DC-Build-Header: hyphy 2.3.14+dfsg-1 / 2019-01-09 21:29:52 +0000 DC-Task: type:rebuild-binarch-only source:hyphy version:2.3.14+dfsg-1 chroot:unstable esttime:279 logfile:/tmp/hyphy_2.3.14+dfsg-1_unstable_clang8.log modes:clang8:binarch-only DC-Sbuild-call: su user42 -c 'sbuild -n --arch-any --apt-update -d unstable -v --chroot-setup-commands=/tmp/clang8 hyphy_2.3.14+dfsg-1' sbuild (Debian sbuild) 0.73.0 (23 Dec 2016) on ip-172-31-4-137.eu-central-1.compute.internal +==============================================================================+ | hyphy 2.3.14+dfsg-1 (amd64) Wed, 09 Jan 2019 21:29:52 +0000 | +==============================================================================+ Package: hyphy Version: 2.3.14+dfsg-1 Source Version: 2.3.14+dfsg-1 Distribution: unstable Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/sid-amd64-sbuild-d3290943-de76-46d8-8333-6c95a15ad55f' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /tmp/clang8 ----------- + echo 'Entering customization script...' Entering customization script... + CLANG_VERSION=8 + echo 'Install of clang-8' Install of clang-8 + echo deb http://127.0.0.1:9999/debian experimental main + apt-get update Get:1 http://127.0.0.1:9999/debian sid InRelease [238 kB] Get:2 http://127.0.0.1:9999/debian experimental InRelease [101 kB] Get:3 http://127.0.0.1:9999/debian sid/main Sources.diff/Index [27.9 kB] Get:4 http://127.0.0.1:9999/debian sid/main amd64 Packages.diff/Index [27.9 kB] Get:5 http://127.0.0.1:9999/debian sid/main Sources 2019-01-09-1430.36.pdiff [24.1 kB] Get:6 http://127.0.0.1:9999/debian sid/main Sources 2019-01-09-2026.40.pdiff [16.8 kB] Get:7 http://127.0.0.1:9999/debian sid/main amd64 Packages 2019-01-09-1430.36.pdiff [40.9 kB] Get:8 http://127.0.0.1:9999/debian sid/main amd64 Packages 2019-01-09-2026.40.pdiff [32.0 kB] Get:6 http://127.0.0.1:9999/debian sid/main Sources 2019-01-09-2026.40.pdiff [16.8 kB] Get:8 http://127.0.0.1:9999/debian sid/main amd64 Packages 2019-01-09-2026.40.pdiff [32.0 kB] Get:9 http://127.0.0.1:9999/debian sid/main Translation-en [6274 kB] Get:10 http://127.0.0.1:9999/debian experimental/main amd64 Packages [248 kB] Get:11 http://127.0.0.1:9999/debian experimental/main Translation-en [173 kB] Fetched 7204 kB in 2s (3364 kB/s) Reading package lists... + apt-get install --yes --no-install-recommends --force-yes clang-8 libomp-8-dev libobjc-8-dev Reading package lists... Building dependency tree... The following additional packages will be installed: lib32gcc1 lib32stdc++6 libbsd0 libc6-i386 libclang-common-8-dev libclang1-8 libedit2 libgc1c2 libllvm8 libobjc4 libomp5-8 Suggested packages: clang-8-doc libomp-8-doc Recommended packages: llvm-8-dev python The following NEW packages will be installed: clang-8 lib32gcc1 lib32stdc++6 libbsd0 libc6-i386 libclang-common-8-dev libclang1-8 libedit2 libgc1c2 libllvm8 libobjc-8-dev libobjc4 libomp-8-dev libomp5-8 0 upgraded, 14 newly installed, 0 to remove and 5 not upgraded. Need to get 35.8 MB of archives. After this operation, 191 MB of additional disk space will be used. Get:1 http://127.0.0.1:9999/debian sid/main amd64 libbsd0 amd64 0.9.1-1 [99.3 kB] Get:2 http://127.0.0.1:9999/debian sid/main amd64 libedit2 amd64 3.1-20181209-1 [94.0 kB] Get:3 http://127.0.0.1:9999/debian experimental/main amd64 libllvm8 amd64 1:8~svn350193-1~exp1 [13.8 MB] Get:4 http://127.0.0.1:9999/debian sid/main amd64 libgc1c2 amd64 1:7.6.4-0.4 [224 kB] Get:5 http://127.0.0.1:9999/debian sid/main amd64 libobjc4 amd64 8.2.0-14 [50.4 kB] Get:6 http://127.0.0.1:9999/debian sid/main amd64 libobjc-8-dev amd64 8.2.0-14 [225 kB] Get:7 http://127.0.0.1:9999/debian sid/main amd64 libc6-i386 amd64 2.28-4 [2873 kB] Get:8 http://127.0.0.1:9999/debian sid/main amd64 lib32gcc1 amd64 1:8.2.0-14 [47.9 kB] Get:9 http://127.0.0.1:9999/debian sid/main amd64 lib32stdc++6 amd64 8.2.0-14 [406 kB] Get:10 http://127.0.0.1:9999/debian experimental/main amd64 libclang-common-8-dev amd64 1:8~svn350193-1~exp1 [3350 kB] Get:11 http://127.0.0.1:9999/debian experimental/main amd64 libclang1-8 amd64 1:8~svn350193-1~exp1 [6255 kB] Get:12 http://127.0.0.1:9999/debian experimental/main amd64 clang-8 amd64 1:8~svn350193-1~exp1 [8025 kB] Get:13 http://127.0.0.1:9999/debian experimental/main amd64 libomp5-8 amd64 1:8~svn350193-1~exp1 [328 kB] Get:14 http://127.0.0.1:9999/debian experimental/main amd64 libomp-8-dev amd64 1:8~svn350193-1~exp1 [58.5 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 35.8 MB in 0s (118 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 ... 11802 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-1_amd64.deb ... Unpacking libbsd0:amd64 (0.9.1-1) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../01-libedit2_3.1-20181209-1_amd64.deb ... Unpacking libedit2:amd64 (3.1-20181209-1) ... Selecting previously unselected package libllvm8:amd64. Preparing to unpack .../02-libllvm8_1%3a8~svn350193-1~exp1_amd64.deb ... Unpacking libllvm8:amd64 (1:8~svn350193-1~exp1) ... Selecting previously unselected package libgc1c2:amd64. Preparing to unpack .../03-libgc1c2_1%3a7.6.4-0.4_amd64.deb ... Unpacking libgc1c2:amd64 (1:7.6.4-0.4) ... Selecting previously unselected package libobjc4:amd64. Preparing to unpack .../04-libobjc4_8.2.0-14_amd64.deb ... Unpacking libobjc4:amd64 (8.2.0-14) ... Selecting previously unselected package libobjc-8-dev:amd64. Preparing to unpack .../05-libobjc-8-dev_8.2.0-14_amd64.deb ... Unpacking libobjc-8-dev:amd64 (8.2.0-14) ... Selecting previously unselected package libc6-i386. Preparing to unpack .../06-libc6-i386_2.28-4_amd64.deb ... Unpacking libc6-i386 (2.28-4) ... Selecting previously unselected package lib32gcc1. Preparing to unpack .../07-lib32gcc1_1%3a8.2.0-14_amd64.deb ... Unpacking lib32gcc1 (1:8.2.0-14) ... Selecting previously unselected package lib32stdc++6. Preparing to unpack .../08-lib32stdc++6_8.2.0-14_amd64.deb ... Unpacking lib32stdc++6 (8.2.0-14) ... Selecting previously unselected package libclang-common-8-dev. Preparing to unpack .../09-libclang-common-8-dev_1%3a8~svn350193-1~exp1_amd64.deb ... Unpacking libclang-common-8-dev (1:8~svn350193-1~exp1) ... Selecting previously unselected package libclang1-8:amd64. Preparing to unpack .../10-libclang1-8_1%3a8~svn350193-1~exp1_amd64.deb ... Unpacking libclang1-8:amd64 (1:8~svn350193-1~exp1) ... Selecting previously unselected package clang-8. Preparing to unpack .../11-clang-8_1%3a8~svn350193-1~exp1_amd64.deb ... Unpacking clang-8 (1:8~svn350193-1~exp1) ... Selecting previously unselected package libomp5-8:amd64. Preparing to unpack .../12-libomp5-8_1%3a8~svn350193-1~exp1_amd64.deb ... Unpacking libomp5-8:amd64 (1:8~svn350193-1~exp1) ... Selecting previously unselected package libomp-8-dev. Preparing to unpack .../13-libomp-8-dev_1%3a8~svn350193-1~exp1_amd64.deb ... Unpacking libomp-8-dev (1:8~svn350193-1~exp1) ... Setting up libomp5-8:amd64 (1:8~svn350193-1~exp1) ... Setting up libgc1c2:amd64 (1:7.6.4-0.4) ... Setting up libc6-i386 (2.28-4) ... Setting up libbsd0:amd64 (0.9.1-1) ... Setting up libomp-8-dev (1:8~svn350193-1~exp1) ... Processing triggers for libc-bin (2.28-4) ... Setting up lib32gcc1 (1:8.2.0-14) ... Setting up libedit2:amd64 (3.1-20181209-1) ... Setting up libobjc4:amd64 (8.2.0-14) ... Setting up libobjc-8-dev:amd64 (8.2.0-14) ... Setting up libllvm8:amd64 (1:8~svn350193-1~exp1) ... Setting up libclang1-8:amd64 (1:8~svn350193-1~exp1) ... Setting up lib32stdc++6 (8.2.0-14) ... Setting up libclang-common-8-dev (1:8~svn350193-1~exp1) ... Setting up clang-8 (1:8~svn350193-1~exp1) ... Processing triggers for libc-bin (2.28-4) ... W: --force-yes is deprecated, use one of the options starting with --allow instead. + echo 'Replace gcc, g++ & cpp by clang' Replace gcc, g++ & cpp by clang + VERSIONS='4.6 4.7 4.8 4.9 5 6 7 8' + cd /usr/bin + for VERSION in $VERSIONS + rm -f g++-4.6 gcc-4.6 cpp-4.6 gcc + ln -s clang++-8 g++-4.6 + ln -s clang-8 gcc-4.6 + ln -s clang-8 cpp-4.6 + ln -s clang-8 gcc + echo 'gcc-4.6 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-4.6 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-4.6 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-4.6 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-4.7 gcc-4.7 cpp-4.7 gcc + ln -s clang++-8 g++-4.7 + ln -s clang-8 gcc-4.7 + ln -s clang-8 cpp-4.7 + ln -s clang-8 gcc + echo 'gcc-4.7 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-4.7 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-4.7 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-4.7 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-4.8 gcc-4.8 cpp-4.8 gcc + ln -s clang++-8 g++-4.8 + ln -s clang-8 gcc-4.8 + ln -s clang-8 cpp-4.8 + ln -s clang-8 gcc + echo 'gcc-4.8 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-4.8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-4.8 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-4.8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-4.9 gcc-4.9 cpp-4.9 gcc + ln -s clang++-8 g++-4.9 + ln -s clang-8 gcc-4.9 + ln -s clang-8 cpp-4.9 + ln -s clang-8 gcc + echo 'gcc-4.9 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-4.9 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-4.9 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-4.9 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-5 gcc-5 cpp-5 gcc + ln -s clang++-8 g++-5 + ln -s clang-8 gcc-5 + ln -s clang-8 cpp-5 + ln -s clang-8 gcc + echo 'gcc-5 hold' + dpkg --set-selections dpkg: warning: package not in status nor available 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; please see the FAQ + echo 'g++-5 hold' + dpkg --set-selections dpkg: warning: package not in status nor available 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; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-6 gcc-6 cpp-6 gcc + ln -s clang++-8 g++-6 + ln -s clang-8 gcc-6 + ln -s clang-8 cpp-6 + ln -s clang-8 gcc + echo 'gcc-6 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-6 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-6 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-6 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-7 gcc-7 cpp-7 gcc + ln -s clang++-8 g++-7 + ln -s clang-8 gcc-7 + ln -s clang-8 cpp-7 + ln -s clang-8 gcc + echo 'gcc-7 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-7 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-7 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-7 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-8 gcc-8 cpp-8 gcc + ln -s clang++-8 g++-8 + ln -s clang-8 gcc-8 + ln -s clang-8 cpp-8 + ln -s clang-8 gcc + echo 'gcc-8 hold' + dpkg --set-selections + echo 'g++-8 hold' + dpkg --set-selections + cd - /build/hyphy-EQPii0 + 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/clang8'. Finished processing commands. -------------------------------------------------------------------------------- +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Hit:1 http://127.0.0.1:9999/debian sid InRelease Hit:2 http://127.0.0.1:9999/debian experimental InRelease Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: libmpfr6 libpam-modules libpam-modules-bin libpam-runtime libpam0g 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 1519 kB of archives. After this operation, 7168 B of additional disk space will be used. Get:1 http://127.0.0.1:9999/debian sid/main amd64 libpam0g amd64 1.1.8-4 [124 kB] Get:2 http://127.0.0.1:9999/debian sid/main amd64 libpam-modules-bin amd64 1.1.8-4 [106 kB] Get:3 http://127.0.0.1:9999/debian sid/main amd64 libpam-modules amd64 1.1.8-4 [305 kB] Get:4 http://127.0.0.1:9999/debian sid/main amd64 libpam-runtime all 1.1.8-4 [211 kB] Get:5 http://127.0.0.1:9999/debian sid/main amd64 libmpfr6 amd64 4.0.2~rc1-1 [773 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 1519 kB in 0s (27.8 MB/s) (Reading database ... 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Processing triggers for libc-bin (2.28-4) ... +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'hyphy' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/hyphy.git Please use: git clone https://salsa.debian.org/med-team/hyphy.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 4586 kB of source archives. Get:1 http://127.0.0.1:9999/debian sid/main hyphy 2.3.14+dfsg-1 (dsc) [2143 B] Get:2 http://127.0.0.1:9999/debian sid/main hyphy 2.3.14+dfsg-1 (tar) [4575 kB] Get:3 http://127.0.0.1:9999/debian sid/main hyphy 2.3.14+dfsg-1 (diff) [8948 B] Fetched 4586 kB in 1s (4878 kB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/hyphy-EQPii0/hyphy-2.3.14+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/hyphy-EQPii0' with '<>' +------------------------------------------------------------------------------+ | Install build-essential | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-meJnVO/apt_archive/sbuild-build-depends-core-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy dpkg-scanpackages: info: Wrote 1 entries to output Packages file. Ign:1 copy:/<>/resolver-meJnVO/apt_archive ./ InRelease Get:2 copy:/<>/resolver-meJnVO/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-meJnVO/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-meJnVO/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-meJnVO/apt_archive ./ Packages [432 B] Fetched 1738 B in 0s (0 B/s) Reading package lists... Reading package lists... Install core build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 856 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-meJnVO/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [856 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 856 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12592 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper (>= 11~), cmake (>= 3.0), mpi-default-dev, libcurl4-gnutls-dev | libcurl4-dev, libssl-dev, libsqlite3-dev Filtered Build-Depends: debhelper (>= 11~), cmake (>= 3.0), mpi-default-dev, libcurl4-gnutls-dev, libssl-dev, libsqlite3-dev dpkg-deb: building package 'sbuild-build-depends-hyphy-dummy' in '/<>/resolver-meJnVO/apt_archive/sbuild-build-depends-hyphy-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-hyphy-dummy dpkg-scanpackages: info: Wrote 2 entries to output Packages file. Ign:1 copy:/<>/resolver-meJnVO/apt_archive ./ InRelease Get:2 copy:/<>/resolver-meJnVO/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-meJnVO/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-meJnVO/apt_archive ./ Sources [540 B] Get:5 copy:/<>/resolver-meJnVO/apt_archive ./ Packages [615 B] Fetched 2118 B in 0s (0 B/s) Reading package lists... Reading package lists... Install hyphy build dependencies (apt-based resolver) ----------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils cmake cmake-data debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base ibverbs-providers intltool-debian libarchive-zip-perl libarchive13 libcroco3 libcurl3-gnutls libcurl4 libcurl4-gnutls-dev libelf1 libevent-2.1-6 libevent-core-2.1-6 libevent-pthreads-2.1-6 libexpat1 libfabric1 libfile-stripnondeterminism-perl libgfortran5 libglib2.0-0 libgssapi-krb5-2 libhwloc-dev libhwloc-plugins libhwloc5 libibverbs-dev libibverbs1 libicu63 libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common libltdl-dev libltdl7 libmagic-mgc libmagic1 libncurses6 libnghttp2-14 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi3 libpciaccess0 libpipeline1 libpmix2 libprocps7 libpsl5 libpsm-infinipath1 libpsm2-2 librdmacm1 librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsqlite3-0 libsqlite3-dev libssh2-1 libssl-dev libssl1.1 libtool libuchardet0 libuv1 libxml2 lsb-base m4 man-db mpi-default-dev ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client po-debconf procps sensible-utils Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation cmake-doc ninja-build dh-make gettext-doc libasprintf-dev libgettextpo-dev groff lrzip libcurl4-doc libgnutls28-dev libidn11-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev pkg-config zlib1g-dev krb5-doc krb5-user libhwloc-contrib-plugins libtool-doc openmpi-doc pciutils sqlite3-doc libssl-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser opencl-icd gfortran keychain libpam-ssh monkeysphere ssh-askpass libmail-box-perl Recommended packages: curl | wget | lynx ca-certificates libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales libgpm2 libcoarrays-openmpi-dev publicsuffix libsasl2-modules xauth libmail-sendmail-perl psmisc The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils cmake cmake-data debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base ibverbs-providers intltool-debian libarchive-zip-perl libarchive13 libcroco3 libcurl3-gnutls libcurl4 libcurl4-gnutls-dev libelf1 libevent-2.1-6 libevent-core-2.1-6 libevent-pthreads-2.1-6 libexpat1 libfabric1 libfile-stripnondeterminism-perl libgfortran5 libglib2.0-0 libgssapi-krb5-2 libhwloc-dev libhwloc-plugins libhwloc5 libibverbs-dev libibverbs1 libicu63 libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common libltdl-dev libltdl7 libmagic-mgc libmagic1 libncurses6 libnghttp2-14 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi3 libpciaccess0 libpipeline1 libpmix2 libprocps7 libpsl5 libpsm-infinipath1 libpsm2-2 librdmacm1 librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsqlite3-0 libsqlite3-dev libssh2-1 libssl-dev libssl1.1 libtool libuchardet0 libuv1 libxml2 lsb-base m4 man-db mpi-default-dev ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client po-debconf procps sbuild-build-depends-hyphy-dummy sensible-utils 0 upgraded, 94 newly installed, 0 to remove and 0 not upgraded. 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Get:1 copy:/<>/resolver-meJnVO/apt_archive ./ sbuild-build-depends-hyphy-dummy 0.invalid.0 [904 B] Get:2 http://127.0.0.1:9999/debian sid/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get:3 http://127.0.0.1:9999/debian sid/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get:4 http://127.0.0.1:9999/debian sid/main amd64 groff-base amd64 1.22.4-2 [917 kB] Get:5 http://127.0.0.1:9999/debian sid/main amd64 libpipeline1 amd64 1.5.0-2 [29.5 kB] Get:6 http://127.0.0.1:9999/debian sid/main amd64 man-db amd64 2.8.5-1 [1274 kB] Get:7 http://127.0.0.1:9999/debian sid/main amd64 libncurses6 amd64 6.1+20181013-1 [102 kB] Get:8 http://127.0.0.1:9999/debian sid/main amd64 libprocps7 amd64 2:3.3.15-2 [61.7 kB] Get:9 http://127.0.0.1:9999/debian sid/main amd64 lsb-base all 10.2018112800 [28.3 kB] Get:10 http://127.0.0.1:9999/debian sid/main amd64 procps amd64 2:3.3.15-2 [259 kB] Get:11 http://127.0.0.1:9999/debian sid/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get:12 http://127.0.0.1:9999/debian sid/main amd64 libmagic-mgc amd64 1:5.34-2 [239 kB] Get:13 http://127.0.0.1:9999/debian sid/main amd64 libmagic1 amd64 1:5.34-2 [116 kB] Get:14 http://127.0.0.1:9999/debian sid/main amd64 file amd64 1:5.34-2 [65.8 kB] Get:15 http://127.0.0.1:9999/debian sid/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get:16 http://127.0.0.1:9999/debian sid/main amd64 libkeyutils1 amd64 1.5.9-9.3 [13.0 kB] Get:17 http://127.0.0.1:9999/debian sid/main amd64 libkrb5support0 amd64 1.16.2-1 [63.3 kB] Get:18 http://127.0.0.1:9999/debian sid/main amd64 libk5crypto3 amd64 1.16.2-1 [121 kB] Get:19 http://127.0.0.1:9999/debian sid/main amd64 libkrb5-3 amd64 1.16.2-1 [320 kB] Get:20 http://127.0.0.1:9999/debian sid/main amd64 libgssapi-krb5-2 amd64 1.16.2-1 [158 kB] Get:21 http://127.0.0.1:9999/debian sid/main amd64 libssl1.1 amd64 1.1.1a-1 [1527 kB] Get:22 http://127.0.0.1:9999/debian sid/main amd64 openssh-client amd64 1:7.9p1-4 [797 kB] Get:23 http://127.0.0.1:9999/debian sid/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get:24 http://127.0.0.1:9999/debian sid/main amd64 m4 amd64 1.4.18-2 [203 kB] Get:25 http://127.0.0.1:9999/debian sid/main amd64 autoconf all 2.69-11 [341 kB] Get:26 http://127.0.0.1:9999/debian sid/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get:27 http://127.0.0.1:9999/debian sid/main amd64 automake all 1:1.16.1-4 [771 kB] Get:28 http://127.0.0.1:9999/debian sid/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get:29 http://127.0.0.1:9999/debian sid/main amd64 cmake-data all 3.13.2-1 [1476 kB] Get:30 http://127.0.0.1:9999/debian sid/main amd64 libicu63 amd64 63.1-5 [8293 kB] Get:31 http://127.0.0.1:9999/debian sid/main amd64 libxml2 amd64 2.9.4+dfsg1-7+b3 [687 kB] Get:32 http://127.0.0.1:9999/debian sid/main amd64 libarchive13 amd64 3.3.3-3 [313 kB] Get:33 http://127.0.0.1:9999/debian sid/main amd64 libsasl2-modules-db amd64 2.1.27~rc8-1 [68.4 kB] Get:34 http://127.0.0.1:9999/debian sid/main amd64 libsasl2-2 amd64 2.1.27~rc8-1 [105 kB] Get:35 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http://127.0.0.1:9999/debian sid/main amd64 cmake amd64 3.13.2-1 [3485 kB] Get:47 http://127.0.0.1:9999/debian sid/main amd64 libtool all 2.4.6-6 [547 kB] Get:48 http://127.0.0.1:9999/debian sid/main amd64 dh-autoreconf all 19 [16.9 kB] Get:49 http://127.0.0.1:9999/debian sid/main amd64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get:50 http://127.0.0.1:9999/debian sid/main amd64 libfile-stripnondeterminism-perl all 1.0.0-1 [19.5 kB] Get:51 http://127.0.0.1:9999/debian sid/main amd64 dh-strip-nondeterminism all 1.0.0-1 [12.5 kB] Get:52 http://127.0.0.1:9999/debian sid/main amd64 libelf1 amd64 0.175-2 [160 kB] Get:53 http://127.0.0.1:9999/debian sid/main amd64 dwz amd64 0.12-3 [78.0 kB] Get:54 http://127.0.0.1:9999/debian sid/main amd64 libglib2.0-0 amd64 2.58.2-3 [1257 kB] Get:55 http://127.0.0.1:9999/debian sid/main amd64 libcroco3 amd64 0.6.12-3 [145 kB] Get:56 http://127.0.0.1:9999/debian sid/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get:57 http://127.0.0.1:9999/debian sid/main 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amd64 libevent-pthreads-2.1-6 amd64 2.1.8-stable-4 [47.9 kB] Get:69 http://127.0.0.1:9999/debian sid/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6 [168 kB] Get:70 http://127.0.0.1:9999/debian sid/main amd64 libnuma1 amd64 2.0.12-1 [26.2 kB] Get:71 http://127.0.0.1:9999/debian sid/main amd64 libpsm2-2 amd64 11.2.68-4 [177 kB] Get:72 http://127.0.0.1:9999/debian sid/main amd64 librdmacm1 amd64 21.0-1 [65.0 kB] Get:73 http://127.0.0.1:9999/debian sid/main amd64 libfabric1 amd64 1.6.1-5 [392 kB] Get:74 http://127.0.0.1:9999/debian sid/main amd64 libgfortran5 amd64 8.2.0-14 [581 kB] Get:75 http://127.0.0.1:9999/debian sid/main amd64 libltdl7 amd64 2.4.6-6 [390 kB] Get:76 http://127.0.0.1:9999/debian sid/main amd64 libhwloc5 amd64 1.11.12-1 [111 kB] Get:77 http://127.0.0.1:9999/debian sid/main amd64 libnuma-dev amd64 2.0.12-1 [39.2 kB] Get:78 http://127.0.0.1:9999/debian sid/main amd64 libltdl-dev amd64 2.4.6-6 [162 kB] Get:79 http://127.0.0.1:9999/debian sid/main amd64 libhwloc-dev amd64 1.11.12-1 [175 kB] Get:80 http://127.0.0.1:9999/debian sid/main amd64 libpciaccess0 amd64 0.14-1 [53.5 kB] Get:81 http://127.0.0.1:9999/debian sid/main amd64 ocl-icd-libopencl1 amd64 2.2.12-2 [37.5 kB] Get:82 http://127.0.0.1:9999/debian sid/main amd64 libhwloc-plugins amd64 1.11.12-1 [17.3 kB] Get:83 http://127.0.0.1:9999/debian sid/main amd64 libnl-3-dev amd64 3.4.0-1 [102 kB] Get:84 http://127.0.0.1:9999/debian sid/main amd64 libnl-route-3-dev amd64 3.4.0-1 [177 kB] Get:85 http://127.0.0.1:9999/debian sid/main amd64 libibverbs-dev amd64 21.0-1 [355 kB] Get:86 http://127.0.0.1:9999/debian sid/main amd64 libpmix2 amd64 3.1.0~rc2-3 [421 kB] Get:87 http://127.0.0.1:9999/debian sid/main amd64 libopenmpi3 amd64 3.1.3-9 [2174 kB] Get:88 http://127.0.0.1:9999/debian sid/main amd64 openmpi-common all 3.1.3-9 [165 kB] Get:89 http://127.0.0.1:9999/debian sid/main amd64 openmpi-bin amd64 3.1.3-9 [200 kB] Get:90 http://127.0.0.1:9999/debian sid/main amd64 libopenmpi-dev amd64 3.1.3-9 [974 kB] Get:91 http://127.0.0.1:9999/debian sid/main amd64 libsqlite3-0 amd64 3.26.0+fossilbc891ac6b-1 [634 kB] Get:92 http://127.0.0.1:9999/debian sid/main amd64 libsqlite3-dev amd64 3.26.0+fossilbc891ac6b-1 [780 kB] Get:93 http://127.0.0.1:9999/debian sid/main amd64 libssl-dev amd64 1.1.1a-1 [1788 kB] Get:94 http://127.0.0.1:9999/debian sid/main amd64 mpi-default-dev amd64 1.13 [5476 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 40.8 MB in 0s (90.5 MB/s) Selecting previously unselected package bsdmainutils. (Reading database ... 12592 files and directories currently installed.) Preparing to unpack .../00-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../01-libuchardet0_0.0.6-3_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-2_amd64.deb ... Unpacking groff-base (1.22.4-2) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../03-libpipeline1_1.5.0-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.0-2) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.8.5-1_amd64.deb ... Unpacking man-db (2.8.5-1) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../05-libncurses6_6.1+20181013-1_amd64.deb ... Unpacking libncurses6:amd64 (6.1+20181013-1) ... 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Setting up libprocps7:amd64 (2:3.3.15-2) ... Setting up libicu63:amd64 (63.1-5) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up libldap-common (2.4.47+dfsg-1) ... Setting up libuv1:amd64 (1.24.0-1) ... Setting up libpsl5:amd64 (0.20.2-2) ... Setting up libnuma1:amd64 (2.0.12-1) ... Setting up libelf1:amd64 (0.175-2) ... Setting up libglib2.0-0:amd64 (2.58.2-3) ... No schema files found: doing nothing. Setting up gettext-base (0.19.8.1-9) ... Setting up cmake-data (3.13.2-1) ... Setting up libpipeline1:amd64 (1.5.0-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2) ... Setting up m4 (1.4.18-2) ... Setting up libxml2:amd64 (2.9.4+dfsg1-7+b3) ... Setting up libuchardet0:amd64 (0.0.6-3) ... Setting up libmagic-mgc (1:5.34-2) ... Setting up libmagic1:amd64 (1:5.34-2) ... Setting up lsb-base (10.2018112800) ... Setting up librhash0:amd64 (1.3.7-1) ... Setting up libcroco3:amd64 (0.6.12-3) ... Setting up libpsm-infinipath1 (3.3+20.604758e7-6) ... update-alternatives: using /usr/lib/libpsm1/libpsm_infinipath.so.1.16 to provide /usr/lib/x86_64-linux-gnu/libpsm_infinipath.so.1 (libpsm_infinipath.so.1) in auto mode Setting up sensible-utils (0.0.12) ... Setting up libssh2-1:amd64 (1.8.0-2) ... Setting up libevent-pthreads-2.1-6:amd64 (2.1.8-stable-4) ... Setting up openmpi-common (3.1.3-9) ... Processing triggers for libc-bin (2.28-4) ... Setting up dwz (0.12-3) ... Setting up autotools-dev (20180224.1) ... Setting up libssl1.1:amd64 (1.1.1a-1) ... Setting up libltdl7:amd64 (2.4.6-6) ... Setting up libsqlite3-0:amd64 (3.26.0+fossilbc891ac6b-1) ... Setting up libpciaccess0:amd64 (0.14-1) ... Setting up libnuma-dev:amd64 (2.0.12-1) ... Setting up ocl-icd-libopencl1:amd64 (2.2.12-2) ... Setting up libkeyutils1:amd64 (1.5.9-9.3) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libnl-3-200:amd64 (3.4.0-1) ... Setting up libgfortran5:amd64 (8.2.0-14) ... Setting up libncurses6:amd64 (6.1+20181013-1) ... Setting up autopoint (0.19.8.1-9) ... Setting up libfile-stripnondeterminism-perl (1.0.0-1) ... Setting up libjsoncpp1:amd64 (1.7.4-3) ... Setting up libpsm2-2 (11.2.68-4) ... Setting up gettext (0.19.8.1-9) ... Setting up libsqlite3-dev:amd64 (3.26.0+fossilbc891ac6b-1) ... Setting up libarchive13:amd64 (3.3.3-3) ... Setting up libssl-dev:amd64 (1.1.1a-1) ... Setting up groff-base (1.22.4-2) ... Setting up libnl-3-dev:amd64 (3.4.0-1) ... Setting up libnl-route-3-200:amd64 (3.4.0-1) ... Setting up autoconf (2.69-11) ... Setting up file (1:5.34-2) ... Setting up libhwloc5:amd64 (1.11.12-1) ... Setting up libkrb5support0:amd64 (1.16.2-1) ... Setting up procps (2:3.3.15-2) ... update-alternatives: using /usr/bin/w.procps to provide /usr/bin/w (w) in auto mode Setting up libhwloc-plugins:amd64 (1.11.12-1) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up man-db (2.8.5-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libtool (2.4.6-6) ... Setting up libibverbs1:amd64 (21.0-1) ... Setting up libk5crypto3:amd64 (1.16.2-1) ... Setting up libltdl-dev:amd64 (2.4.6-6) ... Setting up po-debconf (1.0.21) ... Setting up libhwloc-dev:amd64 (1.11.12-1) ... Setting up libnl-route-3-dev:amd64 (3.4.0-1) ... Setting up libpmix2:amd64 (3.1.0~rc2-3) ... Setting up librdmacm1:amd64 (21.0-1) ... Setting up ibverbs-providers:amd64 (21.0-1) ... Setting up libkrb5-3:amd64 (1.16.2-1) ... Setting up libibverbs-dev:amd64 (21.0-1) ... Setting up libfabric1 (1.6.1-5) ... Setting up libgssapi-krb5-2:amd64 (1.16.2-1) ... Setting up openssh-client (1:7.9p1-4) ... Setting up libopenmpi3:amd64 (3.1.3-9) ... Setting up libsasl2-modules-db:amd64 (2.1.27~rc8-1) ... Setting up libsasl2-2:amd64 (2.1.27~rc8-1) ... Setting up openmpi-bin (3.1.3-9) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up libldap-2.4-2:amd64 (2.4.47+dfsg-1) ... Setting up libcurl3-gnutls:amd64 (7.62.0-1) ... Setting up libopenmpi-dev:amd64 (3.1.3-9) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openmpi/include to provide /usr/include/x86_64-linux-gnu/mpi (mpi-x86_64-linux-gnu) in auto mode Setting up libcurl4:amd64 (7.62.0-1) ... Setting up mpi-default-dev (1.13) ... Setting up cmake (3.13.2-1) ... Setting up libcurl4-gnutls-dev:amd64 (7.62.0-1) ... Setting up dh-autoreconf (19) ... Setting up debhelper (12) ... Setting up sbuild-build-depends-hyphy-dummy (0.invalid.0) ... Setting up dh-strip-nondeterminism (1.0.0-1) ... Processing triggers for libc-bin (2.28-4) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.9.0-8-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.31.1-11 dpkg-dev_1.19.2 g++-8_8.2.0-14 gcc-8_8.2.0-14 libc6-dev_2.28-4 libstdc++-8-dev_8.2.0-14 libstdc++6_8.2.0-14 linux-libc-dev_4.19.13-1 Package versions: adduser_3.118 apt_1.8.0~alpha3 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.1 base-passwd_3.5.45 bash_4.4.18-3.1 binutils_2.31.1-11 binutils-common_2.31.1-11 binutils-x86-64-linux-gnu_2.31.1-11 bsdmainutils_11.1.2+b1 bsdutils_1:2.33-0.2 build-essential_12.5 bzip2_1.0.6-9 clang-8_1:8~svn350193-1~exp1 cmake_3.13.2-1 cmake-data_3.13.2-1 coreutils_8.30-1 cpp_4:8.2.0-2 cpp-8_8.2.0-14 dash_0.5.10.2-4 debconf_1.5.69 debhelper_12 debian-archive-keyring_2018.1 debianutils_4.8.6 dh-autoreconf_19 dh-strip-nondeterminism_1.0.0-1 diffutils_1:3.6-1 dpkg_1.19.2 dpkg-dev_1.19.2 dwz_0.12-3 e2fsprogs_1.44.5-1 fakeroot_1.23-1 fdisk_2.33-0.2 file_1:5.34-2 findutils_4.6.0+git+20181018-1 g++_4:8.2.0-2 g++-8_8.2.0-14 gcc_4:8.2.0-2 gcc-8_8.2.0-14 gcc-8-base_8.2.0-14 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gpgv_2.2.12-1 grep_3.3-1 groff-base_1.22.4-2 gzip_1.9-3 hostname_3.21 ibverbs-providers_21.0-1 init-system-helpers_1.56+nmu1 intltool-debian_0.35.0+20060710.4 lib32gcc1_1:8.2.0-14 lib32stdc++6_8.2.0-14 libacl1_2.2.52-3+b1 libapt-pkg5.0_1.8.0~alpha3 libarchive-zip-perl_1.64-1 libarchive13_3.3.3-3 libasan5_8.2.0-14 libatomic1_8.2.0-14 libattr1_1:2.4.47-2+b2 libaudit-common_1:2.8.4-2 libaudit1_1:2.8.4-2 libbinutils_2.31.1-11 libblkid1_2.33-0.2 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-9 libc-bin_2.28-4 libc-dev-bin_2.28-4 libc6_2.28-4 libc6-dev_2.28-4 libc6-i386_2.28-4 libcap-ng0_0.7.9-1+b1 libcc1-0_8.2.0-14 libclang-common-8-dev_1:8~svn350193-1~exp1 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libjsoncpp1_1.7.4-3 libk5crypto3_1.16.2-1 libkeyutils1_1.5.9-9.3 libkrb5-3_1.16.2-1 libkrb5support0_1.16.2-1 libldap-2.4-2_2.4.47+dfsg-1 libldap-common_2.4.47+dfsg-1 libllvm8_1:8~svn350193-1~exp1 liblsan0_8.2.0-14 libltdl-dev_2.4.6-6 libltdl7_2.4.6-6 liblz4-1_1.8.3-1 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.34-2 libmagic1_1:5.34-2 libmount1_2.33-0.2 libmpc3_1.1.0-1 libmpfr6_4.0.2~rc1-1 libmpx2_8.2.0-14 libncurses6_6.1+20181013-1 libncursesw6_6.1+20181013-1 libnettle6_3.4.1~rc1-1 libnghttp2-14_1.35.1-1+b1 libnl-3-200_3.4.0-1 libnl-3-dev_3.4.0-1 libnl-route-3-200_3.4.0-1 libnl-route-3-dev_3.4.0-1 libnuma-dev_2.0.12-1 libnuma1_2.0.12-1 libobjc-8-dev_8.2.0-14 libobjc4_8.2.0-14 libomp-8-dev_1:8~svn350193-1~exp1 libomp5-8_1:8~svn350193-1~exp1 libopenmpi-dev_3.1.3-9 libopenmpi3_3.1.3-9 libp11-kit0_0.23.14-2 libpam-modules_1.1.8-4 libpam-modules-bin_1.1.8-4 libpam-runtime_1.1.8-4 libpam0g_1.1.8-4 libpciaccess0_0.14-1 libpcre3_2:8.39-11 libperl5.28_5.28.1-3 libpipeline1_1.5.0-2 libpmix2_3.1.0~rc2-3 libprocps7_2:3.3.15-2 libpsl5_0.20.2-2 libpsm-infinipath1_3.3+20.604758e7-6 libpsm2-2_11.2.68-4 libquadmath0_8.2.0-14 librdmacm1_21.0-1 librhash0_1.3.7-1 librtmp1_2.4+20151223.gitfa8646d.1-2 libsasl2-2_2.1.27~rc8-1 libsasl2-modules-db_2.1.27~rc8-1 libseccomp2_2.3.3-3 libselinux1_2.8-1+b1 libsemanage-common_2.8-2 libsemanage1_2.8-2 libsepol1_2.8-1 libsigsegv2_2.12-2 libsmartcols1_2.33-0.2 libsqlite3-0_3.26.0+fossilbc891ac6b-1 libsqlite3-dev_3.26.0+fossilbc891ac6b-1 libss2_1.44.5-1 libssh2-1_1.8.0-2 libssl-dev_1.1.1a-1 libssl1.1_1.1.1a-1 libstdc++-8-dev_8.2.0-14 libstdc++6_8.2.0-14 libsystemd0_240-2 libtasn1-6_4.13-3 libtinfo6_6.1+20181013-1 libtool_2.4.6-6 libtsan0_8.2.0-14 libubsan1_8.2.0-14 libuchardet0_0.0.6-3 libudev1_240-2 libunistring2_0.9.10-1 libuuid1_2.33-0.2 libuv1_1.24.0-1 libxml2_2.9.4+dfsg1-7+b3 libzstd1_1.3.8+dfsg-3 linux-libc-dev_4.19.13-1 login_1:4.5-1.1 lsb-base_10.2018112800 m4_1.4.18-2 make_4.2.1-1.2 man-db_2.8.5-1 mawk_1.3.3-17+b3 mount_2.33-0.2 mpi-default-dev_1.13 ncurses-base_6.1+20181013-1 ncurses-bin_6.1+20181013-1 ocl-icd-libopencl1_2.2.12-2 openmpi-bin_3.1.3-9 openmpi-common_3.1.3-9 openssh-client_1:7.9p1-4 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.28.1-3 perl-base_5.28.1-3 perl-modules-5.28_5.28.1-3 po-debconf_1.0.21 procps_2:3.3.15-2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-hyphy-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 sysvinit-utils_2.93-3 tar_1.30+dfsg-4 tzdata_2018i-1 util-linux_2.33-0.2 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Wed Sep 26 15:04:23 2018 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./hyphy_2.3.14+dfsg-1.dsc dpkg-source: info: extracting hyphy in /<>/hyphy-2.3.14+dfsg dpkg-source: info: unpacking hyphy_2.3.14+dfsg.orig.tar.xz dpkg-source: info: unpacking hyphy_2.3.14+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_sqlite.patch dpkg-source: info: applying spelling.patch dpkg-source: info: applying drop_profiling_option.patch dpkg-source: info: applying remove_unneeded_test.patch dpkg-source: info: applying msse_option_only_if_available.patch dpkg-source: info: applying remove_arch_specific_flags.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANG=en_US.UTF-8 LC_ALL=POSIX LOGNAME=user42 PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=unstable SCHROOT_CHROOT_NAME=sid-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1001 SCHROOT_GROUP=user42 SCHROOT_SESSION_ID=sid-amd64-sbuild-d3290943-de76-46d8-8333-6c95a15ad55f SCHROOT_UID=1001 SCHROOT_USER=user42 SHELL=/bin/sh USER=user42 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package hyphy dpkg-buildpackage: info: source version 2.3.14+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --buildsystem=cmake debian/rules override_dh_auto_clean make[1]: Entering directory '/<>/hyphy-2.3.14+dfsg' dh_auto_clean make[1]: Leaving directory '/<>/hyphy-2.3.14+dfsg' dh_autoreconf_clean -O--buildsystem=cmake dh_clean -O--buildsystem=cmake debian/rules build-arch dh build-arch --buildsystem=cmake dh_update_autotools_config -a -O--buildsystem=cmake dh_autoreconf -a -O--buildsystem=cmake debian/rules override_dh_auto_configure make[1]: Entering directory '/<>/hyphy-2.3.14+dfsg' dh_auto_configure -- -DINSTALL_PREFIX=/usr cd obj-x86_64-linux-gnu && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DINSTALL_PREFIX=/usr .. -- The C compiler identification is Clang 8.0.0 -- The CXX compiler identification is Clang 8.0.0 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Performing Test HAVE_AVX_EXTENSIONS -- Performing Test HAVE_AVX_EXTENSIONS - Failed -- Performing Test HAVE_SSE3_EXTENSIONS -- Performing Test HAVE_SSE3_EXTENSIONS - Success Set compiler flags to -fsigned-char -O3 -msse3 -- Looking for amd_log in libamdlibm.so -- Looking for amd_log in libamdlibm.so - not found -- Found OpenMP_C: -fopenmp=libomp (found version "3.1") -- Found OpenMP_CXX: -fopenmp=libomp (found version "3.1") -- Found OpenMP: TRUE (found version "3.1") -- Found CURL: /usr/lib/x86_64-linux-gnu/libcurl.so (found version "7.62.0") -- Could NOT find PkgConfig (missing: PKG_CONFIG_EXECUTABLE) -- Found SQLITE3: /usr/lib/x86_64-linux-gnu/libsqlite3.so -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) -- Looking for pthread.h -- Looking for pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - not found -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Looking for CL_VERSION_2_2 -- Looking for CL_VERSION_2_2 - not found -- Looking for CL_VERSION_2_1 -- Looking for CL_VERSION_2_1 - not found -- Looking for CL_VERSION_2_0 -- Looking for CL_VERSION_2_0 - not found -- Looking for CL_VERSION_1_2 -- Looking for CL_VERSION_1_2 - not found -- Looking for CL_VERSION_1_1 -- Looking for CL_VERSION_1_1 - not found -- Looking for CL_VERSION_1_0 -- Looking for CL_VERSION_1_0 - not found -- Could NOT find OpenCL (missing: OpenCL_LIBRARY OpenCL_INCLUDE_DIR) -- Found MPI_C: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR INSTALL_PREFIX -- Build files have been written to: /<>/hyphy-2.3.14+dfsg/obj-x86_64-linux-gnu make[1]: Leaving directory '/<>/hyphy-2.3.14+dfsg' debian/rules override_dh_auto_build make[1]: Entering directory '/<>/hyphy-2.3.14+dfsg' # no idea about the purpose of the dynamic library - executables are not simply linked against it dh_auto_build -- MP MPI GTEST # LIB cd obj-x86_64-linux-gnu && make -j4 "INSTALL=install --strip-program=true" MP MPI GTEST make[2]: Entering directory '/<>/hyphy-2.3.14+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/<>/hyphy-2.3.14+dfsg -B/<>/hyphy-2.3.14+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 MP make[3]: Entering directory '/<>/hyphy-2.3.14+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/<>/hyphy-2.3.14+dfsg -B/<>/hyphy-2.3.14+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/hyphy-2.3.14+dfsg/obj-x86_64-linux-gnu/CMakeFiles 24 make -f CMakeFiles/Makefile2 CMakeFiles/MP.dir/all make[4]: Entering directory '/<>/hyphy-2.3.14+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/HYPHYMP.dir/build.make CMakeFiles/HYPHYMP.dir/depend make[5]: Entering directory '/<>/hyphy-2.3.14+dfsg/obj-x86_64-linux-gnu' cd /<>/hyphy-2.3.14+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/hyphy-2.3.14+dfsg /<>/hyphy-2.3.14+dfsg /<>/hyphy-2.3.14+dfsg/obj-x86_64-linux-gnu /<>/hyphy-2.3.14+dfsg/obj-x86_64-linux-gnu /<>/hyphy-2.3.14+dfsg/obj-x86_64-linux-gnu/CMakeFiles/HYPHYMP.dir/DependInfo.cmake --color= Scanning dependencies of target HYPHYMP make[5]: Leaving directory '/<>/hyphy-2.3.14+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/HYPHYMP.dir/build.make CMakeFiles/HYPHYMP.dir/build make[5]: Entering directory '/<>/hyphy-2.3.14+dfsg/obj-x86_64-linux-gnu' [ 0%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/alignment.cpp.o [ 0%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/_hyExecutionContext.cpp.o [ 4%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/avllistx.cpp.o [ 4%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/avllist.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHY_64__ -D__MP2__ -D__MP__ -D__UNIX__ -I/<>/hyphy-2.3.14+dfsg/src/core/include -I/<>/hyphy-2.3.14+dfsg/src/lib/Link -I/<>/hyphy-2.3.14+dfsg/src/new/include -I/<>/hyphy-2.3.14+dfsg/contrib/gtest-1.7.0/include -I/<>/hyphy-2.3.14+dfsg/tests/gtests -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/<>/hyphy-2.3.14+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -msse3 -w -fopenmp=libomp -std=c++14 -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMP.dir/src/core/_hyExecutionContext.cpp.o -c /<>/hyphy-2.3.14+dfsg/src/core/_hyExecutionContext.cpp /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHY_64__ -D__MP2__ -D__MP__ -D__UNIX__ -I/<>/hyphy-2.3.14+dfsg/src/core/include -I/<>/hyphy-2.3.14+dfsg/src/lib/Link -I/<>/hyphy-2.3.14+dfsg/src/new/include -I/<>/hyphy-2.3.14+dfsg/contrib/gtest-1.7.0/include -I/<>/hyphy-2.3.14+dfsg/tests/gtests -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/<>/hyphy-2.3.14+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -msse3 -w -fopenmp=libomp -std=c++14 -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMP.dir/src/core/alignment.cpp.o -c /<>/hyphy-2.3.14+dfsg/src/core/alignment.cpp /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHY_64__ -D__MP2__ -D__MP__ -D__UNIX__ -I/<>/hyphy-2.3.14+dfsg/src/core/include -I/<>/hyphy-2.3.14+dfsg/src/lib/Link -I/<>/hyphy-2.3.14+dfsg/src/new/include -I/<>/hyphy-2.3.14+dfsg/contrib/gtest-1.7.0/include -I/<>/hyphy-2.3.14+dfsg/tests/gtests -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/<>/hyphy-2.3.14+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -msse3 -w -fopenmp=libomp -std=c++14 -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMP.dir/src/core/avllist.cpp.o -c /<>/hyphy-2.3.14+dfsg/src/core/avllist.cpp /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHY_64__ -D__MP2__ -D__MP__ -D__UNIX__ -I/<>/hyphy-2.3.14+dfsg/src/core/include -I/<>/hyphy-2.3.14+dfsg/src/lib/Link -I/<>/hyphy-2.3.14+dfsg/src/new/include -I/<>/hyphy-2.3.14+dfsg/contrib/gtest-1.7.0/include -I/<>/hyphy-2.3.14+dfsg/tests/gtests -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/<>/hyphy-2.3.14+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -msse3 -w -fopenmp=libomp -std=c++14 -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMP.dir/src/core/avllistx.cpp.o -c /<>/hyphy-2.3.14+dfsg/src/core/avllistx.cpp [ 8%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/avllistxl.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHY_64__ -D__MP2__ -D__MP__ -D__UNIX__ -I/<>/hyphy-2.3.14+dfsg/src/core/include -I/<>/hyphy-2.3.14+dfsg/src/lib/Link 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-I/<>/hyphy-2.3.14+dfsg/contrib/gtest-1.7.0/include -I/<>/hyphy-2.3.14+dfsg/tests/gtests -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/<>/hyphy-2.3.14+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -msse3 -w -fopenmp=libomp -std=c++14 -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMP.dir/src/core/nexus.cpp.o -c /<>/hyphy-2.3.14+dfsg/src/core/nexus.cpp [ 54%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/operation.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHY_64__ -D__MP2__ -D__MP__ -D__UNIX__ -I/<>/hyphy-2.3.14+dfsg/src/core/include -I/<>/hyphy-2.3.14+dfsg/src/lib/Link -I/<>/hyphy-2.3.14+dfsg/src/new/include -I/<>/hyphy-2.3.14+dfsg/contrib/gtest-1.7.0/include -I/<>/hyphy-2.3.14+dfsg/tests/gtests 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CMakeFiles/HYPHYMP.dir/src/core/sequence.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHY_64__ -D__MP2__ -D__MP__ -D__UNIX__ -I/<>/hyphy-2.3.14+dfsg/src/core/include -I/<>/hyphy-2.3.14+dfsg/src/lib/Link -I/<>/hyphy-2.3.14+dfsg/src/new/include -I/<>/hyphy-2.3.14+dfsg/contrib/gtest-1.7.0/include -I/<>/hyphy-2.3.14+dfsg/tests/gtests -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/<>/hyphy-2.3.14+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -msse3 -w -fopenmp=libomp -std=c++14 -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMP.dir/src/core/sequence.cpp.o -c /<>/hyphy-2.3.14+dfsg/src/core/sequence.cpp [ 66%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/simplelist.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHY_64__ -D__MP2__ -D__MP__ -D__UNIX__ -I/<>/hyphy-2.3.14+dfsg/src/core/include -I/<>/hyphy-2.3.14+dfsg/src/lib/Link -I/<>/hyphy-2.3.14+dfsg/src/new/include -I/<>/hyphy-2.3.14+dfsg/contrib/gtest-1.7.0/include -I/<>/hyphy-2.3.14+dfsg/tests/gtests -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/<>/hyphy-2.3.14+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -msse3 -w -fopenmp=libomp -std=c++14 -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMP.dir/src/core/simplelist.cpp.o -c /<>/hyphy-2.3.14+dfsg/src/core/simplelist.cpp [ 66%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/site.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHY_64__ -D__MP2__ -D__MP__ -D__UNIX__ -I/<>/hyphy-2.3.14+dfsg/src/core/include -I/<>/hyphy-2.3.14+dfsg/src/lib/Link -I/<>/hyphy-2.3.14+dfsg/src/new/include -I/<>/hyphy-2.3.14+dfsg/contrib/gtest-1.7.0/include -I/<>/hyphy-2.3.14+dfsg/tests/gtests -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/<>/hyphy-2.3.14+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -msse3 -w -fopenmp=libomp -std=c++14 -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMP.dir/src/core/site.cpp.o -c /<>/hyphy-2.3.14+dfsg/src/core/site.cpp [ 70%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/stack.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHY_64__ -D__MP2__ -D__MP__ -D__UNIX__ -I/<>/hyphy-2.3.14+dfsg/src/core/include -I/<>/hyphy-2.3.14+dfsg/src/lib/Link -I/<>/hyphy-2.3.14+dfsg/src/new/include -I/<>/hyphy-2.3.14+dfsg/contrib/gtest-1.7.0/include -I/<>/hyphy-2.3.14+dfsg/tests/gtests -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/<>/hyphy-2.3.14+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -msse3 -w -fopenmp=libomp -std=c++14 -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMP.dir/src/core/stack.cpp.o -c /<>/hyphy-2.3.14+dfsg/src/core/stack.cpp [ 70%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/string_file_wrapper.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHY_64__ -D__MP2__ -D__MP__ -D__UNIX__ -I/<>/hyphy-2.3.14+dfsg/src/core/include -I/<>/hyphy-2.3.14+dfsg/src/lib/Link -I/<>/hyphy-2.3.14+dfsg/src/new/include -I/<>/hyphy-2.3.14+dfsg/contrib/gtest-1.7.0/include -I/<>/hyphy-2.3.14+dfsg/tests/gtests -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/<>/hyphy-2.3.14+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -msse3 -w -fopenmp=libomp -std=c++14 -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMP.dir/src/core/string_file_wrapper.cpp.o -c /<>/hyphy-2.3.14+dfsg/src/core/string_file_wrapper.cpp [ 75%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/strings.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHY_64__ -D__MP2__ -D__MP__ -D__UNIX__ -I/<>/hyphy-2.3.14+dfsg/src/core/include -I/<>/hyphy-2.3.14+dfsg/src/lib/Link -I/<>/hyphy-2.3.14+dfsg/src/new/include -I/<>/hyphy-2.3.14+dfsg/contrib/gtest-1.7.0/include -I/<>/hyphy-2.3.14+dfsg/tests/gtests -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/<>/hyphy-2.3.14+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -msse3 -w -fopenmp=libomp -std=c++14 -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMP.dir/src/core/strings.cpp.o -c /<>/hyphy-2.3.14+dfsg/src/core/strings.cpp /<>/hyphy-2.3.14+dfsg/src/core/string_file_wrapper.cpp:51:27: error: format string is not a string literal (potentially insecure) [-Werror,-Wformat-security] fprintf (file_buffer, buffer); ^~~~~~ /<>/hyphy-2.3.14+dfsg/src/core/string_file_wrapper.cpp:51:27: note: treat the string as an argument to avoid this fprintf (file_buffer, buffer); ^ "%s", 1 error generated. make[5]: *** [CMakeFiles/HYPHYMP.dir/build.make:547: CMakeFiles/HYPHYMP.dir/src/core/string_file_wrapper.cpp.o] Error 1 make[5]: *** Waiting for unfinished jobs.... make[5]: Leaving directory '/<>/hyphy-2.3.14+dfsg/obj-x86_64-linux-gnu' make[4]: *** [CMakeFiles/Makefile2:140: CMakeFiles/HYPHYMP.dir/all] Error 2 make[4]: Leaving directory '/<>/hyphy-2.3.14+dfsg/obj-x86_64-linux-gnu' make[3]: *** [CMakeFiles/Makefile2:184: CMakeFiles/MP.dir/rule] Error 2 make[3]: Leaving directory '/<>/hyphy-2.3.14+dfsg/obj-x86_64-linux-gnu' make[2]: *** [Makefile:206: MP] Error 2 make[2]: Leaving directory '/<>/hyphy-2.3.14+dfsg/obj-x86_64-linux-gnu' dh_auto_build: cd obj-x86_64-linux-gnu && make -j4 "INSTALL=install --strip-program=true" MP MPI GTEST returned exit code 2 make[1]: *** [debian/rules:24: override_dh_auto_build] Error 2 make[1]: Leaving directory '/<>/hyphy-2.3.14+dfsg' make: *** [debian/rules:14: build-arch] Error 2 dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2019-01-09T21:30:40Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: any Build-Space: 46584 Build-Time: 21 Distribution: unstable Fail-Stage: build Host Architecture: amd64 Install-Time: 11 Job: hyphy_2.3.14+dfsg-1 Machine Architecture: amd64 Package: hyphy Package-Time: 48 Source-Version: 2.3.14+dfsg-1 Space: 46584 Status: attempted Version: 2.3.14+dfsg-1 -------------------------------------------------------------------------------- Finished at 2019-01-09T21:30:40Z Build needed 00:00:48, 46584k disk space E: Build failure (dpkg-buildpackage died) DC-Status: Failed 48.181185095s DC-Time-Estimation: 48.181185095 versus expected 279 (r/m: 4.790642124096554 ; m: 48.181185095)