DC-Build-Header: prime-phylo 1.0.11-1 / 2014-06-17 13:23:12 +0000 DC-Task: source:prime-phylo version:1.0.11-1 architecture:any chroot:unstable esttime:558 logfile:/tmp/prime-phylo_1.0.11-1_unstable_clang.log modes:binary-only:parallel: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-172-31-9-162.us-west-2.compute.internal ╔══════════════════════════════════════════════════════════════════════════════╗ ║ prime-phylo 1.0.11-1clang1 (amd64) 17 Jun 2014 13:23 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ 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-DAP0EE/prime-phylo-1.0.11' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/prime-phylo-DAP0EE' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/unstable-amd64-sbuild-b5532e1b-0d82-4504-8247-b90506527fb5' with '«CHROOT»' ┌──────────────────────────────────────────────────────────────────────────────┐ │ Update chroot │ └──────────────────────────────────────────────────────────────────────────────┘ Get:1 http://localhost:9999 unstable InRelease [206 kB] Ign http://localhost:9999 unstable/main Sources/DiffIndex Ign http://localhost:9999 unstable/main amd64 Packages/DiffIndex Get:2 http://localhost:9999 unstable/main Translation-en/DiffIndex [7876 B] Get:3 http://localhost:9999 unstable/main 2014-06-16-2054.31.pdiff [699 B] Get:4 http://localhost:9999 unstable/main 2014-06-16-2054.31.pdiff [699 B] Get:5 http://localhost:9999 unstable/main Sources [9439 kB] Get:6 http://localhost:9999 unstable/main amd64 Packages [9063 kB] Fetched 18.7 MB in 4s (4397 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following packages will be upgraded: libc-bin libc-dev-bin libc6 libc6-dev linux-libc-dev multiarch-support 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 9447 kB of archives. After this operation, 10.2 kB of additional disk space will be used. Get:1 http://localhost:9999/debian/ unstable/main libc6-dev amd64 2.19-2 [2000 kB] Get:2 http://localhost:9999/debian/ unstable/main libc-dev-bin amd64 2.19-2 [235 kB] Get:3 http://localhost:9999/debian/ unstable/main linux-libc-dev amd64 3.14.7-1 [937 kB] Get:4 http://localhost:9999/debian/ unstable/main libc-bin amd64 2.19-2 [1288 kB] Get:5 http://localhost:9999/debian/ unstable/main libc6 amd64 2.19-2 [4816 kB] Get:6 http://localhost:9999/debian/ unstable/main multiarch-support amd64 2.19-2 [171 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 9447 kB in 0s (30.9 MB/s) (Reading database ... 14215 files and directories currently installed.) Preparing to unpack .../libc6-dev_2.19-2_amd64.deb ... Unpacking libc6-dev:amd64 (2.19-2) over (2.19-1) ... Preparing to unpack .../libc-dev-bin_2.19-2_amd64.deb ... Unpacking libc-dev-bin (2.19-2) over (2.19-1) ... Preparing to unpack .../linux-libc-dev_3.14.7-1_amd64.deb ... Unpacking linux-libc-dev:amd64 (3.14.7-1) over (3.14.5-1) ... Preparing to unpack .../libc-bin_2.19-2_amd64.deb ... Unpacking libc-bin (2.19-2) over (2.19-1) ... Preparing to unpack .../libc6_2.19-2_amd64.deb ... Unpacking libc6:amd64 (2.19-2) over (2.19-1) ... Setting up libc6:amd64 (2.19-2) ... Setting up libc-bin (2.19-2) ... (Reading database ... 14216 files and directories currently installed.) Preparing to unpack .../multiarch-support_2.19-2_amd64.deb ... Unpacking multiarch-support (2.19-2) over (2.19-1) ... Setting up multiarch-support (2.19-2) ... Setting up libc-dev-bin (2.19-2) ... Setting up linux-libc-dev:amd64 (3.14.7-1) ... Setting up libc6-dev:amd64 (2.19-2) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ 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 (4328 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-3.4' Install of clang-3.4 + apt-get update Hit http://localhost:9999 unstable InRelease Ign http://localhost:9999 unstable/main Sources/DiffIndex Ign http://localhost:9999 unstable/main amd64 Packages/DiffIndex Hit http://localhost:9999 unstable/main Translation-en/DiffIndex Hit http://localhost:9999 unstable/main Sources Hit http://localhost:9999 unstable/main amd64 Packages Reading package lists... + apt-get install --yes --no-install-recommends --force-yes clang-3.4 Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: libclang-common-3.4-dev libclang1-3.4 libffi6 libllvm3.4 libobjc-4.9-dev libobjc4 Suggested packages: gnustep gnustep-devel Recommended packages: llvm-3.4-dev python The following NEW packages will be installed: clang-3.4 libclang-common-3.4-dev libclang1-3.4 libffi6 libllvm3.4 libobjc-4.9-dev libobjc4 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. Need to get 30.6 MB of archives. After this operation, 118 MB of additional disk space will be used. Get:1 http://localhost:9999/debian/ unstable/main libffi6 amd64 3.1-2 [19.8 kB] Get:2 http://localhost:9999/debian/ unstable/main libllvm3.4 amd64 1:3.4.2-1 [6721 kB] Get:3 http://localhost:9999/debian/ unstable/main libobjc4 amd64 4.9.0-6 [112 kB] Get:4 http://localhost:9999/debian/ unstable/main libobjc-4.9-dev amd64 4.9.0-6 [372 kB] Get:5 http://localhost:9999/debian/ unstable/main libclang1-3.4 amd64 1:3.4.2-1 [3618 kB] Get:6 http://localhost:9999/debian/ unstable/main libclang-common-3.4-dev amd64 1:3.4.2-1 [539 kB] Get:7 http://localhost:9999/debian/ unstable/main clang-3.4 amd64 1:3.4.2-1 [19.2 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 30.6 MB in 0s (33.6 MB/s) Selecting previously unselected package libffi6:amd64. (Reading database ... 14216 files and directories currently installed.) Preparing to unpack .../libffi6_3.1-2_amd64.deb ... Unpacking libffi6:amd64 (3.1-2) ... Selecting previously unselected package libllvm3.4:amd64. Preparing to unpack .../libllvm3.4_1%3a3.4.2-1_amd64.deb ... Unpacking libllvm3.4:amd64 (1:3.4.2-1) ... Selecting previously unselected package libobjc4:amd64. Preparing to unpack .../libobjc4_4.9.0-6_amd64.deb ... Unpacking libobjc4:amd64 (4.9.0-6) ... Selecting previously unselected package libobjc-4.9-dev:amd64. Preparing to unpack .../libobjc-4.9-dev_4.9.0-6_amd64.deb ... Unpacking libobjc-4.9-dev:amd64 (4.9.0-6) ... Selecting previously unselected package libclang1-3.4:amd64. Preparing to unpack .../libclang1-3.4_1%3a3.4.2-1_amd64.deb ... Unpacking libclang1-3.4:amd64 (1:3.4.2-1) ... Selecting previously unselected package libclang-common-3.4-dev. Preparing to unpack .../libclang-common-3.4-dev_1%3a3.4.2-1_amd64.deb ... Unpacking libclang-common-3.4-dev (1:3.4.2-1) ... Selecting previously unselected package clang-3.4. Preparing to unpack .../clang-3.4_1%3a3.4.2-1_amd64.deb ... Unpacking clang-3.4 (1:3.4.2-1) ... Setting up libffi6:amd64 (3.1-2) ... Setting up libllvm3.4:amd64 (1:3.4.2-1) ... Setting up libobjc4:amd64 (4.9.0-6) ... Setting up libobjc-4.9-dev:amd64 (4.9.0-6) ... Setting up libclang1-3.4:amd64 (1:3.4.2-1) ... Setting up libclang-common-3.4-dev (1:3.4.2-1) ... Setting up clang-3.4 (1:3.4.2-1) ... Processing triggers for libc-bin (2.19-2) ... + echo 'Replace gcc, g++ & cpp by clang' Replace gcc, g++ & cpp by clang + VERSIONS='4.6 4.7 4.8 4.9' + cd /usr/bin + for VERSION in '$VERSIONS' + rm -f g++-4.6 gcc-4.6 cpp-4.6 + ln -s clang++ g++-4.6 + ln -s clang gcc-4.6 + ln -s clang cpp-4.6 + echo 'gcc-4.6 hold' + dpkg --set-selections + echo 'g++-4.6 hold' + dpkg --set-selections + for VERSION in '$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 + echo 'gcc-4.7 hold' + dpkg --set-selections + echo 'g++-4.7 hold' + dpkg --set-selections + for VERSION in '$VERSIONS' + rm -f g++-4.8 gcc-4.8 cpp-4.8 + ln -s clang++ g++-4.8 + ln -s clang gcc-4.8 + ln -s clang cpp-4.8 + echo 'gcc-4.8 hold' + dpkg --set-selections dpkg: warning: package not in database at line 1: gcc-4.8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method + echo 'g++-4.8 hold' + dpkg --set-selections dpkg: warning: package not in database at line 1: g++-4.8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method + for VERSION in '$VERSIONS' + rm -f g++-4.9 gcc-4.9 cpp-4.9 + ln -s clang++ g++-4.9 + ln -s clang gcc-4.9 + ln -s clang cpp-4.9 + echo 'gcc-4.9 hold' + dpkg --set-selections + echo 'g++-4.9 hold' + dpkg --set-selections + cd - /«BUILDDIR» + 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/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-Qr_1em/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/818 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 ... 14431 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... 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-TlNwq6/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 file flex gengetopt gettext gettext-base gfortran gfortran-4.9 groff-base intltool-debian libarchive13 libasprintf0c2 libbison-dev libblas-dev libblas3 libboost-dev libboost-mpi-dev libboost-mpi1.55-dev libboost-mpi1.55.0 libboost-serialization-dev libboost-serialization1.55-dev libboost-serialization1.55.0 libboost1.55-dev libcr0 libcroco3 libcurl3 libexpat1 libfl-dev libgcrypt11 libgcrypt20 libgfortran-4.9-dev libgfortran3 libglib2.0-0 libgnutls26 libgpg-error0 libgssapi-krb5-2 libhwloc-dev libhwloc5 libibverbs-dev libibverbs1 libidn11 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack-dev liblapack3 libldap-2.4-2 libltdl7 liblzo2-2 libmagic1 libncursesw5 libnettle4 libnuma1 libopenmpi-dev libopenmpi1.6 libp11-kit0 libpci-dev libpci3 libpipeline1 libprocps3 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh2-1 libssl1.0.0 libtasn1-6 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-4.9-multilib gfortran-4.9-doc libgfortran3-dbg groff lrzip libboost-doc libboost-graph1.55-dev libboost1.55-doc libboost-atomic1.55-dev libboost-chrono1.55-dev libboost-context1.55-dev libboost-coroutine1.55-dev libboost-date-time1.55-dev libboost-exception1.55-dev libboost-filesystem1.55-dev libboost-graph-parallel1.55-dev libboost-iostreams1.55-dev libboost-locale1.55-dev libboost-log1.55-dev libboost-math1.55-dev libboost-mpi-python1.55-dev libboost-program-options1.55-dev libboost-python1.55-dev libboost-random1.55-dev libboost-regex1.55-dev libboost-signals1.55-dev libboost-system1.55-dev libboost-test1.55-dev libboost-thread1.55-dev libboost-timer1.55-dev libboost-wave1.55-dev libboost1.55-tools-dev libmpfrc++-dev libntl-dev blcr-dkms rng-tools krb5-doc krb5-user libhwloc-contrib-plugins 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 libhwloc-plugins krb5-locales libsasl2-modules xml-core libmail-sendmail-perl psmisc The following NEW packages will be installed: adduser bison bsdmainutils cmake cmake-data debhelper file flex gengetopt gettext gettext-base gfortran gfortran-4.9 groff-base intltool-debian libarchive13 libasprintf0c2 libbison-dev libblas-dev libblas3 libboost-dev libboost-mpi-dev libboost-mpi1.55-dev libboost-mpi1.55.0 libboost-serialization-dev libboost-serialization1.55-dev libboost-serialization1.55.0 libboost1.55-dev libcr0 libcroco3 libcurl3 libexpat1 libfl-dev libgcrypt11 libgcrypt20 libgfortran-4.9-dev libgfortran3 libglib2.0-0 libgnutls26 libgpg-error0 libgssapi-krb5-2 libhwloc-dev libhwloc5 libibverbs-dev libibverbs1 libidn11 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack-dev liblapack3 libldap-2.4-2 libltdl7 liblzo2-2 libmagic1 libncursesw5 libnettle4 libnuma1 libopenmpi-dev libopenmpi1.6 libp11-kit0 libpci-dev libpci3 libpipeline1 libprocps3 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh2-1 libssl1.0.0 libtasn1-6 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, 84 newly installed, 0 to remove and 0 not upgraded. Need to get 40.5 MB/40.5 MB of archives. After this operation, 222 MB of additional disk space will be used. Get:1 http://localhost:9999/debian/ unstable/main libncursesw5 amd64 5.9+20140118-1 [120 kB] Get:2 http://localhost:9999/debian/ unstable/main libpipeline1 amd64 1.3.0-1 [25.8 kB] Get:3 http://localhost:9999/debian/ unstable/main libprocps3 amd64 1:3.3.9-5 [55.6 kB] Get:4 http://localhost:9999/debian/ unstable/main libssl1.0.0 amd64 1.0.1h-3 [1011 kB] Get:5 http://localhost:9999/debian/ unstable/main groff-base amd64 1.22.2-5 [1043 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 2.6.7.1-1 [990 kB] Get:8 http://localhost:9999/debian/ unstable/main libasprintf0c2 amd64 0.18.3.2-2 [29.4 kB] Get:9 http://localhost:9999/debian/ unstable/main libgpg-error0 amd64 1.12-0.2 [56.5 kB] Get:10 http://localhost:9999/debian/ unstable/main libgcrypt11 amd64 1.5.3-4 [250 kB] Get:11 http://localhost:9999/debian/ unstable/main libgcrypt20 amd64 1.6.1-2 [381 kB] Get:12 http://localhost:9999/debian/ unstable/main libp11-kit0 amd64 0.20.2-5 [81.1 kB] Get:13 http://localhost:9999/debian/ unstable/main libtasn1-6 amd64 3.6-3 [50.2 kB] Get:14 http://localhost:9999/debian/ unstable/main libgnutls26 amd64 2.12.23-16 [530 kB] Get:15 http://localhost:9999/debian/ unstable/main libkeyutils1 amd64 1.5.9-4 [11.6 kB] Get:16 http://localhost:9999/debian/ unstable/main libkrb5support0 amd64 1.12.1+dfsg-3 [56.9 kB] Get:17 http://localhost:9999/debian/ unstable/main libk5crypto3 amd64 1.12.1+dfsg-3 [111 kB] Get:18 http://localhost:9999/debian/ unstable/main libkrb5-3 amd64 1.12.1+dfsg-3 [297 kB] Get:19 http://localhost:9999/debian/ unstable/main libgssapi-krb5-2 amd64 1.12.1+dfsg-3 [147 kB] Get:20 http://localhost:9999/debian/ unstable/main libidn11 amd64 1.28-2 [158 kB] Get:21 http://localhost:9999/debian/ unstable/main libsasl2-modules-db amd64 2.1.26.dfsg1-9 [66.4 kB] Get:22 http://localhost:9999/debian/ unstable/main libsasl2-2 amd64 2.1.26.dfsg1-9 [103 kB] Get:23 http://localhost:9999/debian/ unstable/main libldap-2.4-2 amd64 2.4.39-1 [212 kB] Get:24 http://localhost:9999/debian/ unstable/main libmagic1 amd64 1:5.19-1 [237 kB] Get:25 http://localhost:9999/debian/ unstable/main libpci3 amd64 1:3.2.1-2 [59.4 kB] Get:26 http://localhost:9999/debian/ unstable/main libxml2 amd64 2.9.1+dfsg1-3 [791 kB] Get:27 http://localhost:9999/debian/ unstable/main libsigsegv2 amd64 2.10-4 [28.8 kB] Get:28 http://localhost:9999/debian/ unstable/main m4 amd64 1.4.17-4 [254 kB] Get:29 http://localhost:9999/debian/ unstable/main libfl-dev amd64 2.5.39-7 [74.7 kB] Get:30 http://localhost:9999/debian/ unstable/main flex amd64 2.5.39-7 [960 kB] Get:31 http://localhost:9999/debian/ unstable/main liblzo2-2 amd64 2.06-1.2 [51.2 kB] Get:32 http://localhost:9999/debian/ unstable/main libnettle4 amd64 2.7.1-2+b1 [172 kB] Get:33 http://localhost:9999/debian/ unstable/main libarchive13 amd64 3.1.2-8 [265 kB] Get:34 http://localhost:9999/debian/ unstable/main libboost-serialization1.55.0 amd64 1.55.0+dfsg-2 [146 kB] Get:35 http://localhost:9999/debian/ unstable/main libltdl7 amd64 2.4.2-1.7 [352 kB] Get:36 http://localhost:9999/debian/ unstable/main libnuma1 amd64 2.0.9~rc5-1 [35.2 kB] Get:37 http://localhost:9999/debian/ unstable/main libhwloc5 amd64 1.9-3 [82.7 kB] Get:38 http://localhost:9999/debian/ unstable/main libcr0 amd64 0.8.5-2.1 [32.4 kB] Get:39 http://localhost:9999/debian/ unstable/main libgfortran3 amd64 4.9.0-6 [254 kB] Get:40 http://localhost:9999/debian/ unstable/main adduser all 3.113+nmu3 [264 kB] Get:41 http://localhost:9999/debian/ unstable/main libibverbs1 amd64 1.1.8-1 [32.0 kB] Get:42 http://localhost:9999/debian/ unstable/main libtorque2 amd64 2.4.16+dfsg-1.4 [105 kB] Get:43 http://localhost:9999/debian/ unstable/main libopenmpi1.6 amd64 1.6.5-8+b1 [1446 kB] Get:44 http://localhost:9999/debian/ unstable/main libboost-mpi1.55.0 amd64 1.55.0+dfsg-2 [66.7 kB] Get:45 http://localhost:9999/debian/ unstable/main libglib2.0-0 amd64 2.40.0-3 [2405 kB] Get:46 http://localhost:9999/debian/ unstable/main libcroco3 amd64 0.6.8-2 [133 kB] Get:47 http://localhost:9999/debian/ unstable/main libssh2-1 amd64 1.4.3-3 [125 kB] Get:48 http://localhost:9999/debian/ unstable/main libcurl3 amd64 7.37.0-1+b1 [252 kB] Get:49 http://localhost:9999/debian/ unstable/main libexpat1 amd64 2.1.0-6 [80.6 kB] Get:50 http://localhost:9999/debian/ unstable/main libunistring0 amd64 0.9.3-5 [434 kB] Get:51 http://localhost:9999/debian/ unstable/main procps amd64 1:3.3.9-5 [233 kB] Get:52 http://localhost:9999/debian/ unstable/main file amd64 1:5.19-1 [58.0 kB] Get:53 http://localhost:9999/debian/ unstable/main gettext-base amd64 0.18.3.2-2 [116 kB] Get:54 http://localhost:9999/debian/ unstable/main libbison-dev amd64 2:3.0.2.dfsg-2 [426 kB] Get:55 http://localhost:9999/debian/ unstable/main bison amd64 2:3.0.2.dfsg-2 [765 kB] Get:56 http://localhost:9999/debian/ unstable/main cmake-data all 2.8.12.1-1.4 [1286 kB] Get:57 http://localhost:9999/debian/ unstable/main cmake amd64 2.8.12.1-1.4 [2612 kB] Get:58 http://localhost:9999/debian/ unstable/main gettext amd64 0.18.3.2-2 [1202 kB] Get:59 http://localhost:9999/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB] Get:60 http://localhost:9999/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB] Get:61 http://localhost:9999/debian/ unstable/main debhelper all 9.20140613 [692 kB] Get:62 http://localhost:9999/debian/ unstable/main gengetopt amd64 2.22.6-2 [320 kB] Get:63 http://localhost:9999/debian/ unstable/main libgfortran-4.9-dev amd64 4.9.0-6 [282 kB] Get:64 http://localhost:9999/debian/ unstable/main gfortran-4.9 amd64 4.9.0-6 [5411 kB] Get:65 http://localhost:9999/debian/ unstable/main gfortran amd64 4:4.9.0-3 [1264 B] Get:66 http://localhost:9999/debian/ unstable/main libblas3 amd64 1.2.20110419-7 [159 kB] Get:67 http://localhost:9999/debian/ unstable/main libblas-dev amd64 1.2.20110419-7 [154 kB] Get:68 http://localhost:9999/debian/ unstable/main libboost1.55-dev amd64 1.55.0+dfsg-2 [5812 kB] Get:69 http://localhost:9999/debian/ unstable/main libboost-dev amd64 1.55.0.2 [3368 B] Get:70 http://localhost:9999/debian/ unstable/main libboost-serialization1.55-dev amd64 1.55.0+dfsg-2 [174 kB] Get:71 http://localhost:9999/debian/ unstable/main openmpi-common all 1.6.5-8 [111 kB] Get:72 http://localhost:9999/debian/ unstable/main libibverbs-dev amd64 1.1.8-1 [85.4 kB] Get:73 http://localhost:9999/debian/ unstable/main libxml2-dev amd64 2.9.1+dfsg1-3 [685 kB] Get:74 http://localhost:9999/debian/ unstable/main zlib1g-dev amd64 1:1.2.8.dfsg-1 [217 kB] Get:75 http://localhost:9999/debian/ unstable/main libpci-dev amd64 1:3.2.1-2 [80.0 kB] Get:76 http://localhost:9999/debian/ unstable/main libhwloc-dev amd64 1.9-3 [136 kB] Get:77 http://localhost:9999/debian/ unstable/main libopenmpi-dev amd64 1.6.5-8+b1 [448 kB] Get:78 http://localhost:9999/debian/ unstable/main mpi-default-dev amd64 1.0.2+nmu1 [3914 B] Get:79 http://localhost:9999/debian/ unstable/main libboost-mpi1.55-dev amd64 1.55.0+dfsg-2 [145 kB] Get:80 http://localhost:9999/debian/ unstable/main libboost-mpi-dev amd64 1.55.0.2 [3096 B] Get:81 http://localhost:9999/debian/ unstable/main libboost-serialization-dev amd64 1.55.0.2 [3240 B] Get:82 http://localhost:9999/debian/ unstable/main liblapack3 amd64 3.5.0-2 [1735 kB] Get:83 http://localhost:9999/debian/ unstable/main liblapack-dev amd64 3.5.0-2 [1747 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 40.5 MB in 1s (24.1 MB/s) Selecting previously unselected package libncursesw5:amd64. 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Setting up libprocps3:amd64 (1:3.3.9-5) ... Setting up libssl1.0.0:amd64 (1.0.1h-3) ... Setting up groff-base (1.22.2-5) ... 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 (2.6.7.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libasprintf0c2:amd64 (0.18.3.2-2) ... Setting up libgpg-error0:amd64 (1.12-0.2) ... Setting up libgcrypt11:amd64 (1.5.3-4) ... Setting up libgcrypt20:amd64 (1.6.1-2) ... Setting up libp11-kit0:amd64 (0.20.2-5) ... Setting up libtasn1-6:amd64 (3.6-3) ... Setting up libgnutls26:amd64 (2.12.23-16) ... Setting up libkeyutils1:amd64 (1.5.9-4) ... Setting up libkrb5support0:amd64 (1.12.1+dfsg-3) ... Setting up libk5crypto3:amd64 (1.12.1+dfsg-3) ... Setting up libkrb5-3:amd64 (1.12.1+dfsg-3) ... Setting up libgssapi-krb5-2:amd64 (1.12.1+dfsg-3) ... Setting up libidn11:amd64 (1.28-2) ... Setting up libsasl2-modules-db:amd64 (2.1.26.dfsg1-9) ... Setting up libsasl2-2:amd64 (2.1.26.dfsg1-9) ... Setting up libldap-2.4-2:amd64 (2.4.39-1) ... Setting up libmagic1:amd64 (1:5.19-1) ... Setting up libpci3:amd64 (1:3.2.1-2) ... Setting up libxml2:amd64 (2.9.1+dfsg1-3) ... Setting up libsigsegv2:amd64 (2.10-4) ... Setting up m4 (1.4.17-4) ... Setting up libfl-dev:amd64 (2.5.39-7) ... Setting up flex (2.5.39-7) ... Setting up liblzo2-2:amd64 (2.06-1.2) ... Setting up libnettle4:amd64 (2.7.1-2+b1) ... Setting up libarchive13:amd64 (3.1.2-8) ... Setting up libboost-serialization1.55.0:amd64 (1.55.0+dfsg-2) ... Setting up libltdl7:amd64 (2.4.2-1.7) ... Setting up libnuma1:amd64 (2.0.9~rc5-1) ... Setting up libhwloc5:amd64 (1.9-3) ... Setting up libcr0 (0.8.5-2.1) ... Setting up libgfortran3:amd64 (4.9.0-6) ... Setting up adduser (3.113+nmu3) ... Setting up libibverbs1 (1.1.8-1) ... Setting up libtorque2 (2.4.16+dfsg-1.4) ... Setting up libopenmpi1.6 (1.6.5-8+b1) ... Setting up libboost-mpi1.55.0 (1.55.0+dfsg-2) ... Setting up libglib2.0-0:amd64 (2.40.0-3) ... No schema files found: doing nothing. Setting up libcroco3:amd64 (0.6.8-2) ... Setting up libssh2-1:amd64 (1.4.3-3) ... Setting up libcurl3:amd64 (7.37.0-1+b1) ... Setting up libexpat1:amd64 (2.1.0-6) ... Setting up libunistring0:amd64 (0.9.3-5) ... Setting up procps (1:3.3.9-5) ... update-alternatives: using /usr/bin/w.procps to provide /usr/bin/w (w) in auto mode All runlevel operations denied by policy invoke-rc.d: policy-rc.d denied execution of start. Setting up file (1:5.19-1) ... Setting up gettext-base (0.18.3.2-2) ... Setting up libbison-dev:amd64 (2:3.0.2.dfsg-2) ... Setting up bison (2:3.0.2.dfsg-2) ... update-alternatives: using /usr/bin/bison.yacc to provide /usr/bin/yacc (yacc) in auto mode Setting up cmake-data (2.8.12.1-1.4) ... Setting up cmake (2.8.12.1-1.4) ... Setting up gettext (0.18.3.2-2) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu2) ... Setting up debhelper (9.20140613) ... Setting up gengetopt (2.22.6-2) ... Setting up libgfortran-4.9-dev:amd64 (4.9.0-6) ... Setting up gfortran-4.9 (4.9.0-6) ... Setting up gfortran (4:4.9.0-3) ... update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode Setting up libblas3 (1.2.20110419-7) ... 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 (1.2.20110419-7) ... update-alternatives: using /usr/lib/libblas/libblas.so to provide /usr/lib/libblas.so (libblas.so) in auto mode Setting up libboost1.55-dev:amd64 (1.55.0+dfsg-2) ... Setting up libboost-dev:amd64 (1.55.0.2) ... Setting up libboost-serialization1.55-dev:amd64 (1.55.0+dfsg-2) ... Setting up openmpi-common (1.6.5-8) ... Setting up libibverbs-dev (1.1.8-1) ... Setting up libxml2-dev:amd64 (2.9.1+dfsg1-3) ... Setting up zlib1g-dev:amd64 (1:1.2.8.dfsg-1) ... Setting up libpci-dev (1:3.2.1-2) ... Setting up libhwloc-dev:amd64 (1.9-3) ... Setting up libopenmpi-dev (1.6.5-8+b1) ... update-alternatives: using /usr/lib/openmpi/include to provide /usr/include/mpi (mpi) in auto mode Setting up mpi-default-dev (1.0.2+nmu1) ... Setting up libboost-mpi1.55-dev (1.55.0+dfsg-2) ... Setting up libboost-mpi-dev (1.55.0.2) ... Setting up libboost-serialization-dev:amd64 (1.55.0.2) ... Setting up liblapack3 (3.5.0-2) ... update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode Setting up liblapack-dev (3.5.0-2) ... update-alternatives: using /usr/lib/lapack/liblapack.so to provide /usr/lib/liblapack.so (liblapack.so) in auto mode Setting up sbuild-build-depends-prime-phylo-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.19-2) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 2.6.32-5-xen-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.24.51.20140604-3 dpkg-dev_1.17.10 g++-4.6_4.6.4-7 g++-4.9_4.9.0-6 gcc-4.6_4.6.4-7 gcc-4.7_4.7.4-1 gcc-4.9_4.9.0-6 libc6-dev_2.19-2 libstdc++-4.9-dev_4.9.0-6 libstdc++6_4.9.0-6 libstdc++6-4.6-dev_4.6.4-7 linux-libc-dev_3.14.7-1 Package versions: adduser_3.113+nmu3 apt_1.0.4 base-files_7.3 base-passwd_3.5.33 bash_4.3-7 binutils_2.24.51.20140604-3 bison_2:3.0.2.dfsg-2 bsdmainutils_9.0.5 bsdutils_1:2.20.1-5.8 build-essential_11.6 bzip2_1.0.6-5 clang-3.4_1:3.4.2-1 cmake_2.8.12.1-1.4 cmake-data_2.8.12.1-1.4 coreutils_8.21-1.2 cpp_4:4.9.0-3 cpp-4.6_4.6.4-7 cpp-4.7_4.7.4-1 cpp-4.9_4.9.0-6 dash_0.5.7-4 debconf_1.5.53 debconf-i18n_1.5.53 debfoster_2.7-1.2 debhelper_9.20140613 debian-archive-keyring_2012.4 debianutils_4.4 diffutils_1:3.3-1 dpkg_1.17.10 dpkg-dev_1.17.10 e2fslibs_1.42.10-1 e2fsprogs_1.42.10-1 fakeroot_1.20-3 file_1:5.19-1 findutils_4.4.2-8 flex_2.5.39-7 g++_4:4.9.0-3 g++-4.6_4.6.4-7 g++-4.9_4.9.0-6 gcc_4:4.9.0-3 gcc-4.4-base_4.4.7-8 gcc-4.5-base_4.5.4-1 gcc-4.6_4.6.4-7 gcc-4.6-base_4.6.4-7 gcc-4.7_4.7.4-1 gcc-4.7-base_4.7.4-1 gcc-4.8-base_4.8.3-3 gcc-4.9_4.9.0-6 gcc-4.9-base_4.9.0-6 gengetopt_2.22.6-2 gettext_0.18.3.2-2 gettext-base_0.18.3.2-2 gfortran_4:4.9.0-3 gfortran-4.9_4.9.0-6 gnupg_1.4.16-1.1 gpgv_1.4.16-1.1 grep_2.18-2 groff-base_1.22.2-5 gzip_1.6-3 hostname_3.15 initscripts_2.88dsf-53.2 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 libacl1_2.2.52-1 libapt-pkg4.12_1.0.4 libarchive-extract-perl_0.72-1 libarchive13_3.1.2-8 libasan1_4.9.0-6 libasprintf0c2_0.18.3.2-2 libatomic1_4.9.0-6 libattr1_1:2.4.47-1 libaudit-common_1:2.3.7-1 libaudit1_1:2.3.7-1 libbison-dev_2:3.0.2.dfsg-2 libblas-dev_1.2.20110419-7 libblas3_1.2.20110419-7 libblkid1_2.20.1-5.8 libboost-dev_1.55.0.2 libboost-mpi-dev_1.55.0.2 libboost-mpi1.55-dev_1.55.0+dfsg-2 libboost-mpi1.55.0_1.55.0+dfsg-2 libboost-serialization-dev_1.55.0.2 libboost-serialization1.55-dev_1.55.0+dfsg-2 libboost-serialization1.55.0_1.55.0+dfsg-2 libboost1.55-dev_1.55.0+dfsg-2 libbz2-1.0_1.0.6-5 libc-bin_2.19-2 libc-dev-bin_2.19-2 libc6_2.19-2 libc6-dev_2.19-2 libcap2_1:2.22-1.2 libcilkrts5_4.9.0-6 libclang-common-3.4-dev_1:3.4.2-1 libclang1-3.4_1:3.4.2-1 libclass-isa-perl_0.36-5 libcloog-isl4_0.18.2-1 libcloog-ppl1_0.16.1-5 libcomerr2_1.42.10-1 libcr0_0.8.5-2.1 libcroco3_0.6.8-2 libcurl3_7.37.0-1+b1 libdb5.1_5.1.29-5 libdb5.3_5.3.28-3 libdebconfclient0_0.191 libdpkg-perl_1.17.10 libexpat1_2.1.0-6 libfakeroot_1.20-3 libffi6_3.1-2 libfile-fcntllock-perl_0.20-1 libfl-dev_2.5.39-7 libgc1c2_1:7.2d-6 libgcc-4.7-dev_4.7.4-1 libgcc-4.9-dev_4.9.0-6 libgcc1_1:4.9.0-6 libgcrypt11_1.5.3-4 libgcrypt20_1.6.1-2 libgdbm3_1.8.3-12 libgfortran-4.9-dev_4.9.0-6 libgfortran3_4.9.0-6 libglib2.0-0_2.40.0-3 libgmp10_2:6.0.0+dfsg-4 libgmpxx4ldbl_2:6.0.0+dfsg-4 libgnutls26_2.12.23-16 libgomp1_4.9.0-6 libgpg-error0_1.12-0.2 libgpm2_1.20.4-6.1 libgssapi-krb5-2_1.12.1+dfsg-3 libhwloc-dev_1.9-3 libhwloc5_1.9-3 libibverbs-dev_1.1.8-1 libibverbs1_1.1.8-1 libidn11_1.28-2 libisl10_0.12.2-1 libitm1_4.9.0-6 libk5crypto3_1.12.1+dfsg-3 libkeyutils1_1.5.9-4 libkrb5-3_1.12.1+dfsg-3 libkrb5support0_1.12.1+dfsg-3 liblapack-dev_3.5.0-2 liblapack3_3.5.0-2 libldap-2.4-2_2.4.39-1 libllvm3.4_1:3.4.2-1 liblocale-gettext-perl_1.05-8 liblog-message-simple-perl_0.10-1 liblsan0_4.9.0-6 libltdl7_2.4.2-1.7 liblzma5_5.1.1alpha+20120614-2 liblzo2-2_2.06-1.2 libmagic1_1:5.19-1 libmodule-pluggable-perl_5.1-1 libmount1_2.20.1-5.8 libmpc2_0.9-4 libmpc3_1.0.1-1 libmpfr4_3.1.2-1 libncurses5_5.9+20140118-1 libncursesw5_5.9+20140118-1 libnettle4_2.7.1-2+b1 libnuma1_2.0.9~rc5-1 libobjc-4.9-dev_4.9.0-6 libobjc4_4.9.0-6 libopenmpi-dev_1.6.5-8+b1 libopenmpi1.6_1.6.5-8+b1 libp11-kit0_0.20.2-5 libpam-modules_1.1.8-3 libpam-modules-bin_1.1.8-3 libpam-runtime_1.1.8-3 libpam0g_1.1.8-3 libpci-dev_1:3.2.1-2 libpci3_1:3.2.1-2 libpcre3_1:8.31-5 libpipeline1_1.3.0-1 libpod-latex-perl_0.61-1 libppl-c4_1:1.1-2+b1 libppl13_1:1.1-2+b1 libprocps3_1:3.3.9-5 libquadmath0_4.9.0-6 libreadline6_6.3-6 libsasl2-2_2.1.26.dfsg1-9 libsasl2-modules-db_2.1.26.dfsg1-9 libselinux1_2.3-1 libsemanage-common_2.3-1 libsemanage1_2.3-1 libsepol1_2.3-1 libsigsegv2_2.10-4 libslang2_2.2.4-16 libss2_1.42.10-1 libssh2-1_1.4.3-3 libssl1.0.0_1.0.1h-3 libstdc++-4.9-dev_4.9.0-6 libstdc++6_4.9.0-6 libstdc++6-4.6-dev_4.6.4-7 libswitch-perl_2.17-1 libtasn1-6_3.6-3 libterm-ui-perl_0.42-1 libtext-charwidth-perl_0.04-7+b2 libtext-iconv-perl_1.7-5+b1 libtext-soundex-perl_3.4-1+b1 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_2.3000-2 libtinfo5_5.9+20140118-1 libtorque2_2.4.16+dfsg-1.4 libtsan0_4.9.0-6 libubsan0_4.9.0-6 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23.3 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.8 libvtv0_4.9.0-6 libxml2_2.9.1+dfsg1-3 libxml2-dev_2.9.1+dfsg1-3 linux-libc-dev_3.14.7-1 login_1:4.2-2 lsb-base_4.1+Debian13 m4_1.4.17-4 make_4.0-8 man-db_2.6.7.1-1 mawk_1.3.3-17 mount_2.20.1-5.8 mpi-default-dev_1.0.2+nmu1 multiarch-support_2.19-2 ncurses-base_5.9+20140118-1 ncurses-bin_5.9+20140118-1 openmpi-common_1.6.5-8 passwd_1:4.2-2 patch_2.7.1-5 perl_5.18.2-4 perl-base_5.18.2-4 perl-modules_5.18.2-4 po-debconf_1.0.16+nmu2 procps_1:3.3.9-5 readline-common_6.3-6 rename_0.20-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-prime-phylo-dummy_0.invalid.0 sed_4.2.2-4 sensible-utils_0.0.9 startpar_0.59-3 sudo_1.8.9p5-1 sysv-rc_2.88dsf-53.2 sysvinit_2.88dsf-53.2 sysvinit-core_2.88dsf-53.2 sysvinit-utils_2.88dsf-53.2 tar_1.27.1-2 tzdata_2014e-1 ucf_3.0030 util-linux_2.20.1-5.8 vim_2:7.4.273-2+b1 vim-common_2:7.4.273-2+b1 vim-runtime_2:7.4.273-2 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 ──────────────── DEB_BUILD_OPTIONS=parallel=10 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-b5532e1b-0d82-4504-8247-b90506527fb5 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-buildpackage: source distribution unstable 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 3.4.2 -- 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 3.4.2 -- 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 "3.0.2") -- Found FLEX: /usr/bin/flex (found version "2.5.39") -- Found MPI_C: /usr/lib/libmpi.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libhwloc.so -- Found MPI_CXX: /usr/lib/libmpi_cxx.so;/usr/lib/libmpi.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libhwloc.so -- Found MPI_Fortran: /usr/lib/libmpi_f90.so;/usr/lib/libmpi_f77.so;/usr/lib/libmpi.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libhwloc.so -- Boost version: 1.55.0 -- 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 /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles [ 0%] [ 1%] [BISON][MyParser2] Building parser with bison 3.0.2 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 [FLEX][MyScanner2] Building scanner with flex 2.5.39 cd /«PKGBUILDDIR»/src/cxx/libraries/sfile && /usr/bin/flex -o/«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/lexer.c seqreader.l gb.y: warning: 1 nonterminal useless in grammar [-Wother] gb.y: warning: 1 rule useless in grammar [-Wother] gb.y:117.47-58: warning: nonterminal useless in grammar: darwin_entry [-Wother] %type gb_entry fasta_entry ig_entry darwin_entry ^^^^^^^^^^^^ gb.y:258.19-61: warning: rule useless in grammar [-Wother] darwin_entry : TEXT {$$ = NULL; /* Not implemented yet */} ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ cd /«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 /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 86 /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 87 [ 1%] [ 2%] [ 3%] [ 4%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/sfile.c.o 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/sfile.c.o -c /«PKGBUILDDIR»/src/cxx/libraries/sfile/sfile.c 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 Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/lexer.c.o 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 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 /«PKGBUILDDIR»/src/cxx/libraries/sfile/gbread.c/«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/gb.tab.c:1235:16: warning: implicit declaration of function 'yylex' is invalid in C99 [-Wimplicit-function-declaration] yychar = yylex (); ^ :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' 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; ^ 1 warning generated. 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 */ ^ /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/lexer.c:1835:17: 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:1876:16: warning: function 'input' is not needed and will not be emitted [-Wunneeded-internal-declaration] static int input (void) ^ 3 warnings generated. 4 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 /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 2 [ 5%] [ 6%] [FLEX][MyScanner] Building scanner with flex 2.5.39 [BISON][MyParser] Building parser with bison 3.0.2 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 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 /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 4 /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 5 /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 6 /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 7 /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 8 /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 9 [ 6%] [ 7%] [ 7%] [ 8%] [ 9%] [ 9%] [ 10%] [ 11%] [ 12%] [ 12%] 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 Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXtree.c.o 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 Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Beep.cc.o 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/Beep.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/Beep.cc Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXparse.c.o 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/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 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/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 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 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 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 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 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 /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/cxx/libraries/prime/NHXparse.c:1278:16: 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:64:25: note: expanded from macro 'yylex' #define yylex yytree_lex ^ /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 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(); ^ /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/cxx/libraries/prime/lexer.c:1323:17: 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:1364:16: warning: function 'input' is not needed and will not be emitted [-Wunneeded-internal-declaration] static int input (void) ^ [ 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 /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 11 [ 13%] [ 14%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PrimeOptionMap.cc.o Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ProbabilityModel.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/ProbabilityModel.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/ProbabilityModel.cc 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 4 warnings generated. /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles [ 14%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DiscreteGamma.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/DiscreteGamma.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/DiscreteGamma.cc 2 warnings generated. /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 12 [ 15%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Probability.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/Probability.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/Probability.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; ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles [ 15%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Tokenizer.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/Tokenizer.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/Tokenizer.cc /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 13 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, ^ [ 16%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TimeEstimator.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/TimeEstimator.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/TimeEstimator.cc /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 14 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 " + ^ [ 17%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BranchSwapping.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/BranchSwapping.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/BranchSwapping.cc /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles [ 17%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DiscTree.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/DiscTree.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/DiscTree.cc /«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. /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 15 make[3]: *** [src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PrimeOptionMap.cc.o] Error 1 src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/build.make:323: recipe for target 'src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PrimeOptionMap.cc.o' failed make[3]: *** Waiting for unfinished jobs.... [ 18%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscPtMaps.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/EdgeDiscPtMaps.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/EdgeDiscPtMaps.cc 36 warnings generated. /«PKGBUILDDIR»/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 '/«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 -j10 returned exit code 2 CMakeFiles/Makefile2:123: recipe for target 'src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/all' failed make[2]: Leaving directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' Makefile:136: recipe for target 'all' failed 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 debian/rules:9: recipe for target 'build-arch' failed ──────────────────────────────────────────────────────────────────────────────── Build finished at 20140617-1324 Finished ──────── E: Build failure (dpkg-buildpackage died) ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /«BUILDDIR» Not cleaning session: cloned chroot in use ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Build Architecture: amd64 Build-Space: 11412 Build-Time: 20 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: 71 Source-Version: 1.0.11-1 Space: 11412 Status: attempted Version: 1.0.11-1clang1 ──────────────────────────────────────────────────────────────────────────────── Finished at 20140617-1324 Build needed 00:01:11, 11412k disc space DC-Status: Failed 71.556804294s DC-Time-Estimation: 71.556804294 versus expected 558 (r/m: 6.798000560608992 ; m: 71.556804294)