DC-Build-Header: prime-phylo 1.0.11-1 / 2013-07-16 10:35:11 +0000 DC-Task: source:prime-phylo version:1.0.11-1 architecture:any chroot:unstable esttime:550 logfile:/tmp/prime-phylo_1.0.11-1_unstable_clang.log modes:binary-only:clang DC-Sbuild-call: su user -c 'sbuild -n --apt-update -d unstable -v --chroot-setup-commands=/tmp/switch-to-clang --append-to-version "clang1" --maintainer "Lucas Nussbaum " --uploader "Lucas Nussbaum " prime-phylo_1.0.11-1' sbuild (Debian sbuild) 0.63.2 (18 Aug 2012) on ip-10-235-9-164.ec2.internal ╔══════════════════════════════════════════════════════════════════════════════╗ ║ prime-phylo 1.0.11-1clang1 (amd64) 16 Jul 2013 10:35 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: prime-phylo Version: 1.0.11-1clang1 Source Version: 1.0.11-1 Distribution: unstable Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 I: NOTICE: Log filtering will replace 'build/prime-phylo-MIokPv/prime-phylo-1.0.11' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/prime-phylo-MIokPv' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/unstable-amd64-sbuild-bfa556f7-5cdd-4e26-b134-53f6ee6938cf' with '«CHROOT»' ┌──────────────────────────────────────────────────────────────────────────────┐ │ Update chroot │ └──────────────────────────────────────────────────────────────────────────────┘ Get:1 http://localhost:9999 unstable InRelease [204 kB] Get:2 http://localhost:9999 unstable/main Sources/DiffIndex [7876 B] Get:3 http://localhost:9999 unstable/main amd64 Packages/DiffIndex [7876 B] Get:4 http://localhost:9999 unstable/main Translation-en/DiffIndex [7876 B] Get:5 http://localhost:9999 unstable/main 2013-07-13-2032.15.pdiff [23.1 kB] Get:6 http://localhost:9999 unstable/main amd64 2013-07-13-2032.15.pdiff [16.9 kB] Get:7 http://localhost:9999 unstable/main 2013-07-13-2032.15.pdiff [23.1 kB] Get:8 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http://localhost:9999 unstable/main amd64 2013-07-14-2031.21.pdiff [9955 B] Get:34 http://localhost:9999 unstable/main 2013-07-15-0229.01.pdiff [9715 B] Get:35 http://localhost:9999 unstable/main 2013-07-14-2031.21.pdiff [2736 B] Get:36 http://localhost:9999 unstable/main amd64 2013-07-15-0229.01.pdiff [12.7 kB] Get:37 http://localhost:9999 unstable/main 2013-07-15-0229.01.pdiff [9715 B] Get:38 http://localhost:9999 unstable/main 2013-07-15-0229.01.pdiff [2239 B] Get:39 http://localhost:9999 unstable/main amd64 2013-07-15-0229.01.pdiff [12.7 kB] Get:40 http://localhost:9999 unstable/main 2013-07-15-0830.19.pdiff [3273 B] Get:41 http://localhost:9999 unstable/main 2013-07-15-0229.01.pdiff [2239 B] Get:42 http://localhost:9999 unstable/main amd64 2013-07-15-0830.19.pdiff [3964 B] Get:43 http://localhost:9999 unstable/main 2013-07-15-0830.19.pdiff [3273 B] Get:44 http://localhost:9999 unstable/main 2013-07-15-0830.19.pdiff [1357 B] Get:45 http://localhost:9999 unstable/main amd64 2013-07-15-0830.19.pdiff [3964 B] Get:46 http://localhost:9999 unstable/main 2013-07-15-1432.36.pdiff [5326 B] Get:47 http://localhost:9999 unstable/main 2013-07-15-0830.19.pdiff [1357 B] Get:48 http://localhost:9999 unstable/main amd64 2013-07-15-1432.36.pdiff [9809 B] Get:49 http://localhost:9999 unstable/main 2013-07-15-1432.36.pdiff [5326 B] Get:50 http://localhost:9999 unstable/main 2013-07-15-1432.36.pdiff [322 B] Get:51 http://localhost:9999 unstable/main amd64 2013-07-15-1432.36.pdiff [9809 B] Get:52 http://localhost:9999 unstable/main 2013-07-15-2031.50.pdiff [12.2 kB] Get:53 http://localhost:9999 unstable/main 2013-07-15-1432.36.pdiff [322 B] Get:54 http://localhost:9999 unstable/main amd64 2013-07-15-2031.50.pdiff [24.4 kB] Get:55 http://localhost:9999 unstable/main 2013-07-15-2031.50.pdiff [12.2 kB] Get:56 http://localhost:9999 unstable/main 2013-07-15-2031.50.pdiff [537 B] Get:57 http://localhost:9999 unstable/main amd64 2013-07-15-2031.50.pdiff [24.4 kB] Get:58 http://localhost:9999 unstable/main 2013-07-16-0233.12.pdiff [14.8 kB] Get:59 http://localhost:9999 unstable/main 2013-07-15-2031.50.pdiff [537 B] Get:60 http://localhost:9999 unstable/main amd64 2013-07-16-0233.12.pdiff [49.5 kB] Get:61 http://localhost:9999 unstable/main 2013-07-16-0233.12.pdiff [14.8 kB] Get:62 http://localhost:9999 unstable/main 2013-07-16-0233.12.pdiff [3247 B] Get:63 http://localhost:9999 unstable/main amd64 2013-07-16-0233.12.pdiff [49.5 kB] Get:64 http://localhost:9999 unstable/main 2013-07-16-0233.12.pdiff [3247 B] Fetched 501 kB in 37s (13.3 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following packages will be upgraded: cpp-4.7 gcc-4.7 gcc-4.7-base initscripts libgcc-4.7-dev sysv-rc sysvinit sysvinit-utils 8 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 14.2 MB of archives. After this operation, 18.4 kB disk space will be freed. Get:1 http://localhost:9999/debian/ unstable/main sysvinit amd64 2.88dsf-42 [134 kB] Get:2 http://localhost:9999/debian/ unstable/main sysv-rc all 2.88dsf-42 [80.4 kB] Get:3 http://localhost:9999/debian/ unstable/main sysvinit-utils amd64 2.88dsf-42 [103 kB] Get:4 http://localhost:9999/debian/ unstable/main initscripts amd64 2.88dsf-42 [87.1 kB] Get:5 http://localhost:9999/debian/ unstable/main gcc-4.7 amd64 4.7.3-6 [5819 kB] Get:6 http://localhost:9999/debian/ unstable/main cpp-4.7 amd64 4.7.3-6 [5385 kB] Get:7 http://localhost:9999/debian/ unstable/main libgcc-4.7-dev amd64 4.7.3-6 [2465 kB] Get:8 http://localhost:9999/debian/ unstable/main gcc-4.7-base amd64 4.7.3-6 [149 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 14.2 MB in 0s (25.3 MB/s) (Reading database ... 13844 files and directories currently installed.) Preparing to replace sysvinit 2.88dsf-41 (using .../sysvinit_2.88dsf-42_amd64.deb) ... Unpacking replacement sysvinit ... Setting up sysvinit (2.88dsf-42) ... Not restarting sysvinit (Reading database ... 13844 files and directories currently installed.) Preparing to replace sysv-rc 2.88dsf-41 (using .../sysv-rc_2.88dsf-42_all.deb) ... Unpacking replacement sysv-rc ... Preparing to replace sysvinit-utils 2.88dsf-41 (using .../sysvinit-utils_2.88dsf-42_amd64.deb) ... Unpacking replacement sysvinit-utils ... Setting up sysvinit-utils (2.88dsf-42) ... Setting up sysv-rc (2.88dsf-42) ... (Reading database ... 13844 files and directories currently installed.) Preparing to replace initscripts 2.88dsf-41 (using .../initscripts_2.88dsf-42_amd64.deb) ... Removing unmodified and obsolete conffile /etc/init.d/mtab.sh ... Unpacking replacement initscripts ... Setting up initscripts (2.88dsf-42) ... Installing new version of config file /etc/init.d/bootmisc.sh ... Installing new version of config file /etc/init.d/checkfs.sh ... Installing new version of config file /etc/init.d/checkroot.sh ... Installing new version of config file /etc/init.d/checkroot-bootclean.sh ... Installing new version of config file /etc/init.d/mountdevsubfs.sh ... Installing new version of config file /etc/init.d/mountkernfs.sh ... Installing new version of config file /etc/init.d/rmnologin ... Installing new version of config file /etc/network/if-up.d/mountnfs ... (Reading database ... 13843 files and directories currently installed.) Preparing to replace gcc-4.7 4.7.3-5 (using .../gcc-4.7_4.7.3-6_amd64.deb) ... Unpacking replacement gcc-4.7 ... Preparing to replace cpp-4.7 4.7.3-5 (using .../cpp-4.7_4.7.3-6_amd64.deb) ... Unpacking replacement cpp-4.7 ... Preparing to replace libgcc-4.7-dev:amd64 4.7.3-5 (using .../libgcc-4.7-dev_4.7.3-6_amd64.deb) ... Unpacking replacement libgcc-4.7-dev:amd64 ... Preparing to replace gcc-4.7-base:amd64 4.7.3-5 (using .../gcc-4.7-base_4.7.3-6_amd64.deb) ... Unpacking replacement gcc-4.7-base:amd64 ... Setting up gcc-4.7-base:amd64 (4.7.3-6) ... Setting up cpp-4.7 (4.7.3-6) ... Setting up libgcc-4.7-dev:amd64 (4.7.3-6) ... Setting up gcc-4.7 (4.7.3-6) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Fetch source files │ └──────────────────────────────────────────────────────────────────────────────┘ Check APT ───────── Checking available source versions... Download source files with APT ────────────────────────────── Reading package lists... Building dependency tree... Reading state information... Need to get 757 kB of source archives. Get:1 http://localhost:9999/debian/ unstable/main prime-phylo 1.0.11-1 (dsc) [1351 B] Get:2 http://localhost:9999/debian/ unstable/main prime-phylo 1.0.11-1 (tar) [751 kB] Get:3 http://localhost:9999/debian/ unstable/main prime-phylo 1.0.11-1 (diff) [5029 B] Fetched 757 kB in 0s (1933 kB/s) Download complete and in download only mode Check arch ────────── ┌──────────────────────────────────────────────────────────────────────────────┐ │ Chroot Setup Commands │ └──────────────────────────────────────────────────────────────────────────────┘ /tmp/switch-to-clang ──────────────────── + echo 'Entering customization script...' Entering customization script... + echo 'Install of clang' Install of clang + apt-get update Hit http://localhost:9999 unstable InRelease Hit http://localhost:9999 unstable/main Sources/DiffIndex Hit http://localhost:9999 unstable/main amd64 Packages/DiffIndex Hit http://localhost:9999 unstable/main Translation-en/DiffIndex Reading package lists... + apt-get install --yes --no-install-recommends --force-yes clang-3.3 Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: libclang-common-3.3-dev libclang1-3.3 libffi6 libllvm3.3 libobjc-4.7-dev libobjc4 libstdc++6-4.7-dev Suggested packages: libstdc++6-4.7-doc Recommended packages: llvm-3.3-dev python The following NEW packages will be installed: clang-3.3 libclang-common-3.3-dev libclang1-3.3 libffi6 libllvm3.3 libobjc-4.7-dev libobjc4 libstdc++6-4.7-dev 0 upgraded, 8 newly installed, 0 to remove and 0 not upgraded. Need to get 27.2 MB of archives. After this operation, 80.8 MB of additional disk space will be used. Get:1 http://localhost:9999/debian/ unstable/main libffi6 amd64 3.0.13-4 [21.6 kB] Get:2 http://localhost:9999/debian/ unstable/main libllvm3.3 amd64 1:3.3-3 [8575 kB] Get:3 http://localhost:9999/debian/ unstable/main libobjc4 amd64 4.8.1-6 [160 kB] Get:4 http://localhost:9999/debian/ unstable/main libstdc++6-4.7-dev amd64 4.7.3-6 [1694 kB] Get:5 http://localhost:9999/debian/ unstable/main libobjc-4.7-dev amd64 4.7.3-6 [719 kB] Get:6 http://localhost:9999/debian/ unstable/main libclang-common-3.3-dev amd64 1:3.3-3 [574 kB] Get:7 http://localhost:9999/debian/ unstable/main libclang1-3.3 amd64 1:3.3-3 [4579 kB] Get:8 http://localhost:9999/debian/ unstable/main clang-3.3 amd64 1:3.3-3 [10.9 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 27.2 MB in 1s (25.8 MB/s) Selecting previously unselected package libffi6:amd64. (Reading database ... 13843 files and directories currently installed.) Unpacking libffi6:amd64 (from .../libffi6_3.0.13-4_amd64.deb) ... Selecting previously unselected package libllvm3.3:amd64. Unpacking libllvm3.3:amd64 (from .../libllvm3.3_1%3a3.3-3_amd64.deb) ... Selecting previously unselected package libobjc4:amd64. Unpacking libobjc4:amd64 (from .../libobjc4_4.8.1-6_amd64.deb) ... Selecting previously unselected package libstdc++6-4.7-dev:amd64. Unpacking libstdc++6-4.7-dev:amd64 (from .../libstdc++6-4.7-dev_4.7.3-6_amd64.deb) ... Selecting previously unselected package libobjc-4.7-dev:amd64. Unpacking libobjc-4.7-dev:amd64 (from .../libobjc-4.7-dev_4.7.3-6_amd64.deb) ... Selecting previously unselected package libclang-common-3.3-dev. Unpacking libclang-common-3.3-dev (from .../libclang-common-3.3-dev_1%3a3.3-3_amd64.deb) ... Selecting previously unselected package libclang1-3.3. Unpacking libclang1-3.3 (from .../libclang1-3.3_1%3a3.3-3_amd64.deb) ... Selecting previously unselected package clang-3.3. Unpacking clang-3.3 (from .../clang-3.3_1%3a3.3-3_amd64.deb) ... Setting up libffi6:amd64 (3.0.13-4) ... Setting up libllvm3.3:amd64 (1:3.3-3) ... Setting up libobjc4:amd64 (4.8.1-6) ... Setting up libstdc++6-4.7-dev:amd64 (4.7.3-6) ... Setting up libobjc-4.7-dev:amd64 (4.7.3-6) ... Setting up libclang-common-3.3-dev (1:3.3-3) ... Setting up libclang1-3.3 (1:3.3-3) ... Setting up clang-3.3 (1:3.3-3) ... Processing triggers for libc-bin ... + echo 'Replace gcc, g++ & cpp by clang' Replace gcc, g++ & cpp by clang + VERSIONS='4.6 4.7 4.8' + cd /usr/bin + for VERSION in '$VERSIONS' + rm -f g++-4.6 gcc-4.6 cpp-4.6 + ln -s clang++ g++-4.6 + ln -s clang gcc-4.6 + ln -s clang cpp-4.6 + for VERSION in '$VERSIONS' + rm -f g++-4.7 gcc-4.7 cpp-4.7 + ln -s clang++ g++-4.7 + ln -s clang gcc-4.7 + ln -s clang cpp-4.7 + for VERSION in '$VERSIONS' + rm -f g++-4.8 gcc-4.8 cpp-4.8 + ln -s clang++ g++-4.8 + ln -s clang gcc-4.8 + ln -s clang cpp-4.8 + cd - /«BUILDDIR» + echo 'Block the installation of new gcc version' Block the installation of new gcc version + dpkg --set-selections + echo 'gcc-4.6 hold' + dpkg --set-selections + echo 'cpp-4.6 hold' + dpkg --set-selections + echo 'g++-4.6 hold' + dpkg --set-selections + echo 'gcc-4.7 hold' + dpkg --set-selections + echo 'cpp-4.7 hold' + dpkg --set-selections + echo 'g++-4.7 hold' + dpkg --set-selections + echo 'gcc-4.8 hold' + dpkg --set-selections + echo 'cpp-4.8 hold' + dpkg --set-selections + echo 'g++-4.8 hold' + echo 'Check if gcc, g++ & cpp are actually clang' Check if gcc, g++ & cpp are actually clang + grep clang + gcc --version + grep clang + cpp --version + grep clang + g++ --version I: Finished running '/tmp/switch-to-clang'. Finished processing commands. ──────────────────────────────────────────────────────────────────────────────── Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-AjM0x1/apt_archive/sbuild-build-depends-core-dummy.deb'. OK 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 debconf: delaying package configuration, since apt-utils is not installed 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 0 B/710 B of archives. After this operation, 0 B of additional disk space will be used. Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 14698 files and directories currently installed.) Unpacking sbuild-build-depends-core-dummy (from .../sbuild-build-depends-core-dummy.deb) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), 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: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), 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 `/«BUILDDIR»/resolver-FDaiZp/apt_archive/sbuild-build-depends-prime-phylo-dummy.deb'. OK 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 extra packages will be installed: adduser bison bsdmainutils cmake cmake-data debhelper emacsen-common file flex gengetopt gettext gettext-base gfortran gfortran-4.8 groff-base intltool-debian libarchive13 libasprintf0c2 libbison-dev libblas-dev libblas3 libboost-dev libboost-mpi-dev libboost-mpi1.49-dev libboost-mpi1.49.0 libboost-serialization-dev libboost-serialization1.49-dev libboost-serialization1.49.0 libboost1.49-dev libcroco3 libcurl3-gnutls libexpat1 libgcrypt11 libgfortran-4.8-dev libgfortran3 libglib2.0-0 libgnutls26 libgpg-error0 libgssapi-krb5-2 libibverbs-dev libibverbs1 libicu48 libidn11 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack-dev liblapack3 libldap-2.4-2 liblzo2-2 libmagic1 libncursesw5 libnettle4 libnuma1 libopenmpi-dev libopenmpi1.3 libp11-kit0 libpipeline1 libprocps1 librtmp0 libsasl2-2 libsasl2-modules libsigsegv2 libssh2-1 libssl1.0.0 libtasn1-3 libtorque2 libunistring0 libxml2 libxml2-dev m4 man-db mpi-default-dev openmpi-common po-debconf procps zlib1g-dev Suggested packages: bison-doc wamerican wordlist whois vacation codeblocks eclipse dh-make gettext-doc gfortran-multilib gfortran-doc gfortran-4.8-multilib gfortran-4.8-doc libgfortran3-dbg groff lrzip libboost-doc libboost-graph1.49-dev libboost1.49-doc libboost-chrono1.49-dev libboost-date-time1.49-dev libboost-filesystem1.49-dev libboost-graph-parallel1.49-dev libboost-iostreams1.49-dev libboost-locale1.49-dev libboost-math1.49-dev libboost-program-options1.49-dev libboost-python1.49-dev libboost-random1.49-dev libboost-regex1.49-dev libboost-signals1.49-dev libboost-system1.49-dev libboost-test1.49-dev libboost-thread1.49-dev libboost-timer1.49-dev libboost-wave1.49-dev xsltproc doxygen docbook-xml docbook-xsl default-jdk fop rng-tools krb5-doc krb5-user libsasl2-modules-otp libsasl2-modules-ldap libsasl2-modules-sql libsasl2-modules-gssapi-mit libsasl2-modules-gssapi-heimdal pkg-config less www-browser libmail-box-perl Recommended packages: curl wget lynx-cur autopoint libasprintf-dev libgettextpo-dev ca-certificates libglib2.0-data shared-mime-info krb5-locales xml-core libmail-sendmail-perl psmisc The following NEW packages will be installed: adduser bison bsdmainutils cmake cmake-data debhelper emacsen-common file flex gengetopt gettext gettext-base gfortran gfortran-4.8 groff-base intltool-debian libarchive13 libasprintf0c2 libbison-dev libblas-dev libblas3 libboost-dev libboost-mpi-dev libboost-mpi1.49-dev libboost-mpi1.49.0 libboost-serialization-dev libboost-serialization1.49-dev libboost-serialization1.49.0 libboost1.49-dev libcroco3 libcurl3-gnutls libexpat1 libgcrypt11 libgfortran-4.8-dev libgfortran3 libglib2.0-0 libgnutls26 libgpg-error0 libgssapi-krb5-2 libibverbs-dev libibverbs1 libicu48 libidn11 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack-dev liblapack3 libldap-2.4-2 liblzo2-2 libmagic1 libncursesw5 libnettle4 libnuma1 libopenmpi-dev libopenmpi1.3 libp11-kit0 libpipeline1 libprocps1 librtmp0 libsasl2-2 libsasl2-modules libsigsegv2 libssh2-1 libssl1.0.0 libtasn1-3 libtorque2 libunistring0 libxml2 libxml2-dev m4 man-db mpi-default-dev openmpi-common po-debconf procps sbuild-build-depends-prime-phylo-dummy zlib1g-dev 0 upgraded, 79 newly installed, 0 to remove and 0 not upgraded. Need to get 62.3 MB/62.3 MB of archives. After this operation, 250 MB of additional disk space will be used. Get:1 http://localhost:9999/debian/ unstable/main libncursesw5 amd64 5.9+20130608-1 [141 kB] Get:2 http://localhost:9999/debian/ unstable/main libpipeline1 amd64 1.2.4-1 [41.0 kB] Get:3 http://localhost:9999/debian/ unstable/main libprocps1 amd64 1:3.3.8-2 [59.8 kB] Get:4 http://localhost:9999/debian/ unstable/main libssl1.0.0 amd64 1.0.1e-3 [1242 kB] Get:5 http://localhost:9999/debian/ unstable/main groff-base amd64 1.22.2-3 [747 kB] Get:6 http://localhost:9999/debian/ unstable/main bsdmainutils amd64 9.0.5 [211 kB] Get:7 http://localhost:9999/debian/ unstable/main man-db amd64 2.6.5-2 [976 kB] Get:8 http://localhost:9999/debian/ unstable/main libasprintf0c2 amd64 0.18.2.1-1 [28.9 kB] Get:9 http://localhost:9999/debian/ unstable/main libgpg-error0 amd64 1.10-3.1 [77.9 kB] Get:10 http://localhost:9999/debian/ unstable/main libgcrypt11 amd64 1.5.2-3 [296 kB] Get:11 http://localhost:9999/debian/ unstable/main libp11-kit0 amd64 0.18.4-1 [115 kB] Get:12 http://localhost:9999/debian/ unstable/main libtasn1-3 amd64 2.14-3 [68.5 kB] Get:13 http://localhost:9999/debian/ unstable/main libgnutls26 amd64 2.12.23-5 [617 kB] Get:14 http://localhost:9999/debian/ unstable/main libkeyutils1 amd64 1.5.5-7 [8808 B] Get:15 http://localhost:9999/debian/ unstable/main libkrb5support0 amd64 1.10.1+dfsg-6.1 [49.3 kB] Get:16 http://localhost:9999/debian/ unstable/main libk5crypto3 amd64 1.10.1+dfsg-6.1 [112 kB] Get:17 http://localhost:9999/debian/ unstable/main libkrb5-3 amd64 1.10.1+dfsg-6.1 [392 kB] Get:18 http://localhost:9999/debian/ unstable/main libgssapi-krb5-2 amd64 1.10.1+dfsg-6.1 [147 kB] Get:19 http://localhost:9999/debian/ unstable/main libidn11 amd64 1.25-2 [178 kB] Get:20 http://localhost:9999/debian/ unstable/main libsasl2-modules amd64 2.1.25.dfsg1-13 [123 kB] Get:21 http://localhost:9999/debian/ unstable/main libsasl2-2 amd64 2.1.25.dfsg1-13 [109 kB] Get:22 http://localhost:9999/debian/ unstable/main libldap-2.4-2 amd64 2.4.31-1+nmu2 [243 kB] Get:23 http://localhost:9999/debian/ unstable/main libmagic1 amd64 1:5.14-2 [216 kB] Get:24 http://localhost:9999/debian/ unstable/main libxml2 amd64 2.9.1+dfsg1-2 [911 kB] Get:25 http://localhost:9999/debian/ unstable/main libsigsegv2 amd64 2.10-2 [29.8 kB] Get:26 http://localhost:9999/debian/ unstable/main m4 amd64 1.4.16-5 [260 kB] Get:27 http://localhost:9999/debian/ unstable/main flex amd64 2.5.35-10.1 [332 kB] Get:28 http://localhost:9999/debian/ unstable/main liblzo2-2 amd64 2.06-1 [57.7 kB] Get:29 http://localhost:9999/debian/ unstable/main libnettle4 amd64 2.7.1-1 [189 kB] Get:30 http://localhost:9999/debian/ unstable/main libarchive13 amd64 3.1.2-7 [319 kB] Get:31 http://localhost:9999/debian/ unstable/main libglib2.0-0 amd64 2.36.3-3 [2048 kB] Get:32 http://localhost:9999/debian/ unstable/main libcroco3 amd64 0.6.8-2 [133 kB] Get:33 http://localhost:9999/debian/ unstable/main librtmp0 amd64 2.4+20121230.gitdf6c518-1 [62.3 kB] Get:34 http://localhost:9999/debian/ unstable/main libssh2-1 amd64 1.4.3-1 [135 kB] Get:35 http://localhost:9999/debian/ unstable/main libcurl3-gnutls amd64 7.31.0-2 [279 kB] Get:36 http://localhost:9999/debian/ unstable/main libexpat1 amd64 2.1.0-4 [138 kB] Get:37 http://localhost:9999/debian/ unstable/main libgfortran3 amd64 4.8.1-6 [345 kB] Get:38 http://localhost:9999/debian/ unstable/main libicu48 amd64 4.8.1.1-12 [4734 kB] Get:39 http://localhost:9999/debian/ unstable/main libunistring0 amd64 0.9.3-5 [434 kB] Get:40 http://localhost:9999/debian/ unstable/main adduser all 3.113+nmu3 [264 kB] Get:41 http://localhost:9999/debian/ unstable/main procps amd64 1:3.3.8-2 [274 kB] Get:42 http://localhost:9999/debian/ unstable/main file amd64 1:5.14-2 [54.0 kB] Get:43 http://localhost:9999/debian/ unstable/main gettext-base amd64 0.18.2.1-1 [156 kB] Get:44 http://localhost:9999/debian/ unstable/main libbison-dev amd64 2:2.7.1.dfsg-1 [346 kB] Get:45 http://localhost:9999/debian/ unstable/main bison amd64 2:2.7.1.dfsg-1 [789 kB] Get:46 http://localhost:9999/debian/ unstable/main emacsen-common all 2.0.5 [20.9 kB] Get:47 http://localhost:9999/debian/ unstable/main cmake-data all 2.8.11.2-1 [1397 kB] Get:48 http://localhost:9999/debian/ unstable/main cmake amd64 2.8.11.2-1 [5129 kB] Get:49 http://localhost:9999/debian/ unstable/main gettext amd64 0.18.2.1-1 [2019 kB] Get:50 http://localhost:9999/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB] Get:51 http://localhost:9999/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB] Get:52 http://localhost:9999/debian/ unstable/main debhelper all 9.20130630 [710 kB] Get:53 http://localhost:9999/debian/ unstable/main gengetopt amd64 2.22.6-2 [320 kB] Get:54 http://localhost:9999/debian/ unstable/main libgfortran-4.8-dev amd64 4.8.1-6 [436 kB] Get:55 http://localhost:9999/debian/ unstable/main gfortran-4.8 amd64 4.8.1-6 [6142 kB] Get:56 http://localhost:9999/debian/ unstable/main gfortran amd64 4:4.8.1-2 [1126 B] Get:57 http://localhost:9999/debian/ unstable/main libblas3 amd64 1.2.20110419-5 [293 kB] Get:58 http://localhost:9999/debian/ unstable/main libblas-dev amd64 1.2.20110419-5 [312 kB] Get:59 http://localhost:9999/debian/ unstable/main libboost1.49-dev amd64 1.49.0-4 [9195 kB] Get:60 http://localhost:9999/debian/ unstable/main libboost-dev amd64 1.49.0.1 [3022 B] Get:61 http://localhost:9999/debian/ unstable/main libboost-serialization1.49.0 amd64 1.49.0-4 [207 kB] Get:62 http://localhost:9999/debian/ unstable/main libboost-serialization1.49-dev amd64 1.49.0-4 [316 kB] Get:63 http://localhost:9999/debian/ unstable/main libibverbs1 amd64 1.1.7-1 [35.4 kB] Get:64 http://localhost:9999/debian/ unstable/main libnuma1 amd64 2.0.8-3 [34.5 kB] Get:65 http://localhost:9999/debian/ unstable/main libtorque2 amd64 2.4.16+dfsg-1 [120 kB] Get:66 http://localhost:9999/debian/ unstable/main libopenmpi1.3 amd64 1.4.5-1 [1436 kB] Get:67 http://localhost:9999/debian/ unstable/main libboost-mpi1.49.0 amd64 1.49.0-4 [80.8 kB] Get:68 http://localhost:9999/debian/ unstable/main openmpi-common all 1.4.5-1 [101 kB] Get:69 http://localhost:9999/debian/ unstable/main libibverbs-dev amd64 1.1.7-1 [86.1 kB] Get:70 http://localhost:9999/debian/ unstable/main libopenmpi-dev amd64 1.4.5-1 [2778 kB] Get:71 http://localhost:9999/debian/ unstable/main mpi-default-dev amd64 1.0.1 [3604 B] Get:72 http://localhost:9999/debian/ unstable/main libboost-mpi1.49-dev amd64 1.49.0-4 [527 kB] Get:73 http://localhost:9999/debian/ unstable/main libboost-mpi-dev amd64 1.49.0.1 [2806 B] Get:74 http://localhost:9999/debian/ unstable/main libboost-serialization-dev amd64 1.49.0.1 [2940 B] Get:75 http://localhost:9999/debian/ unstable/main liblapack3 amd64 3.4.2+dfsg-1 [5088 kB] Get:76 http://localhost:9999/debian/ unstable/main liblapack-dev amd64 3.4.2+dfsg-1 [5602 kB] Get:77 http://localhost:9999/debian/ unstable/main libxml2-dev amd64 2.9.1+dfsg1-2 [915 kB] Get:78 http://localhost:9999/debian/ unstable/main zlib1g-dev amd64 1:1.2.8.dfsg-1 [217 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 62.3 MB in 3s (18.6 MB/s) Selecting previously unselected package libncursesw5:amd64. (Reading database ... 14698 files and directories currently installed.) Unpacking libncursesw5:amd64 (from .../libncursesw5_5.9+20130608-1_amd64.deb) ... Selecting previously unselected package libpipeline1:amd64. Unpacking libpipeline1:amd64 (from .../libpipeline1_1.2.4-1_amd64.deb) ... Selecting previously unselected package libprocps1:amd64. Unpacking libprocps1:amd64 (from .../libprocps1_1%3a3.3.8-2_amd64.deb) ... Selecting previously unselected package libssl1.0.0:amd64. Unpacking libssl1.0.0:amd64 (from .../libssl1.0.0_1.0.1e-3_amd64.deb) ... Selecting previously unselected package groff-base. Unpacking groff-base (from .../groff-base_1.22.2-3_amd64.deb) ... Selecting previously unselected package bsdmainutils. Unpacking bsdmainutils (from .../bsdmainutils_9.0.5_amd64.deb) ... Selecting previously unselected package man-db. Unpacking man-db (from .../man-db_2.6.5-2_amd64.deb) ... Selecting previously unselected package libasprintf0c2:amd64. 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Unpacking libldap-2.4-2:amd64 (from .../libldap-2.4-2_2.4.31-1+nmu2_amd64.deb) ... Selecting previously unselected package libmagic1:amd64. Unpacking libmagic1:amd64 (from .../libmagic1_1%3a5.14-2_amd64.deb) ... Selecting previously unselected package libxml2:amd64. Unpacking libxml2:amd64 (from .../libxml2_2.9.1+dfsg1-2_amd64.deb) ... Selecting previously unselected package libsigsegv2:amd64. Unpacking libsigsegv2:amd64 (from .../libsigsegv2_2.10-2_amd64.deb) ... Selecting previously unselected package m4. Unpacking m4 (from .../archives/m4_1.4.16-5_amd64.deb) ... Selecting previously unselected package flex. Unpacking flex (from .../flex_2.5.35-10.1_amd64.deb) ... Selecting previously unselected package liblzo2-2:amd64. Unpacking liblzo2-2:amd64 (from .../liblzo2-2_2.06-1_amd64.deb) ... Selecting previously unselected package libnettle4:amd64. Unpacking libnettle4:amd64 (from .../libnettle4_2.7.1-1_amd64.deb) ... Selecting previously unselected package libarchive13:amd64. 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Unpacking bison (from .../bison_2%3a2.7.1.dfsg-1_amd64.deb) ... Selecting previously unselected package emacsen-common. Unpacking emacsen-common (from .../emacsen-common_2.0.5_all.deb) ... Selecting previously unselected package cmake-data. Unpacking cmake-data (from .../cmake-data_2.8.11.2-1_all.deb) ... Selecting previously unselected package cmake. Unpacking cmake (from .../cmake_2.8.11.2-1_amd64.deb) ... Selecting previously unselected package gettext. Unpacking gettext (from .../gettext_0.18.2.1-1_amd64.deb) ... Selecting previously unselected package intltool-debian. Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ... Selecting previously unselected package po-debconf. Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ... Selecting previously unselected package debhelper. Unpacking debhelper (from .../debhelper_9.20130630_all.deb) ... Selecting previously unselected package gengetopt. 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Selecting previously unselected package libboost-serialization1.49.0. Unpacking libboost-serialization1.49.0 (from .../libboost-serialization1.49.0_1.49.0-4_amd64.deb) ... Selecting previously unselected package libboost-serialization1.49-dev. Unpacking libboost-serialization1.49-dev (from .../libboost-serialization1.49-dev_1.49.0-4_amd64.deb) ... Selecting previously unselected package libibverbs1. Unpacking libibverbs1 (from .../libibverbs1_1.1.7-1_amd64.deb) ... Selecting previously unselected package libnuma1. Unpacking libnuma1 (from .../libnuma1_2.0.8-3_amd64.deb) ... Selecting previously unselected package libtorque2. Unpacking libtorque2 (from .../libtorque2_2.4.16+dfsg-1_amd64.deb) ... Selecting previously unselected package libopenmpi1.3. Unpacking libopenmpi1.3 (from .../libopenmpi1.3_1.4.5-1_amd64.deb) ... Selecting previously unselected package libboost-mpi1.49.0. Unpacking libboost-mpi1.49.0 (from .../libboost-mpi1.49.0_1.49.0-4_amd64.deb) ... Selecting previously unselected package openmpi-common. Unpacking openmpi-common (from .../openmpi-common_1.4.5-1_all.deb) ... Selecting previously unselected package libibverbs-dev. Unpacking libibverbs-dev (from .../libibverbs-dev_1.1.7-1_amd64.deb) ... Selecting previously unselected package libopenmpi-dev. Unpacking libopenmpi-dev (from .../libopenmpi-dev_1.4.5-1_amd64.deb) ... Selecting previously unselected package mpi-default-dev. Unpacking mpi-default-dev (from .../mpi-default-dev_1.0.1_amd64.deb) ... Selecting previously unselected package libboost-mpi1.49-dev. Unpacking libboost-mpi1.49-dev (from .../libboost-mpi1.49-dev_1.49.0-4_amd64.deb) ... Selecting previously unselected package libboost-mpi-dev. Unpacking libboost-mpi-dev (from .../libboost-mpi-dev_1.49.0.1_amd64.deb) ... Selecting previously unselected package libboost-serialization-dev. Unpacking libboost-serialization-dev (from .../libboost-serialization-dev_1.49.0.1_amd64.deb) ... Selecting previously unselected package liblapack3. Unpacking liblapack3 (from .../liblapack3_3.4.2+dfsg-1_amd64.deb) ... Selecting previously unselected package liblapack-dev. Unpacking liblapack-dev (from .../liblapack-dev_3.4.2+dfsg-1_amd64.deb) ... Selecting previously unselected package libxml2-dev:amd64. Unpacking libxml2-dev:amd64 (from .../libxml2-dev_2.9.1+dfsg1-2_amd64.deb) ... Selecting previously unselected package zlib1g-dev:amd64. Unpacking zlib1g-dev:amd64 (from .../zlib1g-dev_1%3a1.2.8.dfsg-1_amd64.deb) ... Selecting previously unselected package sbuild-build-depends-prime-phylo-dummy. Unpacking sbuild-build-depends-prime-phylo-dummy (from .../sbuild-build-depends-prime-phylo-dummy.deb) ... Setting up libncursesw5:amd64 (5.9+20130608-1) ... Setting up libpipeline1:amd64 (1.2.4-1) ... Setting up libprocps1:amd64 (1:3.3.8-2) ... Setting up libssl1.0.0:amd64 (1.0.1e-3) ... Setting up groff-base (1.22.2-3) ... Setting up bsdmainutils (9.0.5) ... 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 man-db (2.6.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libasprintf0c2:amd64 (0.18.2.1-1) ... Setting up libgpg-error0:amd64 (1.10-3.1) ... Setting up libgcrypt11:amd64 (1.5.2-3) ... Setting up libp11-kit0:amd64 (0.18.4-1) ... Setting up libtasn1-3:amd64 (2.14-3) ... Setting up libgnutls26:amd64 (2.12.23-5) ... Setting up libkeyutils1:amd64 (1.5.5-7) ... Setting up libkrb5support0:amd64 (1.10.1+dfsg-6.1) ... Setting up libk5crypto3:amd64 (1.10.1+dfsg-6.1) ... Setting up libkrb5-3:amd64 (1.10.1+dfsg-6.1) ... Setting up libgssapi-krb5-2:amd64 (1.10.1+dfsg-6.1) ... Setting up libidn11:amd64 (1.25-2) ... Setting up libsasl2-modules:amd64 (2.1.25.dfsg1-13) ... Setting up libsasl2-2:amd64 (2.1.25.dfsg1-13) ... Setting up libldap-2.4-2:amd64 (2.4.31-1+nmu2) ... Setting up libmagic1:amd64 (1:5.14-2) ... Setting up libxml2:amd64 (2.9.1+dfsg1-2) ... Setting up libsigsegv2:amd64 (2.10-2) ... Setting up m4 (1.4.16-5) ... Setting up flex (2.5.35-10.1) ... Setting up liblzo2-2:amd64 (2.06-1) ... Setting up libnettle4:amd64 (2.7.1-1) ... Setting up libarchive13:amd64 (3.1.2-7) ... Setting up libglib2.0-0:amd64 (2.36.3-3) ... No schema files found: doing nothing. Setting up libcroco3:amd64 (0.6.8-2) ... Setting up librtmp0:amd64 (2.4+20121230.gitdf6c518-1) ... Setting up libssh2-1:amd64 (1.4.3-1) ... Setting up libcurl3-gnutls:amd64 (7.31.0-2) ... Setting up libexpat1:amd64 (2.1.0-4) ... Setting up libgfortran3:amd64 (4.8.1-6) ... Setting up libicu48:amd64 (4.8.1.1-12) ... Setting up libunistring0:amd64 (0.9.3-5) ... Setting up adduser (3.113+nmu3) ... Setting up procps (1:3.3.8-2) ... update-alternatives: using /usr/bin/w.procps to provide /usr/bin/w (w) in auto mode update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults All runlevel operations denied by policy invoke-rc.d: policy-rc.d denied execution of start. Setting up file (1:5.14-2) ... Setting up gettext-base (0.18.2.1-1) ... Setting up libbison-dev:amd64 (2:2.7.1.dfsg-1) ... Setting up bison (2:2.7.1.dfsg-1) ... update-alternatives: using /usr/bin/bison.yacc to provide /usr/bin/yacc (yacc) in auto mode Setting up emacsen-common (2.0.5) ... Setting up cmake-data (2.8.11.2-1) ... Install cmake-data for emacs Setting up cmake (2.8.11.2-1) ... Setting up gettext (0.18.2.1-1) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu2) ... Setting up debhelper (9.20130630) ... Setting up gengetopt (2.22.6-2) ... Setting up libgfortran-4.8-dev:amd64 (4.8.1-6) ... Setting up gfortran-4.8 (4.8.1-6) ... Setting up gfortran (4:4.8.1-2) ... update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode Setting up libblas3 (1.2.20110419-5) ... update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode Setting up libblas-dev (1.2.20110419-5) ... update-alternatives: using /usr/lib/libblas/libblas.so to provide /usr/lib/libblas.so (libblas.so) in auto mode Setting up libboost1.49-dev (1.49.0-4) ... Setting up libboost-dev (1.49.0.1) ... Setting up libboost-serialization1.49.0 (1.49.0-4) ... Setting up libboost-serialization1.49-dev (1.49.0-4) ... Setting up libibverbs1 (1.1.7-1) ... Setting up libnuma1 (2.0.8-3) ... Setting up libtorque2 (2.4.16+dfsg-1) ... Setting up libopenmpi1.3 (1.4.5-1) ... Setting up libboost-mpi1.49.0 (1.49.0-4) ... Setting up openmpi-common (1.4.5-1) ... Setting up libibverbs-dev (1.1.7-1) ... Setting up libopenmpi-dev (1.4.5-1) ... update-alternatives: using /usr/lib/openmpi/include to provide /usr/include/mpi (mpi) in auto mode Setting up mpi-default-dev (1.0.1) ... Setting up libboost-mpi1.49-dev (1.49.0-4) ... Setting up libboost-mpi-dev (1.49.0.1) ... Setting up libboost-serialization-dev (1.49.0.1) ... Setting up liblapack3 (3.4.2+dfsg-1) ... update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode Setting up liblapack-dev (3.4.2+dfsg-1) ... update-alternatives: using /usr/lib/lapack/liblapack.so to provide /usr/lib/liblapack.so (liblapack.so) in auto mode Setting up libxml2-dev:amd64 (2.9.1+dfsg1-2) ... Setting up zlib1g-dev:amd64 (1:1.2.8.dfsg-1) ... Setting up sbuild-build-depends-prime-phylo-dummy (0.invalid.0) ... Processing triggers for libc-bin ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 2.6.32-5-xen-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.23.52.20130620-1 dpkg-dev_1.16.10 g++-4.6_4.6.4-4 g++-4.8_4.8.1-6 gcc-4.6_4.6.4-4 gcc-4.7_4.7.3-6 gcc-4.8_4.8.1-6 libc6-dev_2.17-7 libstdc++-4.8-dev_4.8.1-6 libstdc++6_4.8.1-6 libstdc++6-4.6-dev_4.6.4-4 libstdc++6-4.7-dev_4.7.3-6 linux-libc-dev_3.9.8-1 Package versions: adduser_3.113+nmu3 apt_0.9.9.1 base-files_7.2 base-passwd_3.5.26 bash_4.2+dfsg-1 binutils_2.23.52.20130620-1 bison_2:2.7.1.dfsg-1 bsdmainutils_9.0.5 bsdutils_1:2.20.1-5.5 build-essential_11.6 bzip2_1.0.6-4 clang-3.3_1:3.3-3 cmake_2.8.11.2-1 cmake-data_2.8.11.2-1 coreutils_8.20-3 cpp_4:4.8.1-2 cpp-4.6_4.6.4-4 cpp-4.7_4.7.3-6 cpp-4.8_4.8.1-6 dash_0.5.7-3 debconf_1.5.50 debconf-i18n_1.5.50 debfoster_2.7-1.2 debhelper_9.20130630 debian-archive-keyring_2012.4 debianutils_4.3.4 diffutils_1:3.2-8 dpkg_1.16.10 dpkg-dev_1.16.10 e2fslibs_1.42.8-1 e2fsprogs_1.42.8-1 emacsen-common_2.0.5 fakeroot_1.19-2 file_1:5.14-2 findutils_4.4.2-6 flex_2.5.35-10.1 g++_4:4.8.1-2 g++-4.6_4.6.4-4 g++-4.8_4.8.1-6 gcc_4:4.8.1-2 gcc-4.4-base_4.4.7-4 gcc-4.5-base_4.5.4-1 gcc-4.6_4.6.4-4 gcc-4.6-base_4.6.4-4 gcc-4.7_4.7.3-6 gcc-4.7-base_4.7.3-6 gcc-4.8_4.8.1-6 gcc-4.8-base_4.8.1-6 gengetopt_2.22.6-2 gettext_0.18.2.1-1 gettext-base_0.18.2.1-1 gfortran_4:4.8.1-2 gfortran-4.8_4.8.1-6 gnupg_1.4.12-7 gpgv_1.4.12-7 grep_2.14-2 groff-base_1.22.2-3 gzip_1.6-1 hostname_3.13 initscripts_2.88dsf-42 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 libacl1_2.2.52-1 libapt-pkg4.12_0.9.9.1 libarchive13_3.1.2-7 libasan0_4.8.1-6 libasprintf0c2_0.18.2.1-1 libatomic1_4.8.1-6 libattr1_1:2.4.47-1 libbison-dev_2:2.7.1.dfsg-1 libblas-dev_1.2.20110419-5 libblas3_1.2.20110419-5 libblkid1_2.20.1-5.5 libboost-dev_1.49.0.1 libboost-mpi-dev_1.49.0.1 libboost-mpi1.49-dev_1.49.0-4 libboost-mpi1.49.0_1.49.0-4 libboost-serialization-dev_1.49.0.1 libboost-serialization1.49-dev_1.49.0-4 libboost-serialization1.49.0_1.49.0-4 libboost1.49-dev_1.49.0-4 libbz2-1.0_1.0.6-4 libc-bin_2.17-7 libc-dev-bin_2.17-7 libc6_2.17-7 libc6-dev_2.17-7 libcap2_1:2.22-1.2 libclang-common-3.3-dev_1:3.3-3 libclang1-3.3_1:3.3-3 libclass-isa-perl_0.36-5 libcloog-isl4_0.18.0-2 libcloog-ppl1_0.16.1-3 libcomerr2_1.42.8-1 libcroco3_0.6.8-2 libcurl3-gnutls_7.31.0-2 libdb5.1_5.1.29-6 libdpkg-perl_1.16.10 libexpat1_2.1.0-4 libffi6_3.0.13-4 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.2d-5 libgcc-4.7-dev_4.7.3-6 libgcc-4.8-dev_4.8.1-6 libgcc1_1:4.8.1-6 libgcrypt11_1.5.2-3 libgdbm3_1.8.3-12 libgfortran-4.8-dev_4.8.1-6 libgfortran3_4.8.1-6 libglib2.0-0_2.36.3-3 libgmp10_2:5.1.2+dfsg-2 libgmpxx4ldbl_2:5.1.2+dfsg-2 libgnutls26_2.12.23-5 libgomp1_4.8.1-6 libgpg-error0_1.10-3.1 libgpm2_1.20.4-6.1 libgssapi-krb5-2_1.10.1+dfsg-6.1 libibverbs-dev_1.1.7-1 libibverbs1_1.1.7-1 libicu48_4.8.1.1-12 libidn11_1.25-2 libisl10_0.11.2-1 libitm1_4.8.1-6 libk5crypto3_1.10.1+dfsg-6.1 libkeyutils1_1.5.5-7 libkrb5-3_1.10.1+dfsg-6.1 libkrb5support0_1.10.1+dfsg-6.1 liblapack-dev_3.4.2+dfsg-1 liblapack3_3.4.2+dfsg-1 libldap-2.4-2_2.4.31-1+nmu2 libllvm3.3_1:3.3-3 liblocale-gettext-perl_1.05-7+b1 liblzma5_5.1.1alpha+20120614-2 liblzo2-2_2.06-1 libmagic1_1:5.14-2 libmount1_2.20.1-5.5 libmpc2_0.9-4 libmpc3_1.0.1-1 libmpfr4_3.1.1-1 libncurses5_5.9+20130608-1 libncursesw5_5.9+20130608-1 libnettle4_2.7.1-1 libnuma1_2.0.8-3 libobjc-4.7-dev_4.7.3-6 libobjc4_4.8.1-6 libopenmpi-dev_1.4.5-1 libopenmpi1.3_1.4.5-1 libp11-kit0_0.18.4-1 libpam-modules_1.1.3-9 libpam-modules-bin_1.1.3-9 libpam-runtime_1.1.3-9 libpam0g_1.1.3-9 libpcre3_1:8.31-2 libpipeline1_1.2.4-1 libppl-c4_1:1.0-7 libppl12_1:1.0-7 libprocps1_1:3.3.8-2 libquadmath0_4.8.1-6 libreadline6_6.2+dfsg-0.1 librtmp0_2.4+20121230.gitdf6c518-1 libsasl2-2_2.1.25.dfsg1-13 libsasl2-modules_2.1.25.dfsg1-13 libselinux1_2.1.13-2 libsemanage-common_2.1.10-2 libsemanage1_2.1.10-2 libsepol1_2.1.9-2 libsigsegv2_2.10-2 libslang2_2.2.4-15 libss2_1.42.8-1 libssh2-1_1.4.3-1 libssl1.0.0_1.0.1e-3 libstdc++-4.8-dev_4.8.1-6 libstdc++6_4.8.1-6 libstdc++6-4.6-dev_4.6.4-4 libstdc++6-4.7-dev_4.7.3-6 libswitch-perl_2.16-2 libtasn1-3_2.14-3 libtext-charwidth-perl_0.04-7+b1 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9+20130608-1 libtorque2_2.4.16+dfsg-1 libtsan0_4.8.1-6 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23.2 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.5 libxml2_2.9.1+dfsg1-2 libxml2-dev_2.9.1+dfsg1-2 linux-libc-dev_3.9.8-1 login_1:4.1.5.1-1 lsb-base_4.1+Debian12 m4_1.4.16-5 make_3.81-8.2 man-db_2.6.5-2 mawk_1.3.3-17 mount_2.20.1-5.5 mpi-default-dev_1.0.1 multiarch-support_2.17-7 ncurses-base_5.9+20130608-1 ncurses-bin_5.9+20130608-1 openmpi-common_1.4.5-1 passwd_1:4.1.5.1-1 patch_2.7.1-3 perl_5.14.2-21 perl-base_5.14.2-21 perl-modules_5.14.2-21 po-debconf_1.0.16+nmu2 procps_1:3.3.8-2 readline-common_6.2+dfsg-0.1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-prime-phylo-dummy_0.invalid.0 sed_4.2.2-1 sensible-utils_0.0.9 sudo_1.8.5p2-1+nmu1 sysv-rc_2.88dsf-42 sysvinit_2.88dsf-42 sysvinit-utils_2.88dsf-42 tar_1.26+dfsg-6 tzdata_2013c-2 ucf_3.0027+nmu1 util-linux_2.20.1-5.5 vim_2:7.3.923-3 vim-common_2:7.3.923-3 vim-runtime_2:7.3.923-3 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.8.dfsg-1 zlib1g-dev_1:1.2.8.dfsg-1 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error gpgv: Signature made Tue Dec 18 15:40:38 2012 UTC using DSA key ID C09FD35A gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./prime-phylo_1.0.11-1.dsc dpkg-source: info: extracting prime-phylo in prime-phylo-1.0.11 dpkg-source: info: unpacking prime-phylo_1.0.11.orig.tar.gz dpkg-source: info: unpacking prime-phylo_1.0.11-1.debian.tar.gz Check disc space ──────────────── Sufficient free space for build Hack binNMU version ─────────────────── Created changelog entry for binNMU version 1.0.11-1clang1 User Environment ──────────────── HOME=/sbuild-nonexistent LOGNAME=user 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=1000 SCHROOT_GROUP=user SCHROOT_SESSION_ID=unstable-amd64-sbuild-bfa556f7-5cdd-4e26-b134-53f6ee6938cf SCHROOT_UID=1000 SCHROOT_USER=user SHELL=/bin/sh USER=user dpkg-buildpackage ───────────────── dpkg-buildpackage: source package prime-phylo dpkg-buildpackage: source version 1.0.11-1clang1 dpkg-source --before-build prime-phylo-1.0.11 dpkg-buildpackage: host architecture amd64 fakeroot debian/rules clean dh clean --buildsystem=cmake --parallel dh_testdir -O--buildsystem=cmake -O--parallel dh_auto_clean -O--buildsystem=cmake -O--parallel dh_clean -O--buildsystem=cmake -O--parallel debian/rules build-arch dh build-arch --buildsystem=cmake --parallel dh_testdir -a -O--buildsystem=cmake -O--parallel debian/rules override_dh_auto_configure make[1]: Entering directory `/«PKGBUILDDIR»' 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 -- The CXX compiler identification is Clang 3.3.0 -- 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 -- The Fortran compiler identification is GNU -- Check for working Fortran compiler: /usr/bin/f95 -- Check for working Fortran compiler: /usr/bin/f95 -- works -- Detecting Fortran compiler ABI info -- Detecting Fortran compiler ABI info - done -- Checking whether /usr/bin/f95 supports Fortran 90 -- Checking whether /usr/bin/f95 supports Fortran 90 -- yes -- The C compiler identification is Clang 3.3.0 -- 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 -- Looking for Fortran sgemm -- Looking for Fortran sgemm - found -- Looking for include file pthread.h -- Looking for include file pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - not found -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- A library with BLAS API found. hittade /usr/lib/libblas.so -- A library with BLAS API found. -- Looking for Fortran cheev -- Looking for Fortran cheev - found -- A library with LAPACK API found. -- Found BISON: /usr/bin/bison (found version "2.7.12-4996") -- Found FLEX: /usr/bin/flex (found version "2.5.35") -- Found MPI_C: /usr/lib/openmpi/lib/libmpi.so;/usr/lib/openmpi/lib/libopen-rte.so;/usr/lib/openmpi/lib/libopen-pal.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libnsl.so;/usr/lib/x86_64-linux-gnu/libutil.so;/usr/lib/x86_64-linux-gnu/libm.so;/usr/lib/x86_64-linux-gnu/libdl.so -- Found MPI_CXX: /usr/lib/openmpi/lib/libmpi_cxx.so;/usr/lib/openmpi/lib/libmpi.so;/usr/lib/openmpi/lib/libopen-rte.so;/usr/lib/openmpi/lib/libopen-pal.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libnsl.so;/usr/lib/x86_64-linux-gnu/libutil.so;/usr/lib/x86_64-linux-gnu/libm.so;/usr/lib/x86_64-linux-gnu/libdl.so -- Found MPI_Fortran: /usr/lib/openmpi/lib/libmpi_f90.so;/usr/lib/openmpi/lib/libmpi_f77.so;/usr/lib/openmpi/lib/libmpi.so;/usr/lib/openmpi/lib/libopen-rte.so;/usr/lib/openmpi/lib/libopen-pal.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libnsl.so;/usr/lib/x86_64-linux-gnu/libutil.so;/usr/lib/x86_64-linux-gnu/libm.so;/usr/lib/x86_64-linux-gnu/libdl.so -- Boost version: 1.49.0 -- Found the following Boost libraries: -- mpi -- serialization -- Found LibXml2: /usr/lib/x86_64-linux-gnu/libxml2.so (found version "2.9.1") mpilib is /usr/lib/openmpi/include;/usr/lib/openmpi/include/openmpi included path is -- Configuring done -- Generating done -- Build files have been written to: /«PKGBUILDDIR»/obj-x86_64-linux-gnu make[1]: Leaving directory `/«PKGBUILDDIR»' dh_auto_build -a -O--buildsystem=cmake -O--parallel make[1]: Entering directory `/«PKGBUILDDIR»/obj-x86_64-linux-gnu' /usr/bin/cmake -H/«PKGBUILDDIR» -B/«PKGBUILDDIR»/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory `/«PKGBUILDDIR»/obj-x86_64-linux-gnu' make -f src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/build.make src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/depend make[3]: Entering directory `/«PKGBUILDDIR»/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 84 [ 1%] [FLEX][MyScanner2] Building scanner with flex 2.5.35 cd /«PKGBUILDDIR»/src/cxx/libraries/sfile && /usr/bin/flex -o/«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/lexer.c seqreader.l /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles [ 1%] [BISON][MyParser2] Building parser with bison 2.7.12-4996 cd /«PKGBUILDDIR»/src/cxx/libraries/sfile && /usr/bin/bison -d -d -o /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/gb.tab.c gb.y gb.y: warning: 1 nonterminal useless in grammar gb.y: warning: 1 rule useless in grammar gb.y:117.47-58: warning: nonterminal useless in grammar: darwin_entry gb.y:258.19-61: warning: rule useless in grammar: darwin_entry: TEXT cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /«PKGBUILDDIR» /«PKGBUILDDIR»/src/cxx/libraries/sfile /«PKGBUILDDIR»/obj-x86_64-linux-gnu /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/cxx/libraries/sfile /«PKGBUILDDIR»/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 `/«PKGBUILDDIR»/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 `/«PKGBUILDDIR»/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 85 [ 2%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/gbread.c.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/cxx/libraries/sfile -I/«PKGBUILDDIR»/src/cxx/libraries/sfile -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries -o CMakeFiles/prime-phylo-sfile.dir/gbread.c.o -c /«PKGBUILDDIR»/src/cxx/libraries/sfile/gbread.c /«PKGBUILDDIR»/src/cxx/libraries/sfile/gbread.c:17:10: warning: implicitly declaring library function 'strcmp' with type 'int (const char *, const char *)' if (!strcmp(argv[opt], "-d")) { ^ /«PKGBUILDDIR»/src/cxx/libraries/sfile/gbread.c:17:10: note: please include the header or explicitly provide a declaration for 'strcmp' 1 warning generated. /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles [ 2%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/sfile.c.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/cxx/libraries/sfile -I/«PKGBUILDDIR»/src/cxx/libraries/sfile -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries -o CMakeFiles/prime-phylo-sfile.dir/sfile.c.o -c /«PKGBUILDDIR»/src/cxx/libraries/sfile/sfile.c /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 86 [ 3%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/lexer.c.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/cxx/libraries/sfile -I/«PKGBUILDDIR»/src/cxx/libraries/sfile -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries -o CMakeFiles/prime-phylo-sfile.dir/lexer.c.o -c /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/lexer.c seqreader.l:271:9: warning: unused variable 'code' [-Wunused-variable] int code; /* return value */ ^ /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/lexer.c:1832:17: warning: unused function 'yyunput' [-Wunused-function] static void yyunput (int c, register char * yy_bp ) ^ /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/lexer.c:1873:16: warning: function 'input' is not needed and will not be emitted [-Wunneeded-internal-declaration] static int input (void) ^ 3 warnings generated. /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 87 [ 4%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/gb.tab.c.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/cxx/libraries/sfile -I/«PKGBUILDDIR»/src/cxx/libraries/sfile -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries -o CMakeFiles/prime-phylo-sfile.dir/gb.tab.c.o -c /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/gb.tab.c /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/gb.tab.c:1377:16: warning: implicit declaration of function 'yylex' is invalid in C99 [-Wimplicit-function-declaration] yychar = YYLEX; ^ /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/gb.tab.c:726:16: note: expanded from macro 'YYLEX' # define YYLEX 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()); ^ /usr/include/x86_64-linux-gnu/bits/stdio2.h:108:42: note: expanded from macro 'printf' __printf_chk (__USE_FORTIFY_LEVEL - 1, __VA_ARGS__) ^ gb.y:402:9: warning: unused variable 'new_buf' [-Wunused-variable] char *new_buf; ^ 3 warnings generated. Linking C shared library libprime-phylo-sfile.so cd /«PKGBUILDDIR»/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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -Wl,-z,relro -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 `/«PKGBUILDDIR»/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 84 85 86 87 [ 4%] Built target prime-phylo-sfile make -f src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/build.make src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/depend make[3]: Entering directory `/«PKGBUILDDIR»/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 3 [ 5%] [FLEX][MyScanner] Building scanner with flex 2.5.35 cd /«PKGBUILDDIR»/src/cxx/libraries/prime && /usr/bin/flex -Pyytree_ -o/«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/cxx/libraries/prime/lexer.c NHX.l /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 2 [ 6%] [BISON][MyParser] Building parser with bison 2.7.12-4996 cd /«PKGBUILDDIR»/src/cxx/libraries/prime && /usr/bin/bison -d -y -p yytree_ -d -o /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/cxx/libraries/prime/NHXparse.c NHXparse.y cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /«PKGBUILDDIR» /«PKGBUILDDIR»/src/cxx/libraries/prime /«PKGBUILDDIR»/obj-x86_64-linux-gnu /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/cxx/libraries/prime /«PKGBUILDDIR»/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 `/«PKGBUILDDIR»/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 `/«PKGBUILDDIR»/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles [ 6%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXnode.c.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/NHXnode.c.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/NHXnode.c /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 4 [ 7%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXtree.c.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/NHXtree.c.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/NHXtree.c /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles [ 7%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXannotation.c.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/NHXannotation.c.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/NHXannotation.c /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 5 [ 8%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/lexer.c.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/lexer.c.o -c /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/cxx/libraries/prime/lexer.c /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/cxx/libraries/prime/lexer.c:1320:17: warning: unused function 'yyunput' [-Wunused-function] static void yyunput (int c, register char * yy_bp ) ^ /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/cxx/libraries/prime/lexer.c:1361:16: warning: function 'input' is not needed and will not be emitted [-Wunneeded-internal-declaration] static int input (void) ^ 2 warnings generated. /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 6 [ 9%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXparse.c.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/NHXparse.c.o -c /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/cxx/libraries/prime/NHXparse.c /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/cxx/libraries/prime/NHXparse.c:1422:16: warning: implicit declaration of function 'yytree_lex' is invalid in C99 [-Wimplicit-function-declaration] yychar = YYLEX; ^ /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/cxx/libraries/prime/NHXparse.c:771:16: note: expanded from macro 'YYLEX' # define YYLEX yylex () ^ /«PKGBUILDDIR»/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. /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles [ 9%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/AnError.cc.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/AnError.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/AnError.cc /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 7 [ 10%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Beep.cc.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/Beep.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/Beep.cc /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 8 [ 11%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BeepOption.cc.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/BeepOption.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/BeepOption.cc /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles [ 11%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Hacks.cc.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/Hacks.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/Hacks.cc /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 9 [ 12%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ODESolver.cc.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/ODESolver.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/ODESolver.cc In file included from /«PKGBUILDDIR»/src/cxx/libraries/prime/ODESolver.cc:4: /«PKGBUILDDIR»/src/cxx/libraries/prime/ODESolver.hh:359:20: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real C2 = 1.0 / 5.0; ^ ~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/cxx/libraries/prime/ODESolver.hh:360:20: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real C3 = 3.0 / 10.0; ^ ~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/cxx/libraries/prime/ODESolver.hh:361:20: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real C4 = 4.0 / 5.0; ^ ~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/cxx/libraries/prime/ODESolver.hh:362:20: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real C5 = 8.0 / 9.0; ^ ~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/cxx/libraries/prime/ODESolver.hh:363:20: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real A21 = 1.0 / 5.0; ^ ~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/cxx/libraries/prime/ODESolver.hh:364:20: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real A31 = 3.0 / 40.0; ^ ~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/cxx/libraries/prime/ODESolver.hh:365:20: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real A32 = 9.0 / 40.0; ^ ~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/cxx/libraries/prime/ODESolver.hh:366:20: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real A41 = 44.0 / 45.0; ^ ~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/cxx/libraries/prime/ODESolver.hh:367:20: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real A42 = -56.0 / 15.0; ^ ~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/cxx/libraries/prime/ODESolver.hh:368:20: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real A43 = 32.0 / 9.0; ^ ~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/cxx/libraries/prime/ODESolver.hh:369:20: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real A51 = 19372.0 / 6561.0; ^ ~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/cxx/libraries/prime/ODESolver.hh:370:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real A52 = -25360.0 / 2187.0; ^ ~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/cxx/libraries/prime/ODESolver.hh:371:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real A53 = 64448.0 / 6561.0; ^ ~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/cxx/libraries/prime/ODESolver.hh:372:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real A54 = -212.0 / 729.0; ^ ~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/cxx/libraries/prime/ODESolver.hh:373:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real A61 = 9017.0 / 3168.0; ^ ~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/cxx/libraries/prime/ODESolver.hh:374:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real A62 = -355.0 / 33.0; ^ ~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/cxx/libraries/prime/ODESolver.hh:375:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real A63 = 46732.0 / 5247.0; ^ ~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/cxx/libraries/prime/ODESolver.hh:376:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real A64 = 49.0 / 176.0; ^ ~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/cxx/libraries/prime/ODESolver.hh:377:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real A65 = -5103.0 / 18656.0; ^ ~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/cxx/libraries/prime/ODESolver.hh:378:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real A71 = 35.0 / 384.0; ^ ~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/cxx/libraries/prime/ODESolver.hh:379:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real A73 = 500.0 / 1113.0; ^ ~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/cxx/libraries/prime/ODESolver.hh:380:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real A74 = 125.0 / 192.0; ^ ~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/cxx/libraries/prime/ODESolver.hh:381:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real A75 = -2187.0 / 6784.0; ^ ~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/cxx/libraries/prime/ODESolver.hh:382:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real A76 = 11.0 / 84.0; ^ ~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/cxx/libraries/prime/ODESolver.hh:383:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real E1 = 71.0 / 57600.0; ^ ~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/cxx/libraries/prime/ODESolver.hh:384:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real E3 = -71.0 / 16695.0; ^ ~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/cxx/libraries/prime/ODESolver.hh:385:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real E4 = 71.0 / 1920.0; ^ ~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/cxx/libraries/prime/ODESolver.hh:386:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real E5 = -17253.0 / 339200.0; ^ ~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/cxx/libraries/prime/ODESolver.hh:387:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real E6 = 22.0 / 525.0; ^ ~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/cxx/libraries/prime/ODESolver.hh:388:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real E7 = -1.0 / 40.0; ^ ~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/cxx/libraries/prime/ODESolver.hh:391:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real D1 = -12715105075.0 / 11282082432.0; ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/cxx/libraries/prime/ODESolver.hh:392:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real D3 = 87487479700.0 / 32700410799.0; ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/cxx/libraries/prime/ODESolver.hh:393:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real D4 = -10690763975.0 / 1880347072.0; ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/cxx/libraries/prime/ODESolver.hh:394:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real D5 = 701980252875.0 / 199316789632.0; ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/cxx/libraries/prime/ODESolver.hh:395:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real D6 = -1453857185.0 / 822651844.0; ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/cxx/libraries/prime/ODESolver.hh:396:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init] static const Real D7 = 69997945.0 / 29380423.0; ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 36 warnings generated. /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles [ 12%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PRNG.cc.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/PRNG.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/PRNG.cc /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 10 [ 13%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PrimeOptionMap.cc.o cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/PrimeOptionMap.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/PrimeOptionMap.cc In file included from /«PKGBUILDDIR»/src/cxx/libraries/prime/PrimeOptionMap.cc:1: /«PKGBUILDDIR»/src/cxx/libraries/prime/PrimeOptionMap.hh:161:32: error: no function named 'operator<<' with type 'std::ostream &(std::ostream &, const beep::PrimeOptionMap &)' was found in the specified scope friend std::ostream& beep::operator<<(std::ostream& o, ^ /«PKGBUILDDIR»/src/cxx/libraries/prime/PrimeOptionMap.hh:163:32: error: no function named 'operator<<' with type 'std::ostream &(std::ostream &, const beep::PrimeOption &)' was found in the specified scope friend std::ostream& beep::operator<<(std::ostream& o, ^ In file included from /«PKGBUILDDIR»/src/cxx/libraries/prime/PrimeOptionMap.cc:3: /«PKGBUILDDIR»/src/cxx/libraries/prime/PrimeOption.hh:391:2: warning: struct 'UserSubstMatrixParams' was previously declared as a class [-Wmismatched-tags] struct UserSubstMatrixParams tmpVal; ^ /«PKGBUILDDIR»/src/cxx/libraries/prime/PrimeOptionMap.hh:23:9: note: previous use is here class UserSubstMatrixParams ^ /«PKGBUILDDIR»/src/cxx/libraries/prime/PrimeOption.hh:391:2: note: did you mean class here? struct UserSubstMatrixParams tmpVal; ^~~~~~ class /«PKGBUILDDIR»/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); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /«PKGBUILDDIR»/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); ^ & [ ] /«PKGBUILDDIR»/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 " + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ /«PKGBUILDDIR»/src/cxx/libraries/prime/PrimeOption.hh:425:55: note: use array indexing to silence this warning throw AnError("Wrong dimension of R, should be " + ^ /«PKGBUILDDIR»/src/cxx/libraries/prime/PrimeOptionMap.cc:306:18: error: 'optionsInOrderOfIns' is a private member of 'beep::PrimeOptionMap' for(it = pom.optionsInOrderOfIns.begin(); ^ /«PKGBUILDDIR»/src/cxx/libraries/prime/PrimeOptionMap.hh:190:31: note: declared private here std::vector optionsInOrderOfIns; //! Options in insert order ^ /«PKGBUILDDIR»/src/cxx/libraries/prime/PrimeOptionMap.cc:307:12: error: 'optionsInOrderOfIns' is a private member of 'beep::PrimeOptionMap' it != pom.optionsInOrderOfIns.end(); ++it) ^ /«PKGBUILDDIR»/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/PrimeOptionMap.cc.o] Error 1 make[3]: Leaving directory `/«PKGBUILDDIR»/obj-x86_64-linux-gnu' make[2]: *** [src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/all] Error 2 make[1]: *** [all] Error 2 dh_auto_build: make -j1 returned exit code 2 make[2]: Leaving directory `/«PKGBUILDDIR»/obj-x86_64-linux-gnu' make[1]: Leaving directory `/«PKGBUILDDIR»/obj-x86_64-linux-gnu' make: *** [build-arch] Error 2 dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2 ──────────────────────────────────────────────────────────────────────────────── Build finished at 20130716-1036 Finished ──────── E: Build failure (dpkg-buildpackage died) ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /«BUILDDIR» Not cleaning session: cloned chroot in use ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Build Architecture: amd64 Build-Space: 9356 Build-Time: 13 Distribution: unstable Fail-Stage: build Host Architecture: amd64 Install-Time: 21 Job: prime-phylo_1.0.11-1 Machine Architecture: amd64 Package: prime-phylo Package-Time: 94 Source-Version: 1.0.11-1 Space: 9356 Status: attempted Version: 1.0.11-1clang1 ──────────────────────────────────────────────────────────────────────────────── Finished at 20130716-1036 Build needed 00:01:34, 9356k disc space DC-Status: Failed 94.368175309s DC-Time-Estimation: 94.368175309 versus expected 550 (r/m: 4.82823603613268 ; m: 94.368175309)