DC-Build-Header: prime-phylo 1.0.11-4 / 2018-05-02 12:54:35 +0000 DC-Task: type:rebuild-binarch-only source:prime-phylo version:1.0.11-4 chroot:unstable esttime:198 logfile:/tmp/prime-phylo_1.0.11-4_unstable_clang60.log modes:clang60:binarch-only DC-Sbuild-call: su user42 -c 'sbuild -n --arch-any --apt-update -d unstable -v --chroot-setup-commands=/tmp/clang60 prime-phylo_1.0.11-4' sbuild (Debian sbuild) 0.73.0 (23 Dec 2016) on ip-172-31-1-67.eu-central-1.compute.internal +==============================================================================+ | prime-phylo 1.0.11-4 (amd64) Wed, 02 May 2018 12:54:35 +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 Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/unstable-amd64-sbuild-f482c80f-3acc-4976-99d7-7733b1144fff' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /tmp/clang60 ------------ + echo 'Entering customization script...' Entering customization script... + CLANG_VERSION=6.0 + echo 'Install of clang-6.0' Install of clang-6.0 + apt-get update Get:1 http://127.0.0.1:9999/debian unstable InRelease [242 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 Sources 2018-05-02-0830.09.pdiff [16.2 kB] Get:4 http://127.0.0.1:9999/debian unstable/main Sources 2018-05-02-0830.09.pdiff [16.2 kB] Get:5 http://127.0.0.1:9999/debian unstable/main amd64 Packages 2018-05-02-0830.09.pdiff [1781 B] Get:5 http://127.0.0.1:9999/debian unstable/main amd64 Packages 2018-05-02-0830.09.pdiff [1781 B] Get:6 http://127.0.0.1:9999/debian unstable/main Translation-en [6016 kB] Fetched 6332 kB in 2s (3395 kB/s) Reading package lists... + apt-get install --yes --no-install-recommends --force-yes clang-6.0 Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: lib32gcc1 lib32stdc++6 libbsd0 libc6-i386 libclang-common-6.0-dev libclang1-6.0 libedit2 libjsoncpp1 libllvm6.0 libncurses5 libobjc-7-dev libobjc4 Suggested packages: gnustep gnustep-devel clang-6.0-doc Recommended packages: llvm-6.0-dev python libomp-dev libgpm2 The following NEW packages will be installed: clang-6.0 lib32gcc1 lib32stdc++6 libbsd0 libc6-i386 libclang-common-6.0-dev libclang1-6.0 libedit2 libjsoncpp1 libllvm6.0 libncurses5 libobjc-7-dev libobjc4 0 upgraded, 13 newly installed, 0 to remove and 0 not upgraded. Need to get 37.7 MB of archives. After this operation, 187 MB of additional disk space will be used. Get:1 http://127.0.0.1:9999/debian unstable/main amd64 libjsoncpp1 amd64 1.7.4-3 [75.6 kB] Get:2 http://127.0.0.1:9999/debian unstable/main amd64 libbsd0 amd64 0.8.7-1 [92.1 kB] Get:3 http://127.0.0.1:9999/debian unstable/main amd64 libncurses5 amd64 6.1+20180210-2 [95.7 kB] Get:4 http://127.0.0.1:9999/debian unstable/main amd64 libedit2 amd64 3.1-20170329-1 [85.2 kB] Get:5 http://127.0.0.1:9999/debian unstable/main amd64 libllvm6.0 amd64 1:6.0-3 [14.5 MB] Get:6 http://127.0.0.1:9999/debian unstable/main amd64 libobjc4 amd64 8-20180425-1 [52.4 kB] Get:7 http://127.0.0.1:9999/debian unstable/main amd64 libobjc-7-dev amd64 7.3.0-17 [204 kB] Get:8 http://127.0.0.1:9999/debian unstable/main amd64 libc6-i386 amd64 2.27-3 [2855 kB] Get:9 http://127.0.0.1:9999/debian unstable/main amd64 lib32gcc1 amd64 1:8-20180425-1 [47.8 kB] Get:10 http://127.0.0.1:9999/debian unstable/main amd64 lib32stdc++6 amd64 8-20180425-1 [406 kB] Get:11 http://127.0.0.1:9999/debian unstable/main amd64 libclang-common-6.0-dev amd64 1:6.0-3 [3102 kB] Get:12 http://127.0.0.1:9999/debian unstable/main amd64 libclang1-6.0 amd64 1:6.0-3 [6995 kB] Get:13 http://127.0.0.1:9999/debian unstable/main amd64 clang-6.0 amd64 1:6.0-3 [9175 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 37.7 MB in 0s (99.4 MB/s) Selecting previously unselected package libjsoncpp1: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 ... 10022 files and directories currently installed.) Preparing to unpack .../00-libjsoncpp1_1.7.4-3_amd64.deb ... Unpacking libjsoncpp1:amd64 (1.7.4-3) ... Selecting previously unselected package libbsd0:amd64. Preparing to unpack .../01-libbsd0_0.8.7-1_amd64.deb ... Unpacking libbsd0:amd64 (0.8.7-1) ... Selecting previously unselected package libncurses5:amd64. Preparing to unpack .../02-libncurses5_6.1+20180210-2_amd64.deb ... Unpacking libncurses5:amd64 (6.1+20180210-2) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../03-libedit2_3.1-20170329-1_amd64.deb ... Unpacking libedit2:amd64 (3.1-20170329-1) ... Selecting previously unselected package libllvm6.0:amd64. Preparing to unpack .../04-libllvm6.0_1%3a6.0-3_amd64.deb ... Unpacking libllvm6.0:amd64 (1:6.0-3) ... Selecting previously unselected package libobjc4:amd64. Preparing to unpack .../05-libobjc4_8-20180425-1_amd64.deb ... Unpacking libobjc4:amd64 (8-20180425-1) ... Selecting previously unselected package libobjc-7-dev:amd64. Preparing to unpack .../06-libobjc-7-dev_7.3.0-17_amd64.deb ... Unpacking libobjc-7-dev:amd64 (7.3.0-17) ... Selecting previously unselected package libc6-i386. Preparing to unpack .../07-libc6-i386_2.27-3_amd64.deb ... Unpacking libc6-i386 (2.27-3) ... Selecting previously unselected package lib32gcc1. Preparing to unpack .../08-lib32gcc1_1%3a8-20180425-1_amd64.deb ... 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Setting up lib32gcc1 (1:8-20180425-1) ... Setting up libjsoncpp1:amd64 (1.7.4-3) ... Setting up libedit2:amd64 (3.1-20170329-1) ... Setting up libllvm6.0:amd64 (1:6.0-3) ... Setting up libclang1-6.0:amd64 (1:6.0-3) ... Setting up lib32stdc++6 (8-20180425-1) ... Setting up libclang-common-6.0-dev (1:6.0-3) ... Setting up clang-6.0 (1:6.0-3) ... Processing triggers for libc-bin (2.27-3) ... 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 8' + cd /usr/bin + for VERSION in $VERSIONS + rm -f g++-4.6 gcc-4.6 cpp-4.6 gcc + ln -s clang++-6.0 g++-4.6 + ln -s clang-6.0 gcc-4.6 + ln -s clang-6.0 cpp-4.6 + ln -s clang-6.0 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++-6.0 g++-4.7 + ln -s clang-6.0 gcc-4.7 + ln -s clang-6.0 cpp-4.7 + ln -s clang-6.0 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++-6.0 g++-4.8 + ln -s clang-6.0 gcc-4.8 + ln -s clang-6.0 cpp-4.8 + ln -s clang-6.0 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++-6.0 g++-4.9 + ln -s clang-6.0 gcc-4.9 + ln -s clang-6.0 cpp-4.9 + ln -s clang-6.0 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++-6.0 g++-5 + ln -s clang-6.0 gcc-5 + ln -s clang-6.0 cpp-5 + ln -s clang-6.0 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++-6.0 g++-6 + ln -s clang-6.0 gcc-6 + ln -s clang-6.0 cpp-6 + ln -s clang-6.0 gcc + echo 'gcc-6 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-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++-6 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-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++-7 gcc-7 cpp-7 gcc + ln -s clang++-6.0 g++-7 + ln -s clang-6.0 gcc-7 + ln -s clang-6.0 cpp-7 + ln -s clang-6.0 gcc + echo 'gcc-7 hold' + dpkg --set-selections + echo 'g++-7 hold' + dpkg --set-selections + for VERSION in $VERSIONS + rm -f g++-8 gcc-8 cpp-8 gcc + ln -s clang++-6.0 g++-8 + ln -s clang-6.0 gcc-8 + ln -s clang-6.0 cpp-8 + ln -s clang-6.0 gcc + echo 'gcc-8 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-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++-8 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-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 + cd - /build/prime-phylo-gsUC60 + 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/clang60'. 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... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | 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 (5248 kB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/prime-phylo-gsUC60/prime-phylo-1.0.11' with '<>' I: NOTICE: Log filtering will replace 'build/prime-phylo-gsUC60' 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-5paxgd/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-5paxgd/apt_archive ./ InRelease Get:2 copy:/<>/resolver-5paxgd/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-5paxgd/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-5paxgd/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-5paxgd/apt_archive ./ Packages [434 B] Fetched 1740 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 856 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-5paxgd/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [856 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 856 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 10771 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 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-5paxgd/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-core-dummy sbuild-build-depends-prime-phylo-dummy dpkg-scanpackages: info: Wrote 2 entries to output Packages file. Ign:1 copy:/<>/resolver-5paxgd/apt_archive ./ InRelease Get:2 copy:/<>/resolver-5paxgd/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-5paxgd/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-5paxgd/apt_archive ./ Sources [577 B] Get:5 copy:/<>/resolver-5paxgd/apt_archive ./ Packages [660 B] Fetched 2200 B in 0s (0 B/s) Reading package lists... 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-7 groff-base ibverbs-providers icu-devtools intltool-debian libarchive-zip-perl libarchive13 libbison-dev libblas-dev libblas3 libboost-dev libboost-mpi-dev libboost-mpi1.62-dev libboost-mpi1.62.0 libboost-serialization-dev libboost-serialization1.62-dev libboost-serialization1.62.0 libboost1.62-dev libcroco3 libcurl3 libevent-2.1-6 libevent-core-2.1-6 libevent-pthreads-2.1-6 libexpat1 libfabric1 libfile-stripnondeterminism-perl libgfortran-7-dev libgfortran4 libglib2.0-0 libgssapi-krb5-2 libhwloc-dev libhwloc-plugins libhwloc5 libibverbs-dev libibverbs1 libicu-dev libicu57 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack-dev liblapack3 libldap-2.4-2 libldap-common libltdl-dev libltdl7 liblzo2-2 libmagic-mgc libmagic1 libnghttp2-14 libnl-3-200 libnl-route-3-200 libnuma-dev libnuma1 libopenmpi-dev libopenmpi3 libpciaccess0 libpipeline1 libpmix2 libprocps6 libpsl5 libpsm-infinipath1 librdmacm1 librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh2-1 libssl1.0.2 libtimedate-perl libtool libuv1 libxml2 libxml2-dev lsb-base m4 man-db mpi-default-dev ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client po-debconf procps zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc bison-doc wamerican | wordlist whois vacation cmake-doc ninja-build dh-make dwz flex-doc gettext-doc libasprintf-dev libgettextpo-dev gfortran-multilib gfortran-doc gfortran-7-multilib gfortran-7-doc libgfortran4-dbg libcoarrays-dev groff lrzip liblapack-doc libboost-doc libboost-graph1.62-dev libboost1.62-doc libboost-atomic1.62-dev libboost-chrono1.62-dev libboost-context1.62-dev libboost-coroutine1.62-dev libboost-date-time1.62-dev libboost-exception1.62-dev libboost-fiber1.62-dev libboost-filesystem1.62-dev libboost-graph-parallel1.62-dev libboost-iostreams1.62-dev libboost-locale1.62-dev libboost-log1.62-dev libboost-math1.62-dev libboost-mpi-python1.62-dev libboost-program-options1.62-dev libboost-python1.62-dev libboost-random1.62-dev libboost-regex1.62-dev libboost-signals1.62-dev libboost-system1.62-dev libboost-test1.62-dev libboost-thread1.62-dev libboost-timer1.62-dev libboost-type-erasure1.62-dev libboost-wave1.62-dev libboost1.62-tools-dev libmpfrc++-dev libntl-dev krb5-doc krb5-user libhwloc-contrib-plugins icu-doc libtool-doc openmpi-doc pciutils gcj-jdk pkg-config m4-doc apparmor less www-browser opencl-icd keychain libpam-ssh monkeysphere ssh-askpass libmail-box-perl Recommended packages: libfl-dev curl | wget | lynx ca-certificates libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales publicsuffix libsasl2-modules xauth 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-7 groff-base ibverbs-providers icu-devtools intltool-debian libarchive-zip-perl libarchive13 libbison-dev libblas-dev libblas3 libboost-dev libboost-mpi-dev libboost-mpi1.62-dev libboost-mpi1.62.0 libboost-serialization-dev libboost-serialization1.62-dev libboost-serialization1.62.0 libboost1.62-dev libcroco3 libcurl3 libevent-2.1-6 libevent-core-2.1-6 libevent-pthreads-2.1-6 libexpat1 libfabric1 libfile-stripnondeterminism-perl libgfortran-7-dev libgfortran4 libglib2.0-0 libgssapi-krb5-2 libhwloc-dev libhwloc-plugins libhwloc5 libibverbs-dev libibverbs1 libicu-dev libicu57 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack-dev liblapack3 libldap-2.4-2 libldap-common libltdl-dev libltdl7 liblzo2-2 libmagic-mgc libmagic1 libnghttp2-14 libnl-3-200 libnl-route-3-200 libnuma-dev libnuma1 libopenmpi-dev libopenmpi3 libpciaccess0 libpipeline1 libpmix2 libprocps6 libpsl5 libpsm-infinipath1 librdmacm1 librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh2-1 libssl1.0.2 libtimedate-perl libtool libuv1 libxml2 libxml2-dev lsb-base m4 man-db mpi-default-dev ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client po-debconf procps sbuild-build-depends-prime-phylo-dummy zlib1g-dev 0 upgraded, 105 newly installed, 0 to remove and 0 not upgraded. Need to get 75.3 MB of archives. After this operation, 403 MB of additional disk space will be used. Get:1 copy:/<>/resolver-5paxgd/apt_archive ./ sbuild-build-depends-prime-phylo-dummy 0.invalid.0 [948 B] Get:2 http://127.0.0.1:9999/debian unstable/main amd64 bsdmainutils amd64 11.1.2 [190 kB] Get:3 http://127.0.0.1:9999/debian unstable/main amd64 groff-base amd64 1.22.3-10 [1176 kB] Get:4 http://127.0.0.1:9999/debian unstable/main amd64 libpipeline1 amd64 1.5.0-1 [29.0 kB] Get:5 http://127.0.0.1:9999/debian unstable/main amd64 man-db amd64 2.8.3-2 [1180 kB] Get:6 http://127.0.0.1:9999/debian unstable/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get:7 http://127.0.0.1:9999/debian unstable/main amd64 m4 amd64 1.4.18-1 [202 kB] Get:8 http://127.0.0.1:9999/debian unstable/main amd64 flex amd64 2.6.4-6.1 [454 kB] Get:9 http://127.0.0.1:9999/debian unstable/main amd64 libprocps6 amd64 2:3.3.14-1 [60.4 kB] Get:10 http://127.0.0.1:9999/debian unstable/main amd64 lsb-base all 9.20170808 [28.1 kB] Get:11 http://127.0.0.1:9999/debian unstable/main amd64 procps amd64 2:3.3.14-1 [257 kB] Get:12 http://127.0.0.1:9999/debian unstable/main amd64 libmagic-mgc amd64 1:5.33-2 [234 kB] Get:13 http://127.0.0.1:9999/debian unstable/main amd64 libmagic1 amd64 1:5.33-2 [113 kB] Get:14 http://127.0.0.1:9999/debian unstable/main amd64 file amd64 1:5.33-2 [65.6 kB] Get:15 http://127.0.0.1:9999/debian unstable/main amd64 gettext-base amd64 0.19.8.1-6 [122 kB] Get:16 http://127.0.0.1:9999/debian unstable/main amd64 libkeyutils1 amd64 1.5.9-9.2 [12.9 kB] Get:17 http://127.0.0.1:9999/debian unstable/main amd64 libkrb5support0 amd64 1.16-2 [62.8 kB] Get:18 http://127.0.0.1:9999/debian unstable/main amd64 libk5crypto3 amd64 1.16-2 [121 kB] Get:19 http://127.0.0.1:9999/debian unstable/main amd64 libkrb5-3 amd64 1.16-2 [316 kB] Get:20 http://127.0.0.1:9999/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.16-2 [158 kB] Get:21 http://127.0.0.1:9999/debian unstable/main amd64 libssl1.0.2 amd64 1.0.2o-1 [1296 kB] Get:22 http://127.0.0.1:9999/debian unstable/main amd64 openssh-client amd64 1:7.7p1-2 [802 kB] Get:23 http://127.0.0.1:9999/debian unstable/main amd64 autoconf all 2.69-11 [341 kB] Get:24 http://127.0.0.1:9999/debian unstable/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get:25 http://127.0.0.1:9999/debian unstable/main amd64 automake all 1:1.15.1-3.1 [736 kB] Get:26 http://127.0.0.1:9999/debian unstable/main amd64 autopoint all 0.19.8.1-6 [434 kB] Get:27 http://127.0.0.1:9999/debian unstable/main amd64 libbison-dev amd64 2:3.0.4.dfsg-1+b1 [433 kB] Get:28 http://127.0.0.1:9999/debian unstable/main amd64 bison amd64 2:3.0.4.dfsg-1+b1 [786 kB] Get:29 http://127.0.0.1:9999/debian unstable/main amd64 cmake-data all 3.11.1-1 [1386 kB] Get:30 http://127.0.0.1:9999/debian unstable/main amd64 liblzo2-2 amd64 2.08-1.2+b2 [55.0 kB] Get:31 http://127.0.0.1:9999/debian unstable/main amd64 libicu57 amd64 57.1-9 [7698 kB] Get:32 http://127.0.0.1:9999/debian unstable/main amd64 libxml2 amd64 2.9.4+dfsg1-6.1 [725 kB] Get:33 http://127.0.0.1:9999/debian unstable/main amd64 libarchive13 amd64 3.2.2-3.1 [296 kB] Get:34 http://127.0.0.1:9999/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.27~101-g0780600+dfsg-3.1 [68.6 kB] Get:35 http://127.0.0.1:9999/debian unstable/main amd64 libsasl2-2 amd64 2.1.27~101-g0780600+dfsg-3.1 [105 kB] Get:36 http://127.0.0.1:9999/debian unstable/main amd64 libldap-common all 2.4.45+dfsg-1 [87.0 kB] Get:37 http://127.0.0.1:9999/debian unstable/main amd64 libldap-2.4-2 amd64 2.4.45+dfsg-1 [223 kB] Get:38 http://127.0.0.1:9999/debian unstable/main amd64 libnghttp2-14 amd64 1.31.1-1 [80.7 kB] Get:39 http://127.0.0.1:9999/debian unstable/main amd64 libpsl5 amd64 0.20.1-1 [52.6 kB] Get:40 http://127.0.0.1:9999/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-1+b1 [60.4 kB] Get:41 http://127.0.0.1:9999/debian unstable/main amd64 libssh2-1 amd64 1.8.0-1 [138 kB] Get:42 http://127.0.0.1:9999/debian unstable/main amd64 libcurl3 amd64 7.58.0-2 [312 kB] Get:43 http://127.0.0.1:9999/debian unstable/main amd64 libexpat1 amd64 2.2.5-3 [96.8 kB] Get:44 http://127.0.0.1:9999/debian unstable/main amd64 librhash0 amd64 1.3.6-2 [87.1 kB] Get:45 http://127.0.0.1:9999/debian unstable/main amd64 libuv1 amd64 1.18.0-3 [98.5 kB] Get:46 http://127.0.0.1:9999/debian unstable/main amd64 cmake amd64 3.11.1-1 [3190 kB] Get:47 http://127.0.0.1:9999/debian unstable/main amd64 libtool all 2.4.6-2.1 [547 kB] Get:48 http://127.0.0.1:9999/debian unstable/main amd64 dh-autoreconf all 17 [16.5 kB] Get:49 http://127.0.0.1:9999/debian unstable/main amd64 libarchive-zip-perl all 1.60-1 [95.6 kB] Get:50 http://127.0.0.1:9999/debian unstable/main amd64 libfile-stripnondeterminism-perl all 0.041-1 [19.9 kB] Get:51 http://127.0.0.1:9999/debian unstable/main amd64 libtimedate-perl all 2.3000-2 [42.2 kB] Get:52 http://127.0.0.1:9999/debian unstable/main amd64 dh-strip-nondeterminism all 0.041-1 [12.0 kB] Get:53 http://127.0.0.1:9999/debian unstable/main amd64 libglib2.0-0 amd64 2.56.1-2 [2928 kB] Get:54 http://127.0.0.1:9999/debian unstable/main amd64 libcroco3 amd64 0.6.12-2 [144 kB] Get:55 http://127.0.0.1:9999/debian unstable/main amd64 gettext amd64 0.19.8.1-6 [1302 kB] Get:56 http://127.0.0.1:9999/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.4 [26.3 kB] Get:57 http://127.0.0.1:9999/debian unstable/main amd64 po-debconf all 1.0.20 [247 kB] Get:58 http://127.0.0.1:9999/debian unstable/main amd64 debhelper all 11.2.1 [1013 kB] Get:59 http://127.0.0.1:9999/debian unstable/main amd64 gengetopt amd64 2.22.6+dfsg0-2 [174 kB] Get:60 http://127.0.0.1:9999/debian unstable/main amd64 libgfortran4 amd64 7.3.0-17 [487 kB] Get:61 http://127.0.0.1:9999/debian unstable/main amd64 libgfortran-7-dev amd64 7.3.0-17 [526 kB] Get:62 http://127.0.0.1:9999/debian unstable/main amd64 gfortran-7 amd64 7.3.0-17 [7067 kB] Get:63 http://127.0.0.1:9999/debian unstable/main amd64 gfortran amd64 4:7.3.0-3 [1424 B] Get:64 http://127.0.0.1:9999/debian unstable/main amd64 libnl-3-200 amd64 3.2.27-2 [61.5 kB] Get:65 http://127.0.0.1:9999/debian unstable/main amd64 libnl-route-3-200 amd64 3.2.27-2 [136 kB] Get:66 http://127.0.0.1:9999/debian unstable/main amd64 libibverbs1 amd64 17.1-2 [45.2 kB] Get:67 http://127.0.0.1:9999/debian unstable/main amd64 ibverbs-providers amd64 17.1-2 [170 kB] Get:68 http://127.0.0.1:9999/debian unstable/main amd64 icu-devtools amd64 57.1-9 [177 kB] Get:69 http://127.0.0.1:9999/debian unstable/main amd64 libblas3 amd64 3.8.0-1 [150 kB] Get:70 http://127.0.0.1:9999/debian unstable/main amd64 libblas-dev amd64 3.8.0-1 [156 kB] Get:71 http://127.0.0.1:9999/debian unstable/main amd64 libboost1.62-dev amd64 1.62.0+dfsg-5+b1 [7004 kB] Get:72 http://127.0.0.1:9999/debian unstable/main amd64 libboost-dev amd64 1.62.0.1 [3632 B] Get:73 http://127.0.0.1:9999/debian unstable/main amd64 libboost-serialization1.62.0 amd64 1.62.0+dfsg-5+b1 [126 kB] Get:74 http://127.0.0.1:9999/debian unstable/main amd64 libboost-serialization1.62-dev amd64 1.62.0+dfsg-5+b1 [164 kB] Get:75 http://127.0.0.1:9999/debian unstable/main amd64 libevent-2.1-6 amd64 2.1.8-stable-4 [177 kB] Get:76 http://127.0.0.1:9999/debian unstable/main amd64 libevent-core-2.1-6 amd64 2.1.8-stable-4 [129 kB] Get:77 http://127.0.0.1:9999/debian unstable/main amd64 libevent-pthreads-2.1-6 amd64 2.1.8-stable-4 [47.9 kB] Get:78 http://127.0.0.1:9999/debian unstable/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-5 [172 kB] Get:79 http://127.0.0.1:9999/debian unstable/main amd64 librdmacm1 amd64 17.1-2 [65.8 kB] Get:80 http://127.0.0.1:9999/debian unstable/main amd64 libfabric1 amd64 1.5.3-1 [303 kB] Get:81 http://127.0.0.1:9999/debian unstable/main amd64 libltdl7 amd64 2.4.6-2.1 [389 kB] Get:82 http://127.0.0.1:9999/debian unstable/main amd64 libnuma1 amd64 2.0.11-2.2 [33.8 kB] Get:83 http://127.0.0.1:9999/debian unstable/main amd64 libhwloc5 amd64 1.11.10-1 [110 kB] Get:84 http://127.0.0.1:9999/debian unstable/main amd64 libpciaccess0 amd64 0.14-1 [53.5 kB] Get:85 http://127.0.0.1:9999/debian unstable/main amd64 ocl-icd-libopencl1 amd64 2.2.12-1 [37.1 kB] Get:86 http://127.0.0.1:9999/debian unstable/main amd64 libhwloc-plugins amd64 1.11.10-1 [16.7 kB] Get:87 http://127.0.0.1:9999/debian unstable/main amd64 libpmix2 amd64 2.1.1~rc1-4 [340 kB] Get:88 http://127.0.0.1:9999/debian unstable/main amd64 libopenmpi3 amd64 3.0.1.real-1 [2099 kB] Get:89 http://127.0.0.1:9999/debian unstable/main amd64 libboost-mpi1.62.0 amd64 1.62.0+dfsg-5+b1 [71.2 kB] Get:90 http://127.0.0.1:9999/debian unstable/main amd64 openmpi-common all 3.0.1.real-1 [158 kB] Get:91 http://127.0.0.1:9999/debian unstable/main amd64 libibverbs-dev amd64 17.1-2 [104 kB] Get:92 http://127.0.0.1:9999/debian unstable/main amd64 libnuma-dev amd64 2.0.11-2.2 [46.7 kB] Get:93 http://127.0.0.1:9999/debian unstable/main amd64 libltdl-dev amd64 2.4.6-2.1 [161 kB] Get:94 http://127.0.0.1:9999/debian unstable/main amd64 libhwloc-dev amd64 1.11.10-1 [172 kB] Get:95 http://127.0.0.1:9999/debian unstable/main amd64 openmpi-bin amd64 3.0.1.real-1 [203 kB] Get:96 http://127.0.0.1:9999/debian unstable/main amd64 libopenmpi-dev amd64 3.0.1.real-1 [936 kB] Get:97 http://127.0.0.1:9999/debian unstable/main amd64 mpi-default-dev amd64 1.13 [5476 B] Get:98 http://127.0.0.1:9999/debian unstable/main amd64 libboost-mpi1.62-dev amd64 1.62.0+dfsg-5+b1 [155 kB] Get:99 http://127.0.0.1:9999/debian unstable/main amd64 libboost-mpi-dev amd64 1.62.0.1 [3500 B] Get:100 http://127.0.0.1:9999/debian unstable/main amd64 libboost-serialization-dev amd64 1.62.0.1 [3642 B] Get:101 http://127.0.0.1:9999/debian unstable/main amd64 libicu-dev amd64 57.1-9 [16.6 MB] Get:102 http://127.0.0.1:9999/debian unstable/main amd64 liblapack3 amd64 3.8.0-1 [2146 kB] Get:103 http://127.0.0.1:9999/debian unstable/main amd64 liblapack-dev amd64 3.8.0-1 [2174 kB] Get:104 http://127.0.0.1:9999/debian unstable/main amd64 libxml2-dev amd64 2.9.4+dfsg1-6.1 [821 kB] Get:105 http://127.0.0.1:9999/debian unstable/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-1 [214 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 75.3 MB in 1s (90.6 MB/s) Selecting previously unselected package bsdmainutils. (Reading database ... 10771 files and directories currently installed.) Preparing to unpack .../000-bsdmainutils_11.1.2_amd64.deb ... Unpacking bsdmainutils (11.1.2) ... Selecting previously unselected package groff-base. Preparing to unpack .../001-groff-base_1.22.3-10_amd64.deb ... Unpacking groff-base (1.22.3-10) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../002-libpipeline1_1.5.0-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.0-1) ... Selecting previously unselected package man-db. Preparing to unpack .../003-man-db_2.8.3-2_amd64.deb ... Unpacking man-db (2.8.3-2) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../004-libsigsegv2_2.12-2_amd64.deb ... Unpacking libsigsegv2:amd64 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../005-m4_1.4.18-1_amd64.deb ... Unpacking m4 (1.4.18-1) ... Selecting previously unselected package flex. 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Setting up libsasl2-modules-db:amd64 (2.1.27~101-g0780600+dfsg-3.1) ... Setting up libsasl2-2:amd64 (2.1.27~101-g0780600+dfsg-3.1) ... Setting up gettext-base (0.19.8.1-6) ... Setting up cmake-data (3.11.1-1) ... Setting up libpipeline1:amd64 (1.5.0-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-1+b1) ... Setting up m4 (1.4.18-1) ... Setting up gengetopt (2.22.6+dfsg0-2) ... Setting up libicu57:amd64 (57.1-9) ... Setting up libprocps6:amd64 (2:3.3.14-1) ... Setting up libboost-serialization1.62-dev:amd64 (1.62.0+dfsg-5+b1) ... Setting up libxml2:amd64 (2.9.4+dfsg1-6.1) ... Setting up libmagic-mgc (1:5.33-2) ... Setting up libmagic1:amd64 (1:5.33-2) ... Setting up lsb-base (9.20170808) ... Setting up librhash0:amd64 (1.3.6-2) ... Setting up procps (2:3.3.14-1) ... update-alternatives: using /usr/bin/w.procps to provide /usr/bin/w (w) in auto mode Setting up libcroco3:amd64 (0.6.12-2) ... 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Setting up icu-devtools (57.1-9) ... Setting up libboost-dev:amd64 (1.62.0.1) ... Setting up bison (2:3.0.4.dfsg-1+b1) ... update-alternatives: using /usr/bin/bison.yacc to provide /usr/bin/yacc (yacc) in auto mode Setting up libnuma-dev:amd64 (2.0.11-2.2) ... Setting up ocl-icd-libopencl1:amd64 (2.2.12-1) ... Setting up libkeyutils1:amd64 (1.5.9-9.2) ... Setting up bsdmainutils (11.1.2) ... 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 autopoint (0.19.8.1-6) ... Setting up liblzo2-2:amd64 (2.08-1.2+b2) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-1) ... Setting up libfile-stripnondeterminism-perl (0.041-1) ... Setting up gfortran (4:7.3.0-3) ... 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 libboost-serialization-dev:amd64 (1.62.0.1) ... Setting up libltdl-dev:amd64 (2.4.6-2.1) ... Setting up gettext (0.19.8.1-6) ... Setting up flex (2.6.4-6.1) ... Setting up libblas-dev:amd64 (3.8.0-1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode Setting up libarchive13:amd64 (3.2.2-3.1) ... Setting up liblapack3:amd64 (3.8.0-1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libnl-route-3-200:amd64 (3.2.27-2) ... Setting up autoconf (2.69-11) ... Setting up libicu-dev (57.1-9) ... Setting up file (1:5.33-2) ... Setting up libhwloc5:amd64 (1.11.10-1) ... Setting up libkrb5support0:amd64 (1.16-2) ... Setting up libxml2-dev:amd64 (2.9.4+dfsg1-6.1) ... Setting up libhwloc-plugins (1.11.10-1) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up automake (1:1.15.1-3.1) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up man-db (2.8.3-2) ... Not building database; man-db/auto-update is not 'true'. Setting up liblapack-dev:amd64 (3.8.0-1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode Setting up libtool (2.4.6-2.1) ... Setting up libibverbs1:amd64 (17.1-2) ... Setting up libk5crypto3:amd64 (1.16-2) ... Setting up po-debconf (1.0.20) ... Setting up libhwloc-dev:amd64 (1.11.10-1) ... Setting up libpmix2:amd64 (2.1.1~rc1-4) ... Setting up librdmacm1:amd64 (17.1-2) ... Setting up ibverbs-providers:amd64 (17.1-2) ... Setting up libkrb5-3:amd64 (1.16-2) ... Setting up libibverbs-dev:amd64 (17.1-2) ... Setting up libfabric1 (1.5.3-1) ... Setting up libgssapi-krb5-2:amd64 (1.16-2) ... Setting up openssh-client (1:7.7p1-2) ... Setting up libopenmpi3:amd64 (3.0.1.real-1) ... Setting up libcurl3:amd64 (7.58.0-2) ... Setting up openmpi-bin (3.0.1.real-1) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: error: no alternatives for mpi update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up cmake (3.11.1-1) ... Setting up libboost-mpi1.62.0 (1.62.0+dfsg-5+b1) ... Setting up libopenmpi-dev:amd64 (3.0.1.real-1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openmpi/include to provide /usr/include/x86_64-linux-gnu/mpi (mpi-x86_64-linux-gnu) in auto mode Setting up mpi-default-dev (1.13) ... Setting up libboost-mpi1.62-dev (1.62.0+dfsg-5+b1) ... Setting up libboost-mpi-dev (1.62.0.1) ... Setting up dh-autoreconf (17) ... Setting up debhelper (11.2.1) ... Setting up dh-strip-nondeterminism (0.041-1) ... Setting up sbuild-build-depends-prime-phylo-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.27-3) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.9.0-5-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.30-16 dpkg-dev_1.19.0.5 g++-7_7.3.0-17 gcc-7_7.3.0-17 libc6-dev_2.27-3 libstdc++-7-dev_7.3.0-17 libstdc++6_8-20180425-1 linux-libc-dev_4.15.17-1 Package versions: adduser_3.117 apt_1.6.1 autoconf_2.69-11 automake_1:1.15.1-3.1 autopoint_0.19.8.1-6 autotools-dev_20180224.1 base-files_10.1 base-passwd_3.5.45 bash_4.4.18-2 binutils_2.30-16 binutils-common_2.30-16 binutils-x86-64-linux-gnu_2.30-16 bison_2:3.0.4.dfsg-1+b1 bsdmainutils_11.1.2 bsdutils_1:2.31.1-0.5 build-essential_12.5 bzip2_1.0.6-8.1 clang-6.0_1:6.0-3 cmake_3.11.1-1 cmake-data_3.11.1-1 coreutils_8.28-1 cpp_4:7.3.0-3 cpp-7_7.3.0-17 dash_0.5.8-2.10 debconf_1.5.66 debfoster_2.7-2.1+b1 debhelper_11.2.1 debian-archive-keyring_2017.7 debianutils_4.8.4 dh-autoreconf_17 dh-strip-nondeterminism_0.041-1 diffutils_1:3.6-1 dpkg_1.19.0.5 dpkg-dev_1.19.0.5 e2fslibs_1.44.1-2 e2fsprogs_1.44.1-2 eatmydata_105-6 fakeroot_1.22-2 fdisk_2.31.1-0.5 file_1:5.33-2 findutils_4.6.0+git+20171230-2 flex_2.6.4-6.1 g++_4:7.3.0-3 g++-7_7.3.0-17 gcc_4:7.3.0-3 gcc-6-base_6.4.0-17 gcc-7_7.3.0-17 gcc-7-base_7.3.0-17 gcc-8-base_8-20180425-1 gengetopt_2.22.6+dfsg0-2 gettext_0.19.8.1-6 gettext-base_0.19.8.1-6 gfortran_4:7.3.0-3 gfortran-7_7.3.0-17 gpgv_2.2.5-1 grep_3.1-2 groff-base_1.22.3-10 gzip_1.6-5+b1 hostname_3.20 ibverbs-providers_17.1-2 icu-devtools_57.1-9 init-system-helpers_1.51 intltool-debian_0.35.0+20060710.4 lib32gcc1_1:8-20180425-1 lib32stdc++6_8-20180425-1 libacl1_2.2.52-3+b1 libapt-pkg5.0_1.6.1 libarchive-zip-perl_1.60-1 libarchive13_3.2.2-3.1 libasan4_7.3.0-17 libatomic1_8-20180425-1 libattr1_1:2.4.47-2+b2 libaudit-common_1:2.8.3-1 libaudit1_1:2.8.3-1 libbinutils_2.30-16 libbison-dev_2:3.0.4.dfsg-1+b1 libblas-dev_3.8.0-1 libblas3_3.8.0-1 libblkid1_2.31.1-0.5 libboost-dev_1.62.0.1 libboost-mpi-dev_1.62.0.1 libboost-mpi1.62-dev_1.62.0+dfsg-5+b1 libboost-mpi1.62.0_1.62.0+dfsg-5+b1 libboost-serialization-dev_1.62.0.1 libboost-serialization1.62-dev_1.62.0+dfsg-5+b1 libboost-serialization1.62.0_1.62.0+dfsg-5+b1 libboost1.62-dev_1.62.0+dfsg-5+b1 libbsd0_0.8.7-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.27-3 libc-dev-bin_2.27-3 libc6_2.27-3 libc6-dev_2.27-3 libc6-i386_2.27-3 libcap-ng0_0.7.9-1 libcc1-0_8-20180425-1 libcilkrts5_7.3.0-17 libclang-common-6.0-dev_1:6.0-3 libclang1-6.0_1:6.0-3 libcom-err2_1.44.1-2 libcomerr2_1.44.1-2 libcroco3_0.6.12-2 libcurl3_7.58.0-2 libdb5.3_5.3.28-13.1+b1 libdebconfclient0_0.243 libdpkg-perl_1.19.0.5 libeatmydata1_105-6 libedit2_3.1-20170329-1 libevent-2.1-6_2.1.8-stable-4 libevent-core-2.1-6_2.1.8-stable-4 libevent-pthreads-2.1-6_2.1.8-stable-4 libexpat1_2.2.5-3 libext2fs2_1.44.1-2 libfabric1_1.5.3-1 libfakeroot_1.22-2 libfdisk1_2.31.1-0.5 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.041-1 libgc1c2_1:7.4.2-8.2 libgcc-7-dev_7.3.0-17 libgcc1_1:8-20180425-1 libgcrypt20_1.8.2-2 libgdbm-compat4_1.14.1-6 libgdbm3_1.8.3-14 libgdbm5_1.14.1-6 libgfortran-7-dev_7.3.0-17 libgfortran4_7.3.0-17 libglib2.0-0_2.56.1-2 libgmp10_2:6.1.2+dfsg-3 libgnutls30_3.5.18-1 libgomp1_8-20180425-1 libgpg-error0_1.29-4 libgssapi-krb5-2_1.16-2 libhogweed4_3.4-1 libhwloc-dev_1.11.10-1 libhwloc-plugins_1.11.10-1 libhwloc5_1.11.10-1 libibverbs-dev_17.1-2 libibverbs1_17.1-2 libicu-dev_57.1-9 libicu57_57.1-9 libidn2-0_2.0.4-1.1 libisl15_0.18-4 libisl19_0.19-1 libitm1_8-20180425-1 libjsoncpp1_1.7.4-3 libk5crypto3_1.16-2 libkeyutils1_1.5.9-9.2 libkrb5-3_1.16-2 libkrb5support0_1.16-2 liblapack-dev_3.8.0-1 liblapack3_3.8.0-1 libldap-2.4-2_2.4.45+dfsg-1 libldap-common_2.4.45+dfsg-1 libllvm6.0_1:6.0-3 liblsan0_8-20180425-1 libltdl-dev_2.4.6-2.1 libltdl7_2.4.6-2.1 liblz4-1_1.8.1.2-1 liblzma5_5.2.2-1.3 liblzo2-2_2.08-1.2+b2 libmagic-mgc_1:5.33-2 libmagic1_1:5.33-2 libmount1_2.31.1-0.5 libmpc3_1.1.0-1 libmpfr4_3.1.6-1 libmpfr6_4.0.1-1 libmpx2_8-20180425-1 libncurses5_6.1+20180210-2 libncursesw5_6.1+20180210-2 libnettle6_3.4-1 libnghttp2-14_1.31.1-1 libnl-3-200_3.2.27-2 libnl-route-3-200_3.2.27-2 libnuma-dev_2.0.11-2.2 libnuma1_2.0.11-2.2 libobjc-7-dev_7.3.0-17 libobjc4_8-20180425-1 libopenmpi-dev_3.0.1.real-1 libopenmpi3_3.0.1.real-1 libp11-kit0_0.23.10-2 libpam-modules_1.1.8-3.7 libpam-modules-bin_1.1.8-3.7 libpam-runtime_1.1.8-3.7 libpam0g_1.1.8-3.7 libpciaccess0_0.14-1 libpcre3_2:8.39-9 libperl5.26_5.26.2-3 libpipeline1_1.5.0-1 libpmix2_2.1.1~rc1-4 libprocps6_2:3.3.14-1 libpsl5_0.20.1-1 libpsm-infinipath1_3.3+20.604758e7-5 libquadmath0_8-20180425-1 librdmacm1_17.1-2 librhash0_1.3.6-2 librtmp1_2.4+20151223.gitfa8646d.1-1+b1 libsasl2-2_2.1.27~101-g0780600+dfsg-3.1 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3.1 libseccomp2_2.3.3-1 libselinux1_2.7-2+b2 libsemanage-common_2.7-2 libsemanage1_2.7-2+b2 libsepol1_2.7-1 libsigsegv2_2.12-2 libsmartcols1_2.31.1-0.5 libss2_1.44.1-2 libssh2-1_1.8.0-1 libssl1.0.2_1.0.2o-1 libstdc++-7-dev_7.3.0-17 libstdc++6_8-20180425-1 libsystemd0_238-4 libtasn1-6_4.13-2 libtimedate-perl_2.3000-2 libtinfo5_6.1+20180210-2 libtinfo6_6.1+20180210-2 libtool_2.4.6-2.1 libtsan0_8-20180425-1 libubsan0_7.3.0-17 libudev1_238-4 libunistring2_0.9.8-1 libustr-1.0-1_1.0.4-6 libuuid1_2.31.1-0.5 libuv1_1.18.0-3 libxml2_2.9.4+dfsg1-6.1 libxml2-dev_2.9.4+dfsg1-6.1 libzstd1_1.3.4+dfsg-1 linux-libc-dev_4.15.17-1 login_1:4.5-1 lsb-base_9.20170808 m4_1.4.18-1 make_4.2.1-1 man-db_2.8.3-2 mawk_1.3.3-17+b3 mount_2.31.1-0.5 mpi-default-dev_1.13 multiarch-support_2.27-3 ncurses-base_6.1+20180210-2 ncurses-bin_6.1+20180210-2 ocl-icd-libopencl1_2.2.12-1 openmpi-bin_3.0.1.real-1 openmpi-common_3.0.1.real-1 openssh-client_1:7.7p1-2 passwd_1:4.5-1 patch_2.7.6-2 perl_5.26.2-3 perl-base_5.26.2-3 perl-modules-5.26_5.26.2-3 po-debconf_1.0.20 procps_2:3.3.14-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-prime-phylo-dummy_0.invalid.0 sed_4.4-2 sensible-utils_0.0.12 sysvinit-utils_2.88dsf-59.10 tar_1.30+dfsg-1 util-linux_2.31.1-0.5 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1 +------------------------------------------------------------------------------+ | 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 gpgv: using RSA key E8D37AE2F09F4872 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 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-f482c80f-3acc-4976-99d7-7733b1144fff 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_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_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 cd obj-x86_64-linux-gnu && cmake .. -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON "-GUnix Makefiles" -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 6.0.0 -- 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 7.3.0 -- 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 6.0.0 -- 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 -- Found BLAS: /usr/lib/x86_64-linux-gnu/libblas.so hittade /usr/lib/x86_64-linux-gnu/libblas.so -- 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 "2.6.4") -- Found MPI_C: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so (found version "3.1") -- Found MPI_Fortran: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_usempif08.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") -- Boost version: 1.62.0 -- 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/x86_64-linux-gnu/openmpi/include/openmpi;/usr/lib/x86_64-linux-gnu/openmpi/include included path is -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY 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 cd obj-x86_64-linux-gnu && make -j8 -Oline 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 make[1]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[1]: Entering directory '/<>/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /<>/obj-x86_64-linux-gnu/CMakeFiles /<>/obj-x86_64-linux-gnu/CMakeFiles/progress.marks make[1]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f CMakeFiles/Makefile2 all 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 2.6.4 make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 1%] [BISON][MyParser2] Building parser with bison 3.0.4 make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/src/cxx/libraries/sfile && /usr/bin/flex -o/<>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/lexer.c seqreader.l make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' 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 */} ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' 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' [ 2%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/sfile.c.o make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 2%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/gbread.c.o make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 3%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/lexer.c.o make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 3%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/gb.tab.c.o make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' 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/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/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=/<>=. -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. make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' 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/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/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=/<>=. -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 make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' 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/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/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=/<>=. -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. make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' 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/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/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=/<>=. -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:197:10: warning: expression which evaluates to zero treated as a null pointer constant of type 'char *' [-Wnon-literal-null-conversion] last = '\0'; ^~~~ seqreader.l:270:9: warning: unused variable 'code' [-Wunused-variable] int code; /* return value */ ^ /<>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/lexer.c:1821:17: 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:1864:16: warning: function 'input' is not needed and will not be emitted [-Wunneeded-internal-declaration] static int input (void) ^ 4 warnings generated. make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 4%] Linking C shared library libprime-phylo-sfile.so make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' 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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -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,:::::::::::::::::::: make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[2]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 4%] Built target prime-phylo-sfile make[2]: 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/depend make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 4%] [BISON][MyParser] Building parser with bison 3.0.4 make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 5%] [FLEX][MyScanner] Building scanner with flex 2.6.4 make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/src/cxx/libraries/prime && /usr/bin/flex -Pyytree_ -o/<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime/lexer.c NHX.l make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' 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 make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' 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 make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 6%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXtree.c.o make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 7%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXannotation.c.o make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 6%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/lexer.c.o make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 8%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXparse.c.o make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 6%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/AnError.cc.o make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 9%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Beep.cc.o make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 10%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BeepOption.cc.o make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' 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/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<>=. -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 make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 10%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Hacks.cc.o make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' 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/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<>=. -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 make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' 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/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<>=. -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 make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 11%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ODESolver.cc.o make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 11%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PRNG.cc.o make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' 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/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<>=. -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. make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 12%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PrimeOptionMap.cc.o make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' 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/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<>=. -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:1554:17: 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:1597:16: warning: function 'input' is not needed and will not be emitted [-Wunneeded-internal-declaration] static int input (void) ^ 2 warnings generated. make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 12%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ProbabilityModel.cc.o make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' 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/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<>=. -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 make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 13%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DiscreteGamma.cc.o make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' 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/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<>=. -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 make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 14%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Probability.cc.o make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' 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/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<>=. -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 make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' 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/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<>=. -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 make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 14%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Tokenizer.cc.o make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 15%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TimeEstimator.cc.o make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' 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/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<>=. -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. make[3]: *** [src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/build.make:221: src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PrimeOptionMap.cc.o] Error 1 make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: *** Waiting for unfinished jobs.... make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' 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/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<>=. -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/Tokenizer.cc.o -c /<>/src/cxx/libraries/prime/Tokenizer.cc make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' 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/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<>=. -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/TimeEstimator.cc.o -c /<>/src/cxx/libraries/prime/TimeEstimator.cc make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' 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/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<>=. -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/DiscreteGamma.cc.o -c /<>/src/cxx/libraries/prime/DiscreteGamma.cc make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' 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/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<>=. -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 beep::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 beep::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 beep::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 beep::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 beep::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 beep::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 beep::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 beep::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 beep::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 beep::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 beep::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 beep::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 beep::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 beep::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 beep::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 beep::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 beep::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 beep::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 beep::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 beep::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 beep::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 beep::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 beep::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 beep::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 beep::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 beep::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 beep::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 beep::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 beep::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 beep::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 beep::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 beep::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 beep::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 beep::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 beep::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 beep::Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real D7 = 69997945.0 / 29380423.0; ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 36 warnings generated. make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' 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/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<>=. -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/ProbabilityModel.cc.o -c /<>/src/cxx/libraries/prime/ProbabilityModel.cc make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' 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/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<>=. -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 make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' 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/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<>=. -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/Probability.cc.o -c /<>/src/cxx/libraries/prime/Probability.cc /<>/src/cxx/libraries/prime/Probability.cc:201:9: warning: assigning field to itself [-Wself-assign-field] sign = sign; ^ 1 warning generated. make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[2]: *** [CMakeFiles/Makefile2:137: src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/all] Error 2 make[1]: *** [Makefile:155: all] Error 2 dh_auto_build: cd obj-x86_64-linux-gnu && make -j8 -Oline returned exit code 2 make: *** [debian/rules:10: build-arch] Error 25 dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2018-05-02T12:55:12Z 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: 10444 Build-Time: 9 Distribution: unstable Fail-Stage: build Host Architecture: amd64 Install-Time: 15 Job: prime-phylo_1.0.11-4 Machine Architecture: amd64 Package: prime-phylo Package-Time: 37 Source-Version: 1.0.11-4 Space: 10444 Status: attempted Version: 1.0.11-4 -------------------------------------------------------------------------------- Finished at 2018-05-02T12:55:12Z Build needed 00:00:37, 10444k disk space E: Build failure (dpkg-buildpackage died) DC-Status: Failed 38.185546149s DC-Time-Estimation: 38.185546149 versus expected 198 (r/m: 4.185208016336968 ; m: 38.185546149)