237 | system ( fn_cmnd.c_str() ); | ~~~~~~~^~~~~~~~~~~~~~~~~~~ /bin/bash ./libtool --tag=CXX --mode=compile mpicxx.openmpi -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/error.lo src/error.cpp libtool: compile: mpicxx.openmpi -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c src/error.cpp -fPIC -DPIC -o src/.libs/error.o libtool: compile: mpicxx.openmpi -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c src/error.cpp -o src/error.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile mpicxx.openmpi -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/euler.lo src/euler.cpp libtool: compile: mpicxx.openmpi -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c src/euler.cpp -fPIC -DPIC -o src/.libs/euler.o libtool: compile: mpicxx.openmpi -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 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-D_FORTIFY_SOURCE=2 -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c src/tabfuncs.cpp -o src/tabfuncs.o >/dev/null 2>&1 src/time.cpp: In member function ‘int Timer::toc(int)’: src/time.cpp:223:1: warning: no return statement in function returning non-void [-Wreturn-type] 223 | } | ^ libtool: compile: mpicxx.openmpi -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c src/time.cpp -o src/time.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile mpicxx.openmpi -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/transformations.lo src/transformations.cpp libtool: compile: mpicxx.openmpi -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c src/transformations.cpp -fPIC -DPIC -o src/.libs/transformations.o /bin/bash ./libtool --tag=CXX --mode=compile mpicxx.openmpi -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/Healpix_2.15a/cxxutils.lo src/Healpix_2.15a/cxxutils.cc libtool: compile: mpicxx.openmpi -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c src/Healpix_2.15a/cxxutils.cc -fPIC -DPIC -o src/Healpix_2.15a/.libs/cxxutils.o libtool: compile: mpicxx.openmpi -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c src/symmetries.cpp -o src/symmetries.o >/dev/null 2>&1 libtool: compile: mpicxx.openmpi -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c src/transformations.cpp -o src/transformations.o >/dev/null 2>&1 libtool: compile: mpicxx.openmpi -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c src/Healpix_2.15a/cxxutils.cc -o src/Healpix_2.15a/cxxutils.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile mpicxx.openmpi -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/Healpix_2.15a/healpix_base.lo src/Healpix_2.15a/healpix_base.cc libtool: compile: mpicxx.openmpi -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c src/Healpix_2.15a/healpix_base.cc -fPIC -DPIC -o src/Healpix_2.15a/.libs/healpix_base.o /bin/bash ./libtool --tag=CXX --mode=compile mpicxx.openmpi -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/mpi.lo src/mpi.cpp libtool: compile: mpicxx.openmpi -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c src/mpi.cpp -fPIC -DPIC -o src/.libs/mpi.o /bin/bash ./libtool --tag=CXX --mode=compile mpicxx.openmpi -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/autopicker_mpi.lo src/autopicker_mpi.cpp libtool: compile: mpicxx.openmpi -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c src/autopicker_mpi.cpp -fPIC -DPIC -o src/.libs/autopicker_mpi.o In file included from ./src/mpi.h:47, from src/mpi.cpp:46: src/mpi.cpp: In constructor ‘MpiNode::MpiNode(int&, char**)’: /usr/lib/x86_64-linux-gnu/openmpi/include/mpi.h:338:73: error: static assertion failed: MPI_Errhandler_set was removed in MPI-3.0. Use MPI_Comm_set_errhandler instead. 338 | #define THIS_FUNCTION_WAS_REMOVED_IN_MPI30(func, newfunc) static_assert(0, #func " was removed in MPI-3.0. Use " #newfunc " instead.") | ^ /usr/lib/x86_64-linux-gnu/openmpi/include/mpi.h:2864:34: note: in expansion of macro ‘THIS_FUNCTION_WAS_REMOVED_IN_MPI30’ 2864 | #define MPI_Errhandler_set(...) THIS_FUNCTION_WAS_REMOVED_IN_MPI30(MPI_Errhandler_set, MPI_Comm_set_errhandler) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/mpi.cpp:56:5: note: in expansion of macro ‘MPI_Errhandler_set’ 56 | MPI_Errhandler_set(MPI_COMM_WORLD, MPI_ERRORS_RETURN); | ^~~~~~~~~~~~~~~~~~ make[3]: *** [Makefile:1305: src/mpi.lo] Error 1 make[3]: *** Waiting for unfinished jobs.... libtool: compile: mpicxx.openmpi -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c src/Healpix_2.15a/healpix_base.cc -o src/Healpix_2.15a/healpix_base.o >/dev/null 2>&1 libtool: compile: mpicxx.openmpi -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c src/autopicker_mpi.cpp -o src/autopicker_mpi.o >/dev/null 2>&1 make[3]: Leaving directory '/<>' make[2]: *** [Makefile:753: all] Error 2 make[2]: Leaving directory '/<>' make[2]: Entering directory '/<>' /bin/bash ./libtool --tag=CXX --mode=compile mpicxx.openmpi -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/mpi.lo src/mpi.cpp libtool: compile: mpicxx.openmpi -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c src/mpi.cpp -fPIC -DPIC -o src/.libs/mpi.o In file included from ./src/mpi.h:47, from src/mpi.cpp:46: src/mpi.cpp: In constructor ‘MpiNode::MpiNode(int&, char**)’: /usr/lib/x86_64-linux-gnu/openmpi/include/mpi.h:338:73: error: static assertion failed: MPI_Errhandler_set was removed in MPI-3.0. Use MPI_Comm_set_errhandler instead. 338 | #define THIS_FUNCTION_WAS_REMOVED_IN_MPI30(func, newfunc) static_assert(0, #func " was removed in MPI-3.0. Use " #newfunc " instead.") | ^ /usr/lib/x86_64-linux-gnu/openmpi/include/mpi.h:2864:34: note: in expansion of macro ‘THIS_FUNCTION_WAS_REMOVED_IN_MPI30’ 2864 | #define MPI_Errhandler_set(...) THIS_FUNCTION_WAS_REMOVED_IN_MPI30(MPI_Errhandler_set, MPI_Comm_set_errhandler) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/mpi.cpp:56:5: note: in expansion of macro ‘MPI_Errhandler_set’ 56 | MPI_Errhandler_set(MPI_COMM_WORLD, MPI_ERRORS_RETURN); | ^~~~~~~~~~~~~~~~~~ make[2]: *** [Makefile:1305: src/mpi.lo] Error 1 make[2]: Leaving directory '/<>' make[1]: *** [debian/rules:51: override_dh_auto_build] Error 2 make[1]: Leaving directory '/<>' make: *** [debian/rules:37: build] Error 2 dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2020-09-29T18:07:12Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 294112 Build-Time: 192 Distribution: perl-5.32-throwaway Fail-Stage: build Host Architecture: amd64 Install-Time: 15 Job: /srv/debomatic/incoming/relion_1.4+dfsg-4.dsc Machine Architecture: amd64 Package: relion Package-Time: 217 Source-Version: 1.4+dfsg-4 Space: 294112 Status: attempted Version: 1.4+dfsg-4 -------------------------------------------------------------------------------- Finished at 2020-09-29T18:07:12Z Build needed 00:03:37, 294112k disk space