DC-Build-Header: hyphy 2.5.1+dfsg-3 / 2020-02-25 15:37:54 +0000 DC-Task: type:rebuild-binarch-only source:hyphy version:2.5.1+dfsg-3 chroot:unstable esttime:215 logfile:/tmp/hyphy_2.5.1+dfsg-3_unstable_clang8.log modes:clang8:binarch-only DC-Sbuild-call: su user42 -c 'sbuild -n --arch-any --apt-update -d unstable -v --no-run-lintian --chroot-setup-commands=/tmp/clang8 hyphy_2.5.1+dfsg-3' sbuild (Debian sbuild) 0.78.1 (09 February 2019) on ip-172-31-4-163.eu-central-1.compute.internal +==============================================================================+ | hyphy 2.5.1+dfsg-3 (amd64) Tue, 25 Feb 2020 15:37:54 +0000 | +==============================================================================+ Package: hyphy Version: 2.5.1+dfsg-3 Source Version: 2.5.1+dfsg-3 Distribution: unstable Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: binary I: NOTICE: Log filtering will replace 'var/run/schroot/mount/sid-amd64-sbuild-a3f8ce9c-6fa9-4e14-92cd-4743617dd738' 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 + apt-get update Get:1 http://127.0.0.1:12990/debian sid InRelease [142 kB] Get:2 http://127.0.0.1:12990/debian sid/main Sources.diff/Index [27.9 kB] Get:3 http://127.0.0.1:12990/debian sid/main amd64 Packages.diff/Index [27.9 kB] Get:4 http://127.0.0.1:12990/debian sid/main Sources 2020-02-24-0823.32.pdiff [11.0 kB] Get:5 http://127.0.0.1:12990/debian sid/main Sources 2020-02-24-1420.34.pdiff [30.2 kB] Get:6 http://127.0.0.1:12990/debian sid/main Sources 2020-02-24-2014.03.pdiff [16.9 kB] Get:7 http://127.0.0.1:12990/debian sid/main Sources 2020-02-25-0213.11.pdiff [23.2 kB] Get:8 http://127.0.0.1:12990/debian sid/main Sources 2020-02-25-0815.22.pdiff [9222 B] Get:9 http://127.0.0.1:12990/debian sid/main Sources 2020-02-25-1413.15.pdiff [16.3 kB] Get:10 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-02-24-0823.32.pdiff [15.5 kB] Get:11 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-02-24-1420.34.pdiff [27.5 kB] Get:12 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-02-24-2014.03.pdiff [21.6 kB] Get:13 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-02-25-0213.11.pdiff [35.0 kB] Get:14 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-02-25-0815.22.pdiff [20.1 kB] Get:15 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-02-25-1413.15.pdiff [18.4 kB] Get:9 http://127.0.0.1:12990/debian sid/main Sources 2020-02-25-1413.15.pdiff [16.3 kB] Get:15 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-02-25-1413.15.pdiff [18.4 kB] Get:16 http://127.0.0.1:12990/debian sid/main Translation-en [6195 kB] Fetched 6638 kB in 2s (3723 kB/s) Reading package lists... + apt-get install --yes --no-install-recommends --force-yes clang-8 libomp-8-dev libobjc-9-dev Reading package lists... Building dependency tree... The following additional packages will be installed: cpp-9 g++-9 gcc-8-base gcc-9 gcc-9-base lib32gcc-s1 lib32gcc1 lib32stdc++6 libasan5 libbsd0 libc6-i386 libclang-common-8-dev libclang1-8 libedit2 libgc1c2 libgcc-8-dev libgcc-9-dev libllvm8 libmpx2 libobjc-8-dev libobjc4 libomp5-8 libstdc++-8-dev libstdc++-9-dev Suggested packages: clang-8-doc gcc-9-locales g++-9-multilib gcc-9-doc gcc-9-multilib libomp-8-doc libstdc++-8-doc libstdc++-9-doc Recommended packages: llvm-8-dev python3 The following NEW packages will be installed: clang-8 gcc-8-base lib32gcc-s1 lib32gcc1 lib32stdc++6 libbsd0 libc6-i386 libclang-common-8-dev libclang1-8 libedit2 libgc1c2 libgcc-8-dev libllvm8 libmpx2 libobjc-8-dev libobjc-9-dev libobjc4 libomp-8-dev libomp5-8 libstdc++-8-dev The following packages will be upgraded: cpp-9 g++-9 gcc-9 gcc-9-base libasan5 libgcc-9-dev libstdc++-9-dev 7 upgraded, 20 newly installed, 0 to remove and 3 not upgraded. Need to get 74.9 MB of archives. After this operation, 223 MB of additional disk space will be used. Get:1 http://127.0.0.1:12990/debian sid/main amd64 libasan5 amd64 9.2.1-30 [389 kB] Get:2 http://127.0.0.1:12990/debian sid/main amd64 g++-9 amd64 9.2.1-30 [10.7 MB] Get:3 http://127.0.0.1:12990/debian sid/main amd64 gcc-9 amd64 9.2.1-30 [10.0 MB] Get:4 http://127.0.0.1:12990/debian sid/main amd64 libstdc++-9-dev amd64 9.2.1-30 [1697 kB] Get:5 http://127.0.0.1:12990/debian sid/main amd64 libgcc-9-dev amd64 9.2.1-30 [2349 kB] Get:6 http://127.0.0.1:12990/debian sid/main amd64 cpp-9 amd64 9.2.1-30 [9711 kB] Get:7 http://127.0.0.1:12990/debian sid/main amd64 gcc-9-base amd64 9.2.1-30 [196 kB] Get:8 http://127.0.0.1:12990/debian sid/main amd64 libbsd0 amd64 0.10.0-1 [107 kB] Get:9 http://127.0.0.1:12990/debian sid/main amd64 libedit2 amd64 3.1-20191231-1 [95.4 kB] Get:10 http://127.0.0.1:12990/debian sid/main amd64 libllvm8 amd64 1:8.0.1-7 [13.8 MB] Get:11 http://127.0.0.1:12990/debian sid/main amd64 gcc-8-base amd64 8.3.0-29 [194 kB] Get:12 http://127.0.0.1:12990/debian sid/main amd64 libmpx2 amd64 8.3.0-29 [11.4 kB] Get:13 http://127.0.0.1:12990/debian sid/main amd64 libgcc-8-dev amd64 8.3.0-29 [2297 kB] Get:14 http://127.0.0.1:12990/debian sid/main amd64 libstdc++-8-dev amd64 8.3.0-29 [1543 kB] Get:15 http://127.0.0.1:12990/debian sid/main amd64 libgc1c2 amd64 1:7.6.4-0.4 [224 kB] Get:16 http://127.0.0.1:12990/debian sid/main amd64 libobjc4 amd64 10-20200222-1 [41.6 kB] Get:17 http://127.0.0.1:12990/debian sid/main amd64 libobjc-8-dev amd64 8.3.0-29 [227 kB] Get:18 http://127.0.0.1:12990/debian sid/main amd64 libc6-i386 amd64 2.29-10 [2918 kB] Get:19 http://127.0.0.1:12990/debian sid/main amd64 lib32gcc-s1 amd64 10-20200222-1 [49.4 kB] Get:20 http://127.0.0.1:12990/debian sid/main amd64 lib32gcc1 amd64 1:10-20200222-1 [1104 B] Get:21 http://127.0.0.1:12990/debian sid/main amd64 lib32stdc++6 amd64 10-20200222-1 [510 kB] Get:22 http://127.0.0.1:12990/debian sid/main amd64 libclang-common-8-dev amd64 1:8.0.1-7 [2989 kB] Get:23 http://127.0.0.1:12990/debian sid/main amd64 libclang1-8 amd64 1:8.0.1-7 [6244 kB] Get:24 http://127.0.0.1:12990/debian sid/main amd64 clang-8 amd64 1:8.0.1-7 [8010 kB] Get:25 http://127.0.0.1:12990/debian sid/main amd64 libobjc-9-dev amd64 9.2.1-30 [219 kB] Get:26 http://127.0.0.1:12990/debian sid/main amd64 libomp5-8 amd64 1:8.0.1-7 [331 kB] Get:27 http://127.0.0.1:12990/debian sid/main amd64 libomp-8-dev amd64 1:8.0.1-7 [62.3 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 74.9 MB in 1s (100 MB/s) (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 ... 12119 files and directories currently installed.) Preparing to unpack .../00-libasan5_9.2.1-30_amd64.deb ... Unpacking libasan5:amd64 (9.2.1-30) over (9.2.1-29) ... Preparing to unpack .../01-g++-9_9.2.1-30_amd64.deb ... Unpacking g++-9 (9.2.1-30) over (9.2.1-29) ... Preparing to unpack .../02-gcc-9_9.2.1-30_amd64.deb ... Unpacking gcc-9 (9.2.1-30) over (9.2.1-29) ... Preparing to unpack .../03-libstdc++-9-dev_9.2.1-30_amd64.deb ... Unpacking libstdc++-9-dev:amd64 (9.2.1-30) over (9.2.1-29) ... Preparing to unpack .../04-libgcc-9-dev_9.2.1-30_amd64.deb ... Unpacking libgcc-9-dev:amd64 (9.2.1-30) over (9.2.1-29) ... Preparing to unpack .../05-cpp-9_9.2.1-30_amd64.deb ... Unpacking cpp-9 (9.2.1-30) over (9.2.1-29) ... Preparing to unpack .../06-gcc-9-base_9.2.1-30_amd64.deb ... Unpacking gcc-9-base:amd64 (9.2.1-30) over (9.2.1-29) ... Selecting previously unselected package libbsd0:amd64. Preparing to unpack .../07-libbsd0_0.10.0-1_amd64.deb ... Unpacking libbsd0:amd64 (0.10.0-1) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../08-libedit2_3.1-20191231-1_amd64.deb ... Unpacking libedit2:amd64 (3.1-20191231-1) ... Selecting previously unselected package libllvm8:amd64. Preparing to unpack .../09-libllvm8_1%3a8.0.1-7_amd64.deb ... Unpacking libllvm8:amd64 (1:8.0.1-7) ... Selecting previously unselected package gcc-8-base:amd64. Preparing to unpack .../10-gcc-8-base_8.3.0-29_amd64.deb ... Unpacking gcc-8-base:amd64 (8.3.0-29) ... Selecting previously unselected package libmpx2:amd64. Preparing to unpack .../11-libmpx2_8.3.0-29_amd64.deb ... Unpacking libmpx2:amd64 (8.3.0-29) ... Selecting previously unselected package libgcc-8-dev:amd64. Preparing to unpack .../12-libgcc-8-dev_8.3.0-29_amd64.deb ... Unpacking libgcc-8-dev:amd64 (8.3.0-29) ... Selecting previously unselected package libstdc++-8-dev:amd64. Preparing to unpack .../13-libstdc++-8-dev_8.3.0-29_amd64.deb ... Unpacking libstdc++-8-dev:amd64 (8.3.0-29) ... Selecting previously unselected package libgc1c2:amd64. Preparing to unpack .../14-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 .../15-libobjc4_10-20200222-1_amd64.deb ... Unpacking libobjc4:amd64 (10-20200222-1) ... Selecting previously unselected package libobjc-8-dev:amd64. Preparing to unpack .../16-libobjc-8-dev_8.3.0-29_amd64.deb ... Unpacking libobjc-8-dev:amd64 (8.3.0-29) ... Selecting previously unselected package libc6-i386. Preparing to unpack .../17-libc6-i386_2.29-10_amd64.deb ... Unpacking libc6-i386 (2.29-10) ... Selecting previously unselected package lib32gcc-s1. Preparing to unpack .../18-lib32gcc-s1_10-20200222-1_amd64.deb ... Unpacking lib32gcc-s1 (10-20200222-1) ... Selecting previously unselected package lib32gcc1. Preparing to unpack .../19-lib32gcc1_1%3a10-20200222-1_amd64.deb ... Unpacking lib32gcc1 (1:10-20200222-1) ... Selecting previously unselected package lib32stdc++6. Preparing to unpack .../20-lib32stdc++6_10-20200222-1_amd64.deb ... Unpacking lib32stdc++6 (10-20200222-1) ... Selecting previously unselected package libclang-common-8-dev. Preparing to unpack .../21-libclang-common-8-dev_1%3a8.0.1-7_amd64.deb ... Unpacking libclang-common-8-dev (1:8.0.1-7) ... Selecting previously unselected package libclang1-8. Preparing to unpack .../22-libclang1-8_1%3a8.0.1-7_amd64.deb ... Unpacking libclang1-8 (1:8.0.1-7) ... Selecting previously unselected package clang-8. Preparing to unpack .../23-clang-8_1%3a8.0.1-7_amd64.deb ... Unpacking clang-8 (1:8.0.1-7) ... Selecting previously unselected package libobjc-9-dev:amd64. Preparing to unpack .../24-libobjc-9-dev_9.2.1-30_amd64.deb ... Unpacking libobjc-9-dev:amd64 (9.2.1-30) ... Selecting previously unselected package libomp5-8:amd64. Preparing to unpack .../25-libomp5-8_1%3a8.0.1-7_amd64.deb ... Unpacking libomp5-8:amd64 (1:8.0.1-7) ... Selecting previously unselected package libomp-8-dev. Preparing to unpack .../26-libomp-8-dev_1%3a8.0.1-7_amd64.deb ... Unpacking libomp-8-dev (1:8.0.1-7) ... Setting up libgc1c2:amd64 (1:7.6.4-0.4) ... Setting up libobjc4:amd64 (10-20200222-1) ... Setting up gcc-8-base:amd64 (8.3.0-29) ... Setting up libmpx2:amd64 (8.3.0-29) ... Setting up libc6-i386 (2.29-10) ... Setting up libbsd0:amd64 (0.10.0-1) ... Setting up libomp5-8:amd64 (1:8.0.1-7) ... Setting up libomp-8-dev (1:8.0.1-7) ... Setting up gcc-9-base:amd64 (9.2.1-30) ... Setting up libedit2:amd64 (3.1-20191231-1) ... Setting up libasan5:amd64 (9.2.1-30) ... Setting up lib32gcc-s1 (10-20200222-1) ... Setting up libgcc-8-dev:amd64 (8.3.0-29) ... Setting up cpp-9 (9.2.1-30) ... Setting up libstdc++-8-dev:amd64 (8.3.0-29) ... Setting up libllvm8:amd64 (1:8.0.1-7) ... Setting up libclang1-8 (1:8.0.1-7) ... Setting up lib32gcc1 (1:10-20200222-1) ... Setting up libgcc-9-dev:amd64 (9.2.1-30) ... Setting up libobjc-8-dev:amd64 (8.3.0-29) ... Setting up lib32stdc++6 (10-20200222-1) ... Setting up libobjc-9-dev:amd64 (9.2.1-30) ... Setting up gcc-9 (9.2.1-30) ... Setting up libstdc++-9-dev:amd64 (9.2.1-30) ... Setting up libclang-common-8-dev (1:8.0.1-7) ... Setting up g++-9 (9.2.1-30) ... Setting up clang-8 (1:8.0.1-7) ... Processing triggers for libc-bin (2.29-10) ... 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 9 10' + 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 dpkg: warning: package not in status nor available database at line 1: gcc-8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-8 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-9 gcc-9 cpp-9 gcc + ln -s clang++-8 g++-9 + ln -s clang-8 gcc-9 + ln -s clang-8 cpp-9 + ln -s clang-8 gcc + echo 'gcc-9 hold' + dpkg --set-selections + echo 'g++-9 hold' + dpkg --set-selections + for VERSION in $VERSIONS + rm -f g++-10 gcc-10 cpp-10 gcc + ln -s clang++-8 g++-10 + ln -s clang-8 gcc-10 + ln -s clang-8 cpp-10 + ln -s clang-8 gcc + echo 'gcc-10 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-10 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++-10 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-10 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + cd - /build/hyphy-mc01OI + 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. -------------------------------------------------------------------------------- I: NOTICE: Log filtering will replace 'build/hyphy-mc01OI/resolver-lbKcXv' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Hit:1 http://127.0.0.1:12990/debian sid InRelease Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: bash libgmp10 zlib1g 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 1722 kB of archives. After this operation, 4096 B of additional disk space will be used. Get:1 http://127.0.0.1:12990/debian sid/main amd64 bash amd64 5.0-6 [1379 kB] Get:2 http://127.0.0.1:12990/debian sid/main amd64 libgmp10 amd64 2:6.2.0+dfsg-4 [253 kB] Get:3 http://127.0.0.1:12990/debian sid/main amd64 zlib1g amd64 1:1.2.11.dfsg-2 [90.4 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 1722 kB in 0s (72.5 MB/s) (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 ... 13887 files and directories currently installed.) Preparing to unpack .../archives/bash_5.0-6_amd64.deb ... Unpacking bash (5.0-6) over (5.0-5) ... Setting up bash (5.0-6) ... update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode (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 ... 13887 files and directories currently installed.) Preparing to unpack .../libgmp10_2%3a6.2.0+dfsg-4_amd64.deb ... Unpacking libgmp10:amd64 (2:6.2.0+dfsg-4) over (2:6.2.0+dfsg-3) ... Setting up libgmp10:amd64 (2:6.2.0+dfsg-4) ... (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 ... 13887 files and directories currently installed.) Preparing to unpack .../zlib1g_1%3a1.2.11.dfsg-2_amd64.deb ... Unpacking zlib1g:amd64 (1:1.2.11.dfsg-2) over (1:1.2.11.dfsg-1.2) ... Setting up zlib1g:amd64 (1:1.2.11.dfsg-2) ... Processing triggers for libc-bin (2.29-10) ... +------------------------------------------------------------------------------+ | 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 2912 kB of source archives. Get:1 http://127.0.0.1:12990/debian sid/main hyphy 2.5.1+dfsg-3 (dsc) [2171 B] Get:2 http://127.0.0.1:12990/debian sid/main hyphy 2.5.1+dfsg-3 (tar) [2899 kB] Get:3 http://127.0.0.1:12990/debian sid/main hyphy 2.5.1+dfsg-3 (diff) [10.4 kB] Fetched 2912 kB in 0s (22.0 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/hyphy-mc01OI/hyphy-2.5.1+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/hyphy-mc01OI' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 12), cmake, mpi-default-dev, libcurl4-gnutls-dev | libcurl4-dev, libssl-dev, libsqlite3-dev, pkg-config, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 12), cmake, mpi-default-dev, libcurl4-gnutls-dev, libssl-dev, libsqlite3-dev, pkg-config, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [421 B] Get:5 copy:/<>/apt_archive ./ Packages [498 B] Fetched 1876 B in 0s (0 B/s) Reading package lists... Reading package lists... Install main 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 gfortran-9 groff-base ibverbs-providers intltool-debian libarchive-zip-perl libarchive13 libbrotli1 libcbor0 libcroco3 libcurl3-gnutls libcurl4 libcurl4-gnutls-dev libdebhelper-perl libelf1 libevent-2.1-7 libevent-core-2.1-7 libevent-dev libevent-extra-2.1-7 libevent-openssl-2.1-7 libevent-pthreads-2.1-7 libexpat1 libfabric1 libfido2-1 libfile-stripnondeterminism-perl libgfortran-9-dev libgfortran5 libglib2.0-0 libgssapi-krb5-2 libhwloc-dev libhwloc-plugins libhwloc15 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 libprocps8 libpsl5 libpsm-infinipath1 libpsm2-2 librdmacm1 librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsqlite3-0 libsqlite3-dev libssh2-1 libssl-dev libssl1.1 libsub-override-perl libtool libuchardet0 libuv1 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxnvctrl0 m4 man-db mpi-default-dev ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client pkg-config 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 gfortran-9-multilib gfortran-9-doc libcoarrays-dev groff lrzip libcurl4-doc libgnutls28-dev libidn11-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev zlib1g-dev krb5-doc krb5-user libhwloc-contrib-plugins libtool-doc openmpi-doc pciutils sqlite3-doc libssl-doc gcj-jdk m4-doc apparmor less www-browser opencl-icd gfortran | fortran-compiler 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 gfortran-9 groff-base ibverbs-providers intltool-debian libarchive-zip-perl libarchive13 libbrotli1 libcbor0 libcroco3 libcurl3-gnutls libcurl4 libcurl4-gnutls-dev libdebhelper-perl libelf1 libevent-2.1-7 libevent-core-2.1-7 libevent-dev libevent-extra-2.1-7 libevent-openssl-2.1-7 libevent-pthreads-2.1-7 libexpat1 libfabric1 libfido2-1 libfile-stripnondeterminism-perl libgfortran-9-dev libgfortran5 libglib2.0-0 libgssapi-krb5-2 libhwloc-dev libhwloc-plugins libhwloc15 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 libprocps8 libpsl5 libpsm-infinipath1 libpsm2-2 librdmacm1 librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsqlite3-0 libsqlite3-dev libssh2-1 libssl-dev libssl1.1 libsub-override-perl libtool libuchardet0 libuv1 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxnvctrl0 m4 man-db mpi-default-dev ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client pkg-config po-debconf procps sbuild-build-depends-main-dummy sensible-utils 0 upgraded, 111 newly installed, 0 to remove and 0 not upgraded. Need to get 55.2 MB of archives. After this operation, 200 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [928 B] Get:2 http://127.0.0.1:12990/debian sid/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get:3 http://127.0.0.1:12990/debian sid/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get:4 http://127.0.0.1:12990/debian sid/main amd64 groff-base amd64 1.22.4-4 [919 kB] Get:5 http://127.0.0.1:12990/debian sid/main amd64 libpipeline1 amd64 1.5.2-2 [33.9 kB] Get:6 http://127.0.0.1:12990/debian sid/main amd64 man-db amd64 2.9.0-2 [1307 kB] Get:7 http://127.0.0.1:12990/debian sid/main amd64 libncurses6 amd64 6.1+20191019-1 [102 kB] Get:8 http://127.0.0.1:12990/debian sid/main amd64 libprocps8 amd64 2:3.3.16-1+b1 [62.8 kB] Get:9 http://127.0.0.1:12990/debian sid/main amd64 procps amd64 2:3.3.16-1+b1 [263 kB] Get:10 http://127.0.0.1:12990/debian sid/main amd64 sensible-utils all 0.0.12+nmu1 [16.0 kB] Get:11 http://127.0.0.1:12990/debian sid/main amd64 libmagic-mgc amd64 1:5.38-4 [262 kB] Get:12 http://127.0.0.1:12990/debian sid/main amd64 libmagic1 amd64 1:5.38-4 [120 kB] Get:13 http://127.0.0.1:12990/debian sid/main amd64 file amd64 1:5.38-4 [67.9 kB] Get:14 http://127.0.0.1:12990/debian sid/main amd64 gettext-base amd64 0.19.8.1-10 [123 kB] Get:15 http://127.0.0.1:12990/debian sid/main amd64 libcbor0 amd64 0.5.0+dfsg-2 [24.0 kB] Get:16 http://127.0.0.1:12990/debian sid/main amd64 libssl1.1 amd64 1.1.1d-2 [1540 kB] Get:17 http://127.0.0.1:12990/debian sid/main amd64 libfido2-1 amd64 1.3.1-1 [47.4 kB] Get:18 http://127.0.0.1:12990/debian sid/main amd64 libkeyutils1 amd64 1.6.1-2 [15.4 kB] Get:19 http://127.0.0.1:12990/debian sid/main amd64 libkrb5support0 amd64 1.17-6 [64.6 kB] Get:20 http://127.0.0.1:12990/debian sid/main amd64 libk5crypto3 amd64 1.17-6 [116 kB] Get:21 http://127.0.0.1:12990/debian sid/main amd64 libkrb5-3 amd64 1.17-6 [366 kB] Get:22 http://127.0.0.1:12990/debian sid/main amd64 libgssapi-krb5-2 amd64 1.17-6 [156 kB] Get:23 http://127.0.0.1:12990/debian sid/main amd64 openssh-client amd64 1:8.2p1-3 [906 kB] Get:24 http://127.0.0.1:12990/debian sid/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get:25 http://127.0.0.1:12990/debian sid/main amd64 m4 amd64 1.4.18-4 [203 kB] Get:26 http://127.0.0.1:12990/debian sid/main amd64 autoconf all 2.69-11.1 [341 kB] Get:27 http://127.0.0.1:12990/debian sid/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get:28 http://127.0.0.1:12990/debian sid/main amd64 automake all 1:1.16.1-4 [771 kB] Get:29 http://127.0.0.1:12990/debian sid/main amd64 autopoint all 0.19.8.1-10 [435 kB] Get:30 http://127.0.0.1:12990/debian sid/main amd64 cmake-data all 3.16.3-1 [1628 kB] Get:31 http://127.0.0.1:12990/debian sid/main amd64 libicu63 amd64 63.2-2 [8301 kB] Get:32 http://127.0.0.1:12990/debian sid/main amd64 libxml2 amd64 2.9.10+dfsg-3 [709 kB] Get:33 http://127.0.0.1:12990/debian sid/main amd64 libarchive13 amd64 3.4.0-1+b1 [335 kB] Get:34 http://127.0.0.1:12990/debian sid/main amd64 libbrotli1 amd64 1.0.7-6 [266 kB] Get:35 http://127.0.0.1:12990/debian sid/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-2 [69.0 kB] Get:36 http://127.0.0.1:12990/debian sid/main amd64 libsasl2-2 amd64 2.1.27+dfsg-2 [106 kB] Get:37 http://127.0.0.1:12990/debian sid/main amd64 libldap-common all 2.4.49+dfsg-1 [91.9 kB] Get:38 http://127.0.0.1:12990/debian sid/main amd64 libldap-2.4-2 amd64 2.4.49+dfsg-1 [226 kB] Get:39 http://127.0.0.1:12990/debian sid/main amd64 libnghttp2-14 amd64 1.40.0-1 [85.0 kB] Get:40 http://127.0.0.1:12990/debian sid/main amd64 libpsl5 amd64 0.20.2-2 [53.7 kB] Get:41 http://127.0.0.1:12990/debian sid/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b1 [60.8 kB] Get:42 http://127.0.0.1:12990/debian sid/main amd64 libssh2-1 amd64 1.8.0-2.1 [140 kB] Get:43 http://127.0.0.1:12990/debian sid/main amd64 libcurl4 amd64 7.68.0-1 [321 kB] Get:44 http://127.0.0.1:12990/debian sid/main amd64 libexpat1 amd64 2.2.9-1 [94.3 kB] Get:45 http://127.0.0.1:12990/debian sid/main amd64 libjsoncpp1 amd64 1.7.4-3.1 [77.6 kB] Get:46 http://127.0.0.1:12990/debian sid/main amd64 librhash0 amd64 1.3.9-1 [123 kB] Get:47 http://127.0.0.1:12990/debian sid/main amd64 libuv1 amd64 1.34.2-1 [127 kB] Get:48 http://127.0.0.1:12990/debian sid/main amd64 cmake amd64 3.16.3-1 [3673 kB] Get:49 http://127.0.0.1:12990/debian sid/main amd64 libtool all 2.4.6-13 [513 kB] Get:50 http://127.0.0.1:12990/debian sid/main amd64 dh-autoreconf all 19 [16.9 kB] Get:51 http://127.0.0.1:12990/debian sid/main amd64 libdebhelper-perl all 12.9 [183 kB] Get:52 http://127.0.0.1:12990/debian sid/main amd64 libarchive-zip-perl all 1.67-1 [104 kB] Get:53 http://127.0.0.1:12990/debian sid/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get:54 http://127.0.0.1:12990/debian sid/main amd64 libfile-stripnondeterminism-perl all 1.6.3-2 [23.7 kB] Get:55 http://127.0.0.1:12990/debian sid/main amd64 dh-strip-nondeterminism all 1.6.3-2 [14.7 kB] Get:56 http://127.0.0.1:12990/debian sid/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get:57 http://127.0.0.1:12990/debian sid/main amd64 dwz amd64 0.13-5 [151 kB] Get:58 http://127.0.0.1:12990/debian sid/main amd64 libglib2.0-0 amd64 2.62.4-2 [1319 kB] Get:59 http://127.0.0.1:12990/debian sid/main amd64 libcroco3 amd64 0.6.13-1 [146 kB] Get:60 http://127.0.0.1:12990/debian sid/main amd64 gettext amd64 0.19.8.1-10 [1303 kB] Get:61 http://127.0.0.1:12990/debian sid/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:62 http://127.0.0.1:12990/debian sid/main amd64 po-debconf all 1.0.21 [248 kB] Get:63 http://127.0.0.1:12990/debian sid/main amd64 debhelper all 12.9 [994 kB] Get:64 http://127.0.0.1:12990/debian sid/main amd64 libgfortran5 amd64 10-20200222-1 [721 kB] Get:65 http://127.0.0.1:12990/debian sid/main amd64 libgfortran-9-dev amd64 9.2.1-30 [676 kB] Get:66 http://127.0.0.1:12990/debian sid/main amd64 gfortran-9 amd64 9.2.1-30 [10.4 MB] Get:67 http://127.0.0.1:12990/debian sid/main amd64 libnl-3-200 amd64 3.4.0-1+b1 [63.6 kB] Get:68 http://127.0.0.1:12990/debian sid/main amd64 libnl-route-3-200 amd64 3.4.0-1+b1 [161 kB] Get:69 http://127.0.0.1:12990/debian sid/main amd64 libibverbs1 amd64 28.0-1 [54.5 kB] Get:70 http://127.0.0.1:12990/debian sid/main amd64 ibverbs-providers amd64 28.0-1 [234 kB] Get:71 http://127.0.0.1:12990/debian sid/main amd64 libcurl3-gnutls amd64 7.68.0-1 [319 kB] Get:72 http://127.0.0.1:12990/debian sid/main amd64 libcurl4-gnutls-dev amd64 7.68.0-1 [408 kB] Get:73 http://127.0.0.1:12990/debian sid/main amd64 libevent-2.1-7 amd64 2.1.11-stable-1 [186 kB] Get:74 http://127.0.0.1:12990/debian sid/main amd64 libevent-core-2.1-7 amd64 2.1.11-stable-1 [137 kB] Get:75 http://127.0.0.1:12990/debian sid/main amd64 libevent-extra-2.1-7 amd64 2.1.11-stable-1 [108 kB] Get:76 http://127.0.0.1:12990/debian sid/main amd64 libevent-pthreads-2.1-7 amd64 2.1.11-stable-1 [55.1 kB] Get:77 http://127.0.0.1:12990/debian sid/main amd64 libevent-openssl-2.1-7 amd64 2.1.11-stable-1 [62.0 kB] Get:78 http://127.0.0.1:12990/debian sid/main amd64 libevent-dev amd64 2.1.11-stable-1 [309 kB] Get:79 http://127.0.0.1:12990/debian sid/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6+b1 [169 kB] Get:80 http://127.0.0.1:12990/debian sid/main amd64 libnuma1 amd64 2.0.12-1+b1 [26.3 kB] Get:81 http://127.0.0.1:12990/debian sid/main amd64 libpsm2-2 amd64 11.2.86-1 [177 kB] Get:82 http://127.0.0.1:12990/debian sid/main amd64 librdmacm1 amd64 28.0-1 [67.1 kB] Get:83 http://127.0.0.1:12990/debian sid/main amd64 libfabric1 amd64 1.6.2-3+b1 [397 kB] Get:84 http://127.0.0.1:12990/debian sid/main amd64 libltdl7 amd64 2.4.6-13 [390 kB] Get:85 http://127.0.0.1:12990/debian sid/main amd64 libhwloc15 amd64 2.1.0+dfsg-3 [139 kB] Get:86 http://127.0.0.1:12990/debian sid/main amd64 libnuma-dev amd64 2.0.12-1+b1 [39.3 kB] Get:87 http://127.0.0.1:12990/debian sid/main amd64 libltdl-dev amd64 2.4.6-13 [162 kB] Get:88 http://127.0.0.1:12990/debian sid/main amd64 libhwloc-dev amd64 2.1.0+dfsg-3 [210 kB] Get:89 http://127.0.0.1:12990/debian sid/main amd64 libpciaccess0 amd64 0.14-1 [53.5 kB] Get:90 http://127.0.0.1:12990/debian sid/main amd64 libxau6 amd64 1:1.0.8-1+b2 [19.9 kB] Get:91 http://127.0.0.1:12990/debian sid/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:92 http://127.0.0.1:12990/debian sid/main amd64 libxcb1 amd64 1.13.1-5 [137 kB] Get:93 http://127.0.0.1:12990/debian sid/main amd64 libx11-data all 2:1.6.8-1 [298 kB] Get:94 http://127.0.0.1:12990/debian sid/main amd64 libx11-6 amd64 2:1.6.8-1 [756 kB] Get:95 http://127.0.0.1:12990/debian sid/main amd64 libxext6 amd64 2:1.3.3-1+b2 [52.5 kB] Get:96 http://127.0.0.1:12990/debian sid/main amd64 libxnvctrl0 amd64 440.59-1 [26.2 kB] Get:97 http://127.0.0.1:12990/debian sid/main amd64 ocl-icd-libopencl1 amd64 2.2.12-3 [37.7 kB] Get:98 http://127.0.0.1:12990/debian sid/main amd64 libhwloc-plugins amd64 2.1.0+dfsg-3 [19.9 kB] Get:99 http://127.0.0.1:12990/debian sid/main amd64 libnl-3-dev amd64 3.4.0-1+b1 [102 kB] Get:100 http://127.0.0.1:12990/debian sid/main amd64 libnl-route-3-dev amd64 3.4.0-1+b1 [176 kB] Get:101 http://127.0.0.1:12990/debian sid/main amd64 libibverbs-dev amd64 28.0-1 [444 kB] Get:102 http://127.0.0.1:12990/debian sid/main amd64 libpmix2 amd64 3.1.4-1+b1 [431 kB] Get:103 http://127.0.0.1:12990/debian sid/main amd64 libopenmpi3 amd64 4.0.2-5 [1993 kB] Get:104 http://127.0.0.1:12990/debian sid/main amd64 openmpi-common all 4.0.2-5 [169 kB] Get:105 http://127.0.0.1:12990/debian sid/main amd64 openmpi-bin amd64 4.0.2-5 [186 kB] Get:106 http://127.0.0.1:12990/debian sid/main amd64 libopenmpi-dev amd64 4.0.2-5 [915 kB] Get:107 http://127.0.0.1:12990/debian sid/main amd64 libsqlite3-0 amd64 3.31.1-3 [661 kB] Get:108 http://127.0.0.1:12990/debian sid/main amd64 libsqlite3-dev amd64 3.31.1-3 [810 kB] Get:109 http://127.0.0.1:12990/debian sid/main amd64 libssl-dev amd64 1.1.1d-2 [1797 kB] Get:110 http://127.0.0.1:12990/debian sid/main amd64 mpi-default-dev amd64 1.13 [5476 B] Get:111 http://127.0.0.1:12990/debian sid/main amd64 pkg-config amd64 0.29-6 [63.5 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 55.2 MB in 1s (96.8 MB/s) Selecting previously unselected package bsdmainutils. (Reading database ... 13887 files and directories currently installed.) Preparing to unpack .../000-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../001-libuchardet0_0.0.6-3_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../002-groff-base_1.22.4-4_amd64.deb ... Unpacking groff-base (1.22.4-4) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../003-libpipeline1_1.5.2-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.2-2) ... Selecting previously unselected package man-db. Preparing to unpack .../004-man-db_2.9.0-2_amd64.deb ... Unpacking man-db (2.9.0-2) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../005-libncurses6_6.1+20191019-1_amd64.deb ... Unpacking libncurses6:amd64 (6.1+20191019-1) ... Selecting previously unselected package libprocps8:amd64. Preparing to unpack .../006-libprocps8_2%3a3.3.16-1+b1_amd64.deb ... Unpacking libprocps8:amd64 (2:3.3.16-1+b1) ... Selecting previously unselected package procps. Preparing to unpack .../007-procps_2%3a3.3.16-1+b1_amd64.deb ... Unpacking procps (2:3.3.16-1+b1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../008-sensible-utils_0.0.12+nmu1_all.deb ... Unpacking sensible-utils (0.0.12+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../009-libmagic-mgc_1%3a5.38-4_amd64.deb ... Unpacking libmagic-mgc (1:5.38-4) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../010-libmagic1_1%3a5.38-4_amd64.deb ... Unpacking libmagic1:amd64 (1:5.38-4) ... Selecting previously unselected package file. Preparing to unpack .../011-file_1%3a5.38-4_amd64.deb ... Unpacking file (1:5.38-4) ... Selecting previously unselected package gettext-base. Preparing to unpack .../012-gettext-base_0.19.8.1-10_amd64.deb ... Unpacking gettext-base (0.19.8.1-10) ... Selecting previously unselected package libcbor0:amd64. Preparing to unpack .../013-libcbor0_0.5.0+dfsg-2_amd64.deb ... Unpacking libcbor0:amd64 (0.5.0+dfsg-2) ... Selecting previously unselected package libssl1.1:amd64. Preparing to unpack .../014-libssl1.1_1.1.1d-2_amd64.deb ... Unpacking libssl1.1:amd64 (1.1.1d-2) ... Selecting previously unselected package libfido2-1:amd64. Preparing to unpack .../015-libfido2-1_1.3.1-1_amd64.deb ... Unpacking libfido2-1:amd64 (1.3.1-1) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../016-libkeyutils1_1.6.1-2_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.1-2) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../017-libkrb5support0_1.17-6_amd64.deb ... Unpacking libkrb5support0:amd64 (1.17-6) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../018-libk5crypto3_1.17-6_amd64.deb ... Unpacking libk5crypto3:amd64 (1.17-6) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../019-libkrb5-3_1.17-6_amd64.deb ... Unpacking libkrb5-3:amd64 (1.17-6) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../020-libgssapi-krb5-2_1.17-6_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.17-6) ... Selecting previously unselected package openssh-client. Preparing to unpack .../021-openssh-client_1%3a8.2p1-3_amd64.deb ... Unpacking openssh-client (1:8.2p1-3) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../022-libsigsegv2_2.12-2_amd64.deb ... Unpacking libsigsegv2:amd64 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../023-m4_1.4.18-4_amd64.deb ... Unpacking m4 (1.4.18-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../024-autoconf_2.69-11.1_all.deb ... Unpacking autoconf (2.69-11.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../025-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../026-automake_1%3a1.16.1-4_all.deb ... Unpacking automake (1:1.16.1-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../027-autopoint_0.19.8.1-10_all.deb ... Unpacking autopoint (0.19.8.1-10) ... Selecting previously unselected package cmake-data. Preparing to unpack .../028-cmake-data_3.16.3-1_all.deb ... Unpacking cmake-data (3.16.3-1) ... Selecting previously unselected package libicu63:amd64. Preparing to unpack .../029-libicu63_63.2-2_amd64.deb ... Unpacking libicu63:amd64 (63.2-2) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../030-libxml2_2.9.10+dfsg-3_amd64.deb ... Unpacking libxml2:amd64 (2.9.10+dfsg-3) ... Selecting previously unselected package libarchive13:amd64. Preparing to unpack .../031-libarchive13_3.4.0-1+b1_amd64.deb ... Unpacking libarchive13:amd64 (3.4.0-1+b1) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../032-libbrotli1_1.0.7-6_amd64.deb ... Unpacking libbrotli1:amd64 (1.0.7-6) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../033-libsasl2-modules-db_2.1.27+dfsg-2_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.27+dfsg-2) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../034-libsasl2-2_2.1.27+dfsg-2_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.27+dfsg-2) ... Selecting previously unselected package libldap-common. Preparing to unpack .../035-libldap-common_2.4.49+dfsg-1_all.deb ... Unpacking libldap-common (2.4.49+dfsg-1) ... Selecting previously unselected package libldap-2.4-2:amd64. Preparing to unpack .../036-libldap-2.4-2_2.4.49+dfsg-1_amd64.deb ... Unpacking libldap-2.4-2:amd64 (2.4.49+dfsg-1) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../037-libnghttp2-14_1.40.0-1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.40.0-1) ... Selecting previously unselected package libpsl5:amd64. Preparing to unpack .../038-libpsl5_0.20.2-2_amd64.deb ... Unpacking libpsl5:amd64 (0.20.2-2) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../039-librtmp1_2.4+20151223.gitfa8646d.1-2+b1_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b1) ... Selecting previously unselected package libssh2-1:amd64. Preparing to unpack .../040-libssh2-1_1.8.0-2.1_amd64.deb ... Unpacking libssh2-1:amd64 (1.8.0-2.1) ... Selecting previously unselected package libcurl4:amd64. Preparing to unpack .../041-libcurl4_7.68.0-1_amd64.deb ... Unpacking libcurl4:amd64 (7.68.0-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../042-libexpat1_2.2.9-1_amd64.deb ... Unpacking libexpat1:amd64 (2.2.9-1) ... Selecting previously unselected package libjsoncpp1:amd64. Preparing to unpack .../043-libjsoncpp1_1.7.4-3.1_amd64.deb ... Unpacking libjsoncpp1:amd64 (1.7.4-3.1) ... Selecting previously unselected package librhash0:amd64. Preparing to unpack .../044-librhash0_1.3.9-1_amd64.deb ... Unpacking librhash0:amd64 (1.3.9-1) ... Selecting previously unselected package libuv1:amd64. Preparing to unpack .../045-libuv1_1.34.2-1_amd64.deb ... Unpacking libuv1:amd64 (1.34.2-1) ... Selecting previously unselected package cmake. Preparing to unpack .../046-cmake_3.16.3-1_amd64.deb ... Unpacking cmake (3.16.3-1) ... Selecting previously unselected package libtool. Preparing to unpack .../047-libtool_2.4.6-13_all.deb ... Unpacking libtool (2.4.6-13) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../048-dh-autoreconf_19_all.deb ... Unpacking dh-autoreconf (19) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../049-libdebhelper-perl_12.9_all.deb ... Unpacking libdebhelper-perl (12.9) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../050-libarchive-zip-perl_1.67-1_all.deb ... Unpacking libarchive-zip-perl (1.67-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../051-libsub-override-perl_0.09-2_all.deb ... Unpacking libsub-override-perl (0.09-2) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../052-libfile-stripnondeterminism-perl_1.6.3-2_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.6.3-2) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../053-dh-strip-nondeterminism_1.6.3-2_all.deb ... Unpacking dh-strip-nondeterminism (1.6.3-2) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../054-libelf1_0.176-1.1_amd64.deb ... Unpacking libelf1:amd64 (0.176-1.1) ... Selecting previously unselected package dwz. Preparing to unpack .../055-dwz_0.13-5_amd64.deb ... Unpacking dwz (0.13-5) ... Selecting previously unselected package libglib2.0-0:amd64. Preparing to unpack .../056-libglib2.0-0_2.62.4-2_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.62.4-2) ... Selecting previously unselected package libcroco3:amd64. Preparing to unpack .../057-libcroco3_0.6.13-1_amd64.deb ... Unpacking libcroco3:amd64 (0.6.13-1) ... Selecting previously unselected package gettext. Preparing to unpack .../058-gettext_0.19.8.1-10_amd64.deb ... Unpacking gettext (0.19.8.1-10) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../059-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../060-po-debconf_1.0.21_all.deb ... Unpacking po-debconf (1.0.21) ... Selecting previously unselected package debhelper. Preparing to unpack .../061-debhelper_12.9_all.deb ... Unpacking debhelper (12.9) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../062-libgfortran5_10-20200222-1_amd64.deb ... Unpacking libgfortran5:amd64 (10-20200222-1) ... Selecting previously unselected package libgfortran-9-dev:amd64. Preparing to unpack .../063-libgfortran-9-dev_9.2.1-30_amd64.deb ... Unpacking libgfortran-9-dev:amd64 (9.2.1-30) ... Selecting previously unselected package gfortran-9. Preparing to unpack .../064-gfortran-9_9.2.1-30_amd64.deb ... Unpacking gfortran-9 (9.2.1-30) ... Selecting previously unselected package libnl-3-200:amd64. Preparing to unpack .../065-libnl-3-200_3.4.0-1+b1_amd64.deb ... Unpacking libnl-3-200:amd64 (3.4.0-1+b1) ... Selecting previously unselected package libnl-route-3-200:amd64. Preparing to unpack .../066-libnl-route-3-200_3.4.0-1+b1_amd64.deb ... Unpacking libnl-route-3-200:amd64 (3.4.0-1+b1) ... Selecting previously unselected package libibverbs1:amd64. Preparing to unpack .../067-libibverbs1_28.0-1_amd64.deb ... Unpacking libibverbs1:amd64 (28.0-1) ... Selecting previously unselected package ibverbs-providers:amd64. Preparing to unpack .../068-ibverbs-providers_28.0-1_amd64.deb ... Unpacking ibverbs-providers:amd64 (28.0-1) ... Selecting previously unselected package libcurl3-gnutls:amd64. Preparing to unpack .../069-libcurl3-gnutls_7.68.0-1_amd64.deb ... Unpacking libcurl3-gnutls:amd64 (7.68.0-1) ... Selecting previously unselected package libcurl4-gnutls-dev:amd64. Preparing to unpack .../070-libcurl4-gnutls-dev_7.68.0-1_amd64.deb ... Unpacking libcurl4-gnutls-dev:amd64 (7.68.0-1) ... Selecting previously unselected package libevent-2.1-7:amd64. Preparing to unpack .../071-libevent-2.1-7_2.1.11-stable-1_amd64.deb ... Unpacking libevent-2.1-7:amd64 (2.1.11-stable-1) ... Selecting previously unselected package libevent-core-2.1-7:amd64. Preparing to unpack .../072-libevent-core-2.1-7_2.1.11-stable-1_amd64.deb ... Unpacking libevent-core-2.1-7:amd64 (2.1.11-stable-1) ... Selecting previously unselected package libevent-extra-2.1-7:amd64. Preparing to unpack .../073-libevent-extra-2.1-7_2.1.11-stable-1_amd64.deb ... Unpacking libevent-extra-2.1-7:amd64 (2.1.11-stable-1) ... Selecting previously unselected package libevent-pthreads-2.1-7:amd64. Preparing to unpack .../074-libevent-pthreads-2.1-7_2.1.11-stable-1_amd64.deb ... Unpacking libevent-pthreads-2.1-7:amd64 (2.1.11-stable-1) ... Selecting previously unselected package libevent-openssl-2.1-7:amd64. Preparing to unpack .../075-libevent-openssl-2.1-7_2.1.11-stable-1_amd64.deb ... Unpacking libevent-openssl-2.1-7:amd64 (2.1.11-stable-1) ... Selecting previously unselected package libevent-dev. Preparing to unpack .../076-libevent-dev_2.1.11-stable-1_amd64.deb ... Unpacking libevent-dev (2.1.11-stable-1) ... Selecting previously unselected package libpsm-infinipath1. Preparing to unpack .../077-libpsm-infinipath1_3.3+20.604758e7-6+b1_amd64.deb ... Unpacking libpsm-infinipath1 (3.3+20.604758e7-6+b1) ... Selecting previously unselected package libnuma1:amd64. Preparing to unpack .../078-libnuma1_2.0.12-1+b1_amd64.deb ... Unpacking libnuma1:amd64 (2.0.12-1+b1) ... Selecting previously unselected package libpsm2-2. Preparing to unpack .../079-libpsm2-2_11.2.86-1_amd64.deb ... Unpacking libpsm2-2 (11.2.86-1) ... Selecting previously unselected package librdmacm1:amd64. Preparing to unpack .../080-librdmacm1_28.0-1_amd64.deb ... Unpacking librdmacm1:amd64 (28.0-1) ... Selecting previously unselected package libfabric1. Preparing to unpack .../081-libfabric1_1.6.2-3+b1_amd64.deb ... Unpacking libfabric1 (1.6.2-3+b1) ... Selecting previously unselected package libltdl7:amd64. Preparing to unpack .../082-libltdl7_2.4.6-13_amd64.deb ... Unpacking libltdl7:amd64 (2.4.6-13) ... Selecting previously unselected package libhwloc15:amd64. Preparing to unpack .../083-libhwloc15_2.1.0+dfsg-3_amd64.deb ... Unpacking libhwloc15:amd64 (2.1.0+dfsg-3) ... Selecting previously unselected package libnuma-dev:amd64. Preparing to unpack .../084-libnuma-dev_2.0.12-1+b1_amd64.deb ... Unpacking libnuma-dev:amd64 (2.0.12-1+b1) ... Selecting previously unselected package libltdl-dev:amd64. Preparing to unpack .../085-libltdl-dev_2.4.6-13_amd64.deb ... Unpacking libltdl-dev:amd64 (2.4.6-13) ... Selecting previously unselected package libhwloc-dev:amd64. Preparing to unpack .../086-libhwloc-dev_2.1.0+dfsg-3_amd64.deb ... Unpacking libhwloc-dev:amd64 (2.1.0+dfsg-3) ... Selecting previously unselected package libpciaccess0:amd64. Preparing to unpack .../087-libpciaccess0_0.14-1_amd64.deb ... Unpacking libpciaccess0:amd64 (0.14-1) ... Selecting previously unselected package libxau6:amd64. Preparing to unpack .../088-libxau6_1%3a1.0.8-1+b2_amd64.deb ... Unpacking libxau6:amd64 (1:1.0.8-1+b2) ... Selecting previously unselected package libxdmcp6:amd64. Preparing to unpack .../089-libxdmcp6_1%3a1.1.2-3_amd64.deb ... Unpacking libxdmcp6:amd64 (1:1.1.2-3) ... Selecting previously unselected package libxcb1:amd64. Preparing to unpack .../090-libxcb1_1.13.1-5_amd64.deb ... Unpacking libxcb1:amd64 (1.13.1-5) ... Selecting previously unselected package libx11-data. Preparing to unpack .../091-libx11-data_2%3a1.6.8-1_all.deb ... Unpacking libx11-data (2:1.6.8-1) ... Selecting previously unselected package libx11-6:amd64. Preparing to unpack .../092-libx11-6_2%3a1.6.8-1_amd64.deb ... Unpacking libx11-6:amd64 (2:1.6.8-1) ... Selecting previously unselected package libxext6:amd64. Preparing to unpack .../093-libxext6_2%3a1.3.3-1+b2_amd64.deb ... Unpacking libxext6:amd64 (2:1.3.3-1+b2) ... Selecting previously unselected package libxnvctrl0:amd64. Preparing to unpack .../094-libxnvctrl0_440.59-1_amd64.deb ... Unpacking libxnvctrl0:amd64 (440.59-1) ... Selecting previously unselected package ocl-icd-libopencl1:amd64. Preparing to unpack .../095-ocl-icd-libopencl1_2.2.12-3_amd64.deb ... Unpacking ocl-icd-libopencl1:amd64 (2.2.12-3) ... Selecting previously unselected package libhwloc-plugins:amd64. Preparing to unpack .../096-libhwloc-plugins_2.1.0+dfsg-3_amd64.deb ... Unpacking libhwloc-plugins:amd64 (2.1.0+dfsg-3) ... Selecting previously unselected package libnl-3-dev:amd64. Preparing to unpack .../097-libnl-3-dev_3.4.0-1+b1_amd64.deb ... Unpacking libnl-3-dev:amd64 (3.4.0-1+b1) ... Selecting previously unselected package libnl-route-3-dev:amd64. Preparing to unpack .../098-libnl-route-3-dev_3.4.0-1+b1_amd64.deb ... Unpacking libnl-route-3-dev:amd64 (3.4.0-1+b1) ... Selecting previously unselected package libibverbs-dev:amd64. Preparing to unpack .../099-libibverbs-dev_28.0-1_amd64.deb ... Unpacking libibverbs-dev:amd64 (28.0-1) ... Selecting previously unselected package libpmix2:amd64. Preparing to unpack .../100-libpmix2_3.1.4-1+b1_amd64.deb ... Unpacking libpmix2:amd64 (3.1.4-1+b1) ... Selecting previously unselected package libopenmpi3:amd64. Preparing to unpack .../101-libopenmpi3_4.0.2-5_amd64.deb ... Unpacking libopenmpi3:amd64 (4.0.2-5) ... Selecting previously unselected package openmpi-common. Preparing to unpack .../102-openmpi-common_4.0.2-5_all.deb ... Unpacking openmpi-common (4.0.2-5) ... Selecting previously unselected package openmpi-bin. Preparing to unpack .../103-openmpi-bin_4.0.2-5_amd64.deb ... Unpacking openmpi-bin (4.0.2-5) ... Selecting previously unselected package libopenmpi-dev:amd64. Preparing to unpack .../104-libopenmpi-dev_4.0.2-5_amd64.deb ... Unpacking libopenmpi-dev:amd64 (4.0.2-5) ... Selecting previously unselected package libsqlite3-0:amd64. Preparing to unpack .../105-libsqlite3-0_3.31.1-3_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.31.1-3) ... Selecting previously unselected package libsqlite3-dev:amd64. Preparing to unpack .../106-libsqlite3-dev_3.31.1-3_amd64.deb ... Unpacking libsqlite3-dev:amd64 (3.31.1-3) ... Selecting previously unselected package libssl-dev:amd64. Preparing to unpack .../107-libssl-dev_1.1.1d-2_amd64.deb ... Unpacking libssl-dev:amd64 (1.1.1d-2) ... Selecting previously unselected package mpi-default-dev. Preparing to unpack .../108-mpi-default-dev_1.13_amd64.deb ... Unpacking mpi-default-dev (1.13) ... Selecting previously unselected package pkg-config. Preparing to unpack .../109-pkg-config_0.29-6_amd64.deb ... Unpacking pkg-config (0.29-6) ... Selecting previously unselected package sbuild-build-depends-main-dummy. Preparing to unpack .../110-sbuild-build-depends-main-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up libexpat1:amd64 (2.2.9-1) ... Setting up libpipeline1:amd64 (1.5.2-2) ... Setting up libpciaccess0:amd64 (0.14-1) ... Setting up libxau6:amd64 (1:1.0.8-1+b2) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up libkeyutils1:amd64 (1.6.1-2) ... Setting up libpsl5:amd64 (0.20.2-2) ... Setting up libxcb1:amd64 (1.13.1-5) ... Setting up libmagic-mgc (1:5.38-4) ... Setting up libarchive-zip-perl (1.67-1) ... Setting up libglib2.0-0:amd64 (2.62.4-2) ... No schema files found: doing nothing. Setting up libssl1.1:amd64 (1.1.1d-2) ... Setting up libdebhelper-perl (12.9) ... Setting up libbrotli1:amd64 (1.0.7-6) ... Setting up libsqlite3-0:amd64 (3.31.1-3) ... Setting up libcbor0:amd64 (0.5.0+dfsg-2) ... Setting up libnghttp2-14:amd64 (1.40.0-1) ... Setting up libmagic1:amd64 (1:5.38-4) ... Setting up gettext-base (0.19.8.1-10) ... Setting up file (1:5.38-4) ... Setting up libldap-common (2.4.49+dfsg-1) ... Setting up libicu63:amd64 (63.2-2) ... Setting up libkrb5support0:amd64 (1.17-6) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-2) ... Setting up autotools-dev (20180224.1) ... Setting up libuv1:amd64 (1.34.2-1) ... Setting up libsqlite3-dev:amd64 (3.31.1-3) ... Setting up libx11-data (2:1.6.8-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b1) ... Setting up libncurses6:amd64 (6.1+20191019-1) ... Setting up libsigsegv2:amd64 (2.12-2) ... 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 libssl-dev:amd64 (1.1.1d-2) ... Setting up libevent-core-2.1-7:amd64 (2.1.11-stable-1) ... Setting up libevent-2.1-7:amd64 (2.1.11-stable-1) ... Setting up autopoint (0.19.8.1-10) ... Setting up pkg-config (0.29-6) ... Setting up libk5crypto3:amd64 (1.17-6) ... Setting up libltdl7:amd64 (2.4.6-13) ... Setting up libsasl2-2:amd64 (2.1.27+dfsg-2) ... Setting up libgfortran5:amd64 (10-20200222-1) ... Setting up libnuma1:amd64 (2.0.12-1+b1) ... Setting up sensible-utils (0.0.12+nmu1) ... Setting up ocl-icd-libopencl1:amd64 (2.2.12-3) ... Setting up librhash0:amd64 (1.3.9-1) ... Setting up libuchardet0:amd64 (0.0.6-3) ... Setting up libnl-3-200:amd64 (3.4.0-1+b1) ... Setting up libpsm2-2 (11.2.86-1) ... Setting up openmpi-common (4.0.2-5) ... Setting up libsub-override-perl (0.09-2) ... Setting up libx11-6:amd64 (2:1.6.8-1) ... Setting up libssh2-1:amd64 (1.8.0-2.1) ... Setting up cmake-data (3.16.3-1) ... Setting up libkrb5-3:amd64 (1.17-6) ... Setting up libpsm-infinipath1 (3.3+20.604758e7-6+b1) ... 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 libfido2-1:amd64 (1.3.1-1) ... Setting up libelf1:amd64 (0.176-1.1) ... Setting up libxml2:amd64 (2.9.10+dfsg-3) ... Setting up libprocps8:amd64 (2:3.3.16-1+b1) ... Setting up libjsoncpp1:amd64 (1.7.4-3.1) ... Setting up libevent-pthreads-2.1-7:amd64 (2.1.11-stable-1) ... Setting up libfile-stripnondeterminism-perl (1.6.3-2) ... Setting up libevent-extra-2.1-7:amd64 (2.1.11-stable-1) ... Setting up libtool (2.4.6-13) ... Setting up libarchive13:amd64 (3.4.0-1+b1) ... Setting up libxext6:amd64 (2:1.3.3-1+b2) ... Setting up libgfortran-9-dev:amd64 (9.2.1-30) ... Setting up libevent-openssl-2.1-7:amd64 (2.1.11-stable-1) ... Setting up libldap-2.4-2:amd64 (2.4.49+dfsg-1) ... Setting up m4 (1.4.18-4) ... Setting up libnuma-dev:amd64 (2.0.12-1+b1) ... Setting up libnl-route-3-200:amd64 (3.4.0-1+b1) ... Setting up libxnvctrl0:amd64 (440.59-1) ... Setting up libevent-dev (2.1.11-stable-1) ... Setting up libhwloc15:amd64 (2.1.0+dfsg-3) ... Setting up libgssapi-krb5-2:amd64 (1.17-6) ... Setting up libcroco3:amd64 (0.6.13-1) ... Setting up autoconf (2.69-11.1) ... Setting up dh-strip-nondeterminism (1.6.3-2) ... Setting up dwz (0.13-5) ... Setting up libnl-3-dev:amd64 (3.4.0-1+b1) ... Setting up groff-base (1.22.4-4) ... Setting up procps (2:3.3.16-1+b1) ... update-alternatives: using /usr/bin/w.procps to provide /usr/bin/w (w) in auto mode Setting up libcurl4:amd64 (7.68.0-1) ... 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 libibverbs1:amd64 (28.0-1) ... Setting up gettext (0.19.8.1-10) ... Setting up gfortran-9 (9.2.1-30) ... Setting up ibverbs-providers:amd64 (28.0-1) ... Setting up openssh-client (1:8.2p1-3) ... Setting up libcurl3-gnutls:amd64 (7.68.0-1) ... Setting up libcurl4-gnutls-dev:amd64 (7.68.0-1) ... Setting up libhwloc-plugins:amd64 (2.1.0+dfsg-3) ... Setting up man-db (2.9.0-2) ... Not building database; man-db/auto-update is not 'true'. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libnl-route-3-dev:amd64 (3.4.0-1+b1) ... Setting up libltdl-dev:amd64 (2.4.6-13) ... Setting up cmake (3.16.3-1) ... Setting up libhwloc-dev:amd64 (2.1.0+dfsg-3) ... Setting up librdmacm1:amd64 (28.0-1) ... Setting up libpmix2:amd64 (3.1.4-1+b1) ... Setting up po-debconf (1.0.21) ... Setting up libibverbs-dev:amd64 (28.0-1) ... Setting up libfabric1 (1.6.2-3+b1) ... Setting up libopenmpi3:amd64 (4.0.2-5) ... Setting up openmpi-bin (4.0.2-5) ... 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 libopenmpi-dev:amd64 (4.0.2-5) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openmpi/include to provide /usr/include/x86_64-linux-gnu/mpi (mpi-x86_64-linux-gnu) in auto mode Setting up mpi-default-dev (1.13) ... Setting up dh-autoreconf (19) ... Setting up debhelper (12.9) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.29-10) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.19.0-6-cloud-amd64 #1 SMP Debian 4.19.67-2+deb10u2 (2019-11-11) amd64 (x86_64) Toolchain package versions: binutils_2.34-3 dpkg-dev_1.19.7 g++-9_9.2.1-30 gcc-9_9.2.1-30 libc6-dev_2.29-10 libstdc++-8-dev_8.3.0-29 libstdc++-9-dev_9.2.1-30 libstdc++6_10-20200222-1 linux-libc-dev_5.4.19-1 Package versions: adduser_3.118 apt_1.8.4 autoconf_2.69-11.1 automake_1:1.16.1-4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11 base-passwd_3.5.47 bash_5.0-6 binutils_2.34-3 binutils-common_2.34-3 binutils-x86-64-linux-gnu_2.34-3 bsdmainutils_11.1.2+b1 bsdutils_1:2.34-0.1 build-essential_12.8 bzip2_1.0.8-2 clang-8_1:8.0.1-7 cmake_3.16.3-1 cmake-data_3.16.3-1 coreutils_8.30-3+b1 cpp_4:9.2.1-3.1 cpp-9_9.2.1-30 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.9 debian-archive-keyring_2019.1 debianutils_4.9.1 dh-autoreconf_19 dh-strip-nondeterminism_1.6.3-2 diffutils_1:3.7-3 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.5-2 fakeroot_1.24-1 fdisk_2.34-0.1 file_1:5.38-4 findutils_4.7.0-1 g++_4:9.2.1-3.1 g++-9_9.2.1-30 gcc_4:9.2.1-3.1 gcc-10-base_10-20200222-1 gcc-8-base_8.3.0-29 gcc-9_9.2.1-30 gcc-9-base_9.2.1-30 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gfortran-9_9.2.1-30 gpgv_2.2.19-1 grep_3.4-1 groff-base_1.22.4-4 gzip_1.9-3+b1 hostname_3.23 ibverbs-providers_28.0-1 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 lib32gcc-s1_10-20200222-1 lib32gcc1_1:10-20200222-1 lib32stdc++6_10-20200222-1 libacl1_2.2.53-5 libapt-pkg5.0_1.8.4 libarchive-zip-perl_1.67-1 libarchive13_3.4.0-1+b1 libasan5_9.2.1-30 libatomic1_10-20200222-1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2 libaudit1_1:2.8.5-2+b1 libbinutils_2.34-3 libblkid1_2.34-0.1 libbrotli1_1.0.7-6 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.29-10 libc-dev-bin_2.29-10 libc6_2.29-10 libc6-dev_2.29-10 libc6-i386_2.29-10 libcap-ng0_0.7.9-2.1+b1 libcbor0_0.5.0+dfsg-2 libcc1-0_10-20200222-1 libclang-common-8-dev_1:8.0.1-7 libclang1-8_1:8.0.1-7 libcom-err2_1.45.5-2 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.10-10 libcrypt1_1:4.4.10-10 libctf-nobfd0_2.34-3 libctf0_2.34-3 libcurl3-gnutls_7.68.0-1 libcurl4_7.68.0-1 libcurl4-gnutls-dev_7.68.0-1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.251 libdebhelper-perl_12.9 libdpkg-perl_1.19.7 libedit2_3.1-20191231-1 libelf1_0.176-1.1 libevent-2.1-7_2.1.11-stable-1 libevent-core-2.1-7_2.1.11-stable-1 libevent-dev_2.1.11-stable-1 libevent-extra-2.1-7_2.1.11-stable-1 libevent-openssl-2.1-7_2.1.11-stable-1 libevent-pthreads-2.1-7_2.1.11-stable-1 libexpat1_2.2.9-1 libext2fs2_1.45.5-2 libfabric1_1.6.2-3+b1 libfakeroot_1.24-1 libfdisk1_2.34-0.1 libffi7_3.3-3 libfido2-1_1.3.1-1 libfile-stripnondeterminism-perl_1.6.3-2 libgc1c2_1:7.6.4-0.4 libgcc-8-dev_8.3.0-29 libgcc-9-dev_9.2.1-30 libgcc-s1_10-20200222-1 libgcc1_1:10-20200222-1 libgcrypt20_1.8.5-5 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libgfortran-9-dev_9.2.1-30 libgfortran5_10-20200222-1 libglib2.0-0_2.62.4-2 libgmp10_2:6.2.0+dfsg-4 libgnutls30_3.6.12-2 libgomp1_10-20200222-1 libgpg-error0_1.37-1 libgssapi-krb5-2_1.17-6 libhogweed5_3.5.1+really3.5.1-2 libhwloc-dev_2.1.0+dfsg-3 libhwloc-plugins_2.1.0+dfsg-3 libhwloc15_2.1.0+dfsg-3 libibverbs-dev_28.0-1 libibverbs1_28.0-1 libicu63_63.2-2 libidn2-0_2.2.0-2 libisl22_0.22.1-1 libitm1_10-20200222-1 libjsoncpp1_1.7.4-3.1 libk5crypto3_1.17-6 libkeyutils1_1.6.1-2 libkrb5-3_1.17-6 libkrb5support0_1.17-6 libldap-2.4-2_2.4.49+dfsg-1 libldap-common_2.4.49+dfsg-1 libllvm8_1:8.0.1-7 liblsan0_10-20200222-1 libltdl-dev_2.4.6-13 libltdl7_2.4.6-13 liblz4-1_1.9.2-2 liblzma5_5.2.4-1+b1 libmagic-mgc_1:5.38-4 libmagic1_1:5.38-4 libmount1_2.34-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libmpx2_8.3.0-29 libncurses6_6.1+20191019-1 libncursesw6_6.1+20191019-1 libnettle7_3.5.1+really3.5.1-2 libnghttp2-14_1.40.0-1 libnl-3-200_3.4.0-1+b1 libnl-3-dev_3.4.0-1+b1 libnl-route-3-200_3.4.0-1+b1 libnl-route-3-dev_3.4.0-1+b1 libnuma-dev_2.0.12-1+b1 libnuma1_2.0.12-1+b1 libobjc-8-dev_8.3.0-29 libobjc-9-dev_9.2.1-30 libobjc4_10-20200222-1 libomp-8-dev_1:8.0.1-7 libomp5-8_1:8.0.1-7 libopenmpi-dev_4.0.2-5 libopenmpi3_4.0.2-5 libp11-kit0_0.23.20-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpciaccess0_0.14-1 libpcre2-8-0_10.34-7 libpcre3_2:8.39-12+b1 libperl5.30_5.30.0-9 libpipeline1_1.5.2-2 libpmix2_3.1.4-1+b1 libprocps8_2:3.3.16-1+b1 libpsl5_0.20.2-2 libpsm-infinipath1_3.3+20.604758e7-6+b1 libpsm2-2_11.2.86-1 libquadmath0_10-20200222-1 librdmacm1_28.0-1 librhash0_1.3.9-1 librtmp1_2.4+20151223.gitfa8646d.1-2+b1 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.2-2 libselinux1_3.0-1+b1 libsemanage-common_3.0-1 libsemanage1_3.0-1+b1 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1 libsqlite3-0_3.31.1-3 libsqlite3-dev_3.31.1-3 libss2_1.45.5-2 libssh2-1_1.8.0-2.1 libssl-dev_1.1.1d-2 libssl1.1_1.1.1d-2 libstdc++-8-dev_8.3.0-29 libstdc++-9-dev_9.2.1-30 libstdc++6_10-20200222-1 libsub-override-perl_0.09-2 libsystemd0_244.3-1 libtasn1-6_4.16.0-2 libtinfo6_6.1+20191019-1 libtool_2.4.6-13 libtsan0_10-20200222-1 libubsan1_10-20200222-1 libuchardet0_0.0.6-3 libudev1_244.3-1 libunistring2_0.9.10-2 libuuid1_2.34-0.1 libuv1_1.34.2-1 libx11-6_2:1.6.8-1 libx11-data_2:1.6.8-1 libxau6_1:1.0.8-1+b2 libxcb1_1.13.1-5 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.3-1+b2 libxml2_2.9.10+dfsg-3 libxnvctrl0_440.59-1 libzstd1_1.4.4+dfsg-3 linux-libc-dev_5.4.19-1 login_1:4.8.1-1 logsave_1.45.5-2 lsb-base_11.1.0 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.0-2 mawk_1.3.4.20200120-2 mount_2.34-0.1 mpi-default-dev_1.13 ncurses-base_6.1+20191019-1 ncurses-bin_6.1+20191019-1 ocl-icd-libopencl1_2.2.12-3 openmpi-bin_4.0.2-5 openmpi-common_4.0.2-5 openssh-client_1:8.2p1-3 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.30.0-9 perl-base_5.30.0-9 perl-modules-5.30_5.30.0-9 pkg-config_0.29-6 po-debconf_1.0.21 procps_2:3.3.16-1+b1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-2.1 tar_1.30+dfsg-6+b1 tzdata_2019c-3 util-linux_2.34-0.1 xz-utils_5.2.4-1+b1 zlib1g_1:1.2.11.dfsg-2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: hyphy Binary: hyphy-pt, hyphy-mpi, hyphy-common Architecture: any all Version: 2.5.1+dfsg-3 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://hyphy.org/ Standards-Version: 4.4.1 Vcs-Browser: https://salsa.debian.org/med-team/hyphy Vcs-Git: https://salsa.debian.org/med-team/hyphy.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 12), cmake, mpi-default-dev, libcurl4-gnutls-dev | libcurl4-dev, libssl-dev, libsqlite3-dev, pkg-config Package-List: hyphy-common deb science optional arch=all hyphy-mpi deb science optional arch=any hyphy-pt deb science optional arch=any Checksums-Sha1: 3e1253bf9f0d2b5537b3dc55e6fe73a75db9e0d2 2899360 hyphy_2.5.1+dfsg.orig.tar.xz 522cec1b36737ed4ef9ac35e0d486d7fb33d0313 10424 hyphy_2.5.1+dfsg-3.debian.tar.xz Checksums-Sha256: 1ba52718825b34268f9b8ba2e9425f3450f5466750c2dadebc0238385bba989c 2899360 hyphy_2.5.1+dfsg.orig.tar.xz 5af4570bf5d2815550819f09790fd8d80684c01d5521bc2d7e1299f0f8c1c0f1 10424 hyphy_2.5.1+dfsg-3.debian.tar.xz Files: 512d3dc73c4c5ca19865627ff4317db5 2899360 hyphy_2.5.1+dfsg.orig.tar.xz c1479025e5e496e5f1dc5160a187d8dc 10424 hyphy_2.5.1+dfsg-3.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl4U8o8RHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHZQg/+O9TJJyPdxhL8PTyudq1uP/JDsz9pvmBi zEHyGmIS0P4GShHB4HFJeJIiK6lvfwIZgIzX8pztfpOLW4hLwif5S7VzidAYPxSm 8X1cdfPfBrw4iquzCWxEJYTWYGnOotrT60rgSM9Y8pks2jfKQTXYxcqxVaHN3wdR tJH3mVv3kIOjWWHkwlgS6u9qHNxIGoWkyr5eGwM3jsyCyUzxpaw85kLrUjceJs5o aQ6rM/zgMzqW8/YSASxvmpG7SvgDvGhG1XyyB9l/pleCg/KO+xGbmthj+kowsdMI zA37oFhQfYXTuad5i7hjkUBONZZ+ZQvdXXtuhJ+LiGzjj9zJtV25vnqcbeBbPe7+ WPJY9TIsCUhEV97O9ddfQei6jdAX41U3Ky/GfLVkQ4ZpkM8S5PNrrJLYPyVFYYr5 18M+EXyZWxsrXr5CEVF7tlupMZRxUK2zAVW9dw0/SQBUfcqVjlkBrvUAupzthxXU rkfzrGwkoHBd0WhH7kpZj8sZpZDM1COlkLYS8yTzRMsK9tuw0nhzN1vA4tWZkeh5 QaGGFsWSXXravBzNfRQ+FErOOhHrLC3R8CrymibZ3/bDdNRbTuGoc8pBg337XFXb A0GSuG/F5pJLmKPoycWK5b46NDRc8WWyGwcmvzMwW6Kxqs19gx8SJxQEsjQavnE8 wy+7jjR1zq0= =Bz88 -----END PGP SIGNATURE----- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Tue Jan 7 21:05:19 2020 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_2.5.1+dfsg-3.dsc dpkg-source: info: extracting hyphy in /<> dpkg-source: info: unpacking hyphy_2.5.1+dfsg.orig.tar.xz dpkg-source: info: unpacking hyphy_2.5.1+dfsg-3.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 drop_profiling_option.patch dpkg-source: info: applying remove_unneeded_test.patch dpkg-source: info: applying gcc9.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 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-a3f8ce9c-6fa9-4e14-92cd-4743617dd738 SCHROOT_UID=1001 SCHROOT_USER=user42 SHELL=/bin/sh USER=user42 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -b -rfakeroot dpkg-buildpackage: info: source package hyphy dpkg-buildpackage: info: source version 2.5.1+dfsg-3 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 '/<>' dh_auto_clean make[1]: Leaving directory '/<>' dh_autoreconf_clean -O--buildsystem=cmake dh_clean -O--buildsystem=cmake debian/rules build dh build --buildsystem=cmake dh_update_autotools_config -O--buildsystem=cmake dh_autoreconf -O--buildsystem=cmake debian/rules override_dh_auto_configure make[1]: Entering directory '/<>' 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 8.0.1 -- The CXX compiler identification is Clang 8.0.1 -- 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 - Success CMake Warning (dev) in CMakeLists.txt: A logical block opening on the line /<>/CMakeLists.txt:192 (if) closes on the line /<>/CMakeLists.txt:206 (endif) with mis-matching arguments. This warning is for project developers. Use -Wno-dev to suppress it. -- Performing Test HAVE_FMA3 -- Performing Test HAVE_FMA3 - Success Set compiler flags to -fsigned-char -O3 -march=native -mtune=native -mavx -mfma -- 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 "7.68.0") -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29") -- Checking for module 'sqlite3' -- Found sqlite3, version 3.31.1 -- 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 -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- 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 Node not installed; API documentation will not be generated -- 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") -pthread -fopenmp=libomp -- 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: /<>/obj-x86_64-linux-gnu make[1]: Leaving directory '/<>' debian/rules override_dh_auto_build make[1]: Entering directory '/<>' # no idea about the purpose of the dynamic library - executables are not simply linked against it dh_auto_build -- MP MPI cd obj-x86_64-linux-gnu && make -j4 "INSTALL=install --strip-program=true" MP MPI make[2]: Entering directory '/<>/obj-x86_64-linux-gnu' /usr/bin/cmake -S/<> -B/<>/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 MP make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' /usr/bin/cmake -S/<> -B/<>/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/obj-x86_64-linux-gnu/CMakeFiles 17 make -f CMakeFiles/Makefile2 CMakeFiles/MP.dir/all make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' make -f CMakeFiles/hyphy.dir/build.make CMakeFiles/hyphy.dir/depend make[5]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<> /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/CMakeFiles/hyphy.dir/DependInfo.cmake --color= Scanning dependencies of target hyphy make[5]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f CMakeFiles/hyphy.dir/build.make CMakeFiles/hyphy.dir/build make[5]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 0%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllist.cpp.o [ 0%] Building CXX object CMakeFiles/hyphy.dir/src/core/_hyExecutionContext.cpp.o [ 5%] Building CXX object CMakeFiles/hyphy.dir/src/core/associative_list.cpp.o [ 5%] Building CXX object CMakeFiles/hyphy.dir/src/core/alignment.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/<>/src/core/include -I/<>/src/contrib -I/<>/src/lib/Link -I/<>/src/new/include -I/<>/contrib/gtest-1.7.0/include -I/<>/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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -march=native -mtune=native -mavx -mfma -w -g -fopenmp=libomp -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/_hyExecutionContext.cpp.o -c /<>/src/core/_hyExecutionContext.cpp /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/<>/src/core/include -I/<>/src/contrib -I/<>/src/lib/Link -I/<>/src/new/include -I/<>/contrib/gtest-1.7.0/include -I/<>/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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -march=native -mtune=native -mavx -mfma -w -g -fopenmp=libomp -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/avllist.cpp.o -c /<>/src/core/avllist.cpp /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/<>/src/core/include -I/<>/src/contrib -I/<>/src/lib/Link -I/<>/src/new/include -I/<>/contrib/gtest-1.7.0/include -I/<>/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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -march=native -mtune=native -mavx -mfma -w -g -fopenmp=libomp -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/alignment.cpp.o -c /<>/src/core/alignment.cpp /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/<>/src/core/include -I/<>/src/contrib -I/<>/src/lib/Link -I/<>/src/new/include -I/<>/contrib/gtest-1.7.0/include -I/<>/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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -march=native -mtune=native -mavx -mfma -w -g -fopenmp=libomp -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/associative_list.cpp.o -c /<>/src/core/associative_list.cpp [ 5%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllistx.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/<>/src/core/include -I/<>/src/contrib -I/<>/src/lib/Link -I/<>/src/new/include -I/<>/contrib/gtest-1.7.0/include -I/<>/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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -march=native -mtune=native -mavx -mfma -w -g -fopenmp=libomp -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/avllistx.cpp.o -c /<>/src/core/avllistx.cpp [ 11%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllistx_iterator.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/<>/src/core/include -I/<>/src/contrib -I/<>/src/lib/Link -I/<>/src/new/include -I/<>/contrib/gtest-1.7.0/include -I/<>/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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -march=native -mtune=native -mavx -mfma -w -g -fopenmp=libomp -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/avllistx_iterator.cpp.o -c /<>/src/core/avllistx_iterator.cpp [ 11%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllistxl.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/<>/src/core/include -I/<>/src/contrib -I/<>/src/lib/Link -I/<>/src/new/include -I/<>/contrib/gtest-1.7.0/include -I/<>/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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -march=native -mtune=native -mavx -mfma -w -g -fopenmp=libomp -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/avllistxl.cpp.o -c /<>/src/core/avllistxl.cpp [ 11%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllistxl_iterator.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/<>/src/core/include -I/<>/src/contrib -I/<>/src/lib/Link -I/<>/src/new/include -I/<>/contrib/gtest-1.7.0/include -I/<>/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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -march=native -mtune=native -mavx -mfma -w -g -fopenmp=libomp -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/avllistxl_iterator.cpp.o -c /<>/src/core/avllistxl_iterator.cpp [ 11%] Building CXX object CMakeFiles/hyphy.dir/src/core/baseobj.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/<>/src/core/include -I/<>/src/contrib -I/<>/src/lib/Link -I/<>/src/new/include -I/<>/contrib/gtest-1.7.0/include -I/<>/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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -march=native -mtune=native -mavx -mfma -w -g -fopenmp=libomp -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/baseobj.cpp.o -c /<>/src/core/baseobj.cpp [ 17%] Building CXX object CMakeFiles/hyphy.dir/src/core/batchlan.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/<>/src/core/include -I/<>/src/contrib -I/<>/src/lib/Link -I/<>/src/new/include -I/<>/contrib/gtest-1.7.0/include -I/<>/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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -march=native -mtune=native -mavx -mfma -w -g -fopenmp=libomp -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/batchlan.cpp.o -c /<>/src/core/batchlan.cpp [ 17%] Building CXX object CMakeFiles/hyphy.dir/src/core/batchlan2.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/<>/src/core/include -I/<>/src/contrib -I/<>/src/lib/Link -I/<>/src/new/include -I/<>/contrib/gtest-1.7.0/include -I/<>/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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -march=native -mtune=native -mavx -mfma -w -g -fopenmp=libomp -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/batchlan2.cpp.o -c /<>/src/core/batchlan2.cpp [ 17%] Building CXX object CMakeFiles/hyphy.dir/src/core/batchlanhelpers.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/<>/src/core/include -I/<>/src/contrib -I/<>/src/lib/Link -I/<>/src/new/include -I/<>/contrib/gtest-1.7.0/include -I/<>/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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -march=native -mtune=native -mavx -mfma -w -g -fopenmp=libomp -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/batchlanhelpers.cpp.o -c /<>/src/core/batchlanhelpers.cpp [ 17%] Building CXX object CMakeFiles/hyphy.dir/src/core/batchlanruntime.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/<>/src/core/include -I/<>/src/contrib -I/<>/src/lib/Link -I/<>/src/new/include -I/<>/contrib/gtest-1.7.0/include -I/<>/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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -march=native -mtune=native -mavx -mfma -w -g -fopenmp=libomp -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/batchlanruntime.cpp.o -c /<>/src/core/batchlanruntime.cpp [ 23%] Building CXX object CMakeFiles/hyphy.dir/src/core/calcnode.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/<>/src/core/include -I/<>/src/contrib -I/<>/src/lib/Link -I/<>/src/new/include -I/<>/contrib/gtest-1.7.0/include -I/<>/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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -march=native -mtune=native -mavx -mfma -w -g -fopenmp=libomp -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/calcnode.cpp.o -c /<>/src/core/calcnode.cpp [ 23%] Building CXX object CMakeFiles/hyphy.dir/src/core/category.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/<>/src/core/include -I/<>/src/contrib -I/<>/src/lib/Link -I/<>/src/new/include -I/<>/contrib/gtest-1.7.0/include -I/<>/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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -march=native -mtune=native -mavx -mfma -w -g -fopenmp=libomp -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/category.cpp.o -c /<>/src/core/category.cpp [ 23%] Building CXX object CMakeFiles/hyphy.dir/src/core/constant.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/<>/src/core/include -I/<>/src/contrib -I/<>/src/lib/Link -I/<>/src/new/include -I/<>/contrib/gtest-1.7.0/include -I/<>/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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -march=native -mtune=native -mavx -mfma -w -g -fopenmp=libomp -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/constant.cpp.o -c /<>/src/core/constant.cpp [ 29%] Building CXX object CMakeFiles/hyphy.dir/src/core/dataset.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/<>/src/core/include -I/<>/src/contrib -I/<>/src/lib/Link -I/<>/src/new/include -I/<>/contrib/gtest-1.7.0/include -I/<>/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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -march=native -mtune=native -mavx -mfma -w -g -fopenmp=libomp -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/dataset.cpp.o -c /<>/src/core/dataset.cpp [ 29%] Building CXX object CMakeFiles/hyphy.dir/src/core/dataset_filter.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/<>/src/core/include -I/<>/src/contrib -I/<>/src/lib/Link -I/<>/src/new/include -I/<>/contrib/gtest-1.7.0/include -I/<>/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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -march=native -mtune=native -mavx -mfma -w -g -fopenmp=libomp -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/dataset_filter.cpp.o -c /<>/src/core/dataset_filter.cpp [ 29%] Building CXX object CMakeFiles/hyphy.dir/src/core/dataset_filter_numeric.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/<>/src/core/include -I/<>/src/contrib -I/<>/src/lib/Link -I/<>/src/new/include -I/<>/contrib/gtest-1.7.0/include -I/<>/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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -march=native -mtune=native -mavx -mfma -w -g -fopenmp=libomp -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/dataset_filter_numeric.cpp.o -c /<>/src/core/dataset_filter_numeric.cpp [ 29%] Building CXX object CMakeFiles/hyphy.dir/src/core/fisher_exact.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/<>/src/core/include -I/<>/src/contrib -I/<>/src/lib/Link -I/<>/src/new/include -I/<>/contrib/gtest-1.7.0/include -I/<>/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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -march=native -mtune=native -mavx -mfma -w -g -fopenmp=libomp -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/fisher_exact.cpp.o -c /<>/src/core/fisher_exact.cpp [ 35%] Building CXX object CMakeFiles/hyphy.dir/src/core/formula.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/<>/src/core/include -I/<>/src/contrib -I/<>/src/lib/Link -I/<>/src/new/include -I/<>/contrib/gtest-1.7.0/include -I/<>/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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -march=native -mtune=native -mavx -mfma -w -g -fopenmp=libomp -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/formula.cpp.o -c /<>/src/core/formula.cpp [ 35%] Building CXX object CMakeFiles/hyphy.dir/src/core/formula_parsing_context.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/<>/src/core/include -I/<>/src/contrib -I/<>/src/lib/Link -I/<>/src/new/include -I/<>/contrib/gtest-1.7.0/include -I/<>/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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -march=native -mtune=native -mavx -mfma -w -g -fopenmp=libomp -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/formula_parsing_context.cpp.o -c /<>/src/core/formula_parsing_context.cpp [ 35%] Building CXX object CMakeFiles/hyphy.dir/src/core/fstring.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/<>/src/core/include -I/<>/src/contrib -I/<>/src/lib/Link -I/<>/src/new/include -I/<>/contrib/gtest-1.7.0/include -I/<>/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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -march=native -mtune=native -mavx -mfma -w -g -fopenmp=libomp -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/fstring.cpp.o -c /<>/src/core/fstring.cpp [ 35%] Building CXX object CMakeFiles/hyphy.dir/src/core/global_object_lists.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/<>/src/core/include -I/<>/src/contrib -I/<>/src/lib/Link -I/<>/src/new/include -I/<>/contrib/gtest-1.7.0/include -I/<>/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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -march=native -mtune=native -mavx -mfma -w -g -fopenmp=libomp -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/global_object_lists.cpp.o -c /<>/src/core/global_object_lists.cpp [ 41%] Building CXX object CMakeFiles/hyphy.dir/src/core/global_things.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/<>/src/core/include -I/<>/src/contrib -I/<>/src/lib/Link -I/<>/src/new/include -I/<>/contrib/gtest-1.7.0/include -I/<>/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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -march=native -mtune=native -mavx -mfma -w -g -fopenmp=libomp -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/global_things.cpp.o -c /<>/src/core/global_things.cpp [ 41%] Building CXX object CMakeFiles/hyphy.dir/src/core/hbl_env.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/<>/src/core/include -I/<>/src/contrib -I/<>/src/lib/Link -I/<>/src/new/include -I/<>/contrib/gtest-1.7.0/include -I/<>/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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -march=native -mtune=native -mavx -mfma -w -g -fopenmp=libomp -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/hbl_env.cpp.o -c /<>/src/core/hbl_env.cpp [ 41%] Building CXX object CMakeFiles/hyphy.dir/src/core/likefunc.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/<>/src/core/include -I/<>/src/contrib -I/<>/src/lib/Link -I/<>/src/new/include -I/<>/contrib/gtest-1.7.0/include -I/<>/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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -march=native -mtune=native -mavx -mfma -w -g -fopenmp=libomp -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/likefunc.cpp.o -c /<>/src/core/likefunc.cpp [ 41%] Building CXX object CMakeFiles/hyphy.dir/src/core/likefunc2.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/<>/src/core/include -I/<>/src/contrib -I/<>/src/lib/Link -I/<>/src/new/include -I/<>/contrib/gtest-1.7.0/include -I/<>/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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -march=native -mtune=native -mavx -mfma -w -g -fopenmp=libomp -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/likefunc2.cpp.o -c /<>/src/core/likefunc2.cpp [ 47%] Building CXX object CMakeFiles/hyphy.dir/src/core/likefuncocl.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/<>/src/core/include -I/<>/src/contrib -I/<>/src/lib/Link -I/<>/src/new/include -I/<>/contrib/gtest-1.7.0/include -I/<>/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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -march=native -mtune=native -mavx -mfma -w -g -fopenmp=libomp -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/likefuncocl.cpp.o -c /<>/src/core/likefuncocl.cpp [ 47%] Building CXX object CMakeFiles/hyphy.dir/src/core/list.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/<>/src/core/include -I/<>/src/contrib -I/<>/src/lib/Link -I/<>/src/new/include -I/<>/contrib/gtest-1.7.0/include -I/<>/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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -march=native -mtune=native -mavx -mfma -w -g -fopenmp=libomp -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/list.cpp.o -c /<>/src/core/list.cpp [ 47%] Building CXX object CMakeFiles/hyphy.dir/src/core/mathobj.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/<>/src/core/include -I/<>/src/contrib -I/<>/src/lib/Link -I/<>/src/new/include -I/<>/contrib/gtest-1.7.0/include -I/<>/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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -march=native -mtune=native -mavx -mfma -w -g -fopenmp=libomp -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/mathobj.cpp.o -c /<>/src/core/mathobj.cpp [ 47%] Building CXX object CMakeFiles/hyphy.dir/src/core/matrix.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/<>/src/core/include -I/<>/src/contrib -I/<>/src/lib/Link -I/<>/src/new/include -I/<>/contrib/gtest-1.7.0/include -I/<>/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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -march=native -mtune=native -mavx -mfma -w -g -fopenmp=libomp -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/matrix.cpp.o -c /<>/src/core/matrix.cpp [ 52%] Building CXX object CMakeFiles/hyphy.dir/src/core/nexus.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/<>/src/core/include -I/<>/src/contrib -I/<>/src/lib/Link -I/<>/src/new/include -I/<>/contrib/gtest-1.7.0/include -I/<>/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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -march=native -mtune=native -mavx -mfma -w -g -fopenmp=libomp -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/nexus.cpp.o -c /<>/src/core/nexus.cpp [ 52%] Building CXX object CMakeFiles/hyphy.dir/src/core/ntuplestorage.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/<>/src/core/include -I/<>/src/contrib -I/<>/src/lib/Link -I/<>/src/new/include -I/<>/contrib/gtest-1.7.0/include -I/<>/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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -march=native -mtune=native -mavx -mfma -w -g -fopenmp=libomp -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/ntuplestorage.cpp.o -c /<>/src/core/ntuplestorage.cpp [ 52%] Building CXX object CMakeFiles/hyphy.dir/src/core/operation.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/<>/src/core/include -I/<>/src/contrib -I/<>/src/lib/Link -I/<>/src/new/include -I/<>/contrib/gtest-1.7.0/include -I/<>/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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -march=native -mtune=native -mavx -mfma -w -g -fopenmp=libomp -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/operation.cpp.o -c /<>/src/core/operation.cpp [ 52%] Building CXX object CMakeFiles/hyphy.dir/src/core/parser.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/<>/src/core/include -I/<>/src/contrib -I/<>/src/lib/Link -I/<>/src/new/include -I/<>/contrib/gtest-1.7.0/include -I/<>/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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -march=native -mtune=native -mavx -mfma -w -g -fopenmp=libomp -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/parser.cpp.o -c /<>/src/core/parser.cpp [ 58%] Building CXX object CMakeFiles/hyphy.dir/src/core/parser2.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/<>/src/core/include -I/<>/src/contrib -I/<>/src/lib/Link -I/<>/src/new/include -I/<>/contrib/gtest-1.7.0/include -I/<>/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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -march=native -mtune=native -mavx -mfma -w -g -fopenmp=libomp -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/parser2.cpp.o -c /<>/src/core/parser2.cpp [ 58%] Building CXX object CMakeFiles/hyphy.dir/src/core/polynoml.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/<>/src/core/include -I/<>/src/contrib -I/<>/src/lib/Link -I/<>/src/new/include -I/<>/contrib/gtest-1.7.0/include -I/<>/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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -march=native -mtune=native -mavx -mfma -w -g -fopenmp=libomp -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/polynoml.cpp.o -c /<>/src/core/polynoml.cpp [ 58%] Building CXX object CMakeFiles/hyphy.dir/src/core/simplelist.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/<>/src/core/include -I/<>/src/contrib -I/<>/src/lib/Link -I/<>/src/new/include -I/<>/contrib/gtest-1.7.0/include -I/<>/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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -march=native -mtune=native -mavx -mfma -w -g -fopenmp=libomp -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/simplelist.cpp.o -c /<>/src/core/simplelist.cpp [ 58%] Building CXX object CMakeFiles/hyphy.dir/src/core/site.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/<>/src/core/include -I/<>/src/contrib -I/<>/src/lib/Link -I/<>/src/new/include -I/<>/contrib/gtest-1.7.0/include -I/<>/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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -march=native -mtune=native -mavx -mfma -w -g -fopenmp=libomp -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/site.cpp.o -c /<>/src/core/site.cpp [ 64%] Building CXX object CMakeFiles/hyphy.dir/src/core/stack.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/<>/src/core/include -I/<>/src/contrib -I/<>/src/lib/Link -I/<>/src/new/include -I/<>/contrib/gtest-1.7.0/include -I/<>/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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -march=native -mtune=native -mavx -mfma -w -g -fopenmp=libomp -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/stack.cpp.o -c /<>/src/core/stack.cpp [ 64%] Building CXX object CMakeFiles/hyphy.dir/src/core/string_buffer.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/<>/src/core/include -I/<>/src/contrib -I/<>/src/lib/Link -I/<>/src/new/include -I/<>/contrib/gtest-1.7.0/include -I/<>/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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -march=native -mtune=native -mavx -mfma -w -g -fopenmp=libomp -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/string_buffer.cpp.o -c /<>/src/core/string_buffer.cpp [ 64%] Building CXX object CMakeFiles/hyphy.dir/src/core/string_file_wrapper.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/<>/src/core/include -I/<>/src/contrib -I/<>/src/lib/Link -I/<>/src/new/include -I/<>/contrib/gtest-1.7.0/include -I/<>/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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -march=native -mtune=native -mavx -mfma -w -g -fopenmp=libomp -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/string_file_wrapper.cpp.o -c /<>/src/core/string_file_wrapper.cpp [ 64%] Building CXX object CMakeFiles/hyphy.dir/src/core/strings.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/lib/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/<>/src/core/include -I/<>/src/contrib -I/<>/src/lib/Link -I/<>/src/new/include -I/<>/contrib/gtest-1.7.0/include -I/<>/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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -march=native -mtune=native -mavx -mfma -w -g -fopenmp=libomp -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/strings.cpp.o -c /<>/src/core/strings.cpp /<>/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); ^~~~~~ /<>/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/hyphy.dir/build.make:612: CMakeFiles/hyphy.dir/src/core/string_file_wrapper.cpp.o] Error 1 make[5]: *** Waiting for unfinished jobs.... make[5]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[4]: *** [CMakeFiles/Makefile2:220: CMakeFiles/hyphy.dir/all] Error 2 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: *** [CMakeFiles/Makefile2:281: CMakeFiles/MP.dir/rule] Error 2 make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[2]: *** [Makefile:245: MP] Error 2 make[2]: Leaving directory '/<>/obj-x86_64-linux-gnu' dh_auto_build: error: cd obj-x86_64-linux-gnu && make -j4 "INSTALL=install --strip-program=true" MP MPI returned exit code 2 make[1]: *** [debian/rules:24: override_dh_auto_build] Error 25 make[1]: Leaving directory '/<>' make: *** [debian/rules:14: build] Error 2 dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2020-02-25T15:38:46Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: binary Build-Space: 44200 Build-Time: 26 Distribution: unstable Fail-Stage: build Host Architecture: amd64 Install-Time: 9 Job: hyphy_2.5.1+dfsg-3 Machine Architecture: amd64 Package: hyphy Package-Time: 52 Source-Version: 2.5.1+dfsg-3 Space: 44200 Status: attempted Version: 2.5.1+dfsg-3 -------------------------------------------------------------------------------- Finished at 2020-02-25T15:38:46Z Build needed 00:00:52, 44200k disk space E: Build failure (dpkg-buildpackage died) DC-Status: Failed 52.989399381s DC-Time-Estimation: 52.989399381 versus expected 215 (r/m: 3.057415304033261 ; m: 52.989399381)