DC-Build-Header: prime-phylo 1.0.11-4 / 2016-08-29 16:39:07 +0000 DC-Task: type:rebuild-binarch-only source:prime-phylo version:1.0.11-4 chroot:unstable esttime:368 logfile:/tmp/prime-phylo_1.0.11-4_unstable_clang3.8.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 prime-phylo_1.0.11-4' sbuild (Debian sbuild) 0.70.0 (03 Aug 2016) on ip-172-31-7-230.eu-central-1.compute.internal +==============================================================================+ | prime-phylo 1.0.11-4 (amd64) Mon, 29 Aug 2016 16:39:08 +0000 | +==============================================================================+ Package: prime-phylo Version: 1.0.11-4 Source Version: 1.0.11-4 Distribution: unstable Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/unstable-amd64-sbuild-bc5932bd-71e2-4d5f-a243-9cedd68680a4' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /tmp/clang ---------- + echo 'Entering customization script...' Entering customization script... + CLANG_VERSION=3.8 + echo 'Install of clang-3.8' Install of clang-3.8 + apt-get update Get:1 http://127.0.0.1:9999/debian unstable InRelease [209 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 [5451 kB] Get:5 http://127.0.0.1:9999/debian unstable/main Sources 2016-08-29-0319.00.pdiff [16.7 kB] Get:6 http://127.0.0.1:9999/debian unstable/main Sources 2016-08-29-0916.07.pdiff [5442 B] Get:6 http://127.0.0.1:9999/debian unstable/main Sources 2016-08-29-0916.07.pdiff [5442 B] Get:7 http://127.0.0.1:9999/debian unstable/main amd64 Packages 2016-08-29-0319.00.pdiff [13.2 kB] Get:8 http://127.0.0.1:9999/debian unstable/main amd64 Packages 2016-08-29-0916.07.pdiff [3300 B] Get:8 http://127.0.0.1:9999/debian unstable/main amd64 Packages 2016-08-29-0916.07.pdiff [3300 B] Fetched 5755 kB in 3s (1825 kB/s) Reading package lists... W: No sandbox user '_apt' on the system, can not drop privileges + apt-get install --yes --no-install-recommends --force-yes clang-3.8 Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: libbsd0 libclang-common-3.8-dev libclang1-3.8 libedit2 libffi6 libllvm3.8 libobjc-6-dev libobjc4 Suggested packages: gnustep gnustep-devel clang-3.8-doc Recommended packages: llvm-3.8-dev python The following NEW packages will be installed: clang-3.8 libbsd0 libclang-common-3.8-dev libclang1-3.8 libedit2 libffi6 libllvm3.8 libobjc-6-dev libobjc4 0 upgraded, 9 newly installed, 0 to remove and 1 not upgraded. Need to get 38.3 MB of archives. After this operation, 162 MB of additional disk space will be used. Get:1 http://127.0.0.1:9999/debian unstable/main amd64 libbsd0 amd64 0.8.3-1 [83.0 kB] Get:2 http://127.0.0.1:9999/debian unstable/main amd64 libedit2 amd64 3.1-20150325-1+b1 [85.2 kB] Get:3 http://127.0.0.1:9999/debian unstable/main amd64 libffi6 amd64 3.2.1-4 [20.4 kB] Get:4 http://127.0.0.1:9999/debian unstable/main amd64 libllvm3.8 amd64 1:3.8.1-9 [10.3 MB] Get:5 http://127.0.0.1:9999/debian unstable/main amd64 libobjc4 amd64 6.2.0-1 [110 kB] Get:6 http://127.0.0.1:9999/debian unstable/main amd64 libobjc-6-dev amd64 6.2.0-1 [394 kB] Get:7 http://127.0.0.1:9999/debian unstable/main amd64 libclang1-3.8 amd64 1:3.8.1-9 [4188 kB] Get:8 http://127.0.0.1:9999/debian unstable/main amd64 libclang-common-3.8-dev amd64 1:3.8.1-9 [1477 kB] Get:9 http://127.0.0.1:9999/debian unstable/main amd64 clang-3.8 amd64 1:3.8.1-9 [21.6 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 38.3 MB in 7s (5407 kB/s) Selecting previously unselected package libbsd0:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 9446 files and directories currently installed.) Preparing to unpack .../0-libbsd0_0.8.3-1_amd64.deb ... Unpacking libbsd0:amd64 (0.8.3-1) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../1-libedit2_3.1-20150325-1+b1_amd64.deb ... Unpacking libedit2:amd64 (3.1-20150325-1+b1) ... Selecting previously unselected package libffi6:amd64. Preparing to unpack .../2-libffi6_3.2.1-4_amd64.deb ... Unpacking libffi6:amd64 (3.2.1-4) ... Selecting previously unselected package libllvm3.8:amd64. Preparing to unpack .../3-libllvm3.8_1%3a3.8.1-9_amd64.deb ... Unpacking libllvm3.8:amd64 (1:3.8.1-9) ... Selecting previously unselected package libobjc4:amd64. Preparing to unpack .../4-libobjc4_6.2.0-1_amd64.deb ... Unpacking libobjc4:amd64 (6.2.0-1) ... Selecting previously unselected package libobjc-6-dev:amd64. Preparing to unpack .../5-libobjc-6-dev_6.2.0-1_amd64.deb ... Unpacking libobjc-6-dev:amd64 (6.2.0-1) ... Selecting previously unselected package libclang1-3.8:amd64. Preparing to unpack .../6-libclang1-3.8_1%3a3.8.1-9_amd64.deb ... Unpacking libclang1-3.8:amd64 (1:3.8.1-9) ... Selecting previously unselected package libclang-common-3.8-dev. Preparing to unpack .../7-libclang-common-3.8-dev_1%3a3.8.1-9_amd64.deb ... Unpacking libclang-common-3.8-dev (1:3.8.1-9) ... Selecting previously unselected package clang-3.8. Preparing to unpack .../8-clang-3.8_1%3a3.8.1-9_amd64.deb ... Unpacking clang-3.8 (1:3.8.1-9) ... Setting up libobjc4:amd64 (6.2.0-1) ... Setting up libbsd0:amd64 (0.8.3-1) ... Processing triggers for libc-bin (2.23-5) ... Setting up libobjc-6-dev:amd64 (6.2.0-1) ... Setting up libffi6:amd64 (3.2.1-4) ... Setting up libedit2:amd64 (3.1-20150325-1+b1) ... Setting up libllvm3.8:amd64 (1:3.8.1-9) ... Setting up libclang-common-3.8-dev (1:3.8.1-9) ... Setting up libclang1-3.8:amd64 (1:3.8.1-9) ... Setting up clang-3.8 (1:3.8.1-9) ... Processing triggers for libc-bin (2.23-5) ... W: --force-yes is deprecated, use one of the options starting with --allow instead. W: No sandbox user '_apt' on the system, can not drop privileges + echo 'Replace gcc, g++ & cpp by clang' Replace gcc, g++ & cpp by clang + VERSIONS='4.6 4.7 4.8 4.9 5 6' + cd /usr/bin + for VERSION in '$VERSIONS' + rm -f g++-4.6 gcc-4.6 cpp-4.6 gcc + ln -s clang++-3.8 g++-4.6 + ln -s clang-3.8 gcc-4.6 + ln -s clang-3.8 cpp-4.6 + ln -s clang-3.8 gcc + echo 'gcc-4.6 hold' + dpkg --set-selections dpkg: warning: package not in database at line 1: gcc-4.6 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method + echo 'g++-4.6 hold' + dpkg --set-selections dpkg: warning: package not in database at line 1: g++-4.6 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method + for VERSION in '$VERSIONS' + rm -f g++-4.7 gcc-4.7 cpp-4.7 gcc + ln -s clang++-3.8 g++-4.7 + ln -s clang-3.8 gcc-4.7 + ln -s clang-3.8 cpp-4.7 + ln -s clang-3.8 gcc + echo 'gcc-4.7 hold' + dpkg --set-selections dpkg: warning: package not in 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 + echo 'g++-4.7 hold' + dpkg --set-selections dpkg: warning: package not in 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 + for VERSION in '$VERSIONS' + rm -f g++-4.8 gcc-4.8 cpp-4.8 gcc + ln -s clang++-3.8 g++-4.8 + ln -s clang-3.8 gcc-4.8 + ln -s clang-3.8 cpp-4.8 + ln -s clang-3.8 gcc + echo 'gcc-4.8 hold' + dpkg --set-selections dpkg: warning: package not in database at line 1: gcc-4.8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method + echo 'g++-4.8 hold' + dpkg --set-selections dpkg: warning: package not in database at line 1: g++-4.8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method + for VERSION in '$VERSIONS' + rm -f g++-4.9 gcc-4.9 cpp-4.9 gcc + ln -s clang++-3.8 g++-4.9 + ln -s clang-3.8 gcc-4.9 + ln -s clang-3.8 cpp-4.9 + ln -s clang-3.8 gcc + echo 'gcc-4.9 hold' + dpkg --set-selections dpkg: warning: package not in 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 + echo 'g++-4.9 hold' + dpkg --set-selections dpkg: warning: package not in 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 + for VERSION in '$VERSIONS' + rm -f g++-5 gcc-5 cpp-5 gcc + ln -s clang++-3.8 g++-5 + ln -s clang-3.8 gcc-5 + ln -s clang-3.8 cpp-5 + ln -s clang-3.8 gcc + echo 'gcc-5 hold' + dpkg --set-selections + echo 'g++-5 hold' + dpkg --set-selections + for VERSION in '$VERSIONS' + rm -f g++-6 gcc-6 cpp-6 gcc + ln -s clang++-3.8 g++-6 + ln -s clang-3.8 gcc-6 + ln -s clang-3.8 cpp-6 + ln -s clang-3.8 gcc + echo 'gcc-6 hold' + dpkg --set-selections + echo 'g++-6 hold' + dpkg --set-selections + cd - /build/prime-phylo-SSLzKr + 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... W: No sandbox user '_apt' on the system, can not drop privileges Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: linux-libc-dev 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 1158 kB of archives. After this operation, 60.4 kB of additional disk space will be used. Get:1 http://127.0.0.1:9999/debian unstable/main amd64 linux-libc-dev amd64 4.7.2-1 [1158 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 1158 kB in 0s (69.1 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 9769 files and directories currently installed.) Preparing to unpack .../linux-libc-dev_4.7.2-1_amd64.deb ... Unpacking linux-libc-dev:amd64 (4.7.2-1) over (4.6.4-1) ... Setting up linux-libc-dev:amd64 (4.7.2-1) ... W: No sandbox user '_apt' on the system, can not drop privileges +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'prime-phylo' packaging is maintained in the 'Git' version control system at: https://anonscm.debian.org/git/debian-med/prime-phylo.git Please use: git clone https://anonscm.debian.org/git/debian-med/prime-phylo.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 759 kB of source archives. Get:1 http://127.0.0.1:9999/debian unstable/main prime-phylo 1.0.11-4 (dsc) [2134 B] Get:2 http://127.0.0.1:9999/debian unstable/main prime-phylo 1.0.11-4 (tar) [751 kB] Get:3 http://127.0.0.1:9999/debian unstable/main prime-phylo 1.0.11-4 (diff) [5892 B] Fetched 759 kB in 0s (4792 kB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/prime-phylo-SSLzKr/prime-phylo-1.0.11' with '<>' I: NOTICE: Log filtering will replace 'build/prime-phylo-SSLzKr' 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-5YLeiV/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-5YLeiV/apt_archive ./ InRelease Get:2 copy:/<>/resolver-5YLeiV/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-5YLeiV/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-5YLeiV/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-5YLeiV/apt_archive ./ Packages [431 B] Fetched 1737 B in 0s (0 B/s) Reading package lists... W: No sandbox user '_apt' on the system, can not drop privileges 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 774 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-5YLeiV/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [774 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 774 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 9775 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) ... W: No sandbox user '_apt' on the system, can not drop privileges +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper (>= 9.0.0), gengetopt, cmake, libblas-dev, liblapack-dev, gfortran, bison, flex, libopenmpi-dev, libxml2-dev, libboost-dev, libboost-mpi-dev, libboost-serialization-dev, zlib1g-dev Filtered Build-Depends: debhelper (>= 9.0.0), gengetopt, cmake, libblas-dev, liblapack-dev, gfortran, bison, flex, libopenmpi-dev, libxml2-dev, libboost-dev, libboost-mpi-dev, libboost-serialization-dev, zlib1g-dev dpkg-deb: building package 'sbuild-build-depends-prime-phylo-dummy' in '/<>/resolver-WOUPbS/apt_archive/sbuild-build-depends-prime-phylo-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-prime-phylo-dummy dpkg-scanpackages: info: Wrote 1 entries to output Packages file. Ign:1 copy:/<>/resolver-WOUPbS/apt_archive ./ InRelease Get:2 copy:/<>/resolver-WOUPbS/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-WOUPbS/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-WOUPbS/apt_archive ./ Sources [431 B] Get:5 copy:/<>/resolver-WOUPbS/apt_archive ./ Packages [520 B] Fetched 1908 B in 0s (0 B/s) Reading package lists... W: No sandbox user '_apt' on the system, can not drop privileges Reading package lists... Install prime-phylo 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 bison bsdmainutils cmake cmake-data debhelper dh-autoreconf dh-strip-nondeterminism file flex gengetopt gettext gettext-base gfortran gfortran-6 groff-base icu-devtools intltool-debian libarchive-zip-perl libarchive13 libbison-dev libblas-common libblas-dev libblas3 libboost-dev libboost-mpi-dev libboost-mpi1.61-dev libboost-mpi1.61.0 libboost-serialization-dev libboost-serialization1.61-dev libboost-serialization1.61.0 libboost1.61-dev libcroco3 libcurl3 libexpat1 libfile-stripnondeterminism-perl libfl-dev libgfortran-6-dev libgfortran3 libglib2.0-0 libgnutls30 libgssapi-krb5-2 libhogweed4 libhwloc-dev libhwloc-plugins libhwloc5 libibverbs-dev libibverbs1 libicu-dev libicu57 libidn11 libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack-dev liblapack3 libldap-2.4-2 libltdl-dev libltdl7 liblzo2-2 libmagic-mgc libmagic1 libnettle6 libnghttp2-14 libnl-3-200 libnl-route-3-200 libnuma-dev libnuma1 libopenmpi-dev libopenmpi1.10 libp11-kit0 libpciaccess0 libpipeline1 libprocps6 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh2-1 libssl1.0.2 libtasn1-6 libtimedate-perl libtool libunistring0 libxml2 libxml2-dev lsb-base m4 man-db mpi-default-dev ocl-icd-libopencl1 openmpi-common po-debconf procps zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc bison-doc wamerican | wordlist whois vacation codeblocks eclipse ninja-build dh-make gettext-doc libasprintf-dev libgettextpo-dev gfortran-multilib gfortran-doc gfortran-6-multilib gfortran-6-doc libgfortran3-dbg libcoarrays-dev groff lrzip liblapack-doc-man liblapack-doc libboost-doc libboost-graph1.61-dev libboost1.61-doc libboost-atomic1.61-dev libboost-chrono1.61-dev libboost-context1.61-dev libboost-coroutine1.61-dev libboost-date-time1.61-dev libboost-exception1.61-dev libboost-filesystem1.61-dev libboost-graph-parallel1.61-dev libboost-iostreams1.61-dev libboost-locale1.61-dev libboost-log1.61-dev libboost-math1.61-dev libboost-mpi-python1.61-dev libboost-program-options1.61-dev libboost-python1.61-dev libboost-random1.61-dev libboost-regex1.61-dev libboost-signals1.61-dev libboost-system1.61-dev libboost-test1.61-dev libboost-thread1.61-dev libboost-timer1.61-dev libboost-wave1.61-dev libboost1.61-tools-dev libmpfrc++-dev libntl-dev gnutls-bin krb5-doc krb5-user libhwloc-contrib-plugins icu-doc libtool-doc opennmpi-doc pciutils gcj-jdk pkg-config less www-browser opencl-icd libmail-box-perl Recommended packages: curl | wget | lynx-cur ca-certificates libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales openmpi-bin libsasl2-modules xml-core libmail-sendmail-perl psmisc The following NEW packages will be installed: autoconf automake autopoint autotools-dev bison bsdmainutils cmake cmake-data debhelper dh-autoreconf dh-strip-nondeterminism file flex gengetopt gettext gettext-base gfortran gfortran-6 groff-base icu-devtools intltool-debian libarchive-zip-perl libarchive13 libbison-dev libblas-common libblas-dev libblas3 libboost-dev libboost-mpi-dev libboost-mpi1.61-dev libboost-mpi1.61.0 libboost-serialization-dev libboost-serialization1.61-dev libboost-serialization1.61.0 libboost1.61-dev libcroco3 libcurl3 libexpat1 libfile-stripnondeterminism-perl libfl-dev libgfortran-6-dev libgfortran3 libglib2.0-0 libgnutls30 libgssapi-krb5-2 libhogweed4 libhwloc-dev libhwloc-plugins libhwloc5 libibverbs-dev libibverbs1 libicu-dev libicu57 libidn11 libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack-dev liblapack3 libldap-2.4-2 libltdl-dev libltdl7 liblzo2-2 libmagic-mgc libmagic1 libnettle6 libnghttp2-14 libnl-3-200 libnl-route-3-200 libnuma-dev libnuma1 libopenmpi-dev libopenmpi1.10 libp11-kit0 libpciaccess0 libpipeline1 libprocps6 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh2-1 libssl1.0.2 libtasn1-6 libtimedate-perl libtool libunistring0 libxml2 libxml2-dev lsb-base m4 man-db mpi-default-dev ocl-icd-libopencl1 openmpi-common po-debconf procps sbuild-build-depends-prime-phylo-dummy zlib1g-dev 0 upgraded, 101 newly installed, 0 to remove and 0 not upgraded. Need to get 96.1 MB of archives. After this operation, 514 MB of additional disk space will be used. Get:1 copy:/<>/resolver-WOUPbS/apt_archive ./ sbuild-build-depends-prime-phylo-dummy 0.invalid.0 [862 B] Get:2 http://127.0.0.1:9999/debian unstable/main amd64 groff-base amd64 1.22.3-8 [1162 kB] Get:3 http://127.0.0.1:9999/debian unstable/main amd64 bsdmainutils amd64 9.0.10 [184 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 2.7.5-1 [1003 kB] Get:6 http://127.0.0.1:9999/debian unstable/main amd64 cmake-data all 3.6.1-1 [1152 kB] Get:7 http://127.0.0.1:9999/debian unstable/main amd64 libprocps6 amd64 2:3.3.12-2 [57.7 kB] Get:8 http://127.0.0.1:9999/debian unstable/main amd64 lsb-base all 9.20160629 [27.6 kB] Get:9 http://127.0.0.1:9999/debian unstable/main amd64 procps amd64 2:3.3.12-2 [250 kB] Get:10 http://127.0.0.1:9999/debian unstable/main amd64 liblzo2-2 amd64 2.08-1.2 [54.6 kB] Get:11 http://127.0.0.1:9999/debian unstable/main amd64 libnettle6 amd64 3.2-1 [191 kB] Get:12 http://127.0.0.1:9999/debian unstable/main amd64 libicu57 amd64 57.1-3 [7676 kB] Get:13 http://127.0.0.1:9999/debian unstable/main amd64 libxml2 amd64 2.9.4+dfsg1-1+b1 [919 kB] Get:14 http://127.0.0.1:9999/debian unstable/main amd64 libarchive13 amd64 3.2.1-2 [288 kB] Get:15 http://127.0.0.1:9999/debian unstable/main amd64 libkeyutils1 amd64 1.5.9-9 [12.4 kB] Get:16 http://127.0.0.1:9999/debian unstable/main amd64 libkrb5support0 amd64 1.14.3+dfsg-1 [61.0 kB] Get:17 http://127.0.0.1:9999/debian unstable/main amd64 libk5crypto3 amd64 1.14.3+dfsg-1 [115 kB] Get:18 http://127.0.0.1:9999/debian unstable/main amd64 libkrb5-3 amd64 1.14.3+dfsg-1 [311 kB] Get:19 http://127.0.0.1:9999/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.14.3+dfsg-1 [154 kB] Get:20 http://127.0.0.1:9999/debian unstable/main amd64 libidn11 amd64 1.33-1 [115 kB] Get:21 http://127.0.0.1:9999/debian unstable/main amd64 libhogweed4 amd64 3.2-1 [136 kB] Get:22 http://127.0.0.1:9999/debian unstable/main amd64 libp11-kit0 amd64 0.23.2-5 [111 kB] Get:23 http://127.0.0.1:9999/debian unstable/main amd64 libtasn1-6 amd64 4.9-4 [50.0 kB] Get:24 http://127.0.0.1:9999/debian unstable/main amd64 libgnutls30 amd64 3.5.3-3 [801 kB] Get:25 http://127.0.0.1:9999/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.26.dfsg1-15 [66.9 kB] Get:26 http://127.0.0.1:9999/debian unstable/main amd64 libsasl2-2 amd64 2.1.26.dfsg1-15 [103 kB] Get:27 http://127.0.0.1:9999/debian unstable/main amd64 libldap-2.4-2 amd64 2.4.42+dfsg-2+b2 [222 kB] Get:28 http://127.0.0.1:9999/debian unstable/main amd64 libnghttp2-14 amd64 1.13.0-1 [79.4 kB] Get:29 http://127.0.0.1:9999/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-1 [60.0 kB] Get:30 http://127.0.0.1:9999/debian unstable/main amd64 libssh2-1 amd64 1.7.0-1 [138 kB] Get:31 http://127.0.0.1:9999/debian unstable/main amd64 libssl1.0.2 amd64 1.0.2h-1 [1287 kB] Get:32 http://127.0.0.1:9999/debian unstable/main amd64 libcurl3 amd64 7.50.1-1 [280 kB] Get:33 http://127.0.0.1:9999/debian unstable/main amd64 libexpat1 amd64 2.2.0-1 [82.0 kB] Get:34 http://127.0.0.1:9999/debian unstable/main amd64 libjsoncpp1 amd64 1.7.4-3 [75.6 kB] Get:35 http://127.0.0.1:9999/debian unstable/main amd64 cmake amd64 3.6.1-1 [2736 kB] Get:36 http://127.0.0.1:9999/debian unstable/main amd64 libsigsegv2 amd64 2.10-5 [28.9 kB] Get:37 http://127.0.0.1:9999/debian unstable/main amd64 m4 amd64 1.4.17-5 [255 kB] Get:38 http://127.0.0.1:9999/debian unstable/main amd64 libfl-dev amd64 2.6.1-1 [92.5 kB] Get:39 http://127.0.0.1:9999/debian unstable/main amd64 flex amd64 2.6.1-1 [428 kB] Get:40 http://127.0.0.1:9999/debian unstable/main amd64 libmagic-mgc amd64 1:5.28-4 [210 kB] Get:41 http://127.0.0.1:9999/debian unstable/main amd64 libmagic1 amd64 1:5.28-4 [109 kB] Get:42 http://127.0.0.1:9999/debian unstable/main amd64 file amd64 1:5.28-4 [62.9 kB] Get:43 http://127.0.0.1:9999/debian unstable/main amd64 gettext-base amd64 0.19.8.1-1 [121 kB] Get:44 http://127.0.0.1:9999/debian unstable/main amd64 autoconf all 2.69-10 [338 kB] Get:45 http://127.0.0.1:9999/debian unstable/main amd64 autotools-dev all 20160430.1 [72.6 kB] Get:46 http://127.0.0.1:9999/debian unstable/main amd64 automake all 1:1.15-4 [735 kB] Get:47 http://127.0.0.1:9999/debian unstable/main amd64 autopoint all 0.19.8.1-1 [433 kB] Get:48 http://127.0.0.1:9999/debian unstable/main amd64 libbison-dev amd64 2:3.0.4.dfsg-1 [432 kB] Get:49 http://127.0.0.1:9999/debian unstable/main amd64 bison amd64 2:3.0.4.dfsg-1 [780 kB] Get:50 http://127.0.0.1:9999/debian unstable/main amd64 libglib2.0-0 amd64 2.48.1-3 [2707 kB] Get:51 http://127.0.0.1:9999/debian unstable/main amd64 libcroco3 amd64 0.6.11-1 [143 kB] Get:52 http://127.0.0.1:9999/debian unstable/main amd64 libunistring0 amd64 0.9.6+really0.9.3-0.1 [279 kB] Get:53 http://127.0.0.1:9999/debian unstable/main amd64 gettext amd64 0.19.8.1-1 [1493 kB] Get:54 http://127.0.0.1:9999/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.4 [26.3 kB] Get:55 http://127.0.0.1:9999/debian unstable/main amd64 po-debconf all 1.0.19 [249 kB] Get:56 http://127.0.0.1:9999/debian unstable/main amd64 libarchive-zip-perl all 1.59-1 [95.5 kB] Get:57 http://127.0.0.1:9999/debian unstable/main amd64 libfile-stripnondeterminism-perl all 0.023-2 [13.4 kB] Get:58 http://127.0.0.1:9999/debian unstable/main amd64 libtimedate-perl all 2.3000-2 [42.2 kB] Get:59 http://127.0.0.1:9999/debian unstable/main amd64 dh-strip-nondeterminism all 0.023-2 [8202 B] Get:60 http://127.0.0.1:9999/debian unstable/main amd64 libtool all 2.4.6-2 [545 kB] Get:61 http://127.0.0.1:9999/debian unstable/main amd64 dh-autoreconf all 12 [15.8 kB] Get:62 http://127.0.0.1:9999/debian unstable/main amd64 debhelper all 9.20160814 [800 kB] Get:63 http://127.0.0.1:9999/debian unstable/main amd64 gengetopt amd64 2.22.6+dfsg0-1+b1 [176 kB] Get:64 http://127.0.0.1:9999/debian unstable/main amd64 libgfortran3 amd64 6.2.0-1 [264 kB] Get:65 http://127.0.0.1:9999/debian unstable/main amd64 libgfortran-6-dev amd64 6.2.0-1 [295 kB] Get:66 http://127.0.0.1:9999/debian unstable/main amd64 gfortran-6 amd64 6.2.0-1 [31.7 MB] Get:67 http://127.0.0.1:9999/debian unstable/main amd64 gfortran amd64 4:6.1.1-1 [1352 B] Get:68 http://127.0.0.1:9999/debian unstable/main amd64 icu-devtools amd64 57.1-3 [172 kB] Get:69 http://127.0.0.1:9999/debian unstable/main amd64 libblas-common amd64 3.6.1-2 [13.9 kB] Get:70 http://127.0.0.1:9999/debian unstable/main amd64 libblas3 amd64 3.6.1-2 [157 kB] Get:71 http://127.0.0.1:9999/debian unstable/main amd64 libblas-dev amd64 3.6.1-2 [18.9 kB] Get:72 http://127.0.0.1:9999/debian unstable/main amd64 libboost1.61-dev amd64 1.61.0+dfsg-2.1 [6843 kB] Get:73 http://127.0.0.1:9999/debian unstable/main amd64 libboost-dev amd64 1.61.0.2 [3746 B] Get:74 http://127.0.0.1:9999/debian unstable/main amd64 libboost-serialization1.61.0 amd64 1.61.0+dfsg-2.1 [125 kB] Get:75 http://127.0.0.1:9999/debian unstable/main amd64 libboost-serialization1.61-dev amd64 1.61.0+dfsg-2.1 [160 kB] Get:76 http://127.0.0.1:9999/debian unstable/main amd64 libltdl7 amd64 2.4.6-2 [389 kB] Get:77 http://127.0.0.1:9999/debian unstable/main amd64 libnuma1 amd64 2.0.11-1 [32.5 kB] Get:78 http://127.0.0.1:9999/debian unstable/main amd64 libhwloc5 amd64 1.11.3-2 [104 kB] Get:79 http://127.0.0.1:9999/debian unstable/main amd64 libnl-3-200 amd64 3.2.27-1 [61.4 kB] Get:80 http://127.0.0.1:9999/debian unstable/main amd64 libnl-route-3-200 amd64 3.2.27-1 [135 kB] Get:81 http://127.0.0.1:9999/debian unstable/main amd64 libibverbs1 amd64 1.2.0-2 [37.7 kB] Get:82 http://127.0.0.1:9999/debian unstable/main amd64 libpciaccess0 amd64 0.13.4-1 [49.8 kB] Get:83 http://127.0.0.1:9999/debian unstable/main amd64 ocl-icd-libopencl1 amd64 2.2.9-1 [36.1 kB] Get:84 http://127.0.0.1:9999/debian unstable/main amd64 libhwloc-plugins amd64 1.11.3-2 [16.0 kB] Get:85 http://127.0.0.1:9999/debian unstable/main amd64 libopenmpi1.10 amd64 1.10.3-3 [2109 kB] Get:86 http://127.0.0.1:9999/debian unstable/main amd64 libboost-mpi1.61.0 amd64 1.61.0+dfsg-2.1 [70.4 kB] Get:87 http://127.0.0.1:9999/debian unstable/main amd64 openmpi-common all 1.10.3-3 [143 kB] Get:88 http://127.0.0.1:9999/debian unstable/main amd64 libibverbs-dev amd64 1.2.0-2 [93.7 kB] Get:89 http://127.0.0.1:9999/debian unstable/main amd64 libnuma-dev amd64 2.0.11-1 [45.5 kB] Get:90 http://127.0.0.1:9999/debian unstable/main amd64 libltdl-dev amd64 2.4.6-2 [161 kB] Get:91 http://127.0.0.1:9999/debian unstable/main amd64 libhwloc-dev amd64 1.11.3-2 [161 kB] Get:92 http://127.0.0.1:9999/debian unstable/main amd64 libopenmpi-dev amd64 1.10.3-3 [628 kB] Get:93 http://127.0.0.1:9999/debian unstable/main amd64 mpi-default-dev amd64 1.7 [4786 B] Get:94 http://127.0.0.1:9999/debian unstable/main amd64 libboost-mpi1.61-dev amd64 1.61.0+dfsg-2.1 [152 kB] Get:95 http://127.0.0.1:9999/debian unstable/main amd64 libboost-mpi-dev amd64 1.61.0.2 [3470 B] Get:96 http://127.0.0.1:9999/debian unstable/main amd64 libboost-serialization-dev amd64 1.61.0.2 [3614 B] Get:97 http://127.0.0.1:9999/debian unstable/main amd64 libicu-dev amd64 57.1-3 [16.3 MB] Get:98 http://127.0.0.1:9999/debian unstable/main amd64 liblapack3 amd64 3.6.1-2 [1963 kB] Get:99 http://127.0.0.1:9999/debian unstable/main amd64 liblapack-dev amd64 3.6.1-2 [1977 kB] Get:100 http://127.0.0.1:9999/debian unstable/main amd64 libxml2-dev amd64 2.9.4+dfsg1-1+b1 [812 kB] Get:101 http://127.0.0.1:9999/debian unstable/main amd64 zlib1g-dev amd64 1:1.2.8.dfsg-2+b1 [206 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 96.1 MB in 11s (8212 kB/s) Selecting previously unselected package groff-base. (Reading database ... 9775 files and directories currently installed.) Preparing to unpack .../000-groff-base_1.22.3-8_amd64.deb ... Unpacking groff-base (1.22.3-8) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../001-bsdmainutils_9.0.10_amd64.deb ... Unpacking bsdmainutils (9.0.10) ... 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_2.7.5-1_amd64.deb ... Unpacking man-db (2.7.5-1) ... Selecting previously unselected package cmake-data. Preparing to unpack .../004-cmake-data_3.6.1-1_all.deb ... Unpacking cmake-data (3.6.1-1) ... Selecting previously unselected package libprocps6:amd64. Preparing to unpack .../005-libprocps6_2%3a3.3.12-2_amd64.deb ... Unpacking libprocps6:amd64 (2:3.3.12-2) ... Selecting previously unselected package lsb-base. Preparing to unpack .../006-lsb-base_9.20160629_all.deb ... Unpacking lsb-base (9.20160629) ... Selecting previously unselected package procps. Preparing to unpack .../007-procps_2%3a3.3.12-2_amd64.deb ... Unpacking procps (2:3.3.12-2) ... Selecting previously unselected package liblzo2-2:amd64. Preparing to unpack .../008-liblzo2-2_2.08-1.2_amd64.deb ... Unpacking liblzo2-2:amd64 (2.08-1.2) ... Selecting previously unselected package libnettle6:amd64. Preparing to unpack .../009-libnettle6_3.2-1_amd64.deb ... Unpacking libnettle6:amd64 (3.2-1) ... Selecting previously unselected package libicu57:amd64. Preparing to unpack .../010-libicu57_57.1-3_amd64.deb ... Unpacking libicu57:amd64 (57.1-3) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../011-libxml2_2.9.4+dfsg1-1+b1_amd64.deb ... Unpacking libxml2:amd64 (2.9.4+dfsg1-1+b1) ... Selecting previously unselected package libarchive13:amd64. Preparing to unpack .../012-libarchive13_3.2.1-2_amd64.deb ... Unpacking libarchive13:amd64 (3.2.1-2) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../013-libkeyutils1_1.5.9-9_amd64.deb ... Unpacking libkeyutils1:amd64 (1.5.9-9) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../014-libkrb5support0_1.14.3+dfsg-1_amd64.deb ... Unpacking libkrb5support0:amd64 (1.14.3+dfsg-1) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../015-libk5crypto3_1.14.3+dfsg-1_amd64.deb ... Unpacking libk5crypto3:amd64 (1.14.3+dfsg-1) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../016-libkrb5-3_1.14.3+dfsg-1_amd64.deb ... Unpacking libkrb5-3:amd64 (1.14.3+dfsg-1) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../017-libgssapi-krb5-2_1.14.3+dfsg-1_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.14.3+dfsg-1) ... Selecting previously unselected package libidn11:amd64. Preparing to unpack .../018-libidn11_1.33-1_amd64.deb ... Unpacking libidn11:amd64 (1.33-1) ... Selecting previously unselected package libhogweed4:amd64. Preparing to unpack .../019-libhogweed4_3.2-1_amd64.deb ... Unpacking libhogweed4:amd64 (3.2-1) ... Selecting previously unselected package libp11-kit0:amd64. Preparing to unpack .../020-libp11-kit0_0.23.2-5_amd64.deb ... Unpacking libp11-kit0:amd64 (0.23.2-5) ... Selecting previously unselected package libtasn1-6:amd64. Preparing to unpack .../021-libtasn1-6_4.9-4_amd64.deb ... Unpacking libtasn1-6:amd64 (4.9-4) ... Selecting previously unselected package libgnutls30:amd64. Preparing to unpack .../022-libgnutls30_3.5.3-3_amd64.deb ... Unpacking libgnutls30:amd64 (3.5.3-3) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../023-libsasl2-modules-db_2.1.26.dfsg1-15_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.26.dfsg1-15) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../024-libsasl2-2_2.1.26.dfsg1-15_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.26.dfsg1-15) ... Selecting previously unselected package libldap-2.4-2:amd64. Preparing to unpack .../025-libldap-2.4-2_2.4.42+dfsg-2+b2_amd64.deb ... Unpacking libldap-2.4-2:amd64 (2.4.42+dfsg-2+b2) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../026-libnghttp2-14_1.13.0-1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.13.0-1) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../027-librtmp1_2.4+20151223.gitfa8646d.1-1_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-1) ... Selecting previously unselected package libssh2-1:amd64. Preparing to unpack .../028-libssh2-1_1.7.0-1_amd64.deb ... Unpacking libssh2-1:amd64 (1.7.0-1) ... Selecting previously unselected package libssl1.0.2:amd64. Preparing to unpack .../029-libssl1.0.2_1.0.2h-1_amd64.deb ... Unpacking libssl1.0.2:amd64 (1.0.2h-1) ... Selecting previously unselected package libcurl3:amd64. Preparing to unpack .../030-libcurl3_7.50.1-1_amd64.deb ... Unpacking libcurl3:amd64 (7.50.1-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../031-libexpat1_2.2.0-1_amd64.deb ... Unpacking libexpat1:amd64 (2.2.0-1) ... Selecting previously unselected package libjsoncpp1:amd64. Preparing to unpack .../032-libjsoncpp1_1.7.4-3_amd64.deb ... Unpacking libjsoncpp1:amd64 (1.7.4-3) ... Selecting previously unselected package cmake. Preparing to unpack .../033-cmake_3.6.1-1_amd64.deb ... Unpacking cmake (3.6.1-1) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../034-libsigsegv2_2.10-5_amd64.deb ... Unpacking libsigsegv2:amd64 (2.10-5) ... Selecting previously unselected package m4. Preparing to unpack .../035-m4_1.4.17-5_amd64.deb ... Unpacking m4 (1.4.17-5) ... Selecting previously unselected package libfl-dev:amd64. 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Unpacking sbuild-build-depends-prime-phylo-dummy (0.invalid.0) ... Setting up libnettle6:amd64 (3.2-1) ... Setting up libexpat1:amd64 (2.2.0-1) ... Setting up libarchive-zip-perl (1.59-1) ... Setting up libnghttp2-14:amd64 (1.13.0-1) ... Setting up libtimedate-perl (2.3000-2) ... Setting up libsigsegv2:amd64 (2.10-5) ... Setting up libblas-common (3.6.1-2) ... Setting up libnuma1:amd64 (2.0.11-1) ... Setting up libgfortran3:amd64 (6.2.0-1) ... Setting up groff-base (1.22.3-8) ... Setting up libglib2.0-0:amd64 (2.48.1-3) ... No schema files found: doing nothing. Setting up libsasl2-modules-db:amd64 (2.1.26.dfsg1-15) ... Setting up libgfortran-6-dev:amd64 (6.2.0-1) ... Setting up libsasl2-2:amd64 (2.1.26.dfsg1-15) ... Setting up gettext-base (0.19.8.1-1) ... Setting up cmake-data (3.6.1-1) ... Setting up libpipeline1:amd64 (1.4.1-2) ... Setting up m4 (1.4.17-5) ... Setting up gengetopt (2.22.6+dfsg0-1+b1) ... Setting up libicu57:amd64 (57.1-3) ... Setting up libboost1.61-dev:amd64 (1.61.0+dfsg-2.1) ... Setting up libprocps6:amd64 (2:3.3.12-2) ... Setting up libxml2:amd64 (2.9.4+dfsg1-1+b1) ... Setting up libtasn1-6:amd64 (4.9-4) ... Setting up libmagic-mgc (1:5.28-4) ... Setting up libfl-dev:amd64 (2.6.1-1) ... Setting up libmagic1:amd64 (1:5.28-4) ... Setting up libhogweed4:amd64 (3.2-1) ... Setting up lsb-base (9.20160629) ... Setting up procps (2:3.3.12-2) ... update-alternatives: using /usr/bin/w.procps to provide /usr/bin/w (w) in auto mode Setting up libcroco3:amd64 (0.6.11-1) ... Setting up libssl1.0.2:amd64 (1.0.2h-1) ... Setting up libblas3 (3.6.1-2) ... update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode Setting up libssh2-1:amd64 (1.7.0-1) ... Setting up openmpi-common (1.10.3-3) ... Processing triggers for libc-bin (2.23-5) ... Setting up autotools-dev (20160430.1) ... Setting up libunistring0:amd64 (0.9.6+really0.9.3-0.1) ... Setting up libp11-kit0:amd64 (0.23.2-5) ... Setting up libltdl7:amd64 (2.4.6-2) ... Setting up libbison-dev:amd64 (2:3.0.4.dfsg-1) ... Setting up libpciaccess0:amd64 (0.13.4-1) ... Setting up icu-devtools (57.1-3) ... Setting up libboost-dev:amd64 (1.61.0.2) ... Setting up bison (2:3.0.4.dfsg-1) ... update-alternatives: using /usr/bin/bison.yacc to provide /usr/bin/yacc (yacc) in auto mode Setting up libnuma-dev:amd64 (2.0.11-1) ... Setting up ocl-icd-libopencl1:amd64 (2.2.9-1) ... Setting up libkeyutils1:amd64 (1.5.9-9) ... Setting up bsdmainutils (9.0.10) ... 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 (3.2.27-1) ... Setting up libboost-serialization1.61.0:amd64 (1.61.0+dfsg-2.1) ... Setting up autopoint (0.19.8.1-1) ... Setting up libidn11:amd64 (1.33-1) ... Setting up liblzo2-2:amd64 (2.08-1.2) ... Setting up zlib1g-dev:amd64 (1:1.2.8.dfsg-2+b1) ... Setting up libfile-stripnondeterminism-perl (0.023-2) ... Setting up libjsoncpp1:amd64 (1.7.4-3) ... Setting up gfortran-6 (6.2.0-1) ... Setting up libltdl-dev:amd64 (2.4.6-2) ... Setting up gettext (0.19.8.1-1) ... Setting up flex (2.6.1-1) ... Setting up libboost-serialization1.61-dev:amd64 (1.61.0+dfsg-2.1) ... Setting up libarchive13:amd64 (3.2.1-2) ... Setting up liblapack3 (3.6.1-2) ... update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode Setting up libgnutls30:amd64 (3.5.3-3) ... Setting up libnl-route-3-200:amd64 (3.2.27-1) ... Setting up autoconf (2.69-10) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-1) ... Setting up libicu-dev (57.1-3) ... Setting up file (1:5.28-4) ... Setting up libhwloc5:amd64 (1.11.3-2) ... Setting up libkrb5support0:amd64 (1.14.3+dfsg-1) ... Setting up libxml2-dev:amd64 (2.9.4+dfsg1-1+b1) ... Setting up libhwloc-plugins (1.11.3-2) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up libldap-2.4-2:amd64 (2.4.42+dfsg-2+b2) ... Setting up automake (1:1.15-4) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up man-db (2.7.5-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libtool (2.4.6-2) ... Setting up gfortran (4:6.1.1-1) ... update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode Setting up libibverbs1 (1.2.0-2) ... Setting up libboost-serialization-dev:amd64 (1.61.0.2) ... Setting up libk5crypto3:amd64 (1.14.3+dfsg-1) ... Setting up po-debconf (1.0.19) ... Setting up libhwloc-dev:amd64 (1.11.3-2) ... Setting up libblas-dev (3.6.1-2) ... update-alternatives: using /usr/lib/libblas/libblas.so to provide /usr/lib/libblas.so (libblas.so) in auto mode Setting up libopenmpi1.10 (1.10.3-3) ... Setting up libkrb5-3:amd64 (1.14.3+dfsg-1) ... Setting up libibverbs-dev (1.2.0-2) ... Setting up liblapack-dev (3.6.1-2) ... update-alternatives: using /usr/lib/lapack/liblapack.so to provide /usr/lib/liblapack.so (liblapack.so) in auto mode Setting up libboost-mpi1.61.0 (1.61.0+dfsg-2.1) ... Setting up libopenmpi-dev (1.10.3-3) ... update-alternatives: using /usr/lib/openmpi/include to provide /usr/include/mpi (mpi) in auto mode Setting up mpi-default-dev (1.7) ... Setting up libgssapi-krb5-2:amd64 (1.14.3+dfsg-1) ... Setting up libcurl3:amd64 (7.50.1-1) ... Setting up libboost-mpi1.61-dev (1.61.0+dfsg-2.1) ... Setting up libboost-mpi-dev (1.61.0.2) ... Setting up cmake (3.6.1-1) ... Setting up dh-strip-nondeterminism (0.023-2) ... Setting up debhelper (9.20160814) ... Setting up dh-autoreconf (12) ... Setting up sbuild-build-depends-prime-phylo-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.23-5) ... W: No sandbox user '_apt' on the system, can not drop privileges +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 3.16.0-4-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.27-6 dpkg-dev_1.18.10 g++-6_6.2.0-1 gcc-6_6.2.0-1 libc6-dev_2.23-5 libstdc++-6-dev_6.2.0-1 libstdc++6_6.2.0-1 linux-libc-dev_4.7.2-1 Package versions: adduser_3.115 apt_1.3~rc2 autoconf_2.69-10 automake_1:1.15-4 autopoint_0.19.8.1-1 autotools-dev_20160430.1 base-files_9.6 base-passwd_3.5.40 bash_4.3-15 binutils_2.27-6 bison_2:3.0.4.dfsg-1 bsdmainutils_9.0.10 bsdutils_1:2.28.1-1 build-essential_12.2 bzip2_1.0.6-8 clang-3.8_1:3.8.1-9 cmake_3.6.1-1 cmake-data_3.6.1-1 coreutils_8.25-2 cpp_4:6.1.1-1 cpp-6_6.2.0-1 dash_0.5.8-2.3 debconf_1.5.59 debfoster_2.7-2.1 debhelper_9.20160814 debian-archive-keyring_2014.3 debianutils_4.8 dh-autoreconf_12 dh-strip-nondeterminism_0.023-2 diffutils_1:3.3-3 dpkg_1.18.10 dpkg-dev_1.18.10 e2fslibs_1.43.1-1 e2fsprogs_1.43.1-1 eatmydata_105-3 fakeroot_1.21-1 file_1:5.28-4 findutils_4.6.0+git+20160703-2 flex_2.6.1-1 g++_4:6.1.1-1 g++-6_6.2.0-1 gcc_4:6.1.1-1 gcc-6_6.2.0-1 gcc-6-base_6.2.0-1 gengetopt_2.22.6+dfsg0-1+b1 gettext_0.19.8.1-1 gettext-base_0.19.8.1-1 gfortran_4:6.1.1-1 gfortran-6_6.2.0-1 gpgv_2.1.14-5 grep_2.25-6 groff-base_1.22.3-8 gzip_1.6-5 hostname_3.18 icu-devtools_57.1-3 init-system-helpers_1.42 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3 libapt-pkg5.0_1.3~rc2 libarchive-zip-perl_1.59-1 libarchive13_3.2.1-2 libasan3_6.2.0-1 libatomic1_6.2.0-1 libattr1_1:2.4.47-2 libaudit-common_1:2.6.6-1 libaudit1_1:2.6.6-1 libbison-dev_2:3.0.4.dfsg-1 libblas-common_3.6.1-2 libblas-dev_3.6.1-2 libblas3_3.6.1-2 libblkid1_2.28.1-1 libboost-dev_1.61.0.2 libboost-mpi-dev_1.61.0.2 libboost-mpi1.61-dev_1.61.0+dfsg-2.1 libboost-mpi1.61.0_1.61.0+dfsg-2.1 libboost-serialization-dev_1.61.0.2 libboost-serialization1.61-dev_1.61.0+dfsg-2.1 libboost-serialization1.61.0_1.61.0+dfsg-2.1 libboost1.61-dev_1.61.0+dfsg-2.1 libbsd0_0.8.3-1 libbz2-1.0_1.0.6-8 libc-bin_2.23-5 libc-dev-bin_2.23-5 libc6_2.23-5 libc6-dev_2.23-5 libcap-ng0_0.7.7-3 libcc1-0_6.2.0-1 libcilkrts5_6.2.0-1 libclang-common-3.8-dev_1:3.8.1-9 libclang1-3.8_1:3.8.1-9 libcomerr2_1.43.1-1 libcroco3_0.6.11-1 libcurl3_7.50.1-1 libdb5.3_5.3.28-12 libdebconfclient0_0.215 libdpkg-perl_1.18.10 libeatmydata1_105-3 libedit2_3.1-20150325-1+b1 libexpat1_2.2.0-1 libfakeroot_1.21-1 libfdisk1_2.28.1-1 libffi6_3.2.1-4 libfile-stripnondeterminism-perl_0.023-2 libfl-dev_2.6.1-1 libgc1c2_1:7.4.2-8 libgcc-6-dev_6.2.0-1 libgcc1_1:6.2.0-1 libgcrypt20_1.7.3-1 libgdbm3_1.8.3-14 libgfortran-6-dev_6.2.0-1 libgfortran3_6.2.0-1 libglib2.0-0_2.48.1-3 libgmp10_2:6.1.1+dfsg-1 libgnutls30_3.5.3-3 libgomp1_6.2.0-1 libgpg-error0_1.24-1 libgssapi-krb5-2_1.14.3+dfsg-1 libhogweed4_3.2-1 libhwloc-dev_1.11.3-2 libhwloc-plugins_1.11.3-2 libhwloc5_1.11.3-2 libibverbs-dev_1.2.0-2 libibverbs1_1.2.0-2 libicu-dev_57.1-3 libicu57_57.1-3 libidn11_1.33-1 libisl15_0.17.1-1 libitm1_6.2.0-1 libjsoncpp1_1.7.4-3 libk5crypto3_1.14.3+dfsg-1 libkeyutils1_1.5.9-9 libkrb5-3_1.14.3+dfsg-1 libkrb5support0_1.14.3+dfsg-1 liblapack-dev_3.6.1-2 liblapack3_3.6.1-2 libldap-2.4-2_2.4.42+dfsg-2+b2 libllvm3.8_1:3.8.1-9 liblsan0_6.2.0-1 libltdl-dev_2.4.6-2 libltdl7_2.4.6-2 liblz4-1_0.0~r131-2 liblzma5_5.1.1alpha+20120614-2.1 liblzo2-2_2.08-1.2 libmagic-mgc_1:5.28-4 libmagic1_1:5.28-4 libmount1_2.28.1-1 libmpc3_1.0.3-1 libmpfr4_3.1.4-2 libmpx2_6.2.0-1 libncurses5_6.0+20160625-1 libncursesw5_6.0+20160625-1 libnettle6_3.2-1 libnghttp2-14_1.13.0-1 libnl-3-200_3.2.27-1 libnl-route-3-200_3.2.27-1 libnuma-dev_2.0.11-1 libnuma1_2.0.11-1 libobjc-6-dev_6.2.0-1 libobjc4_6.2.0-1 libopenmpi-dev_1.10.3-3 libopenmpi1.10_1.10.3-3 libp11-kit0_0.23.2-5 libpam-modules_1.1.8-3.3 libpam-modules-bin_1.1.8-3.3 libpam-runtime_1.1.8-3.3 libpam0g_1.1.8-3.3 libpciaccess0_0.13.4-1 libpcre3_2:8.39-2 libperl5.22_5.22.2-3 libpipeline1_1.4.1-2 libprocps6_2:3.3.12-2 libquadmath0_6.2.0-1 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.26.dfsg1-15 libsasl2-modules-db_2.1.26.dfsg1-15 libselinux1_2.5-3 libsemanage-common_2.5-1 libsemanage1_2.5-1 libsepol1_2.5-1 libsigsegv2_2.10-5 libsmartcols1_2.28.1-1 libss2_1.43.1-1 libssh2-1_1.7.0-1 libssl1.0.2_1.0.2h-1 libstdc++-6-dev_6.2.0-1 libstdc++6_6.2.0-1 libsystemd0_231-5 libtasn1-6_4.9-4 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160625-1 libtool_2.4.6-2 libtsan0_6.2.0-1 libubsan0_6.2.0-1 libudev1_231-5 libunistring0_0.9.6+really0.9.3-0.1 libustr-1.0-1_1.0.4-5 libuuid1_2.28.1-1 libxml2_2.9.4+dfsg1-1+b1 libxml2-dev_2.9.4+dfsg1-1+b1 linux-libc-dev_4.7.2-1 login_1:4.2-3.1 lsb-base_9.20160629 m4_1.4.17-5 make_4.1-9 man-db_2.7.5-1 mawk_1.3.3-17 mount_2.28.1-1 mpi-default-dev_1.7 multiarch-support_2.23-5 ncurses-base_6.0+20160625-1 ncurses-bin_6.0+20160625-1 ocl-icd-libopencl1_2.2.9-1 openmpi-common_1.10.3-3 passwd_1:4.2-3.1 patch_2.7.5-1 perl_5.22.2-3 perl-base_5.22.2-3 perl-modules-5.22_5.22.2-3 po-debconf_1.0.19 procps_2:3.3.12-2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-prime-phylo-dummy_0.invalid.0 sed_4.2.2-7.1 sensible-utils_0.0.9 sysvinit-utils_2.88dsf-59.8 tar_1.29b-1 util-linux_2.28.1-1 xz-utils_5.1.1alpha+20120614-2.1 zlib1g_1:1.2.8.dfsg-2+b1 zlib1g-dev_1:1.2.8.dfsg-2+b1 +------------------------------------------------------------------------------+ | 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 Aug 3 11:30:28 2016 UTC using RSA key ID gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./prime-phylo_1.0.11-4.dsc dpkg-source: info: extracting prime-phylo in /<> dpkg-source: info: unpacking prime-phylo_1.0.11.orig.tar.gz dpkg-source: info: unpacking prime-phylo_1.0.11-4.debian.tar.xz dpkg-source: info: applying fix-gcc-6.patch dpkg-source: info: applying fix-ftbfs-with-Boost160.patch Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent 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-bc5932bd-71e2-4d5f-a243-9cedd68680a4 SCHROOT_UID=1001 SCHROOT_USER=user42 SHELL=/bin/sh USER=user42 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package prime-phylo dpkg-buildpackage: info: source version 1.0.11-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Sascha Steinbiss dpkg-source --before-build prime-phylo-1.0.11 dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --buildsystem=cmake --parallel dh_testdir -O--buildsystem=cmake -O--parallel dh_auto_clean -O--buildsystem=cmake -O--parallel dh_clean -O--buildsystem=cmake -O--parallel debian/rules build-arch dh build-arch --buildsystem=cmake --parallel dh_testdir -a -O--buildsystem=cmake -O--parallel dh_update_autotools_config -a -O--buildsystem=cmake -O--parallel debian/rules override_dh_auto_configure make[1]: Entering directory '/<>' dh_auto_configure -- \ -Dofficial_binary_packaging=on \ -Dprime_dynamic=on \ -DCMAKE_INSTALL_PREFIX=/usr \ -DCMAKE_INSTALL_RPATH=/usr/lib/prime-phylo \ -DCMAKE_BUILD_TYPE=RELEASE cmake .. -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -Dofficial_binary_packaging=on -Dprime_dynamic=on -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_INSTALL_RPATH=/usr/lib/prime-phylo -DCMAKE_BUILD_TYPE=RELEASE -- The CXX compiler identification is Clang 3.8.1 -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- The Fortran compiler identification is GNU 6.2.0 -- Check for working Fortran compiler: /usr/bin/f95 -- Check for working Fortran compiler: /usr/bin/f95 -- works -- Detecting Fortran compiler ABI info -- Detecting Fortran compiler ABI info - done -- Checking whether /usr/bin/f95 supports Fortran 90 -- Checking whether /usr/bin/f95 supports Fortran 90 -- yes -- The C compiler identification is Clang 3.8.1 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Looking for Fortran sgemm -- Looking for Fortran sgemm - found -- Looking for pthread.h -- Looking for pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - not found -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- A library with BLAS API found. hittade /usr/lib/libblas.so -- A library with BLAS API found. -- Looking for Fortran cheev -- Looking for Fortran cheev - found -- A library with LAPACK API found. -- Found BISON: /usr/bin/bison (found version "3.0.4") -- Found FLEX: /usr/bin/flex (found version "2.6.1") -- Found MPI_C: /usr/lib/openmpi/lib/libmpi.so -- Found MPI_CXX: /usr/lib/openmpi/lib/libmpi_cxx.so;/usr/lib/openmpi/lib/libmpi.so -- Found MPI_Fortran: /usr/lib/openmpi/lib/libmpi_usempif08.so;/usr/lib/openmpi/lib/libmpi_usempi_ignore_tkr.so;/usr/lib/openmpi/lib/libmpi_mpifh.so;/usr/lib/openmpi/lib/libmpi.so -- Boost version: 1.61.0 -- Found the following Boost libraries: -- mpi -- serialization -- Found LibXml2: /usr/lib/x86_64-linux-gnu/libxml2.so (found version "2.9.4") mpilib is /usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2021/libevent;/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2021/libevent/include;/usr/lib/openmpi/include;/usr/lib/openmpi/include/openmpi included path is -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_SYSCONFDIR -- Build files have been written to: /<>/obj-x86_64-linux-gnu make[1]: Leaving directory '/<>' dh_auto_build -a -O--buildsystem=cmake -O--parallel make -j1 make[1]: Entering directory '/<>/obj-x86_64-linux-gnu' /usr/bin/cmake -H/<> -B/<>/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/obj-x86_64-linux-gnu/CMakeFiles /<>/obj-x86_64-linux-gnu/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/<>/obj-x86_64-linux-gnu' make -f src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/build.make src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/depend make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 1%] [FLEX][MyScanner2] Building scanner with flex 2.6.1 cd /<>/src/cxx/libraries/sfile && /usr/bin/flex -o/<>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/lexer.c seqreader.l [ 1%] [BISON][MyParser2] Building parser with bison 3.0.4 cd /<>/src/cxx/libraries/sfile && /usr/bin/bison -d -d -o /<>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/gb.tab.c gb.y gb.y: warning: 1 nonterminal useless in grammar [-Wother] gb.y: warning: 1 rule useless in grammar [-Wother] gb.y:117.47-58: warning: nonterminal useless in grammar: darwin_entry [-Wother] %type gb_entry fasta_entry ig_entry darwin_entry ^^^^^^^^^^^^ gb.y:258.19-61: warning: rule useless in grammar [-Wother] darwin_entry : TEXT {$$ = NULL; /* Not implemented yet */} ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/cxx/libraries/sfile /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile /<>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/DependInfo.cmake --color= Scanning dependencies of target prime-phylo-sfile make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/build.make src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 1%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/gbread.c.o cd /<>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/<>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile -I/<>/src/cxx/libraries/sfile -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2021/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2021/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries/prime -I/<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<>/src/cxx/libraries -g -O2 -fdebug-prefix-map=/<>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo-sfile.dir/gbread.c.o -c /<>/src/cxx/libraries/sfile/gbread.c /<>/src/cxx/libraries/sfile/gbread.c:17:10: warning: implicitly declaring library function 'strcmp' with type 'int (const char *, const char *)' [-Wimplicit-function-declaration] if (!strcmp(argv[opt], "-d")) { ^ /<>/src/cxx/libraries/sfile/gbread.c:17:10: note: include the header or explicitly provide a declaration for 'strcmp' 1 warning generated. [ 2%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/sfile.c.o cd /<>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/<>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile -I/<>/src/cxx/libraries/sfile -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2021/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2021/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries/prime -I/<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<>/src/cxx/libraries -g -O2 -fdebug-prefix-map=/<>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo-sfile.dir/sfile.c.o -c /<>/src/cxx/libraries/sfile/sfile.c [ 3%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/lexer.c.o cd /<>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/<>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile -I/<>/src/cxx/libraries/sfile -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2021/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2021/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries/prime -I/<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<>/src/cxx/libraries -g -O2 -fdebug-prefix-map=/<>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo-sfile.dir/lexer.c.o -c /<>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/lexer.c seqreader.l:198:10: warning: expression which evaluates to zero treated as a null pointer constant of type 'char *' [-Wnon-literal-null-conversion] last = '\0'; ^~~~ seqreader.l:271:9: warning: unused variable 'code' [-Wunused-variable] int code; /* return value */ ^ /<>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/lexer.c:1832:17: warning: unused function 'yyunput' [-Wunused-function] static void yyunput (int c, char * yy_bp ) ^ /<>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/lexer.c:1875:16: warning: function 'input' is not needed and will not be emitted [-Wunneeded-internal-declaration] static int input (void) ^ 4 warnings generated. [ 3%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/gb.tab.c.o cd /<>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/<>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile -I/<>/src/cxx/libraries/sfile -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2021/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2021/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries/prime -I/<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<>/src/cxx/libraries -g -O2 -fdebug-prefix-map=/<>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo-sfile.dir/gb.tab.c.o -c /<>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/gb.tab.c /<>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/gb.tab.c:1237:16: warning: implicit declaration of function 'yylex' is invalid in C99 [-Wimplicit-function-declaration] yychar = yylex (); ^ gb.y:291:70: warning: implicit declaration of function 'linenumber' is invalid in C99 [-Wimplicit-function-declaration] printf("Can't parse file. Error is '%s', on line %d.\n", msg, linenumber()); ^ gb.y:402:9: warning: unused variable 'new_buf' [-Wunused-variable] char *new_buf; ^ 3 warnings generated. [ 4%] Linking C shared library libprime-phylo-sfile.so cd /<>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cmake -E cmake_link_script CMakeFiles/prime-phylo-sfile.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIE -pie -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libprime-phylo-sfile.so -o libprime-phylo-sfile.so CMakeFiles/prime-phylo-sfile.dir/gbread.c.o CMakeFiles/prime-phylo-sfile.dir/sfile.c.o CMakeFiles/prime-phylo-sfile.dir/lexer.c.o CMakeFiles/prime-phylo-sfile.dir/gb.tab.c.o -Wl,-rpath,:::::::::::::::::::: clang: warning: argument unused during compilation: '-pie' make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 4%] Built target prime-phylo-sfile make -f src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/build.make src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/depend make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 5%] [FLEX][MyScanner] Building scanner with flex 2.6.1 cd /<>/src/cxx/libraries/prime && /usr/bin/flex -Pyytree_ -o/<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime/lexer.c NHX.l [ 5%] [BISON][MyParser] Building parser with bison 3.0.4 cd /<>/src/cxx/libraries/prime && /usr/bin/bison -d -y -p yytree_ -d -o /<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime/NHXparse.c NHXparse.y cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/cxx/libraries/prime /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime /<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DependInfo.cmake --color= Scanning dependencies of target prime-phylo make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/build.make src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 6%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXnode.c.o cd /<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2021/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2021/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/NHXnode.c.o -c /<>/src/cxx/libraries/prime/NHXnode.c [ 6%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXtree.c.o cd /<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2021/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2021/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/NHXtree.c.o -c /<>/src/cxx/libraries/prime/NHXtree.c [ 7%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXannotation.c.o cd /<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2021/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2021/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/NHXannotation.c.o -c /<>/src/cxx/libraries/prime/NHXannotation.c [ 7%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/lexer.c.o cd /<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2021/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2021/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/lexer.c.o -c /<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime/lexer.c /<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime/lexer.c:1320:17: warning: unused function 'yyunput' [-Wunused-function] static void yyunput (int c, char * yy_bp ) ^ /<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime/lexer.c:1363:16: warning: function 'input' is not needed and will not be emitted [-Wunneeded-internal-declaration] static int input (void) ^ 2 warnings generated. [ 8%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXparse.c.o cd /<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2021/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2021/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/NHXparse.c.o -c /<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime/NHXparse.c /<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime/NHXparse.c:1280:16: warning: implicit declaration of function 'yytree_lex' is invalid in C99 [-Wimplicit-function-declaration] yychar = yylex (); ^ /<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime/NHXparse.c:64:25: note: expanded from macro 'yylex' #define yylex yytree_lex ^ NHXparse.y:351:5: warning: implicit declaration of function 'close' is invalid in C99 [-Wimplicit-function-declaration] close(f); ^ NHXparse.y:399:3: warning: implicit declaration of function 'read_from_string' is invalid in C99 [-Wimplicit-function-declaration] read_from_string(str); ^ NHXparse.y:404:3: warning: implicit declaration of function 'close_string_buffer' is invalid in C99 [-Wimplicit-function-declaration] close_string_buffer(); ^ 4 warnings generated. [ 8%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/AnError.cc.o cd /<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2021/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2021/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -std=gnu++98 -o CMakeFiles/prime-phylo.dir/AnError.cc.o -c /<>/src/cxx/libraries/prime/AnError.cc [ 9%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Beep.cc.o cd /<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2021/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2021/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -std=gnu++98 -o CMakeFiles/prime-phylo.dir/Beep.cc.o -c /<>/src/cxx/libraries/prime/Beep.cc [ 10%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BeepOption.cc.o cd /<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2021/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2021/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -std=gnu++98 -o CMakeFiles/prime-phylo.dir/BeepOption.cc.o -c /<>/src/cxx/libraries/prime/BeepOption.cc [ 10%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Hacks.cc.o cd /<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2021/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2021/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -std=gnu++98 -o CMakeFiles/prime-phylo.dir/Hacks.cc.o -c /<>/src/cxx/libraries/prime/Hacks.cc [ 11%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ODESolver.cc.o cd /<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2021/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2021/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -std=gnu++98 -o CMakeFiles/prime-phylo.dir/ODESolver.cc.o -c /<>/src/cxx/libraries/prime/ODESolver.cc In file included from /<>/src/cxx/libraries/prime/ODESolver.cc:4: /<>/src/cxx/libraries/prime/ODESolver.hh:359:20: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real C2 = 1.0 / 5.0; ^ ~~~~~~~~~~~~~~ /<>/src/cxx/libraries/prime/ODESolver.hh:360:20: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real C3 = 3.0 / 10.0; ^ ~~~~~~~~~~~~~~ /<>/src/cxx/libraries/prime/ODESolver.hh:361:20: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real C4 = 4.0 / 5.0; ^ ~~~~~~~~~~~~~~ /<>/src/cxx/libraries/prime/ODESolver.hh:362:20: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real C5 = 8.0 / 9.0; ^ ~~~~~~~~~~~~~~ /<>/src/cxx/libraries/prime/ODESolver.hh:363:20: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real A21 = 1.0 / 5.0; ^ ~~~~~~~~~~~~~~ /<>/src/cxx/libraries/prime/ODESolver.hh:364:20: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real A31 = 3.0 / 40.0; ^ ~~~~~~~~~~~~~~ /<>/src/cxx/libraries/prime/ODESolver.hh:365:20: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real A32 = 9.0 / 40.0; ^ ~~~~~~~~~~~~~~ /<>/src/cxx/libraries/prime/ODESolver.hh:366:20: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real A41 = 44.0 / 45.0; ^ ~~~~~~~~~~~~~~~ /<>/src/cxx/libraries/prime/ODESolver.hh:367:20: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real A42 = -56.0 / 15.0; ^ ~~~~~~~~~~~~~~~~ /<>/src/cxx/libraries/prime/ODESolver.hh:368:20: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real A43 = 32.0 / 9.0; ^ ~~~~~~~~~~~~~~~ /<>/src/cxx/libraries/prime/ODESolver.hh:369:20: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real A51 = 19372.0 / 6561.0; ^ ~~~~~~~~~~~~~~~~~~ /<>/src/cxx/libraries/prime/ODESolver.hh:370:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real A52 = -25360.0 / 2187.0; ^ ~~~~~~~~~~~~~~~~~~~ /<>/src/cxx/libraries/prime/ODESolver.hh:371:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real A53 = 64448.0 / 6561.0; ^ ~~~~~~~~~~~~~~~~~~ /<>/src/cxx/libraries/prime/ODESolver.hh:372:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real A54 = -212.0 / 729.0; ^ ~~~~~~~~~~~~~~~~~ /<>/src/cxx/libraries/prime/ODESolver.hh:373:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real A61 = 9017.0 / 3168.0; ^ ~~~~~~~~~~~~~~~~~ /<>/src/cxx/libraries/prime/ODESolver.hh:374:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real A62 = -355.0 / 33.0; ^ ~~~~~~~~~~~~~~~~~ /<>/src/cxx/libraries/prime/ODESolver.hh:375:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real A63 = 46732.0 / 5247.0; ^ ~~~~~~~~~~~~~~~~~~ /<>/src/cxx/libraries/prime/ODESolver.hh:376:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real A64 = 49.0 / 176.0; ^ ~~~~~~~~~~~~~~~ /<>/src/cxx/libraries/prime/ODESolver.hh:377:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real A65 = -5103.0 / 18656.0; ^ ~~~~~~~~~~~~~~~~~~ /<>/src/cxx/libraries/prime/ODESolver.hh:378:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real A71 = 35.0 / 384.0; ^ ~~~~~~~~~~~~~~~ /<>/src/cxx/libraries/prime/ODESolver.hh:379:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real A73 = 500.0 / 1113.0; ^ ~~~~~~~~~~~~~~~~ /<>/src/cxx/libraries/prime/ODESolver.hh:380:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real A74 = 125.0 / 192.0; ^ ~~~~~~~~~~~~~~~~ /<>/src/cxx/libraries/prime/ODESolver.hh:381:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real A75 = -2187.0 / 6784.0; ^ ~~~~~~~~~~~~~~~~~~ /<>/src/cxx/libraries/prime/ODESolver.hh:382:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real A76 = 11.0 / 84.0; ^ ~~~~~~~~~~~~~~~ /<>/src/cxx/libraries/prime/ODESolver.hh:383:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real E1 = 71.0 / 57600.0; ^ ~~~~~~~~~~~~~~~ /<>/src/cxx/libraries/prime/ODESolver.hh:384:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real E3 = -71.0 / 16695.0; ^ ~~~~~~~~~~~~~~~~ /<>/src/cxx/libraries/prime/ODESolver.hh:385:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real E4 = 71.0 / 1920.0; ^ ~~~~~~~~~~~~~~~ /<>/src/cxx/libraries/prime/ODESolver.hh:386:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real E5 = -17253.0 / 339200.0; ^ ~~~~~~~~~~~~~~~~~~~ /<>/src/cxx/libraries/prime/ODESolver.hh:387:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real E6 = 22.0 / 525.0; ^ ~~~~~~~~~~~~~~~ /<>/src/cxx/libraries/prime/ODESolver.hh:388:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real E7 = -1.0 / 40.0; ^ ~~~~~~~~~~~~~~~ /<>/src/cxx/libraries/prime/ODESolver.hh:391:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real D1 = -12715105075.0 / 11282082432.0; ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/cxx/libraries/prime/ODESolver.hh:392:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real D3 = 87487479700.0 / 32700410799.0; ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/cxx/libraries/prime/ODESolver.hh:393:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real D4 = -10690763975.0 / 1880347072.0; ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/cxx/libraries/prime/ODESolver.hh:394:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real D5 = 701980252875.0 / 199316789632.0; ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/cxx/libraries/prime/ODESolver.hh:395:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real D6 = -1453857185.0 / 822651844.0; ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/cxx/libraries/prime/ODESolver.hh:396:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real D7 = 69997945.0 / 29380423.0; ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 36 warnings generated. [ 11%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PRNG.cc.o cd /<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2021/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2021/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -std=gnu++98 -o CMakeFiles/prime-phylo.dir/PRNG.cc.o -c /<>/src/cxx/libraries/prime/PRNG.cc [ 12%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PrimeOptionMap.cc.o cd /<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2021/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2021/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -std=gnu++98 -o CMakeFiles/prime-phylo.dir/PrimeOptionMap.cc.o -c /<>/src/cxx/libraries/prime/PrimeOptionMap.cc In file included from /<>/src/cxx/libraries/prime/PrimeOptionMap.cc:1: /<>/src/cxx/libraries/prime/PrimeOptionMap.hh:161:32: error: no function named 'operator<<' with type 'std::ostream &(std::ostream &, const beep::PrimeOptionMap &)' (aka 'basic_ostream &(basic_ostream &, const beep::PrimeOptionMap &)') was found in the specified scope friend std::ostream& beep::operator<<(std::ostream& o, ^ /<>/src/cxx/libraries/prime/PrimeOptionMap.hh:163:32: error: no function named 'operator<<' with type 'std::ostream &(std::ostream &, const beep::PrimeOption &)' (aka 'basic_ostream &(basic_ostream &, const beep::PrimeOption &)') was found in the specified scope friend std::ostream& beep::operator<<(std::ostream& o, ^ In file included from /<>/src/cxx/libraries/prime/PrimeOptionMap.cc:3: /<>/src/cxx/libraries/prime/PrimeOption.hh:391:2: warning: struct 'UserSubstMatrixParams' was previously declared as a class [-Wmismatched-tags] struct UserSubstMatrixParams tmpVal; ^ /<>/src/cxx/libraries/prime/PrimeOptionMap.hh:23:9: note: previous use is here class UserSubstMatrixParams ^ /<>/src/cxx/libraries/prime/PrimeOption.hh:391:2: note: did you mean class here? struct UserSubstMatrixParams tmpVal; ^~~~~~ class /<>/src/cxx/libraries/prime/PrimeOption.hh:407:56: warning: adding 'unsigned int' to a string does not append to the string [-Wstring-plus-int] throw AnError("Wrong dimension of Pi, should be " + dim, 1); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /<>/src/cxx/libraries/prime/PrimeOption.hh:407:56: note: use array indexing to silence this warning throw AnError("Wrong dimension of Pi, should be " + dim, 1); ^ & [ ] /<>/src/cxx/libraries/prime/PrimeOption.hh:425:55: warning: adding 'unsigned int' to a string does not append to the string [-Wstring-plus-int] throw AnError("Wrong dimension of R, should be " + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ /<>/src/cxx/libraries/prime/PrimeOption.hh:425:55: note: use array indexing to silence this warning throw AnError("Wrong dimension of R, should be " + ^ /<>/src/cxx/libraries/prime/PrimeOptionMap.cc:306:18: error: 'optionsInOrderOfIns' is a private member of 'beep::PrimeOptionMap' for(it = pom.optionsInOrderOfIns.begin(); ^ /<>/src/cxx/libraries/prime/PrimeOptionMap.hh:190:31: note: declared private here std::vector optionsInOrderOfIns; //! Options in insert order ^ /<>/src/cxx/libraries/prime/PrimeOptionMap.cc:307:12: error: 'optionsInOrderOfIns' is a private member of 'beep::PrimeOptionMap' it != pom.optionsInOrderOfIns.end(); ++it) ^ /<>/src/cxx/libraries/prime/PrimeOptionMap.hh:190:31: note: declared private here std::vector optionsInOrderOfIns; //! Options in insert order ^ 3 warnings and 4 errors generated. src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/build.make:341: recipe for target 'src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PrimeOptionMap.cc.o' failed make[3]: *** [src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PrimeOptionMap.cc.o] Error 1 make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' CMakeFiles/Makefile2:136: recipe for target 'src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/all' failed make[2]: *** [src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/all] Error 2 make[2]: Leaving directory '/<>/obj-x86_64-linux-gnu' Makefile:152: recipe for target 'all' failed make[1]: *** [all] Error 2 make[1]: Leaving directory '/<>/obj-x86_64-linux-gnu' dh_auto_build: make -j1 returned exit code 2 debian/rules:10: 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 2016-08-29T16:45:36Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build-Space: 0 Build-Time: 8 Distribution: unstable Fail-Stage: build Host Architecture: amd64 Install-Time: 265 Job: prime-phylo_1.0.11-4 Machine Architecture: amd64 Package: prime-phylo Package-Time: 388 Source-Version: 1.0.11-4 Space: 0 Status: failed Version: 1.0.11-4 -------------------------------------------------------------------------------- Finished at 2016-08-29T16:45:36Z Build needed 00:00:00, 0k disc space E: Build failure (dpkg-buildpackage died) DC-Status: Failed 389.649317865s