DC-Build-Header: prime-phylo 1.0.11-2 / 2015-03-26 13:28:43 +0000 DC-Task: source:prime-phylo version:1.0.11-2 architecture:any chroot:unstable esttime:2074 logfile:/tmp/prime-phylo_1.0.11-2_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/clang prime-phylo_1.0.11-2' sbuild (Debian sbuild) 0.63.2 (18 Aug 2012) on ip-172-31-0-156.us-west-2.compute.internal ╔══════════════════════════════════════════════════════════════════════════════╗ ║ prime-phylo 1.0.11-2 (amd64) 26 Mar 2015 13:28 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: prime-phylo Version: 1.0.11-2 Source Version: 1.0.11-2 Distribution: unstable Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 I: NOTICE: Log filtering will replace 'build/prime-phylo-LFM_G4/prime-phylo-1.0.11' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/prime-phylo-LFM_G4' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/unstable-amd64-sbuild-dca46ce2-233f-4471-a5fe-3a88d65810b2' with '«CHROOT»' ┌──────────────────────────────────────────────────────────────────────────────┐ │ Update chroot │ └──────────────────────────────────────────────────────────────────────────────┘ Get:1 http://localhost:9999 unstable InRelease [257 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 2015-03-25-1448.37.pdiff [3021 B] Get:6 http://localhost:9999 unstable/main 2015-03-25-2049.47.pdiff [5545 B] Get:7 http://localhost:9999 unstable/main 2015-03-26-0248.39.pdiff [3389 B] Get:8 http://localhost:9999 unstable/main 2015-03-26-0844.35.pdiff [2242 B] Get:9 http://localhost:9999 unstable/main 2015-03-26-0844.35.pdiff [2242 B] Get:10 http://localhost:9999 unstable/main amd64 2015-03-25-1448.37.pdiff [4095 B] Get:11 http://localhost:9999 unstable/main amd64 2015-03-25-2049.47.pdiff [4595 B] Get:12 http://localhost:9999 unstable/main amd64 2015-03-26-0248.39.pdiff [3173 B] Get:13 http://localhost:9999 unstable/main amd64 2015-03-26-0844.35.pdiff [1129 B] Get:14 http://localhost:9999 unstable/main 2015-03-25-2049.47.pdiff [2032 B] Get:15 http://localhost:9999 unstable/main 2015-03-26-0844.35.pdiff [464 B] Get:16 http://localhost:9999 unstable/main amd64 2015-03-26-0844.35.pdiff [1129 B] Get:17 http://localhost:9999 unstable/main 2015-03-26-0844.35.pdiff [464 B] Fetched 310 kB in 4s (69.8 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. ┌──────────────────────────────────────────────────────────────────────────────┐ │ Fetch source files │ └──────────────────────────────────────────────────────────────────────────────┘ Check APT ───────── Checking available source versions... Download source files with APT ────────────────────────────── Reading package lists... Building dependency tree... Reading state information... NOTICE: 'prime-phylo' packaging is maintained in the 'Git' version control system at: git://anonscm.debian.org/debian-med/prime-phylo.git Need to get 758 kB of source archives. Get:1 http://localhost:9999/debian/ unstable/main prime-phylo 1.0.11-2 (dsc) [2146 B] Get:2 http://localhost:9999/debian/ unstable/main prime-phylo 1.0.11-2 (tar) [751 kB] Get:3 http://localhost:9999/debian/ unstable/main prime-phylo 1.0.11-2 (diff) [5008 B] Fetched 758 kB in 1s (384 kB/s) Download complete and in download only mode Check arch ────────── ┌──────────────────────────────────────────────────────────────────────────────┐ │ Chroot Setup Commands │ └──────────────────────────────────────────────────────────────────────────────┘ /tmp/clang ────────── + echo 'Entering customization script...' Entering customization script... + CLANG_VERSION=3.6 + echo 'Install of clang-3.6' Install of clang-3.6 + apt-get update Hit http://localhost:9999 unstable InRelease Get:1 http://localhost:9999 unstable/main Sources/DiffIndex [7876 B] Get:2 http://localhost:9999 unstable/main amd64 Packages/DiffIndex [7876 B] Get:3 http://localhost:9999 unstable/main Translation-en/DiffIndex [7876 B] Fetched 23.6 kB in 1s (13.9 kB/s) Reading package lists... + apt-get install --yes --no-install-recommends --force-yes clang-3.6 Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: libbsd0 libclang-common-3.6-dev libclang1-3.6 libedit2 libffi6 libllvm3.6 libobjc-4.9-dev libobjc4 Suggested packages: gnustep gnustep-devel clang-3.6-doc Recommended packages: llvm-3.6-dev python The following NEW packages will be installed: clang-3.6 libbsd0 libclang-common-3.6-dev libclang1-3.6 libedit2 libffi6 libllvm3.6 libobjc-4.9-dev libobjc4 0 upgraded, 9 newly installed, 0 to remove and 0 not upgraded. Need to get 39.2 MB of archives. After this operation, 153 MB of additional disk space will be used. Get:1 http://localhost:9999/debian/ unstable/main libbsd0 amd64 0.7.0-2 [67.9 kB] Get:2 http://localhost:9999/debian/ unstable/main libedit2 amd64 3.1-20140620-2 [85.1 kB] Get:3 http://localhost:9999/debian/ unstable/main libffi6 amd64 3.1-2+b2 [20.1 kB] Get:4 http://localhost:9999/debian/ unstable/main libllvm3.6 amd64 1:3.6-2 [8137 kB] Get:5 http://localhost:9999/debian/ unstable/main libobjc4 amd64 4.9.2-10 [112 kB] Get:6 http://localhost:9999/debian/ unstable/main libobjc-4.9-dev amd64 4.9.2-10 [372 kB] Get:7 http://localhost:9999/debian/ unstable/main libclang1-3.6 amd64 1:3.6-2 [3839 kB] Get:8 http://localhost:9999/debian/ unstable/main libclang-common-3.6-dev amd64 1:3.6-2 [706 kB] Get:9 http://localhost:9999/debian/ unstable/main clang-3.6 amd64 1:3.6-2 [25.8 MB] debconf: unable to initialize frontend: Dialog debconf: (Dialog frontend will not work on a dumb terminal, an emacs shell buffer, or without a controlling terminal.) debconf: falling back to frontend: Readline debconf: unable to initialize frontend: Readline debconf: (This frontend requires a controlling tty.) debconf: falling back to frontend: Teletype dpkg-preconfigure: unable to re-open stdin: Fetched 39.2 MB in 0s (39.4 MB/s) Selecting previously unselected package libbsd0:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11980 files and directories currently installed.) Preparing to unpack .../libbsd0_0.7.0-2_amd64.deb ... Unpacking libbsd0:amd64 (0.7.0-2) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../libedit2_3.1-20140620-2_amd64.deb ... Unpacking libedit2:amd64 (3.1-20140620-2) ... Selecting previously unselected package libffi6:amd64. Preparing to unpack .../libffi6_3.1-2+b2_amd64.deb ... Unpacking libffi6:amd64 (3.1-2+b2) ... Selecting previously unselected package libllvm3.6:amd64. Preparing to unpack .../libllvm3.6_1%3a3.6-2_amd64.deb ... Unpacking libllvm3.6:amd64 (1:3.6-2) ... Selecting previously unselected package libobjc4:amd64. Preparing to unpack .../libobjc4_4.9.2-10_amd64.deb ... Unpacking libobjc4:amd64 (4.9.2-10) ... Selecting previously unselected package libobjc-4.9-dev:amd64. Preparing to unpack .../libobjc-4.9-dev_4.9.2-10_amd64.deb ... Unpacking libobjc-4.9-dev:amd64 (4.9.2-10) ... Selecting previously unselected package libclang1-3.6:amd64. Preparing to unpack .../libclang1-3.6_1%3a3.6-2_amd64.deb ... Unpacking libclang1-3.6:amd64 (1:3.6-2) ... Selecting previously unselected package libclang-common-3.6-dev. Preparing to unpack .../libclang-common-3.6-dev_1%3a3.6-2_amd64.deb ... Unpacking libclang-common-3.6-dev (1:3.6-2) ... Selecting previously unselected package clang-3.6. Preparing to unpack .../clang-3.6_1%3a3.6-2_amd64.deb ... Unpacking clang-3.6 (1:3.6-2) ... Setting up libbsd0:amd64 (0.7.0-2) ... Setting up libedit2:amd64 (3.1-20140620-2) ... Setting up libffi6:amd64 (3.1-2+b2) ... Setting up libllvm3.6:amd64 (1:3.6-2) ... Setting up libobjc4:amd64 (4.9.2-10) ... Setting up libobjc-4.9-dev:amd64 (4.9.2-10) ... Setting up libclang1-3.6:amd64 (1:3.6-2) ... Setting up libclang-common-3.6-dev (1:3.6-2) ... Setting up clang-3.6 (1:3.6-2) ... Processing triggers for libc-bin (2.19-17) ... + echo 'Replace gcc, g++ & cpp by clang' Replace gcc, g++ & cpp by clang + VERSIONS='4.6 4.7 4.8 4.9 5' + cd /usr/bin + for VERSION in '$VERSIONS' + rm -f g++-4.6 gcc-4.6 cpp-4.6 gcc + ln -s clang++-3.6 g++-4.6 + ln -s clang-3.6 gcc-4.6 + ln -s clang-3.6 cpp-4.6 + ln -s clang-3.6 gcc + echo 'gcc-4.6 hold' + dpkg --set-selections + echo 'g++-4.6 hold' + dpkg --set-selections + for VERSION in '$VERSIONS' + rm -f g++-4.7 gcc-4.7 cpp-4.7 gcc + ln -s clang++-3.6 g++-4.7 + ln -s clang-3.6 gcc-4.7 + ln -s clang-3.6 cpp-4.7 + ln -s clang-3.6 gcc + echo 'gcc-4.7 hold' + dpkg --set-selections + echo 'g++-4.7 hold' + dpkg --set-selections + for VERSION in '$VERSIONS' + rm -f g++-4.8 gcc-4.8 cpp-4.8 gcc + ln -s clang++-3.6 g++-4.8 + ln -s clang-3.6 gcc-4.8 + ln -s clang-3.6 cpp-4.8 + ln -s clang-3.6 gcc + echo 'gcc-4.8 hold' + dpkg --set-selections dpkg: warning: package not in database at line 1: gcc-4.8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method + echo 'g++-4.8 hold' + dpkg --set-selections dpkg: warning: package not in database at line 1: g++-4.8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method + for VERSION in '$VERSIONS' + rm -f g++-4.9 gcc-4.9 cpp-4.9 gcc + ln -s clang++-3.6 g++-4.9 + ln -s clang-3.6 gcc-4.9 + ln -s clang-3.6 cpp-4.9 + ln -s clang-3.6 gcc + echo 'gcc-4.9 hold' + dpkg --set-selections + echo 'g++-4.9 hold' + dpkg --set-selections + for VERSION in '$VERSIONS' + rm -f g++-5 gcc-5 cpp-5 gcc + ln -s clang++-3.6 g++-5 + ln -s clang-3.6 gcc-5 + ln -s clang-3.6 cpp-5 + ln -s clang-3.6 gcc + echo 'gcc-5 hold' + dpkg --set-selections dpkg: warning: package not in database at line 1: gcc-5 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method + echo 'g++-5 hold' + dpkg --set-selections dpkg: warning: package not in database at line 1: g++-5 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method + 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/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-LspxI8/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 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 ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12200 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, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), 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, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), 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-5tuC8P/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: bison bsdmainutils cmake cmake-data debhelper file flex gengetopt gettext gettext-base gfortran gfortran-4.9 groff-base icu-devtools intltool-debian libarchive13 libasprintf0c2 libbison-dev libblas-common 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 libgfortran-4.9-dev libgfortran3 libglib2.0-0 libgnutls-deb0-28 libgssapi-krb5-2 libhogweed2 libhwloc-dev libhwloc5 libibverbs-dev libibverbs1 libicu-dev libicu52 libidn11 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack-dev liblapack3 libldap-2.4-2 libltdl-dev libltdl7 liblzo2-2 libmagic1 libnettle4 libnuma-dev libnuma1 libopenmpi-dev libopenmpi1.6 libp11-kit0 libpipeline1 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh2-1 libssl1.0.0 libtasn1-6 libunistring0 libxml2 libxml2-dev m4 man-db mpi-default-dev openmpi-common po-debconf zlib1g-dev Suggested packages: bison-doc wamerican wordlist whois vacation codeblocks eclipse ninja-build 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 gnutls-bin krb5-doc krb5-user libhwloc-contrib-plugins icu-doc libtool-doc pkg-config www-browser libmail-box-perl Recommended packages: curl wget lynx-cur autopoint libasprintf-dev libgettextpo-dev ca-certificates libglib2.0-data shared-mime-info xdg-user-dirs libhwloc-plugins krb5-locales libtool libsasl2-modules xml-core libmail-sendmail-perl The following NEW packages will be installed: bison bsdmainutils cmake cmake-data debhelper file flex gengetopt gettext gettext-base gfortran gfortran-4.9 groff-base icu-devtools intltool-debian libarchive13 libasprintf0c2 libbison-dev libblas-common 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 libgfortran-4.9-dev libgfortran3 libglib2.0-0 libgnutls-deb0-28 libgssapi-krb5-2 libhogweed2 libhwloc-dev libhwloc5 libibverbs-dev libibverbs1 libicu-dev libicu52 libidn11 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack-dev liblapack3 libldap-2.4-2 libltdl-dev libltdl7 liblzo2-2 libmagic1 libnettle4 libnuma-dev libnuma1 libopenmpi-dev libopenmpi1.6 libp11-kit0 libpipeline1 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh2-1 libssl1.0.0 libtasn1-6 libunistring0 libxml2 libxml2-dev m4 man-db mpi-default-dev openmpi-common po-debconf sbuild-build-depends-prime-phylo-dummy zlib1g-dev 0 upgraded, 82 newly installed, 0 to remove and 0 not upgraded. Need to get 53.4 MB/53.4 MB of archives. After this operation, 287 MB of additional disk space will be used. Get:1 http://localhost:9999/debian/ unstable/main libpipeline1 amd64 1.4.0-1 [27.9 kB] Get:2 http://localhost:9999/debian/ unstable/main libssl1.0.0 amd64 1.0.1k-3 [1037 kB] Get:3 http://localhost:9999/debian/ unstable/main groff-base amd64 1.22.3-1 [1205 kB] Get:4 http://localhost:9999/debian/ unstable/main bsdmainutils amd64 9.0.6 [183 kB] Get:5 http://localhost:9999/debian/ unstable/main man-db amd64 2.7.0.2-5 [1000 kB] Get:6 http://localhost:9999/debian/ unstable/main libasprintf0c2 amd64 0.19.3-2 [31.3 kB] Get:7 http://localhost:9999/debian/ unstable/main libnettle4 amd64 2.7.1-5 [176 kB] Get:8 http://localhost:9999/debian/ unstable/main libhogweed2 amd64 2.7.1-5 [125 kB] Get:9 http://localhost:9999/debian/ unstable/main libp11-kit0 amd64 0.20.7-1 [81.2 kB] Get:10 http://localhost:9999/debian/ unstable/main libtasn1-6 amd64 4.2-2 [48.6 kB] Get:11 http://localhost:9999/debian/ unstable/main libgnutls-deb0-28 amd64 3.3.8-6 [694 kB] Get:12 http://localhost:9999/debian/ unstable/main libkeyutils1 amd64 1.5.9-5+b1 [12.0 kB] Get:13 http://localhost:9999/debian/ unstable/main libkrb5support0 amd64 1.12.1+dfsg-19 [58.5 kB] Get:14 http://localhost:9999/debian/ unstable/main libk5crypto3 amd64 1.12.1+dfsg-19 [115 kB] Get:15 http://localhost:9999/debian/ unstable/main libkrb5-3 amd64 1.12.1+dfsg-19 [303 kB] Get:16 http://localhost:9999/debian/ unstable/main libgssapi-krb5-2 amd64 1.12.1+dfsg-19 [150 kB] Get:17 http://localhost:9999/debian/ unstable/main libidn11 amd64 1.29-1+b2 [136 kB] Get:18 http://localhost:9999/debian/ unstable/main libsasl2-modules-db amd64 2.1.26.dfsg1-13 [67.0 kB] Get:19 http://localhost:9999/debian/ unstable/main libsasl2-2 amd64 2.1.26.dfsg1-13 [104 kB] Get:20 http://localhost:9999/debian/ unstable/main libldap-2.4-2 amd64 2.4.40-4 [217 kB] Get:21 http://localhost:9999/debian/ unstable/main libmagic1 amd64 1:5.22+15-2 [249 kB] Get:22 http://localhost:9999/debian/ unstable/main libicu52 amd64 52.1-8 [6780 kB] Get:23 http://localhost:9999/debian/ unstable/main libxml2 amd64 2.9.2+dfsg1-3 [934 kB] Get:24 http://localhost:9999/debian/ unstable/main cmake-data all 3.0.2-1 [929 kB] Get:25 http://localhost:9999/debian/ unstable/main liblzo2-2 amd64 2.08-1.2 [54.6 kB] Get:26 http://localhost:9999/debian/ unstable/main libarchive13 amd64 3.1.2-11 [269 kB] Get:27 http://localhost:9999/debian/ unstable/main librtmp1 amd64 2.4+20131018.git79459a2-5 [59.6 kB] Get:28 http://localhost:9999/debian/ unstable/main libssh2-1 amd64 1.4.3-4.1 [125 kB] Get:29 http://localhost:9999/debian/ unstable/main libcurl3 amd64 7.38.0-4 [259 kB] Get:30 http://localhost:9999/debian/ unstable/main libexpat1 amd64 2.1.0-6+b3 [80.3 kB] Get:31 http://localhost:9999/debian/ unstable/main cmake amd64 3.0.2-1 [2384 kB] Get:32 http://localhost:9999/debian/ unstable/main libsigsegv2 amd64 2.10-4+b1 [29.2 kB] Get:33 http://localhost:9999/debian/ unstable/main m4 amd64 1.4.17-4 [254 kB] Get:34 http://localhost:9999/debian/ unstable/main libfl-dev amd64 2.5.39-8+b1 [75.4 kB] Get:35 http://localhost:9999/debian/ unstable/main flex amd64 2.5.39-8+b1 [422 kB] Get:36 http://localhost:9999/debian/ unstable/main libboost-serialization1.55.0 amd64 1.55.0+dfsg-3 [153 kB] Get:37 http://localhost:9999/debian/ unstable/main libltdl7 amd64 2.4.2-1.11 [45.2 kB] Get:38 http://localhost:9999/debian/ unstable/main libnuma1 amd64 2.0.10-1 [32.5 kB] Get:39 http://localhost:9999/debian/ unstable/main libhwloc5 amd64 1.10.0-3 [86.9 kB] Get:40 http://localhost:9999/debian/ unstable/main libcr0 amd64 0.8.5-2.2 [32.7 kB] Get:41 http://localhost:9999/debian/ unstable/main libgfortran3 amd64 4.9.2-10 [255 kB] Get:42 http://localhost:9999/debian/ unstable/main libibverbs1 amd64 1.1.8-1 [32.0 kB] Get:43 http://localhost:9999/debian/ unstable/main libopenmpi1.6 amd64 1.6.5-9.2 [1457 kB] Get:44 http://localhost:9999/debian/ unstable/main libboost-mpi1.55.0 amd64 1.55.0+dfsg-3 [69.7 kB] Get:45 http://localhost:9999/debian/ unstable/main libglib2.0-0 amd64 2.42.1-1 [2401 kB] Get:46 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http://localhost:9999/debian/ unstable/main libgfortran-4.9-dev amd64 4.9.2-10 [281 kB] Get:58 http://localhost:9999/debian/ unstable/main gfortran-4.9 amd64 4.9.2-10 [5465 kB] Get:59 http://localhost:9999/debian/ unstable/main gfortran amd64 4:4.9.2-2 [1292 B] Get:60 http://localhost:9999/debian/ unstable/main icu-devtools amd64 52.1-8 [172 kB] Get:61 http://localhost:9999/debian/ unstable/main libblas-common amd64 1.2.20110419-10 [8496 B] Get:62 http://localhost:9999/debian/ unstable/main libblas3 amd64 1.2.20110419-10 [167 kB] Get:63 http://localhost:9999/debian/ unstable/main libblas-dev amd64 1.2.20110419-10 [163 kB] Get:64 http://localhost:9999/debian/ unstable/main libboost1.55-dev amd64 1.55.0+dfsg-3 [5818 kB] Get:65 http://localhost:9999/debian/ unstable/main libboost-dev amd64 1.55.0.2 [3368 B] Get:66 http://localhost:9999/debian/ unstable/main libboost-serialization1.55-dev amd64 1.55.0+dfsg-3 [191 kB] Get:67 http://localhost:9999/debian/ unstable/main openmpi-common all 1.6.5-9.2 [110 kB] Get:68 http://localhost:9999/debian/ unstable/main libibverbs-dev amd64 1.1.8-1 [85.4 kB] Get:69 http://localhost:9999/debian/ unstable/main libnuma-dev amd64 2.0.10-1 [45.3 kB] Get:70 http://localhost:9999/debian/ unstable/main libltdl-dev amd64 2.4.2-1.11 [157 kB] Get:71 http://localhost:9999/debian/ unstable/main libhwloc-dev amd64 1.10.0-3 [142 kB] Get:72 http://localhost:9999/debian/ unstable/main libopenmpi-dev amd64 1.6.5-9.2 [450 kB] Get:73 http://localhost:9999/debian/ unstable/main mpi-default-dev amd64 1.0.2+nmu2 [3962 B] Get:74 http://localhost:9999/debian/ unstable/main libboost-mpi1.55-dev amd64 1.55.0+dfsg-3 [170 kB] Get:75 http://localhost:9999/debian/ unstable/main libboost-mpi-dev amd64 1.55.0.2 [3096 B] Get:76 http://localhost:9999/debian/ unstable/main libboost-serialization-dev amd64 1.55.0.2 [3240 B] Get:77 http://localhost:9999/debian/ unstable/main libicu-dev amd64 52.1-8 [7645 kB] Get:78 http://localhost:9999/debian/ unstable/main liblapack3 amd64 3.5.0-4 [1852 kB] Get:79 http://localhost:9999/debian/ unstable/main liblapack-dev amd64 3.5.0-4 [1884 kB] Get:80 http://localhost:9999/debian/ unstable/main libxml2-dev amd64 2.9.2+dfsg1-3 [827 kB] Get:81 http://localhost:9999/debian/ unstable/main zlib1g-dev amd64 1:1.2.8.dfsg-2+b1 [206 kB] Extracting templates from packages: 36% Extracting templates from packages: 73% Extracting templates from packages: 100% Preconfiguring packages ... Fetched 53.4 MB in 8s (6114 kB/s) Selecting previously unselected package libpipeline1:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12200 files and directories currently installed.) Preparing to unpack .../libpipeline1_1.4.0-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.4.0-1) ... Selecting previously unselected package libssl1.0.0:amd64. Preparing to unpack .../libssl1.0.0_1.0.1k-3_amd64.deb ... Unpacking libssl1.0.0:amd64 (1.0.1k-3) ... 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Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-2+b1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.2.8.dfsg-2+b1) ... Selecting previously unselected package sbuild-build-depends-prime-phylo-dummy. Preparing to unpack .../sbuild-build-depends-prime-phylo-dummy.deb ... Unpacking sbuild-build-depends-prime-phylo-dummy (0.invalid.0) ... Setting up libpipeline1:amd64 (1.4.0-1) ... Setting up libssl1.0.0:amd64 (1.0.1k-3) ... Setting up groff-base (1.22.3-1) ... Setting up bsdmainutils (9.0.6) ... 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 (2.7.0.2-5) ... Not building database; man-db/auto-update is not 'true'. Setting up libasprintf0c2:amd64 (0.19.3-2) ... Setting up libnettle4:amd64 (2.7.1-5) ... Setting up libhogweed2:amd64 (2.7.1-5) ... Setting up libp11-kit0:amd64 (0.20.7-1) ... Setting up libtasn1-6:amd64 (4.2-2) ... 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Setting up libsigsegv2:amd64 (2.10-4+b1) ... Setting up m4 (1.4.17-4) ... Setting up libfl-dev:amd64 (2.5.39-8+b1) ... Setting up flex (2.5.39-8+b1) ... Setting up libboost-serialization1.55.0:amd64 (1.55.0+dfsg-3) ... Setting up libltdl7:amd64 (2.4.2-1.11) ... Setting up libnuma1:amd64 (2.0.10-1) ... Setting up libhwloc5:amd64 (1.10.0-3) ... Setting up libcr0 (0.8.5-2.2) ... Setting up libgfortran3:amd64 (4.9.2-10) ... Setting up libibverbs1 (1.1.8-1) ... Setting up libopenmpi1.6 (1.6.5-9.2) ... Setting up libboost-mpi1.55.0 (1.55.0+dfsg-3) ... Setting up libglib2.0-0:amd64 (2.42.1-1) ... No schema files found: doing nothing. Setting up libcroco3:amd64 (0.6.8-3+b1) ... Setting up libunistring0:amd64 (0.9.3-5.2+b1) ... Setting up file (1:5.22+15-2) ... Setting up gettext-base (0.19.3-2) ... 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 gettext (0.19.3-2) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu3) ... Setting up debhelper (9.20150101) ... Setting up gengetopt (2.22.6+dfsg0-1) ... Setting up libgfortran-4.9-dev:amd64 (4.9.2-10) ... Setting up gfortran-4.9 (4.9.2-10) ... Setting up gfortran (4:4.9.2-2) ... update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode Setting up icu-devtools (52.1-8) ... Setting up libblas-common (1.2.20110419-10) ... Setting up libblas3 (1.2.20110419-10) ... 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 (1.2.20110419-10) ... 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-3) ... Setting up libboost-dev:amd64 (1.55.0.2) ... Setting up libboost-serialization1.55-dev:amd64 (1.55.0+dfsg-3) ... Setting up openmpi-common (1.6.5-9.2) ... Setting up libibverbs-dev (1.1.8-1) ... Setting up libnuma-dev:amd64 (2.0.10-1) ... Setting up libltdl-dev:amd64 (2.4.2-1.11) ... Setting up libhwloc-dev:amd64 (1.10.0-3) ... Setting up libopenmpi-dev (1.6.5-9.2) ... update-alternatives: using /usr/lib/openmpi/include to provide /usr/include/mpi (mpi) in auto mode Setting up mpi-default-dev (1.0.2+nmu2) ... Setting up libboost-mpi1.55-dev (1.55.0+dfsg-3) ... Setting up libboost-mpi-dev (1.55.0.2) ... Setting up libboost-serialization-dev:amd64 (1.55.0.2) ... Setting up libicu-dev:amd64 (52.1-8) ... Setting up liblapack3 (3.5.0-4) ... 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 (3.5.0-4) ... update-alternatives: using /usr/lib/lapack/liblapack.so to provide /usr/lib/liblapack.so (liblapack.so) in auto mode Setting up libxml2-dev:amd64 (2.9.2+dfsg1-3) ... Setting up zlib1g-dev:amd64 (1:1.2.8.dfsg-2+b1) ... Setting up sbuild-build-depends-prime-phylo-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.19-17) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 3.2.0-4-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.25-5 dpkg-dev_1.17.24 g++-4.9_4.9.2-10 gcc-4.9_4.9.2-10 libc6-dev_2.19-17 libstdc++-4.9-dev_4.9.2-10 libstdc++6_4.9.2-10 linux-libc-dev_3.16.7-ckt7-1 Package versions: acl_2.2.52-2 adduser_3.113+nmu3 apt_1.0.9.7 apt-utils_1.0.9.7 base-files_8 base-passwd_3.5.37 bash_4.3-12 binutils_2.25-5 bison_2:3.0.2.dfsg-2 bsdmainutils_9.0.6 bsdutils_1:2.25.2-5 build-essential_11.7 bzip2_1.0.6-7+b2 clang-3.6_1:3.6-2 cmake_3.0.2-1 cmake-data_3.0.2-1 coreutils_8.23-4 cpp_4:4.9.2-2 cpp-4.9_4.9.2-10 dash_0.5.7-4+b1 debconf_1.5.56 debfoster_2.7-2 debhelper_9.20150101 debian-archive-keyring_2014.3 debianutils_4.4+b1 diffutils_1:3.3-1+b1 dmsetup_2:1.02.90-2.1 dpkg_1.17.24 dpkg-dev_1.17.24 e2fslibs_1.42.12-1.1 e2fsprogs_1.42.12-1.1 fakeroot_1.20.2-1 file_1:5.22+15-2 findutils_4.4.2-9+b1 flex_2.5.39-8+b1 g++_4:4.9.2-2 g++-4.9_4.9.2-10 gcc_4:4.9.2-2 gcc-4.9_4.9.2-10 gcc-4.9-base_4.9.2-10 gengetopt_2.22.6+dfsg0-1 gettext_0.19.3-2 gettext-base_0.19.3-2 gfortran_4:4.9.2-2 gfortran-4.9_4.9.2-10 gnupg_1.4.18-7 gpgv_1.4.18-7 grep_2.20-4.1 groff-base_1.22.3-1 gzip_1.6-4 hostname_3.15 icu-devtools_52.1-8 init_1.22 initscripts_2.88dsf-58 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 less_458-3 libacl1_2.2.52-2 libapt-inst1.5_1.0.9.7 libapt-pkg4.12_1.0.9.7 libarchive13_3.1.2-11 libasan1_4.9.2-10 libasprintf0c2_0.19.3-2 libatomic1_4.9.2-10 libattr1_1:2.4.47-2 libaudit-common_1:2.4-1 libaudit1_1:2.4-1+b1 libbison-dev_2:3.0.2.dfsg-2 libblas-common_1.2.20110419-10 libblas-dev_1.2.20110419-10 libblas3_1.2.20110419-10 libblkid1_2.25.2-5 libboost-dev_1.55.0.2 libboost-mpi-dev_1.55.0.2 libboost-mpi1.55-dev_1.55.0+dfsg-3 libboost-mpi1.55.0_1.55.0+dfsg-3 libboost-serialization-dev_1.55.0.2 libboost-serialization1.55-dev_1.55.0+dfsg-3 libboost-serialization1.55.0_1.55.0+dfsg-3 libboost1.55-dev_1.55.0+dfsg-3 libbsd0_0.7.0-2 libbz2-1.0_1.0.6-7+b2 libc-bin_2.19-17 libc-dev-bin_2.19-17 libc6_2.19-17 libc6-dev_2.19-17 libcap2_1:2.24-7 libcap2-bin_1:2.24-7 libcilkrts5_4.9.2-10 libclang-common-3.6-dev_1:3.6-2 libclang1-3.6_1:3.6-2 libcloog-isl4_0.18.2-1+b2 libcomerr2_1.42.12-1.1 libcr0_0.8.5-2.2 libcroco3_0.6.8-3+b1 libcryptsetup4_2:1.6.6-5 libcurl3_7.38.0-4 libdb5.3_5.3.28-9 libdebconfclient0_0.192 libdevmapper1.02.1_2:1.02.90-2.1 libdpkg-perl_1.17.24 libedit2_3.1-20140620-2 libexpat1_2.1.0-6+b3 libfakeroot_1.20.2-1 libffi6_3.1-2+b2 libfl-dev_2.5.39-8+b1 libgc1c2_1:7.2d-6.4 libgcc-4.9-dev_4.9.2-10 libgcc1_1:4.9.2-10 libgcrypt20_1.6.3-2 libgdbm3_1.8.3-13.1 libgfortran-4.9-dev_4.9.2-10 libgfortran3_4.9.2-10 libglib2.0-0_2.42.1-1 libgmp10_2:6.0.0+dfsg-6 libgnutls-deb0-28_3.3.8-6 libgomp1_4.9.2-10 libgpg-error0_1.17-3 libgssapi-krb5-2_1.12.1+dfsg-19 libhogweed2_2.7.1-5 libhwloc-dev_1.10.0-3 libhwloc5_1.10.0-3 libibverbs-dev_1.1.8-1 libibverbs1_1.1.8-1 libicu-dev_52.1-8 libicu52_52.1-8 libidn11_1.29-1+b2 libisl10_0.12.2-2 libitm1_4.9.2-10 libk5crypto3_1.12.1+dfsg-19 libkeyutils1_1.5.9-5+b1 libkmod2_20-1 libkrb5-3_1.12.1+dfsg-19 libkrb5support0_1.12.1+dfsg-19 liblapack-dev_3.5.0-4 liblapack3_3.5.0-4 libldap-2.4-2_2.4.40-4 libllvm3.6_1:3.6-2 liblsan0_4.9.2-10 libltdl-dev_2.4.2-1.11 libltdl7_2.4.2-1.11 liblzma5_5.1.1alpha+20120614-2+b3 liblzo2-2_2.08-1.2 libmagic1_1:5.22+15-2 libmount1_2.25.2-5 libmpc3_1.0.3-1 libmpfr4_3.1.2-3 libncurses5_5.9+20140913-1+b1 libncursesw5_5.9+20140913-1+b1 libnettle4_2.7.1-5 libnuma-dev_2.0.10-1 libnuma1_2.0.10-1 libobjc-4.9-dev_4.9.2-10 libobjc4_4.9.2-10 libopenmpi-dev_1.6.5-9.2 libopenmpi1.6_1.6.5-9.2 libp11-kit0_0.20.7-1 libpam-modules_1.1.8-3.1 libpam-modules-bin_1.1.8-3.1 libpam-runtime_1.1.8-3.1 libpam0g_1.1.8-3.1 libpcre3_2:8.35-3.3 libpipeline1_1.4.0-1 libprocps3_2:3.3.9-9 libquadmath0_4.9.2-10 libreadline6_6.3-8+b3 librtmp1_2.4+20131018.git79459a2-5 libsasl2-2_2.1.26.dfsg1-13 libsasl2-modules-db_2.1.26.dfsg1-13 libselinux1_2.3-2 libsemanage-common_2.3-1 libsemanage1_2.3-1+b1 libsepol1_2.3-2 libsigsegv2_2.10-4+b1 libslang2_2.3.0-2 libsmartcols1_2.25.2-5 libss2_1.42.12-1.1 libssh2-1_1.4.3-4.1 libssl1.0.0_1.0.1k-3 libstdc++-4.9-dev_4.9.2-10 libstdc++6_4.9.2-10 libsystemd0_215-12 libtasn1-6_4.2-2 libtimedate-perl_2.3000-2 libtinfo5_5.9+20140913-1+b1 libtsan0_4.9.2-10 libubsan0_4.9.2-10 libudev1_215-12 libunistring0_0.9.3-5.2+b1 libusb-0.1-4_2:0.1.12-25 libustr-1.0-1_1.0.4-3+b2 libuuid1_2.25.2-5 libxml2_2.9.2+dfsg1-3 libxml2-dev_2.9.2+dfsg1-3 linux-libc-dev_3.16.7-ckt7-1 login_1:4.2-3 lsb-base_4.1+Debian13+nmu1 m4_1.4.17-4 make_4.0-8.1 man-db_2.7.0.2-5 mawk_1.3.3-17 mount_2.25.2-5 mpi-default-dev_1.0.2+nmu2 multiarch-support_2.19-17 ncurses-base_5.9+20140913-1 ncurses-bin_5.9+20140913-1+b1 nvi_1.81.6-11+b1 openmpi-common_1.6.5-9.2 passwd_1:4.2-3 patch_2.7.5-1 perl_5.20.2-2 perl-base_5.20.2-2 perl-modules_5.20.2-2 po-debconf_1.0.16+nmu3 procps_2:3.3.9-9 readline-common_6.3-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-prime-phylo-dummy_0.invalid.0 sed_4.2.2-4+b1 sensible-utils_0.0.9 startpar_0.59-3 sudo_1.8.12-1 systemd_215-12 systemd-sysv_215-12 sysv-rc_2.88dsf-58 sysvinit-utils_2.88dsf-58 tar_1.27.1-2+b1 tzdata_2015b-1 udev_215-12 util-linux_2.25.2-5 xz-utils_5.1.1alpha+20120614-2+b3 zlib1g_1:1.2.8.dfsg-2+b1 zlib1g-dev_1:1.2.8.dfsg-2+b1 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error gpgv: Signature made Fri Oct 17 08:07:35 2014 UTC using RSA key ID D1C646D1 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./prime-phylo_1.0.11-2.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_1.0.11-2.debian.tar.xz Check disc space ──────────────── Sufficient free space for build 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=1001 SCHROOT_GROUP=user SCHROOT_SESSION_ID=unstable-amd64-sbuild-dca46ce2-233f-4471-a5fe-3a88d65810b2 SCHROOT_UID=1001 SCHROOT_USER=user SHELL=/bin/sh USER=user dpkg-buildpackage ───────────────── dpkg-buildpackage: source package prime-phylo dpkg-buildpackage: source version 1.0.11-2 dpkg-buildpackage: source distribution unstable dpkg-buildpackage: source changed by Andreas Tille 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 3.6.0 -- 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 3.6.0 -- 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 "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 "2.9.2") mpilib is /usr/lib/openmpi/include;/usr/lib/openmpi/include/openmpi included path is CMake Warning (dev) at src/cxx/CMakeLists.txt:366 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The LOCATION property should not be read from target "primeDTLSR". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate. Call Stack (most recent call first): src/cxx/applications/primeDTLSR/CMakeLists.txt:30 (prime_add_tests) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at src/cxx/CMakeLists.txt:366 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The LOCATION property should not be read from target "primeDLRS". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate. Call Stack (most recent call first): src/cxx/applications/primeDLRS/CMakeLists.txt:27 (prime_add_tests) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at src/cxx/CMakeLists.txt:366 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The LOCATION property should not be read from target "showtree". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate. Call Stack (most recent call first): src/cxx/tools/showtree/CMakeLists.txt:12 (prime_add_tests) This warning is for project developers. Use -Wno-dev to suppress it. -- 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 [ 1%] [ 1%] [BISON][MyParser2] Building parser with bison 3.0.2 [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 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 [-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 [ 2%] [ 3%] [ 4%] [ 4%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/gbread.c.o 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-strong -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 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-strong -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-strong -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 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-strong -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 /«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: include the header or explicitly provide a declaration for 'strcmp' 1/«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/gb.tab.c warning:1235:16: warning: implicit declaration of function 'yylex' is invalid in C99 [-Wimplicit-function-declaration] generated. yychar = yylex (); ^ gb.y:291:70: warning: implicit declaration of function 'linenumber' is invalid in C99 [-Wimplicit-function-declaration] printf("Can't parse file. Error is '%s', on line %d.\n", msg, linenumber()); ^ /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; ^ 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-strong -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/bison -d -y -p yytree_ -d -o /«PKGBUILDDIR»/obj-x86_64-linux-gnu/src/cxx/libraries/prime/NHXparse.c NHXparse.y 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»/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%] [ 8%] [ 8%] [ 8%] [ 9%] [ 10%] [ 10%] [ 11%] [ 12%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXannotation.c.o Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXnode.c.o 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-strong -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 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-strong -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 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-strong -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/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector-strong -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 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-strong -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/NHXtree.c.o Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BeepOption.cc.o Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/lexer.c.o 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-strong -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/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector-strong -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 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-strong -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/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-strong -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 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-strong -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 /«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[ 12%] /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 10 :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) ^ /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 11 [ 13%] 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-strong -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 [ 14%] 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-strong -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 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-strong -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 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-strong -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-strong -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 /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 13 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-strong -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 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-strong -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 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 " + ^ /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 14 [ 17%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BranchSwapping.cc.o /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-x86_64-linux-gnu/CMakeFiles 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-strong -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 /«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 ^ [ 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-strong -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 3 warnings and 4 errors generated. make[3]: *** [src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PrimeOptionMap.cc.o] Error 1 make[3]: *** Waiting for unfinished jobs.... 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 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 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' make[1]: *** [all] Error 2 Makefile:140: recipe for target 'all' failed make[1]: Leaving directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu' dh_auto_build: make -j10 returned exit code 2 make: *** [build-arch] Error 2 debian/rules:9: recipe for target 'build-arch' failed dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2 ──────────────────────────────────────────────────────────────────────────────── Build finished at 20150326-1329 Finished ──────── E: Build failure (dpkg-buildpackage died) ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /«BUILDDIR» Not cleaning session: cloned chroot in use ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Build Architecture: amd64 Build-Space: 9936 Build-Time: 15 Distribution: unstable Fail-Stage: build Host Architecture: amd64 Install-Time: 30 Job: prime-phylo_1.0.11-2 Machine Architecture: amd64 Package: prime-phylo Package-Time: 70 Source-Version: 1.0.11-2 Space: 9936 Status: attempted Version: 1.0.11-2 ──────────────────────────────────────────────────────────────────────────────── Finished at 20150326-1329 Build needed 00:01:10, 9936k disc space DC-Status: Failed 70.648853492s DC-Time-Estimation: 70.648853492 versus expected 2074 (r/m: 28.356456580499948 ; m: 70.648853492)