DC-Build-Header: relion 1.4+dfsg-2 / 2017-07-06 17:08:18 +0000 DC-Task: type:rebuild-binarch-only source:relion version:1.4+dfsg-2 chroot:unstable esttime:1314 logfile:/tmp/relion_1.4+dfsg-2_unstable_clang3.9.log modes:clang:binarch-only DC-Sbuild-call: su user42 -c 'sbuild -n --arch-any --apt-update -d unstable -v --chroot-setup-commands=/tmp/clang relion_1.4+dfsg-2' sbuild (Debian sbuild) 0.73.0 (23 Dec 2016) on ip-172-31-43-157.eu-central-1.compute.internal +==============================================================================+ | relion 1.4+dfsg-2 (amd64) Thu, 06 Jul 2017 17:08:18 +0000 | +==============================================================================+ Package: relion Version: 1.4+dfsg-2 Source Version: 1.4+dfsg-2 Distribution: unstable Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/unstable-amd64-sbuild-7a87e29f-ae81-43e3-a3f9-b1aa90617837' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /tmp/clang ---------- + echo 'Entering customization script...' Entering customization script... + CLANG_VERSION=3.9 + echo 'Install of clang-3.9' Install of clang-3.9 + apt-get update Get:1 http://127.0.0.1:9999/debian unstable InRelease [255 kB] Get:2 http://127.0.0.1:9999/debian unstable/main Sources.diff/Index [27.9 kB] Get:3 http://127.0.0.1:9999/debian unstable/main amd64 Packages.diff/Index [27.9 kB] Get:4 http://127.0.0.1:9999/debian unstable/main Translation-en.diff/Index [27.9 kB] Get:5 http://127.0.0.1:9999/debian unstable/main Sources 2017-07-02-0216.39.pdiff [15.0 kB] Get:6 http://127.0.0.1:9999/debian unstable/main Sources 2017-07-02-0817.00.pdiff [7416 B] Get:7 http://127.0.0.1:9999/debian unstable/main Sources 2017-07-02-1415.16.pdiff [17.0 kB] Get:8 http://127.0.0.1:9999/debian unstable/main Sources 2017-07-02-2015.53.pdiff [15.2 kB] Get:9 http://127.0.0.1:9999/debian unstable/main Sources 2017-07-03-0215.43.pdiff [50.2 kB] Get:10 http://127.0.0.1:9999/debian unstable/main Sources 2017-07-03-0815.58.pdiff [5500 B] Get:11 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2017-07-04-1416.28.pdiff [484 B] Get:50 http://127.0.0.1:9999/debian unstable/main Translation-en 2017-07-04-2017.16.pdiff [1126 B] Get:51 http://127.0.0.1:9999/debian unstable/main Translation-en 2017-07-05-0215.45.pdiff [214 B] Get:52 http://127.0.0.1:9999/debian unstable/main Translation-en 2017-07-05-0817.10.pdiff [606 B] Get:53 http://127.0.0.1:9999/debian unstable/main Translation-en 2017-07-05-1416.09.pdiff [214 B] Get:54 http://127.0.0.1:9999/debian unstable/main Translation-en 2017-07-05-2019.56.pdiff [2615 B] Get:55 http://127.0.0.1:9999/debian unstable/main Translation-en 2017-07-06-0216.07.pdiff [1869 B] Get:56 http://127.0.0.1:9999/debian unstable/main Translation-en 2017-07-06-0817.23.pdiff [915 B] Get:56 http://127.0.0.1:9999/debian unstable/main Translation-en 2017-07-06-0817.23.pdiff [915 B] Fetched 974 kB in 1s (755 kB/s) Reading package lists... + apt-get install --yes --no-install-recommends --force-yes clang-3.9 Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: cpp-6 g++-6 gcc-6 gcc-6-base gcc-7-base libasan3 libatomic1 libbsd0 libcc1-0 libcilkrts5 libclang-common-3.9-dev libclang1-3.9 libedit2 libffi6 libgcc-6-dev libgcc1 libgomp1 libitm1 libjsoncpp1 libllvm3.9 liblsan0 libmpx2 libncurses5 libobjc-6-dev libobjc4 libquadmath0 libstdc++-6-dev libstdc++6 libtsan0 libubsan0 Suggested packages: gnustep gnustep-devel clang-3.9-doc gcc-6-locales g++-6-multilib gcc-6-doc libstdc++6-6-dbg gcc-6-multilib libgcc1-dbg libgomp1-dbg libitm1-dbg libatomic1-dbg libasan3-dbg liblsan0-dbg libtsan0-dbg libubsan0-dbg libcilkrts5-dbg libmpx2-dbg libquadmath0-dbg libstdc++-6-doc Recommended packages: llvm-3.9-dev python libgpm2 The following NEW packages will be installed: clang-3.9 libbsd0 libclang-common-3.9-dev libclang1-3.9 libedit2 libffi6 libjsoncpp1 libllvm3.9 libncurses5 libobjc-6-dev libobjc4 The following packages will be upgraded: cpp-6 g++-6 gcc-6 gcc-6-base gcc-7-base libasan3 libatomic1 libcc1-0 libcilkrts5 libgcc-6-dev libgcc1 libgomp1 libitm1 liblsan0 libmpx2 libquadmath0 libstdc++-6-dev libstdc++6 libtsan0 libubsan0 20 upgraded, 11 newly installed, 0 to remove and 13 not upgraded. Need to get 83.9 MB of archives. After this operation, 251 MB of additional disk space will be used. 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Preparing to unpack .../16-libclang-common-3.9-dev_1%3a3.9.1-10_amd64.deb ... Unpacking libclang-common-3.9-dev (1:3.9.1-10) ... Selecting previously unselected package clang-3.9. Preparing to unpack .../17-clang-3.9_1%3a3.9.1-10_amd64.deb ... Unpacking clang-3.9 (1:3.9.1-10) ... Setting up libquadmath0:amd64 (7.1.0-9) ... Setting up libncurses5:amd64 (6.0+20161126-1) ... Setting up libgomp1:amd64 (7.1.0-9) ... Setting up libatomic1:amd64 (7.1.0-9) ... Setting up libcc1-0:amd64 (7.1.0-9) ... Setting up libobjc4:amd64 (7.1.0-9) ... Setting up libcilkrts5:amd64 (7.1.0-9) ... Setting up libubsan0:amd64 (7.1.0-9) ... Setting up libtsan0:amd64 (7.1.0-9) ... Setting up gcc-6-base:amd64 (6.4.0-1) ... Setting up libbsd0:amd64 (0.8.5-1) ... Setting up liblsan0:amd64 (7.1.0-9) ... Setting up libmpx2:amd64 (7.1.0-9) ... Processing triggers for libc-bin (2.24-12) ... Setting up libffi6:amd64 (3.2.1-6) ... Setting up cpp-6 (6.4.0-1) ... Setting up libitm1:amd64 (7.1.0-9) ... Setting up libjsoncpp1:amd64 (1.7.4-3) ... Setting up libedit2:amd64 (3.1-20170329-1) ... Setting up libasan3:amd64 (6.4.0-1) ... Setting up libgcc-6-dev:amd64 (6.4.0-1) ... Setting up libstdc++-6-dev:amd64 (6.4.0-1) ... Setting up libllvm3.9:amd64 (1:3.9.1-10) ... Setting up libclang-common-3.9-dev (1:3.9.1-10) ... Setting up gcc-6 (6.4.0-1) ... Setting up g++-6 (6.4.0-1) ... Setting up libobjc-6-dev:amd64 (6.4.0-1) ... Setting up libclang1-3.9:amd64 (1:3.9.1-10) ... Setting up clang-3.9 (1:3.9.1-10) ... Processing triggers for libc-bin (2.24-12) ... W: --force-yes is deprecated, use one of the options starting with --allow instead. + echo 'Replace gcc, g++ & cpp by clang' Replace gcc, g++ & cpp by clang + VERSIONS='4.6 4.7 4.8 4.9 5 6 7' + cd /usr/bin + for VERSION in $VERSIONS + rm -f g++-4.6 gcc-4.6 cpp-4.6 gcc + ln -s clang++-3.9 g++-4.6 + ln -s clang-3.9 gcc-4.6 + ln -s clang-3.9 cpp-4.6 + ln -s clang-3.9 gcc + echo 'gcc-4.6 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-4.6 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-4.6 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-4.6 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-4.7 gcc-4.7 cpp-4.7 gcc + ln -s clang++-3.9 g++-4.7 + ln -s clang-3.9 gcc-4.7 + ln -s clang-3.9 cpp-4.7 + ln -s clang-3.9 gcc + echo 'gcc-4.7 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-4.7 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-4.7 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-4.7 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-4.8 gcc-4.8 cpp-4.8 gcc + ln -s clang++-3.9 g++-4.8 + ln -s clang-3.9 gcc-4.8 + ln -s clang-3.9 cpp-4.8 + ln -s clang-3.9 gcc + echo 'gcc-4.8 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-4.8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-4.8 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-4.8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-4.9 gcc-4.9 cpp-4.9 gcc + ln -s clang++-3.9 g++-4.9 + ln -s clang-3.9 gcc-4.9 + ln -s clang-3.9 cpp-4.9 + ln -s clang-3.9 gcc + echo 'gcc-4.9 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-4.9 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-4.9 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-4.9 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-5 gcc-5 cpp-5 gcc + ln -s clang++-3.9 g++-5 + ln -s clang-3.9 gcc-5 + ln -s clang-3.9 cpp-5 + ln -s clang-3.9 gcc + echo 'gcc-5 hold' + dpkg --set-selections + echo 'g++-5 hold' + dpkg --set-selections + for VERSION in $VERSIONS + rm -f g++-6 gcc-6 cpp-6 gcc + ln -s clang++-3.9 g++-6 + ln -s clang-3.9 gcc-6 + ln -s clang-3.9 cpp-6 + ln -s clang-3.9 gcc + echo 'gcc-6 hold' + dpkg --set-selections + echo 'g++-6 hold' + dpkg --set-selections + for VERSION in $VERSIONS + rm -f g++-7 gcc-7 cpp-7 gcc + ln -s clang++-3.9 g++-7 + ln -s clang-3.9 gcc-7 + ln -s clang-3.9 cpp-7 + ln -s clang-3.9 gcc + echo 'gcc-7 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-7 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-7 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-7 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + cd - /build/relion-tAVDwT + echo 'Check if gcc, g++ & cpp are actually clang' Check if gcc, g++ & cpp are actually clang + gcc --version + grep clang + cpp --version + grep clang + g++ --version + grep clang I: Finished running '/tmp/clang'. Finished processing commands. -------------------------------------------------------------------------------- +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Hit:1 http://127.0.0.1:9999/debian unstable InRelease Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: libgnutls30 libhogweed4 libidn2-0 libnettle6 libp11-kit0 libtasn1-6 libunistring2 The following packages will be upgraded: apt cpp debconf g++ gcc libapt-pkg5.0 libdebconfclient0 libperl5.24 libsystemd0 libudev1 perl perl-base perl-modules-5.24 13 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. Need to get 12.5 MB of archives. After this operation, 6330 kB of additional disk space will be used. Get:1 http://127.0.0.1:9999/debian unstable/main amd64 libperl5.24 amd64 5.24.1-6 [3525 kB] Get:2 http://127.0.0.1:9999/debian unstable/main amd64 perl amd64 5.24.1-6 [218 kB] Get:3 http://127.0.0.1:9999/debian unstable/main amd64 perl-base amd64 5.24.1-6 [1344 kB] Get:4 http://127.0.0.1:9999/debian unstable/main amd64 perl-modules-5.24 all 5.24.1-6 [2723 kB] Get:5 http://127.0.0.1:9999/debian unstable/main amd64 libapt-pkg5.0 amd64 1.5~beta1 [922 kB] Get:6 http://127.0.0.1:9999/debian unstable/main amd64 libnettle6 amd64 3.3-1+b1 [191 kB] Get:7 http://127.0.0.1:9999/debian unstable/main amd64 libhogweed4 amd64 3.3-1+b1 [136 kB] Get:8 http://127.0.0.1:9999/debian unstable/main amd64 libunistring2 amd64 0.9.7-2 [377 kB] Get:9 http://127.0.0.1:9999/debian unstable/main amd64 libidn2-0 amd64 0.16-1+b1 [56.6 kB] Get:10 http://127.0.0.1:9999/debian unstable/main amd64 libp11-kit0 amd64 0.23.7-2 [193 kB] Get:11 http://127.0.0.1:9999/debian unstable/main amd64 libtasn1-6 amd64 4.12-2 [51.0 kB] Get:12 http://127.0.0.1:9999/debian unstable/main amd64 libgnutls30 amd64 3.5.13-2 [914 kB] Get:13 http://127.0.0.1:9999/debian unstable/main amd64 apt amd64 1.5~beta1 [1237 kB] Get:14 http://127.0.0.1:9999/debian unstable/main amd64 debconf all 1.5.62 [160 kB] Get:15 http://127.0.0.1:9999/debian unstable/main amd64 libsystemd0 amd64 233-10 [281 kB] Get:16 http://127.0.0.1:9999/debian unstable/main amd64 libudev1 amd64 233-10 [126 kB] Get:17 http://127.0.0.1:9999/debian unstable/main amd64 libdebconfclient0 amd64 0.229 [47.9 kB] Get:18 http://127.0.0.1:9999/debian unstable/main amd64 cpp amd64 4:6.3.0-4d1 [18.8 kB] Get:19 http://127.0.0.1:9999/debian unstable/main amd64 gcc amd64 4:6.3.0-4d1 [5252 B] Get:20 http://127.0.0.1:9999/debian unstable/main amd64 g++ amd64 4:6.3.0-4d1 [1548 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 12.5 MB in 0s (83.0 MB/s) (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 10176 files and directories currently installed.) Preparing to unpack .../cpp_4%3a6.3.0-4d1_amd64.deb ... Unpacking cpp (4:6.3.0-4d1) over (4:6.3.0-4) ... Preparing to unpack .../gcc_4%3a6.3.0-4d1_amd64.deb ... Removing old gcc doc directory. Unpacking gcc (4:6.3.0-4d1) over (4:6.3.0-4) ... Preparing to unpack .../g++_4%3a6.3.0-4d1_amd64.deb ... Unpacking g++ (4:6.3.0-4d1) over (4:6.3.0-4) ... Setting up cpp (4:6.3.0-4d1) ... Setting up perl-modules-5.24 (5.24.1-6) ... Setting up libperl5.24:amd64 (5.24.1-6) ... Setting up gcc (4:6.3.0-4d1) ... Setting up perl (5.24.1-6) ... Processing triggers for libc-bin (2.24-12) ... Setting up g++ (4:6.3.0-4d1) ... +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'relion' packaging is maintained in the 'Git' version control system at: git://anonscm.debian.org/debian-med/relion.git Please use: git clone git://anonscm.debian.org/debian-med/relion.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 560 kB of source archives. Get:1 http://127.0.0.1:9999/debian unstable/main relion 1.4+dfsg-2 (dsc) [3043 B] Get:2 http://127.0.0.1:9999/debian unstable/main relion 1.4+dfsg-2 (tar) [548 kB] Get:3 http://127.0.0.1:9999/debian unstable/main relion 1.4+dfsg-2 (diff) [8292 B] Fetched 560 kB in 0s (3156 kB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/relion-tAVDwT/relion-1.4+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/relion-tAVDwT' with '<>' +------------------------------------------------------------------------------+ | Install build-essential | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-JqzGgp/apt_archive/sbuild-build-depends-core-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy dpkg-scanpackages: info: Wrote 1 entries to output Packages file. Ign:1 copy:/<>/resolver-JqzGgp/apt_archive ./ InRelease Get:2 copy:/<>/resolver-JqzGgp/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-JqzGgp/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-JqzGgp/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-JqzGgp/apt_archive ./ Packages [430 B] Fetched 1736 B in 0s (0 B/s) Reading package lists... Reading package lists... Install core build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 784 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-JqzGgp/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [784 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 784 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 10178 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in i386 amd64 all) +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper (>= 9), dh-autoreconf, dh-exec (>= 0.3), libfltk1.3-dev, libfftw3-dev, libopenmpi-dev Filtered Build-Depends: debhelper (>= 9), dh-autoreconf, dh-exec (>= 0.3), libfltk1.3-dev, libfftw3-dev, libopenmpi-dev dpkg-deb: building package 'sbuild-build-depends-relion-dummy' in '/<>/resolver-JqzGgp/apt_archive/sbuild-build-depends-relion-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-relion-dummy dpkg-scanpackages: info: Wrote 2 entries to output Packages file. Ign:1 copy:/<>/resolver-JqzGgp/apt_archive ./ InRelease Get:2 copy:/<>/resolver-JqzGgp/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-JqzGgp/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-JqzGgp/apt_archive ./ Sources [530 B] Get:5 copy:/<>/resolver-JqzGgp/apt_archive ./ Packages [607 B] Fetched 2100 B in 0s (0 B/s) Reading package lists... Reading package lists... Install relion 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 bsdmainutils debhelper dh-autoreconf dh-exec dh-strip-nondeterminism file fontconfig-config fonts-dejavu-core gettext gettext-base groff-base intltool-debian libarchive-zip-perl libcairo2 libcroco3 libdrm2 libexpat1 libfabric1 libfftw3-bin libfftw3-dev libfftw3-double3 libfftw3-long3 libfftw3-quad3 libfftw3-single3 libfile-stripnondeterminism-perl libfltk-cairo1.3 libfltk-forms1.3 libfltk-gl1.3 libfltk-images1.3 libfltk1.3 libfltk1.3-dev libfontconfig1 libfreetype6 libgfortran3 libgl1-mesa-glx libglapi-mesa libglib2.0-0 libhwloc-dev libhwloc-plugins libhwloc5 libibverbs-dev libibverbs1 libicu57 libjpeg62-turbo libltdl-dev libltdl7 libmagic-mgc libmagic1 libnl-3-200 libnl-route-3-200 libnuma-dev libnuma1 libopenmpi-dev libopenmpi2 libpciaccess0 libpipeline1 libpixman-1-0 libpng16-16 libpsm-infinipath1 libpthread-stubs0-dev librdmacm1 libsigsegv2 libtimedate-perl libtool libx11-6 libx11-data libx11-dev libx11-xcb1 libxau-dev libxau6 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcb1 libxcb1-dev libxcursor1 libxdamage1 libxdmcp-dev libxdmcp6 libxext6 libxfixes3 libxft2 libxinerama1 libxml2 libxrender1 libxshmfence1 libxxf86vm1 m4 man-db ocl-icd-libopencl1 openmpi-common po-debconf ucf x11proto-core-dev x11proto-input-dev x11proto-kb-dev xorg-sgml-doctools xtrans-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libfftw3-doc fltk1.3-doc libcairo2-dev libjpeg-dev libpng-dev libxext-dev libxft-dev libxinerama-dev zlib1g-dev | libz-dev libhwloc-contrib-plugins libtool-doc openmpi-doc pciutils gfortran | fortran95-compiler gcj-jdk libxcb-doc m4-doc less www-browser opencl-icd libmail-box-perl Recommended packages: curl | wget | lynx-cur libarchive-cpio-perl fluid libgl1-mesa-dev | libgl-dev libglu1-mesa-dev | libglu-dev libgl1-mesa-dri libglib2.0-data shared-mime-info xdg-user-dirs openmpi-bin libx11-doc xml-core libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-exec dh-strip-nondeterminism file fontconfig-config fonts-dejavu-core gettext gettext-base groff-base intltool-debian libarchive-zip-perl libcairo2 libcroco3 libdrm2 libexpat1 libfabric1 libfftw3-bin libfftw3-dev libfftw3-double3 libfftw3-long3 libfftw3-quad3 libfftw3-single3 libfile-stripnondeterminism-perl libfltk-cairo1.3 libfltk-forms1.3 libfltk-gl1.3 libfltk-images1.3 libfltk1.3 libfltk1.3-dev libfontconfig1 libfreetype6 libgfortran3 libgl1-mesa-glx libglapi-mesa libglib2.0-0 libhwloc-dev libhwloc-plugins libhwloc5 libibverbs-dev libibverbs1 libicu57 libjpeg62-turbo libltdl-dev libltdl7 libmagic-mgc libmagic1 libnl-3-200 libnl-route-3-200 libnuma-dev libnuma1 libopenmpi-dev libopenmpi2 libpciaccess0 libpipeline1 libpixman-1-0 libpng16-16 libpsm-infinipath1 libpthread-stubs0-dev librdmacm1 libsigsegv2 libtimedate-perl libtool libx11-6 libx11-data libx11-dev libx11-xcb1 libxau-dev libxau6 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcb1 libxcb1-dev libxcursor1 libxdamage1 libxdmcp-dev libxdmcp6 libxext6 libxfixes3 libxft2 libxinerama1 libxml2 libxrender1 libxshmfence1 libxxf86vm1 m4 man-db ocl-icd-libopencl1 openmpi-common po-debconf sbuild-build-depends-relion-dummy ucf x11proto-core-dev x11proto-input-dev x11proto-kb-dev xorg-sgml-doctools xtrans-dev 0 upgraded, 108 newly installed, 0 to remove and 0 not upgraded. Need to get 39.9 MB of archives. After this operation, 138 MB of additional disk space will be used. Get:1 copy:/<>/resolver-JqzGgp/apt_archive ./ sbuild-build-depends-relion-dummy 0.invalid.0 [824 B] Get:2 http://127.0.0.1:9999/debian unstable/main amd64 groff-base amd64 1.22.3-9 [1160 kB] Get:3 http://127.0.0.1:9999/debian unstable/main amd64 bsdmainutils amd64 9.0.12+nmu1 [186 kB] Get:4 http://127.0.0.1:9999/debian unstable/main amd64 libpipeline1 amd64 1.4.1-2 [27.6 kB] Get:5 http://127.0.0.1:9999/debian unstable/main amd64 man-db amd64 2.7.6.1-2 [1044 kB] Get:6 http://127.0.0.1:9999/debian unstable/main amd64 libxau6 amd64 1:1.0.8-1 [20.7 kB] Get:7 http://127.0.0.1:9999/debian unstable/main amd64 libmagic-mgc amd64 1:5.30-1 [222 kB] Get:8 http://127.0.0.1:9999/debian unstable/main amd64 libmagic1 amd64 1:5.30-1 [111 kB] Get:9 http://127.0.0.1:9999/debian unstable/main amd64 file amd64 1:5.30-1 [63.9 kB] Get:10 http://127.0.0.1:9999/debian unstable/main amd64 gettext-base amd64 0.19.8.1-2+b1 [122 kB] Get:11 http://127.0.0.1:9999/debian unstable/main amd64 libicu57 amd64 57.1-6 [7701 kB] Get:12 http://127.0.0.1:9999/debian unstable/main amd64 libxml2 amd64 2.9.4+dfsg1-3 [715 kB] Get:13 http://127.0.0.1:9999/debian unstable/main amd64 ucf all 3.0036 [70.2 kB] Get:14 http://127.0.0.1:9999/debian unstable/main amd64 libsigsegv2 amd64 2.11-1 [29.9 kB] Get:15 http://127.0.0.1:9999/debian unstable/main amd64 m4 amd64 1.4.18-1 [202 kB] Get:16 http://127.0.0.1:9999/debian unstable/main amd64 autoconf all 2.69-10 [338 kB] Get:17 http://127.0.0.1:9999/debian unstable/main amd64 autotools-dev all 20161112.1 [73.4 kB] Get:18 http://127.0.0.1:9999/debian unstable/main amd64 automake all 1:1.15.1-2 [736 kB] Get:19 http://127.0.0.1:9999/debian unstable/main amd64 autopoint all 0.19.8.1-2 [433 kB] Get:20 http://127.0.0.1:9999/debian unstable/main amd64 libtool all 2.4.6-2 [545 kB] Get:21 http://127.0.0.1:9999/debian unstable/main amd64 dh-autoreconf all 14 [15.9 kB] Get:22 http://127.0.0.1:9999/debian unstable/main amd64 libarchive-zip-perl all 1.59-1 [95.5 kB] Get:23 http://127.0.0.1:9999/debian unstable/main amd64 libfile-stripnondeterminism-perl all 0.035-2 [17.0 kB] Get:24 http://127.0.0.1:9999/debian unstable/main amd64 libtimedate-perl all 2.3000-2 [42.2 kB] Get:25 http://127.0.0.1:9999/debian unstable/main amd64 dh-strip-nondeterminism all 0.035-2 [10.7 kB] Get:26 http://127.0.0.1:9999/debian unstable/main amd64 libglib2.0-0 amd64 2.52.3-1 [2742 kB] Get:27 http://127.0.0.1:9999/debian unstable/main amd64 libcroco3 amd64 0.6.12-1 [144 kB] Get:28 http://127.0.0.1:9999/debian unstable/main amd64 gettext amd64 0.19.8.1-2+b1 [1301 kB] Get:29 http://127.0.0.1:9999/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.4 [26.3 kB] Get:30 http://127.0.0.1:9999/debian unstable/main amd64 po-debconf all 1.0.20 [247 kB] Get:31 http://127.0.0.1:9999/debian unstable/main amd64 debhelper all 10.6.2 [968 kB] Get:32 http://127.0.0.1:9999/debian unstable/main amd64 dh-exec amd64 0.23+b1 [26.7 kB] Get:33 http://127.0.0.1:9999/debian unstable/main amd64 fonts-dejavu-core all 2.37-1 [1068 kB] Get:34 http://127.0.0.1:9999/debian unstable/main amd64 fontconfig-config all 2.12.3-0.1 [303 kB] Get:35 http://127.0.0.1:9999/debian unstable/main amd64 libexpat1 amd64 2.2.1-3 [85.6 kB] Get:36 http://127.0.0.1:9999/debian unstable/main amd64 libpng16-16 amd64 1.6.29-3 [281 kB] Get:37 http://127.0.0.1:9999/debian unstable/main amd64 libfreetype6 amd64 2.8-0.2 [449 kB] Get:38 http://127.0.0.1:9999/debian unstable/main amd64 libfontconfig1 amd64 2.12.3-0.1 [366 kB] Get:39 http://127.0.0.1:9999/debian unstable/main amd64 libpixman-1-0 amd64 0.34.0-1 [530 kB] Get:40 http://127.0.0.1:9999/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:41 http://127.0.0.1:9999/debian unstable/main amd64 libxcb1 amd64 1.12-1 [133 kB] Get:42 http://127.0.0.1:9999/debian unstable/main amd64 libx11-data all 2:1.6.4-3 [290 kB] Get:43 http://127.0.0.1:9999/debian unstable/main amd64 libx11-6 amd64 2:1.6.4-3 [747 kB] Get:44 http://127.0.0.1:9999/debian unstable/main amd64 libxcb-render0 amd64 1.12-1 [105 kB] Get:45 http://127.0.0.1:9999/debian unstable/main amd64 libxcb-shm0 amd64 1.12-1 [95.9 kB] Get:46 http://127.0.0.1:9999/debian unstable/main amd64 libxext6 amd64 2:1.3.3-1+b2 [52.5 kB] Get:47 http://127.0.0.1:9999/debian unstable/main amd64 libxrender1 amd64 1:0.9.10-1 [33.0 kB] Get:48 http://127.0.0.1:9999/debian unstable/main amd64 libcairo2 amd64 1.14.10-1 [774 kB] Get:49 http://127.0.0.1:9999/debian unstable/main amd64 libdrm2 amd64 2.4.81-2 [38.4 kB] Get:50 http://127.0.0.1:9999/debian unstable/main amd64 libnl-3-200 amd64 3.2.27-2 [61.5 kB] Get:51 http://127.0.0.1:9999/debian unstable/main amd64 libnl-route-3-200 amd64 3.2.27-2 [136 kB] Get:52 http://127.0.0.1:9999/debian unstable/main amd64 libibverbs1 amd64 1.2.1-2 [39.3 kB] Get:53 http://127.0.0.1:9999/debian unstable/main amd64 libpsm-infinipath1 amd64 3.3+19.g67c0807.open-3 [169 kB] Get:54 http://127.0.0.1:9999/debian unstable/main amd64 librdmacm1 amd64 1.1.0-2 [49.4 kB] Get:55 http://127.0.0.1:9999/debian unstable/main amd64 libfabric1 amd64 1.4.0-1 [259 kB] Get:56 http://127.0.0.1:9999/debian unstable/main amd64 libfftw3-double3 amd64 3.3.6p2-1 [732 kB] Get:57 http://127.0.0.1:9999/debian unstable/main amd64 libfftw3-long3 amd64 3.3.6p2-1 [315 kB] Get:58 http://127.0.0.1:9999/debian unstable/main amd64 libfftw3-quad3 amd64 3.3.6p2-1 [556 kB] Get:59 http://127.0.0.1:9999/debian unstable/main amd64 libfftw3-single3 amd64 3.3.6p2-1 [764 kB] Get:60 http://127.0.0.1:9999/debian unstable/main amd64 libfftw3-bin amd64 3.3.6p2-1 [50.1 kB] Get:61 http://127.0.0.1:9999/debian unstable/main amd64 libfftw3-dev amd64 3.3.6p2-1 [2123 kB] Get:62 http://127.0.0.1:9999/debian unstable/main amd64 libxfixes3 amd64 1:5.0.3-1 [21.9 kB] Get:63 http://127.0.0.1:9999/debian unstable/main amd64 libxcursor1 amd64 1:1.1.14-1+b4 [35.0 kB] Get:64 http://127.0.0.1:9999/debian unstable/main amd64 libxft2 amd64 2.3.2-1+b2 [56.5 kB] Get:65 http://127.0.0.1:9999/debian unstable/main amd64 libxinerama1 amd64 2:1.1.3-1+b3 [16.7 kB] Get:66 http://127.0.0.1:9999/debian unstable/main amd64 libfltk1.3 amd64 1.3.4-4 [550 kB] Get:67 http://127.0.0.1:9999/debian unstable/main amd64 libfltk-cairo1.3 amd64 1.3.4-4 [39.8 kB] Get:68 http://127.0.0.1:9999/debian unstable/main amd64 libfltk-forms1.3 amd64 1.3.4-4 [46.1 kB] Get:69 http://127.0.0.1:9999/debian unstable/main amd64 libglapi-mesa amd64 17.1.4-1 [59.7 kB] Get:70 http://127.0.0.1:9999/debian unstable/main amd64 libx11-xcb1 amd64 2:1.6.4-3 [183 kB] Get:71 http://127.0.0.1:9999/debian unstable/main amd64 libxcb-dri2-0 amd64 1.12-1 [97.2 kB] Get:72 http://127.0.0.1:9999/debian unstable/main amd64 libxcb-dri3-0 amd64 1.12-1 [95.6 kB] Get:73 http://127.0.0.1:9999/debian unstable/main amd64 libxcb-glx0 amd64 1.12-1 [113 kB] Get:74 http://127.0.0.1:9999/debian unstable/main amd64 libxcb-present0 amd64 1.12-1 [95.8 kB] Get:75 http://127.0.0.1:9999/debian unstable/main amd64 libxcb-sync1 amd64 1.12-1 [99.2 kB] Get:76 http://127.0.0.1:9999/debian unstable/main amd64 libxcb-xfixes0 amd64 1.12-1 [99.6 kB] Get:77 http://127.0.0.1:9999/debian unstable/main amd64 libxdamage1 amd64 1:1.1.4-2+b3 [14.5 kB] Get:78 http://127.0.0.1:9999/debian unstable/main amd64 libxshmfence1 amd64 1.2-1+b2 [7922 B] Get:79 http://127.0.0.1:9999/debian unstable/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b2 [20.8 kB] Get:80 http://127.0.0.1:9999/debian unstable/main amd64 libgl1-mesa-glx amd64 17.1.4-1 [167 kB] Get:81 http://127.0.0.1:9999/debian unstable/main amd64 libfltk-gl1.3 amd64 1.3.4-4 [70.7 kB] Get:82 http://127.0.0.1:9999/debian unstable/main amd64 libjpeg62-turbo amd64 1:1.5.1-2 [134 kB] Get:83 http://127.0.0.1:9999/debian unstable/main amd64 libfltk-images1.3 amd64 1.3.4-4 [57.9 kB] Get:84 http://127.0.0.1:9999/debian unstable/main amd64 xorg-sgml-doctools all 1:1.11-1 [21.9 kB] Get:85 http://127.0.0.1:9999/debian unstable/main amd64 x11proto-core-dev all 7.0.31-1 [728 kB] Get:86 http://127.0.0.1:9999/debian unstable/main amd64 libxau-dev amd64 1:1.0.8-1 [23.6 kB] Get:87 http://127.0.0.1:9999/debian unstable/main amd64 libxdmcp-dev amd64 1:1.1.2-3 [42.2 kB] Get:88 http://127.0.0.1:9999/debian unstable/main amd64 x11proto-input-dev all 2.3.2-1 [158 kB] Get:89 http://127.0.0.1:9999/debian unstable/main amd64 x11proto-kb-dev all 1.0.7-1 [233 kB] Get:90 http://127.0.0.1:9999/debian unstable/main amd64 xtrans-dev all 1.3.5-1 [100 kB] Get:91 http://127.0.0.1:9999/debian unstable/main amd64 libpthread-stubs0-dev amd64 0.3-4 [3866 B] Get:92 http://127.0.0.1:9999/debian unstable/main amd64 libxcb1-dev amd64 1.12-1 [169 kB] Get:93 http://127.0.0.1:9999/debian unstable/main amd64 libx11-dev amd64 2:1.6.4-3 [815 kB] Get:94 http://127.0.0.1:9999/debian unstable/main amd64 libfltk1.3-dev amd64 1.3.4-4 [830 kB] Get:95 http://127.0.0.1:9999/debian unstable/main amd64 libgfortran3 amd64 6.4.0-1 [265 kB] Get:96 http://127.0.0.1:9999/debian unstable/main amd64 libltdl7 amd64 2.4.6-2 [389 kB] Get:97 http://127.0.0.1:9999/debian unstable/main amd64 libnuma1 amd64 2.0.11-2.1 [33.3 kB] Get:98 http://127.0.0.1:9999/debian unstable/main amd64 libhwloc5 amd64 1.11.5-1 [105 kB] Get:99 http://127.0.0.1:9999/debian unstable/main amd64 libnuma-dev amd64 2.0.11-2.1 [46.0 kB] Get:100 http://127.0.0.1:9999/debian unstable/main amd64 libltdl-dev amd64 2.4.6-2 [161 kB] Get:101 http://127.0.0.1:9999/debian unstable/main amd64 libhwloc-dev amd64 1.11.5-1 [167 kB] Get:102 http://127.0.0.1:9999/debian unstable/main amd64 libpciaccess0 amd64 0.13.4-1+b2 [50.0 kB] Get:103 http://127.0.0.1:9999/debian unstable/main amd64 ocl-icd-libopencl1 amd64 2.2.11-1 [36.8 kB] Get:104 http://127.0.0.1:9999/debian unstable/main amd64 libhwloc-plugins amd64 1.11.5-1 [16.1 kB] Get:105 http://127.0.0.1:9999/debian unstable/main amd64 libibverbs-dev amd64 1.2.1-2 [107 kB] Get:106 http://127.0.0.1:9999/debian unstable/main amd64 libopenmpi2 amd64 2.1.1-6 [2062 kB] Get:107 http://127.0.0.1:9999/debian unstable/main amd64 openmpi-common all 2.1.1-6 [154 kB] Get:108 http://127.0.0.1:9999/debian unstable/main amd64 libopenmpi-dev amd64 2.1.1-6 [1026 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 39.9 MB in 0s (86.7 MB/s) Selecting previously unselected package groff-base. (Reading database ... 10178 files and directories currently installed.) Preparing to unpack .../000-groff-base_1.22.3-9_amd64.deb ... Unpacking groff-base (1.22.3-9) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../001-bsdmainutils_9.0.12+nmu1_amd64.deb ... Unpacking bsdmainutils (9.0.12+nmu1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../002-libpipeline1_1.4.1-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.4.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../003-man-db_2.7.6.1-2_amd64.deb ... Unpacking man-db (2.7.6.1-2) ... Selecting previously unselected package libxau6:amd64. Preparing to unpack .../004-libxau6_1%3a1.0.8-1_amd64.deb ... Unpacking libxau6:amd64 (1:1.0.8-1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../005-libmagic-mgc_1%3a5.30-1_amd64.deb ... Unpacking libmagic-mgc (1:5.30-1) ... 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Setting up libxshmfence1:amd64 (1.2-1+b2) ... Setting up xorg-sgml-doctools (1:1.11-1) ... Setting up gettext-base (0.19.8.1-2+b1) ... Setting up libpipeline1:amd64 (1.4.1-2) ... Setting up x11proto-kb-dev (1.0.7-1) ... Setting up libglapi-mesa:amd64 (17.1.4-1) ... Setting up m4 (1.4.18-1) ... Setting up libfftw3-double3:amd64 (3.3.6p2-1) ... Setting up libicu57:amd64 (57.1-6) ... Setting up ucf (3.0036) ... Setting up libxml2:amd64 (2.9.4+dfsg1-3) ... Setting up libfreetype6:amd64 (2.8-0.2) ... Setting up libmagic-mgc (1:5.30-1) ... Setting up libdrm2:amd64 (2.4.81-2) ... Setting up libmagic1:amd64 (1:5.30-1) ... Setting up libcroco3:amd64 (0.6.12-1) ... Setting up libpsm-infinipath1 (3.3+19.g67c0807.open-3) ... Setting up libfftw3-quad3:amd64 (3.3.6p2-1) ... Setting up libx11-xcb1:amd64 (2:1.6.4-3) ... Setting up libpixman-1-0:amd64 (0.34.0-1) ... Setting up xtrans-dev (1.3.5-1) ... Setting up openmpi-common (2.1.1-6) ... Processing triggers for libc-bin (2.24-12) ... Setting up autotools-dev (20161112.1) ... Setting up libltdl7:amd64 (2.4.6-2) ... Setting up libpciaccess0:amd64 (0.13.4-1+b2) ... Setting up libfftw3-single3:amd64 (3.3.6p2-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up libnuma-dev:amd64 (2.0.11-2.1) ... Setting up ocl-icd-libopencl1:amd64 (2.2.11-1) ... Setting up bsdmainutils (9.0.12+nmu1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libnl-3-200:amd64 (3.2.27-2) ... Setting up libfftw3-long3:amd64 (3.3.6p2-1) ... Setting up libx11-data (2:1.6.4-3) ... Setting up libxau6:amd64 (1:1.0.8-1) ... Setting up autopoint (0.19.8.1-2) ... Setting up libfile-stripnondeterminism-perl (0.035-2) ... Setting up libfftw3-bin (3.3.6p2-1) ... Setting up fontconfig-config (2.12.3-0.1) ... Setting up x11proto-core-dev (7.0.31-1) ... Setting up libltdl-dev:amd64 (2.4.6-2) ... Setting up gettext (0.19.8.1-2+b1) ... Setting up libxau-dev:amd64 (1:1.0.8-1) ... Setting up libnl-route-3-200:amd64 (3.2.27-2) ... Setting up autoconf (2.69-10) ... Setting up file (1:5.30-1) ... Setting up libhwloc5:amd64 (1.11.5-1) ... Setting up libhwloc-plugins (1.11.5-1) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up libxdmcp-dev:amd64 (1:1.1.2-3) ... Setting up libfftw3-dev:amd64 (3.3.6p2-1) ... Setting up automake (1:1.15.1-2) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up man-db (2.7.6.1-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libxcb1:amd64 (1.12-1) ... Setting up x11proto-input-dev (2.3.2-1) ... Setting up libtool (2.4.6-2) ... Setting up libibverbs1 (1.2.1-2) ... Setting up libxcb-present0:amd64 (1.12-1) ... Setting up libfontconfig1:amd64 (2.12.3-0.1) ... Setting up libxcb-dri2-0:amd64 (1.12-1) ... Setting up libxcb-dri3-0:amd64 (1.12-1) ... Setting up libxcb-glx0:amd64 (1.12-1) ... Setting up libxcb-xfixes0:amd64 (1.12-1) ... Setting up libxcb-render0:amd64 (1.12-1) ... Setting up po-debconf (1.0.20) ... Setting up libhwloc-dev:amd64 (1.11.5-1) ... Setting up libx11-6:amd64 (2:1.6.4-3) ... Setting up librdmacm1 (1.1.0-2) ... Setting up libxcb-sync1:amd64 (1.12-1) ... Setting up libxcb-shm0:amd64 (1.12-1) ... Setting up libxrender1:amd64 (1:0.9.10-1) ... Setting up libxcb1-dev:amd64 (1.12-1) ... Setting up libx11-dev:amd64 (2:1.6.4-3) ... Setting up libxft2:amd64 (2.3.2-1+b2) ... Setting up libibverbs-dev (1.2.1-2) ... Setting up libxext6:amd64 (2:1.3.3-1+b2) ... Setting up libxfixes3:amd64 (1:5.0.3-1) ... Setting up libfabric1 (1.4.0-1) ... Setting up libxcursor1:amd64 (1:1.1.14-1+b4) ... Setting up libopenmpi2:amd64 (2.1.1-6) ... Setting up libxxf86vm1:amd64 (1:1.1.4-1+b2) ... Setting up libcairo2:amd64 (1.14.10-1) ... Setting up libxinerama1:amd64 (2:1.1.3-1+b3) ... Setting up libxdamage1:amd64 (1:1.1.4-2+b3) ... Setting up libopenmpi-dev (2.1.1-6) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openmpi/include to provide /usr/include/mpi (mpi) in auto mode Setting up libgl1-mesa-glx:amd64 (17.1.4-1) ... Setting up libfltk1.3:amd64 (1.3.4-4) ... Setting up libfltk-images1.3:amd64 (1.3.4-4) ... Setting up libfltk-forms1.3:amd64 (1.3.4-4) ... Setting up libfltk-gl1.3:amd64 (1.3.4-4) ... Setting up libfltk-cairo1.3:amd64 (1.3.4-4) ... Setting up libfltk1.3-dev (1.3.4-4) ... Setting up dh-strip-nondeterminism (0.035-2) ... Setting up debhelper (10.6.2) ... Setting up dh-autoreconf (14) ... Setting up dh-exec (0.23+b1) ... Setting up sbuild-build-depends-relion-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.24-12) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.9.0-2-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.28-6 dpkg-dev_1.18.24 g++-6_6.4.0-1 gcc-6_6.4.0-1 libc6-dev_2.24-12 libstdc++-6-dev_6.4.0-1 libstdc++6_7.1.0-9 linux-libc-dev_4.11.6-1 Package versions: adduser_3.115 apt_1.5~beta1 autoconf_2.69-10 automake_1:1.15.1-2 autopoint_0.19.8.1-2 autotools-dev_20161112.1 base-files_10 base-passwd_3.5.43 bash_4.4-5 binutils_2.28-6 bsdmainutils_9.0.12+nmu1 bsdutils_1:2.29.2-1 build-essential_12.3 bzip2_1.0.6-8.1 clang-3.9_1:3.9.1-10 coreutils_8.26-3 cpp_4:6.3.0-4d1 cpp-6_6.4.0-1 dash_0.5.8-2.4 debconf_1.5.62 debfoster_2.7-2.1+b1 debhelper_10.6.2 debian-archive-keyring_2017.5 debianutils_4.8.1.1 dh-autoreconf_14 dh-exec_0.23+b1 dh-strip-nondeterminism_0.035-2 diffutils_1:3.5-3 dpkg_1.18.24 dpkg-dev_1.18.24 e2fslibs_1.43.4-2 e2fsprogs_1.43.4-2 eatmydata_105-5 fakeroot_1.21-3.1 file_1:5.30-1 findutils_4.6.0+git+20170606-2 fontconfig-config_2.12.3-0.1 fonts-dejavu-core_2.37-1 g++_4:6.3.0-4d1 g++-6_6.4.0-1 gcc_4:6.3.0-4d1 gcc-6_6.4.0-1 gcc-6-base_6.4.0-1 gcc-7-base_7.1.0-9 gettext_0.19.8.1-2+b1 gettext-base_0.19.8.1-2+b1 gpgv_2.1.18-8 grep_2.27-2 groff-base_1.22.3-9 gzip_1.6-5+b1 hostname_3.18+b1 init-system-helpers_1.48 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3+b1 libapt-pkg5.0_1.5~beta1 libarchive-zip-perl_1.59-1 libasan3_6.4.0-1 libatomic1_7.1.0-9 libattr1_1:2.4.47-2+b2 libaudit-common_1:2.7.7-1 libaudit1_1:2.7.7-1+b1 libblkid1_2.29.2-1 libbsd0_0.8.5-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.24-12 libc-dev-bin_2.24-12 libc6_2.24-12 libc6-dev_2.24-12 libcairo2_1.14.10-1 libcap-ng0_0.7.7-3+b1 libcc1-0_7.1.0-9 libcilkrts5_7.1.0-9 libclang-common-3.9-dev_1:3.9.1-10 libclang1-3.9_1:3.9.1-10 libcomerr2_1.43.4-2 libcroco3_0.6.12-1 libdb5.3_5.3.28-12+b1 libdebconfclient0_0.229 libdpkg-perl_1.18.24 libdrm2_2.4.81-2 libeatmydata1_105-5 libedit2_3.1-20170329-1 libexpat1_2.2.1-3 libfabric1_1.4.0-1 libfakeroot_1.21-3.1 libfdisk1_2.29.2-1 libffi6_3.2.1-6 libfftw3-bin_3.3.6p2-1 libfftw3-dev_3.3.6p2-1 libfftw3-double3_3.3.6p2-1 libfftw3-long3_3.3.6p2-1 libfftw3-quad3_3.3.6p2-1 libfftw3-single3_3.3.6p2-1 libfile-stripnondeterminism-perl_0.035-2 libfltk-cairo1.3_1.3.4-4 libfltk-forms1.3_1.3.4-4 libfltk-gl1.3_1.3.4-4 libfltk-images1.3_1.3.4-4 libfltk1.3_1.3.4-4 libfltk1.3-dev_1.3.4-4 libfontconfig1_2.12.3-0.1 libfreetype6_2.8-0.2 libgc1c2_1:7.4.2-8 libgcc-6-dev_6.4.0-1 libgcc1_1:7.1.0-9 libgcrypt20_1.7.8-1 libgdbm3_1.8.3-14 libgfortran3_6.4.0-1 libgl1-mesa-glx_17.1.4-1 libglapi-mesa_17.1.4-1 libglib2.0-0_2.52.3-1 libgmp10_2:6.1.2+dfsg-1 libgnutls30_3.5.13-2 libgomp1_7.1.0-9 libgpg-error0_1.27-3 libhogweed4_3.3-1+b1 libhwloc-dev_1.11.5-1 libhwloc-plugins_1.11.5-1 libhwloc5_1.11.5-1 libibverbs-dev_1.2.1-2 libibverbs1_1.2.1-2 libicu57_57.1-6 libidn2-0_0.16-1+b1 libisl15_0.18-1 libitm1_7.1.0-9 libjpeg62-turbo_1:1.5.1-2 libjsoncpp1_1.7.4-3 libllvm3.9_1:3.9.1-10 liblsan0_7.1.0-9 libltdl-dev_2.4.6-2 libltdl7_2.4.6-2 liblz4-1_0.0~r131-2+b1 liblzma5_5.2.2-1.2+b1 libmagic-mgc_1:5.30-1 libmagic1_1:5.30-1 libmount1_2.29.2-1 libmpc3_1.0.3-1+b2 libmpfr4_3.1.5-1 libmpx2_7.1.0-9 libncurses5_6.0+20161126-1 libncursesw5_6.0+20161126-1 libnettle6_3.3-1+b1 libnl-3-200_3.2.27-2 libnl-route-3-200_3.2.27-2 libnuma-dev_2.0.11-2.1 libnuma1_2.0.11-2.1 libobjc-6-dev_6.4.0-1 libobjc4_7.1.0-9 libopenmpi-dev_2.1.1-6 libopenmpi2_2.1.1-6 libp11-kit0_0.23.7-2 libpam-modules_1.1.8-3.6 libpam-modules-bin_1.1.8-3.6 libpam-runtime_1.1.8-3.6 libpam0g_1.1.8-3.6 libpciaccess0_0.13.4-1+b2 libpcre3_2:8.39-3 libperl5.24_5.24.1-6 libpipeline1_1.4.1-2 libpixman-1-0_0.34.0-1 libpng16-16_1.6.29-3 libpsm-infinipath1_3.3+19.g67c0807.open-3 libpthread-stubs0-dev_0.3-4 libquadmath0_7.1.0-9 librdmacm1_1.1.0-2 libselinux1_2.6-3+b2 libsemanage-common_2.6-2 libsemanage1_2.6-2+b1 libsepol1_2.6-2 libsigsegv2_2.11-1 libsmartcols1_2.29.2-1 libss2_1.43.4-2 libstdc++-6-dev_6.4.0-1 libstdc++6_7.1.0-9 libsystemd0_233-10 libtasn1-6_4.12-2 libtimedate-perl_2.3000-2 libtinfo5_6.0+20161126-1 libtool_2.4.6-2 libtsan0_7.1.0-9 libubsan0_7.1.0-9 libudev1_233-10 libunistring2_0.9.7-2 libustr-1.0-1_1.0.4-6 libuuid1_2.29.2-1 libx11-6_2:1.6.4-3 libx11-data_2:1.6.4-3 libx11-dev_2:1.6.4-3 libx11-xcb1_2:1.6.4-3 libxau-dev_1:1.0.8-1 libxau6_1:1.0.8-1 libxcb-dri2-0_1.12-1 libxcb-dri3-0_1.12-1 libxcb-glx0_1.12-1 libxcb-present0_1.12-1 libxcb-render0_1.12-1 libxcb-shm0_1.12-1 libxcb-sync1_1.12-1 libxcb-xfixes0_1.12-1 libxcb1_1.12-1 libxcb1-dev_1.12-1 libxcursor1_1:1.1.14-1+b4 libxdamage1_1:1.1.4-2+b3 libxdmcp-dev_1:1.1.2-3 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.3-1+b2 libxfixes3_1:5.0.3-1 libxft2_2.3.2-1+b2 libxinerama1_2:1.1.3-1+b3 libxml2_2.9.4+dfsg1-3 libxrender1_1:0.9.10-1 libxshmfence1_1.2-1+b2 libxxf86vm1_1:1.1.4-1+b2 linux-libc-dev_4.11.6-1 login_1:4.4-4.1 m4_1.4.18-1 make_4.1-9.1 man-db_2.7.6.1-2 mawk_1.3.3-17+b3 mount_2.29.2-1 multiarch-support_2.24-12 ncurses-base_6.0+20161126-1 ncurses-bin_6.0+20161126-1 ocl-icd-libopencl1_2.2.11-1 openmpi-common_2.1.1-6 passwd_1:4.4-4.1 patch_2.7.5-1+b2 perl_5.24.1-6 perl-base_5.24.1-6 perl-modules-5.24_5.24.1-6 po-debconf_1.0.20 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-relion-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.9 sysvinit-utils_2.88dsf-59.9 tar_1.29b-1.1 ucf_3.0036 util-linux_2.29.2-1 x11proto-core-dev_7.0.31-1 x11proto-input-dev_2.3.2-1 x11proto-kb-dev_1.0.7-1 xorg-sgml-doctools_1:1.11-1 xtrans-dev_1.3.5-1 xz-utils_5.2.2-1.2+b1 zlib1g_1:1.2.8.dfsg-5 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Wed Jun 29 19:09:44 2016 UTC gpgv: using RSA key 578A0494D1C646D1 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./relion_1.4+dfsg-2.dsc dpkg-source: info: extracting relion in /<>/relion-1.4+dfsg dpkg-source: info: unpacking relion_1.4+dfsg.orig.tar.xz dpkg-source: info: unpacking relion_1.4+dfsg-2.debian.tar.xz 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 User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANG=en_US.UTF-8 LC_ALL=POSIX LOGNAME=user42 PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=unstable-amd64-sbuild SCHROOT_CHROOT_NAME=unstable-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1001 SCHROOT_GROUP=user42 SCHROOT_SESSION_ID=unstable-amd64-sbuild-7a87e29f-ae81-43e3-a3f9-b1aa90617837 SCHROOT_UID=1001 SCHROOT_USER=user42 SHELL=/bin/sh USER=user42 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package relion dpkg-buildpackage: info: source version 1.4+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Gert Wollny dpkg-source --before-build relion-1.4+dfsg 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 --parallel --with autoreconf dh_testdir -O--parallel dh_auto_clean -O--parallel dh_autoreconf_clean -O--parallel dh_clean -O--parallel debian/rules build-arch Relion API Version = 1.4 Relion most recent (current) lib interface = 1 dh build-arch --parallel --with autoreconf dh_testdir -a -O--parallel dh_update_autotools_config -a -O--parallel dh_autoreconf -a -O--parallel 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-1.15/am/ltlibrary.am: warning: 'librelion-@RELION_API_VERSION@.la': linking libtool libraries using a non-POSIX /usr/share/automake-1.15/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-1.4+dfsg' 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-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --libexecdir=\${prefix}/lib/x86_64-linux-gnu --disable-maintainer-mode --disable-dependency-tracking --libdir=\${prefix}/lib/x86_64-linux-gnu --disable-gui configure: WARNING: unrecognized options: --disable-maintainer-mode 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 for style of include used by make... GNU 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... yes 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 configure: WARNING: unrecognized options: --disable-maintainer-mode make -j16; make install prefix=/<>/relion-1.4+dfsg/debian/tmp/simple/usr make[2]: Entering directory '/<>/relion-1.4+dfsg' make all-am make[3]: Entering directory '/<>/relion-1.4+dfsg' /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/relion-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/args.lo src/args.cpp /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/relion-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/assembly.lo src/assembly.cpp /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/relion-1.4+dfsg=. -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=/<>/relion-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/backprojector.lo src/backprojector.cpp /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/relion-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/complex.lo src/complex.cpp /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/relion-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/ctf.lo src/ctf.cpp /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/relion-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/ctffind_runner.lo src/ctffind_runner.cpp /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/relion-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/error.lo src/error.cpp /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/relion-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/euler.lo src/euler.cpp /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/relion-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/exp_model.lo src/exp_model.cpp /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/relion-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/fftw.lo src/fftw.cpp /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/relion-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/filename.lo src/filename.cpp /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/relion-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/funcs.lo src/funcs.cpp /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/relion-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/healpix_sampling.lo src/healpix_sampling.cpp /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/relion-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/image.lo src/image.cpp /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/relion-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/mask.lo src/mask.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/relion-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c src/assembly.cpp -fPIC -DPIC -o src/.libs/assembly.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/relion-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c src/ctffind_runner.cpp -fPIC -DPIC -o src/.libs/ctffind_runner.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/relion-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c src/error.cpp -fPIC -DPIC -o src/.libs/error.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/relion-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c src/fftw.cpp -fPIC -DPIC -o src/.libs/fftw.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/relion-1.4+dfsg=. -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=/<>/relion-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c src/args.cpp -fPIC -DPIC -o src/.libs/args.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/relion-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c src/image.cpp -fPIC -DPIC -o src/.libs/image.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/relion-1.4+dfsg=. -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=/<>/relion-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c src/exp_model.cpp -fPIC -DPIC -o src/.libs/exp_model.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/relion-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c src/ctf.cpp -fPIC -DPIC -o src/.libs/ctf.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/relion-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c src/euler.cpp -fPIC -DPIC -o src/.libs/euler.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/relion-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c src/funcs.cpp -fPIC -DPIC -o src/.libs/funcs.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/relion-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c src/backprojector.cpp -fPIC -DPIC -o src/.libs/backprojector.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/relion-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c src/mask.cpp -fPIC -DPIC -o src/.libs/mask.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/relion-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c src/filename.cpp -fPIC -DPIC -o src/.libs/filename.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/relion-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c src/healpix_sampling.cpp -fPIC -DPIC -o src/.libs/healpix_sampling.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/relion-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c src/error.cpp -o src/error.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/relion-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c src/complex.cpp -o src/complex.o >/dev/null 2>&1 src/args.cpp:104:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ src/assembly.cpp:356:33: warning: format specifies type 'int' but the argument has type 'long' [-Wformat] atomnum, molecules[imol].residues[ires].atoms[iatom].name.c_str(), molecules[imol].residues[ires].name.c_str(), ^~~~~~~ src/funcs.cpp:754:8: error: 'log2' is missing exception specification 'throw()' DOUBLE log2(DOUBLE value) ^ throw() ./src/funcs.h:316:8: note: previous declaration is here DOUBLE log2(DOUBLE value); ^ 1 error generated. In file included from src/exp_model.cpp:20: In file included from ./src/exp_model.h:24: In file included from ./src/image.h:60: ./src/multidim_array.h:3888:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] system((static_cast("(gnuplot PPP") + fn_tmp + ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/multidim_array.h:3906:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] system((static_cast< std::string >("xmipp_edit -i " + nam + ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from src/euler.cpp:48: In file included from ./src/euler.h:48: ./src/multidim_array.h:3888:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] Makefile:1243: recipe for target 'src/funcs.lo' failed make[3]: *** [src/funcs.lo] Error 1 make[3]: *** Waiting for unfinished jobs.... system((static_cast("(gnuplot PPP") + fn_tmp + ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/multidim_array.h:3906:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] system((static_cast< std::string >("xmipp_edit -i " + nam + ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from src/ctf.cpp:45: In file included from ./src/ctf.h:48: ./src/multidim_array.h:3888:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] system((static_cast("(gnuplot PPP") + fn_tmp + ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/multidim_array.h:3906:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] system((static_cast< std::string >("xmipp_edit -i " + nam + ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from src/fftw.cpp:46: In file included from ./src/fftw.h:50: ./src/multidim_array.h:3888:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] system((static_cast("(gnuplot PPP") + fn_tmp + ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/multidim_array.h:3906:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] system((static_cast< std::string >("xmipp_edit -i " + nam + ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from src/image.cpp:20: In file included from ./src/image.h:60: ./src/multidim_array.h:3888:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] system((static_cast("(gnuplot PPP") + fn_tmp + ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/multidim_array.h:3906:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] system((static_cast< std::string >("xmipp_edit -i " + nam + ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from src/autopicker.cpp:20: In file included from ./src/autopicker.h:10: In file included from ./src/image.h:60: ./src/multidim_array.h:3888:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] system((static_cast("(gnuplot PPP") + fn_tmp + ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/multidim_array.h:3906:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] system((static_cast< std::string >("xmipp_edit -i " + nam + ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from src/mask.cpp:20: In file included from ./src/mask.h:24: ./src/multidim_array.h:3888:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] system((static_cast("(gnuplot PPP") + fn_tmp + ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/multidim_array.h:3906:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] system((static_cast< std::string >("xmipp_edit -i " + nam + ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from src/backprojector.cpp:27: In file included from ./src/backprojector.h:31: In file included from ./src/projector.h:23: In file included from ./src/fftw.h:50: ./src/multidim_array.h:3888:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] system((static_cast("(gnuplot PPP") + fn_tmp + ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/multidim_array.h:3906:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] system((static_cast< std::string >("xmipp_edit -i " + nam + ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from src/ctffind_runner.cpp:20: In file included from ./src/ctffind_runner.h:30: In file included from ./src/image.h:60: ./src/multidim_array.h:3888:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] system((static_cast("(gnuplot PPP") + fn_tmp + ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/multidim_array.h:3906:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] system((static_cast< std::string >("xmipp_edit -i " + nam + ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from src/healpix_sampling.cpp:20: In file included from ./src/healpix_sampling.h:27: ./src/multidim_array.h:3888:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] system((static_cast("(gnuplot PPP") + fn_tmp + ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/multidim_array.h:3906:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] system((static_cast< std::string >("xmipp_edit -i " + nam + ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from src/exp_model.cpp:20: In file included from ./src/exp_model.h:24: ./src/image.h:1047:25: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] if (_exists = exists(fileName)) ~~~~~~~~^~~~~~~~~~~~~~~~~~ ./src/image.h:1047:25: note: place parentheses around the assignment to silence this warning if (_exists = exists(fileName)) ^ ( ) ./src/image.h:1047:25: note: use '==' to turn this assignment into an equality comparison if (_exists = exists(fileName)) ^ == In file included from src/ctffind_runner.cpp:20: In file included from ./src/ctffind_runner.h:30: ./src/image.h:1047:25: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] if (_exists = exists(fileName)) ~~~~~~~~^~~~~~~~~~~~~~~~~~ ./src/image.h:1047:25: note: place parentheses around the assignment to silence this warning if (_exists = exists(fileName)) ^ ( ) ./src/image.h:1047:25: note: use '==' to turn this assignment into an equality comparison if (_exists = exists(fileName)) ^ == In file included from src/image.cpp:20: ./src/image.h:1047:25: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] if (_exists = exists(fileName)) ~~~~~~~~^~~~~~~~~~~~~~~~~~ ./src/image.h:1047:25: note: place parentheses around the assignment to silence this warning if (_exists = exists(fileName)) ^ ( ) ./src/image.h:1047:25: note: use '==' to turn this assignment into an equality comparison if (_exists = exists(fileName)) ^ == In file included from src/autopicker.cpp:20: In file included from ./src/autopicker.h:10: ./src/image.h:1047:25: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] if (_exists = exists(fileName)) ~~~~~~~~^~~~~~~~~~~~~~~~~~ ./src/image.h:1047:25: note: place parentheses around the assignment to silence this warning if (_exists = exists(fileName)) ^ ( ) ./src/image.h:1047:25: note: use '==' to turn this assignment into an equality comparison if (_exists = exists(fileName)) ^ == In file included from src/backprojector.cpp:27: In file included from ./src/backprojector.h:31: In file included from ./src/projector.h:25: ./src/image.h:1047:25: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] if (_exists = exists(fileName)) ~~~~~~~~^~~~~~~~~~~~~~~~~~ ./src/image.h:1047:25: note: place parentheses around the assignment to silence this warning if (_exists = exists(fileName)) ^ ( ) ./src/image.h:1047:25: note: use '==' to turn this assignment into an equality comparison if (_exists = exists(fileName)) ^ == src/ctffind_runner.cpp:237:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] system ( fn_cmnd.c_str() ); ^~~~~~ ~~~~~~~~~~~~~~~ src/healpix_sampling.cpp:1508:42: warning: '&&' within '||' [-Wlogical-op-parentheses] if (rot_angles[i] >= 90. && ~~~~~~~~~~~~~~~~~~~~~~~~~^~ src/healpix_sampling.cpp:1508:42: note: place parentheses around the '&&' expression to silence this warning if (rot_angles[i] >= 90. && ^ In file included from src/ctffind_runner.cpp:20: In file included from ./src/ctffind_runner.h:30: ./src/image.h:1047:25: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] if (_exists = exists(fileName)) ~~~~~~~~^~~~~~~~~~~~~~~~~~ ./src/image.h:255:32: note: in instantiation of member function 'Image::openFile' requested here fImageHandler* hFile = openFile(name); ^ src/ctffind_runner.cpp:206:15: note: in instantiation of member function 'Image::read' requested here I.read(fn_mic); ^ ./src/image.h:1047:25: note: place parentheses around the assignment to silence this warning if (_exists = exists(fileName)) ^ ( ) ./src/image.h:1047:25: note: use '==' to turn this assignment into an equality comparison if (_exists = exists(fileName)) ^ == ./src/image.h:1047:25: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] if (_exists = exists(fileName)) ~~~~~~~~^~~~~~~~~~~~~~~~~~ ./src/image.h:255:32: note: in instantiation of member function 'Image::openFile' requested here fImageHandler* hFile = openFile(name); ^ src/autopicker.cpp:121:9: note: in instantiation of member function 'Image::read' requested here Iref.read(fn_img); ^ ./src/image.h:1047:25: note: place parentheses around the assignment to silence this warning if (_exists = exists(fileName)) ^ ( ) ./src/image.h:1047:25: note: use '==' to turn this assignment into an equality comparison if (_exists = exists(fileName)) ^ == 2 warnings generated. libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/relion-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c src/euler.cpp -o src/euler.o >/dev/null 2>&1 ./src/image.h:1047:25: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] if (_exists = exists(fileName)) ~~~~~~~~^~~~~~~~~~~~~~~~~~ ./src/image.h:255:32: note: in instantiation of member function 'Image::openFile' requested here fImageHandler* hFile = openFile(name); ^ src/exp_model.cpp:673:7: note: in instantiation of member function 'Image::read' requested here img.read(fn_exp, false); // false means skip data, only read header ^ ./src/image.h:1047:25: note: place parentheses around the assignment to silence this warning if (_exists = exists(fileName)) ^ ( ) ./src/image.h:1047:25: note: use '==' to turn this assignment into an equality comparison if (_exists = exists(fileName)) ^ == 2 warnings generated. libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/relion-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c src/ctf.cpp -o src/ctf.o >/dev/null 2>&1 2 warnings generated. libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/relion-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c src/mask.cpp -o src/mask.o >/dev/null 2>&1 3 warnings generated. libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/relion-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c src/image.cpp -o src/image.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/relion-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c src/filename.cpp -o src/filename.o >/dev/null 2>&1 1 warning generated. libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/relion-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c src/args.cpp -o src/args.o >/dev/null 2>&1 2 warnings generated. libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/relion-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c src/fftw.cpp -o src/fftw.o >/dev/null 2>&1 1 warning generated. libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/relion-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c src/assembly.cpp -o src/assembly.o >/dev/null 2>&1 3 warnings generated. libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/relion-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c src/backprojector.cpp -o src/backprojector.o >/dev/null 2>&1 5 warnings generated. libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/relion-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c src/ctffind_runner.cpp -o src/ctffind_runner.o >/dev/null 2>&1 4 warnings generated. libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/relion-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c src/autopicker.cpp -o src/autopicker.o >/dev/null 2>&1 4 warnings generated. libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/relion-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c src/exp_model.cpp -o src/exp_model.o >/dev/null 2>&1 3 warnings generated. libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/relion-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c src/healpix_sampling.cpp -o src/healpix_sampling.o >/dev/null 2>&1 make[3]: Leaving directory '/<>/relion-1.4+dfsg' Makefile:697: recipe for target 'all' failed make[2]: *** [all] Error 2 make[2]: Leaving directory '/<>/relion-1.4+dfsg' make[2]: Entering directory '/<>/relion-1.4+dfsg' /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/relion-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/funcs.lo src/funcs.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/relion-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c src/funcs.cpp -fPIC -DPIC -o src/.libs/funcs.o src/funcs.cpp:754:8: error: 'log2' is missing exception specification 'throw()' DOUBLE log2(DOUBLE value) ^ throw() ./src/funcs.h:316:8: note: previous declaration is here DOUBLE log2(DOUBLE value); ^ 1 error generated. Makefile:1243: recipe for target 'src/funcs.lo' failed make[2]: *** [src/funcs.lo] Error 1 make[2]: Leaving directory '/<>/relion-1.4+dfsg' debian/rules:42: recipe for target 'override_dh_auto_build' failed make[1]: *** [override_dh_auto_build] Error 2 make[1]: Leaving directory '/<>/relion-1.4+dfsg' debian/rules:37: recipe for target 'build-arch' failed make: *** [build-arch] Error 2 dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2 -------------------------------------------------------------------------------- Build finished at 2017-07-06T17:09:07Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: any Build-Space: 32676 Build-Time: 20 Distribution: unstable Fail-Stage: build Host Architecture: amd64 Install-Time: 9 Job: relion_1.4+dfsg-2 Machine Architecture: amd64 Package: relion Package-Time: 49 Source-Version: 1.4+dfsg-2 Space: 32676 Status: attempted Version: 1.4+dfsg-2 -------------------------------------------------------------------------------- Finished at 2017-07-06T17:09:07Z Build needed 00:00:49, 32676k disk space E: Build failure (dpkg-buildpackage died) DC-Status: Failed 50.089922466s DC-Time-Estimation: 50.089922466 versus expected 1314 (r/m: 25.232821599832103 ; m: 50.089922466)