DC-Build-Header: hyphy 2.5.33+dfsg-1 / 2021-10-26 21:44:19 +0000 DC-Task: type:rebuild-binarch-only source:hyphy version:2.5.33+dfsg-1 chroot:unstable esttime:312 logfile:/tmp/hyphy_2.5.33+dfsg-1_unstable_clang13.log modes:clang13:binarch-only DC-Sbuild-call: su user42 -c 'sbuild -n --arch-any --apt-update -d unstable -v --no-run-lintian --chroot-setup-commands=/tmp/clang13 hyphy_2.5.33+dfsg-1' sbuild (Debian sbuild) 0.78.1 (09 February 2019) on ip-172-31-4-209.eu-central-1.compute.internal +==============================================================================+ | hyphy 2.5.33+dfsg-1 (amd64) Tue, 26 Oct 2021 21:44:19 +0000 | +==============================================================================+ Package: hyphy Version: 2.5.33+dfsg-1 Source Version: 2.5.33+dfsg-1 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-fa31d336-3089-413b-beec-07aff9fab658' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /tmp/clang13 ------------ + echo 'Entering customization script...' Entering customization script... + CLANG_VERSION=13 + echo 'Install of clang-13' Install of clang-13 + apt-get update Get:1 http://127.0.0.1:12990/debian sid InRelease [165 kB] Get:2 http://127.0.0.1:12990/debian sid/main Sources.diff/Index [63.6 kB] Get:3 http://127.0.0.1:12990/debian sid/main amd64 Packages.diff/Index [63.6 kB] Get:4 http://127.0.0.1:12990/debian sid/main Sources T-2021-10-26-2004.40-F-2021-10-26-0202.15.pdiff [47.3 kB] Get:4 http://127.0.0.1:12990/debian sid/main Sources T-2021-10-26-2004.40-F-2021-10-26-0202.15.pdiff [47.3 kB] Get:5 http://127.0.0.1:12990/debian sid/main amd64 Packages T-2021-10-26-2004.40-F-2021-10-26-0202.15.pdiff [55.9 kB] Get:5 http://127.0.0.1:12990/debian sid/main amd64 Packages T-2021-10-26-2004.40-F-2021-10-26-0202.15.pdiff [55.9 kB] Get:6 http://127.0.0.1:12990/debian sid/main Translation-en [6586 kB] Fetched 6981 kB in 3s (2729 kB/s) Reading package lists... + apt-get install --yes --no-install-recommends --force-yes clang-13 libomp-13-dev libobjc-9-dev Reading package lists... Building dependency tree... The following additional packages will be installed: lib32gcc-s1 lib32stdc++6 libasan5 libbsd0 libc6-i386 libclang-common-13-dev libclang-cpp13 libclang1-13 libedit2 libgc1 libgcc-9-dev libicu67 libllvm13 libmd0 libobjc-11-dev libobjc4 libomp5-13 libxml2 libz3-4 Suggested packages: clang-13-doc libomp-13-doc Recommended packages: llvm-13-dev python3 The following NEW packages will be installed: clang-13 lib32gcc-s1 lib32stdc++6 libasan5 libbsd0 libc6-i386 libclang-common-13-dev libclang-cpp13 libclang1-13 libedit2 libgc1 libgcc-9-dev libicu67 libllvm13 libmd0 libobjc-11-dev libobjc-9-dev libobjc4 libomp-13-dev libomp5-13 libxml2 libz3-4 0 upgraded, 22 newly installed, 0 to remove and 0 not upgraded. Need to get 68.5 MB of archives. After this operation, 379 MB of additional disk space will be used. Get:1 http://127.0.0.1:12990/debian sid/main amd64 libmd0 amd64 1.0.4-1 [29.6 kB] Get:2 http://127.0.0.1:12990/debian sid/main amd64 libbsd0 amd64 0.11.3-1 [108 kB] Get:3 http://127.0.0.1:12990/debian sid/main amd64 libedit2 amd64 3.1-20210910-1 [97.5 kB] Get:4 http://127.0.0.1:12990/debian sid/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get:5 http://127.0.0.1:12990/debian sid/main amd64 libxml2 amd64 2.9.12+dfsg-5 [696 kB] Get:6 http://127.0.0.1:12990/debian sid/main amd64 libz3-4 amd64 4.8.12-1+b1 [6997 kB] Get:7 http://127.0.0.1:12990/debian sid/main amd64 libllvm13 amd64 1:13.0.0-8 [19.7 MB] Get:8 http://127.0.0.1:12990/debian sid/main amd64 libclang-cpp13 amd64 1:13.0.0-8 [10.5 MB] Get:9 http://127.0.0.1:12990/debian sid/main amd64 libgc1 amd64 1:8.0.4-3 [239 kB] Get:10 http://127.0.0.1:12990/debian sid/main amd64 libobjc4 amd64 11.2.0-10 [43.2 kB] Get:11 http://127.0.0.1:12990/debian sid/main amd64 libobjc-11-dev amd64 11.2.0-10 [170 kB] Get:12 http://127.0.0.1:12990/debian sid/main amd64 libc6-i386 amd64 2.32-4 [2624 kB] Get:13 http://127.0.0.1:12990/debian sid/main amd64 lib32gcc-s1 amd64 11.2.0-10 [49.9 kB] Get:14 http://127.0.0.1:12990/debian sid/main amd64 lib32stdc++6 amd64 11.2.0-10 [601 kB] Get:15 http://127.0.0.1:12990/debian sid/main amd64 libclang-common-13-dev amd64 1:13.0.0-8 [5730 kB] Get:16 http://127.0.0.1:12990/debian sid/main amd64 libclang1-13 amd64 1:13.0.0-8 [6093 kB] Get:17 http://127.0.0.1:12990/debian sid/main amd64 clang-13 amd64 1:13.0.0-8 [119 kB] Get:18 http://127.0.0.1:12990/debian sid/main amd64 libasan5 amd64 9.4.0-3 [2734 kB] Get:19 http://127.0.0.1:12990/debian sid/main amd64 libgcc-9-dev amd64 9.4.0-3 [2343 kB] Get:20 http://127.0.0.1:12990/debian sid/main amd64 libobjc-9-dev amd64 9.4.0-3 [219 kB] Get:21 http://127.0.0.1:12990/debian sid/main amd64 libomp5-13 amd64 1:13.0.0-8 [377 kB] Get:22 http://127.0.0.1:12990/debian sid/main amd64 libomp-13-dev amd64 1:13.0.0-8 [482 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 68.5 MB in 0s (149 MB/s) Selecting previously unselected package libmd0:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12431 files and directories currently installed.) Preparing to unpack .../00-libmd0_1.0.4-1_amd64.deb ... Unpacking libmd0:amd64 (1.0.4-1) ... Selecting previously unselected package libbsd0:amd64. Preparing to unpack .../01-libbsd0_0.11.3-1_amd64.deb ... Unpacking libbsd0:amd64 (0.11.3-1) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../02-libedit2_3.1-20210910-1_amd64.deb ... Unpacking libedit2:amd64 (3.1-20210910-1) ... Selecting previously unselected package libicu67:amd64. Preparing to unpack .../03-libicu67_67.1-7_amd64.deb ... Unpacking libicu67:amd64 (67.1-7) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../04-libxml2_2.9.12+dfsg-5_amd64.deb ... Unpacking libxml2:amd64 (2.9.12+dfsg-5) ... Selecting previously unselected package libz3-4:amd64. Preparing to unpack .../05-libz3-4_4.8.12-1+b1_amd64.deb ... Unpacking libz3-4:amd64 (4.8.12-1+b1) ... Selecting previously unselected package libllvm13:amd64. Preparing to unpack .../06-libllvm13_1%3a13.0.0-8_amd64.deb ... Unpacking libllvm13:amd64 (1:13.0.0-8) ... Selecting previously unselected package libclang-cpp13. Preparing to unpack .../07-libclang-cpp13_1%3a13.0.0-8_amd64.deb ... Unpacking libclang-cpp13 (1:13.0.0-8) ... Selecting previously unselected package libgc1:amd64. Preparing to unpack .../08-libgc1_1%3a8.0.4-3_amd64.deb ... Unpacking libgc1:amd64 (1:8.0.4-3) ... Selecting previously unselected package libobjc4:amd64. Preparing to unpack .../09-libobjc4_11.2.0-10_amd64.deb ... Unpacking libobjc4:amd64 (11.2.0-10) ... Selecting previously unselected package libobjc-11-dev:amd64. Preparing to unpack .../10-libobjc-11-dev_11.2.0-10_amd64.deb ... Unpacking libobjc-11-dev:amd64 (11.2.0-10) ... Selecting previously unselected package libc6-i386. Preparing to unpack .../11-libc6-i386_2.32-4_amd64.deb ... Unpacking libc6-i386 (2.32-4) ... Selecting previously unselected package lib32gcc-s1. Preparing to unpack .../12-lib32gcc-s1_11.2.0-10_amd64.deb ... Unpacking lib32gcc-s1 (11.2.0-10) ... Selecting previously unselected package lib32stdc++6. Preparing to unpack .../13-lib32stdc++6_11.2.0-10_amd64.deb ... Unpacking lib32stdc++6 (11.2.0-10) ... Selecting previously unselected package libclang-common-13-dev. Preparing to unpack .../14-libclang-common-13-dev_1%3a13.0.0-8_amd64.deb ... Unpacking libclang-common-13-dev (1:13.0.0-8) ... Selecting previously unselected package libclang1-13. Preparing to unpack .../15-libclang1-13_1%3a13.0.0-8_amd64.deb ... Unpacking libclang1-13 (1:13.0.0-8) ... Selecting previously unselected package clang-13. Preparing to unpack .../16-clang-13_1%3a13.0.0-8_amd64.deb ... Unpacking clang-13 (1:13.0.0-8) ... Selecting previously unselected package libasan5:amd64. Preparing to unpack .../17-libasan5_9.4.0-3_amd64.deb ... Unpacking libasan5:amd64 (9.4.0-3) ... Selecting previously unselected package libgcc-9-dev:amd64. Preparing to unpack .../18-libgcc-9-dev_9.4.0-3_amd64.deb ... Unpacking libgcc-9-dev:amd64 (9.4.0-3) ... Selecting previously unselected package libobjc-9-dev:amd64. Preparing to unpack .../19-libobjc-9-dev_9.4.0-3_amd64.deb ... Unpacking libobjc-9-dev:amd64 (9.4.0-3) ... Selecting previously unselected package libomp5-13:amd64. Preparing to unpack .../20-libomp5-13_1%3a13.0.0-8_amd64.deb ... Unpacking libomp5-13:amd64 (1:13.0.0-8) ... Selecting previously unselected package libomp-13-dev. Preparing to unpack .../21-libomp-13-dev_1%3a13.0.0-8_amd64.deb ... Unpacking libomp-13-dev (1:13.0.0-8) ... Setting up libicu67:amd64 (67.1-7) ... Setting up libasan5:amd64 (9.4.0-3) ... Setting up libz3-4:amd64 (4.8.12-1+b1) ... Setting up libgc1:amd64 (1:8.0.4-3) ... Setting up libmd0:amd64 (1.0.4-1) ... Setting up libc6-i386 (2.32-4) ... Setting up libomp5-13:amd64 (1:13.0.0-8) ... Setting up libbsd0:amd64 (0.11.3-1) ... Setting up libxml2:amd64 (2.9.12+dfsg-5) ... Setting up libedit2:amd64 (3.1-20210910-1) ... Setting up libobjc4:amd64 (11.2.0-10) ... Setting up libgcc-9-dev:amd64 (9.4.0-3) ... Setting up lib32gcc-s1 (11.2.0-10) ... Setting up lib32stdc++6 (11.2.0-10) ... Setting up libllvm13:amd64 (1:13.0.0-8) ... Setting up libobjc-9-dev:amd64 (9.4.0-3) ... Setting up libclang-common-13-dev (1:13.0.0-8) ... Setting up libomp-13-dev (1:13.0.0-8) ... Setting up libobjc-11-dev:amd64 (11.2.0-10) ... Setting up libclang1-13 (1:13.0.0-8) ... Setting up libclang-cpp13 (1:13.0.0-8) ... Setting up clang-13 (1:13.0.0-8) ... Processing triggers for libc-bin (2.32-4) ... W: --force-yes is deprecated, use one of the options starting with --allow instead. + echo 'Replace gcc, g++ & cpp by clang' Replace gcc, g++ & cpp by clang + VERSIONS='4.6 4.7 4.8 4.9 5 6 7 8 9 10 11' + cd /usr/bin + for VERSION in $VERSIONS + rm -f g++-4.6 gcc-4.6 cpp-4.6 gcc + ln -s clang++-13 g++-4.6 + ln -s clang-13 gcc-4.6 + ln -s clang-13 cpp-4.6 + ln -s clang-13 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++-13 g++-4.7 + ln -s clang-13 gcc-4.7 + ln -s clang-13 cpp-4.7 + ln -s clang-13 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++-13 g++-4.8 + ln -s clang-13 gcc-4.8 + ln -s clang-13 cpp-4.8 + ln -s clang-13 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++-13 g++-4.9 + ln -s clang-13 gcc-4.9 + ln -s clang-13 cpp-4.9 + ln -s clang-13 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++-13 g++-5 + ln -s clang-13 gcc-5 + ln -s clang-13 cpp-5 + ln -s clang-13 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++-13 g++-6 + ln -s clang-13 gcc-6 + ln -s clang-13 cpp-6 + ln -s clang-13 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++-13 g++-7 + ln -s clang-13 gcc-7 + ln -s clang-13 cpp-7 + ln -s clang-13 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++-13 g++-8 + ln -s clang-13 gcc-8 + ln -s clang-13 cpp-8 + ln -s clang-13 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++-13 g++-9 + ln -s clang-13 gcc-9 + ln -s clang-13 cpp-9 + ln -s clang-13 gcc + echo 'gcc-9 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-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++-9 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-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++-10 gcc-10 cpp-10 gcc + ln -s clang++-13 g++-10 + ln -s clang-13 gcc-10 + ln -s clang-13 cpp-10 + ln -s clang-13 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 + for VERSION in $VERSIONS + rm -f g++-11 gcc-11 cpp-11 gcc + ln -s clang++-13 g++-11 + ln -s clang-13 gcc-11 + ln -s clang-13 cpp-11 + ln -s clang-13 gcc + echo 'gcc-11 hold' + dpkg --set-selections + echo 'g++-11 hold' + dpkg --set-selections + cd - /build/hyphy-D2Eg1h + 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 + cd /usr/bin/ + rm -f clang++ clang + ln -s clang-13 clang++ + ln -s clang-13 clang + clang++ --version Debian clang version 13.0.0-8 Target: x86_64-pc-linux-gnu Thread model: posix InstalledDir: /usr/bin + clang --version Debian clang version 13.0.0-8 Target: x86_64-pc-linux-gnu Thread model: posix InstalledDir: /usr/bin + cd - /build/hyphy-D2Eg1h + apt install --yes --no-install-recommends --force-yes qt5-qmake WARNING: apt does not have a stable CLI interface. Use with caution in scripts. Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: qt5-qmake-bin qtchooser The following NEW packages will be installed: qt5-qmake qt5-qmake-bin qtchooser 0 upgraded, 3 newly installed, 0 to remove and 0 not upgraded. Need to get 1322 kB of archives. After this operation, 4914 kB of additional disk space will be used. Get:1 http://127.0.0.1:12990/debian sid/main amd64 qt5-qmake-bin amd64 5.15.2+dfsg-12 [1046 kB] Get:2 http://127.0.0.1:12990/debian sid/main amd64 qtchooser amd64 66-2 [26.3 kB] Get:3 http://127.0.0.1:12990/debian sid/main amd64 qt5-qmake amd64 5.15.2+dfsg-12 [249 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 1322 kB in 0s (20.9 MB/s) Selecting previously unselected package qt5-qmake-bin. (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 ... 13528 files and directories currently installed.) Preparing to unpack .../qt5-qmake-bin_5.15.2+dfsg-12_amd64.deb ... Unpacking qt5-qmake-bin (5.15.2+dfsg-12) ... Selecting previously unselected package qtchooser. Preparing to unpack .../qtchooser_66-2_amd64.deb ... Unpacking qtchooser (66-2) ... Selecting previously unselected package qt5-qmake:amd64. Preparing to unpack .../qt5-qmake_5.15.2+dfsg-12_amd64.deb ... Unpacking qt5-qmake:amd64 (5.15.2+dfsg-12) ... Setting up qt5-qmake-bin (5.15.2+dfsg-12) ... Setting up qtchooser (66-2) ... Setting up qt5-qmake:amd64 (5.15.2+dfsg-12) ... W: --force-yes is deprecated, use one of the options starting with --allow instead. + cp /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-clang/qmake.conf /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-clang/qplatformdefs.h /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++/ + ls -al /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++/ total 16 drwxr-xr-x 2 root root 4096 Oct 26 21:44 . drwxr-xr-x 76 root root 4096 Oct 26 21:44 .. -rw-r--r-- 1 root root 276 Oct 26 21:44 qmake.conf -rw-r--r-- 1 root root 3218 Oct 26 21:44 qplatformdefs.h + cat /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++/qmake.conf # # qmake configuration for linux-clang # MAKEFILE_GENERATOR = UNIX CONFIG += incremental QMAKE_INCREMENTAL_STYLE = sublib include(../common/linux.conf) include(../common/gcc-base-unix.conf) include(../common/clang.conf) QMAKE_LFLAGS += -ccc-gcc-name g++ load(qt_config) + export QMAKESPEC=/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-clang/ + QMAKESPEC=/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-clang/ + sed -i -e 's|compare_problem(2,|compare_problem(0,|g' /usr/bin/dpkg-gensymbols + sed -i -e 's|compare_problem(1,|compare_problem(0,|g' /usr/bin/dpkg-gensymbols + grep 'compare_problem(' /usr/bin/dpkg-gensymbols compare_problem(4, g_('new libraries appeared in the symbols file: %s'), "@libs"); compare_problem(3, g_('some libraries disappeared in the symbols file: %s'), "@libs"); compare_problem(0, g_('some new symbols appeared in the symbols file: %s'), compare_problem(0, g_('some symbols or patterns disappeared in the symbols file: %s'), I: Finished running '/tmp/clang13'. Finished processing commands. -------------------------------------------------------------------------------- I: NOTICE: Log filtering will replace 'build/hyphy-D2Eg1h/resolver-4s9f4x' 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... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... 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 2498 kB of source archives. Get:1 http://127.0.0.1:12990/debian sid/main hyphy 2.5.33+dfsg-1 (dsc) [2261 B] Get:2 http://127.0.0.1:12990/debian sid/main hyphy 2.5.33+dfsg-1 (tar) [2480 kB] Get:3 http://127.0.0.1:12990/debian sid/main hyphy 2.5.33+dfsg-1 (diff) [16.5 kB] Fetched 2498 kB in 0s (26.1 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/hyphy-D2Eg1h/hyphy-2.5.33+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/hyphy-D2Eg1h' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), cmake, mpi-default-dev, libcurl4-gnutls-dev | libcurl4-dev, libssl-dev, libsqlite3-dev, pkg-config, chrpath, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), cmake, mpi-default-dev, libcurl4-gnutls-dev, libssl-dev, libsqlite3-dev, pkg-config, chrpath, 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 [428 B] Get:5 copy:/<>/apt_archive ./ Packages [502 B] Fetched 1887 B in 0s (183 kB/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 bsdextrautils chrpath cmake cmake-data cpp-10 debhelper dh-autoreconf dh-elpa-helper dh-strip-nondeterminism dwz emacsen-common file gcc-10 gettext gettext-base gfortran-10 groff-base ibverbs-providers intltool-debian libarchive-zip-perl libarchive13 libbrotli1 libcbor0.8 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 libgcc-10-dev libgfortran-10-dev libgfortran5 libglib2.0-0 libhwloc-dev libhwloc-plugins libhwloc15 libibverbs-dev libibverbs1 libjs-jquery libjs-jquery-ui libjsoncpp24 libldap-2.4-2 libltdl-dev libltdl7 libmagic-mgc libmagic1 libncurses6 libncursesw6 libnghttp2-14 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi3 libpciaccess0 libpipeline1 libpmix-dev libpmix2 libprocps8 libpsl5 libpsm-infinipath1 libpsm2-2 librdmacm1 librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsqlite3-0 libsqlite3-dev libssh2-1 libssl-dev libsub-override-perl libtool libuchardet0 libucx0 libuv1 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxnvctrl0 m4 man-db mpi-default-dev ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client pkg-config po-debconf procps sensible-utils zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc cmake-doc ninja-build gcc-10-locales dh-make gcc-10-multilib gcc-10-doc gettext-doc libasprintf-dev libgettextpo-dev gfortran-10-multilib gfortran-10-doc libcoarrays-dev groff lrzip libcurl4-doc libgnutls28-dev libidn11-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev libhwloc-contrib-plugins libjs-jquery-ui-docs 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 javascript-common libldap-common libgpm2 libcoarrays-openmpi-dev publicsuffix libsasl2-modules xauth libmail-sendmail-perl psmisc The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils chrpath cmake cmake-data cpp-10 debhelper dh-autoreconf dh-elpa-helper dh-strip-nondeterminism dwz emacsen-common file gcc-10 gettext gettext-base gfortran-10 groff-base ibverbs-providers intltool-debian libarchive-zip-perl libarchive13 libbrotli1 libcbor0.8 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 libgcc-10-dev libgfortran-10-dev libgfortran5 libglib2.0-0 libhwloc-dev libhwloc-plugins libhwloc15 libibverbs-dev libibverbs1 libjs-jquery libjs-jquery-ui libjsoncpp24 libldap-2.4-2 libltdl-dev libltdl7 libmagic-mgc libmagic1 libncurses6 libncursesw6 libnghttp2-14 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi3 libpciaccess0 libpipeline1 libpmix-dev libpmix2 libprocps8 libpsl5 libpsm-infinipath1 libpsm2-2 librdmacm1 librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsqlite3-0 libsqlite3-dev libssh2-1 libssl-dev libsub-override-perl libtool libuchardet0 libucx0 libuv1 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 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 zlib1g-dev 0 upgraded, 113 newly installed, 0 to remove and 0 not upgraded. Need to get 79.9 MB of archives. After this operation, 282 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [932 B] Get:2 http://127.0.0.1:12990/debian sid/main amd64 bsdextrautils amd64 2.37.2-4 [143 kB] Get:3 http://127.0.0.1:12990/debian sid/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get:4 http://127.0.0.1:12990/debian sid/main amd64 groff-base amd64 1.22.4-7 [935 kB] Get:5 http://127.0.0.1:12990/debian sid/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get:6 http://127.0.0.1:12990/debian sid/main amd64 man-db amd64 2.9.4-2 [1354 kB] Get:7 http://127.0.0.1:12990/debian sid/main amd64 libncurses6 amd64 6.2+20210905-1 [102 kB] Get:8 http://127.0.0.1:12990/debian sid/main amd64 libncursesw6 amd64 6.2+20210905-1 [133 kB] Get:9 http://127.0.0.1:12990/debian sid/main amd64 libprocps8 amd64 2:3.3.17-5 [63.9 kB] Get:10 http://127.0.0.1:12990/debian sid/main amd64 procps amd64 2:3.3.17-5 [502 kB] Get:11 http://127.0.0.1:12990/debian sid/main amd64 sensible-utils all 0.0.17 [21.5 kB] Get:12 http://127.0.0.1:12990/debian sid/main amd64 libmagic-mgc amd64 1:5.39-3 [273 kB] Get:13 http://127.0.0.1:12990/debian sid/main amd64 libmagic1 amd64 1:5.39-3 [126 kB] Get:14 http://127.0.0.1:12990/debian sid/main amd64 file amd64 1:5.39-3 [69.1 kB] Get:15 http://127.0.0.1:12990/debian sid/main amd64 gettext-base amd64 0.21-4 [175 kB] Get:16 http://127.0.0.1:12990/debian sid/main amd64 libcbor0.8 amd64 0.8.0-1 [27.1 kB] Get:17 http://127.0.0.1:12990/debian sid/main amd64 libfido2-1 amd64 1.8.0-1+b1 [63.4 kB] Get:18 http://127.0.0.1:12990/debian sid/main amd64 openssh-client amd64 1:8.4p1-6 [929 kB] Get:19 http://127.0.0.1:12990/debian sid/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get:20 http://127.0.0.1:12990/debian sid/main amd64 m4 amd64 1.4.18-5 [204 kB] Get:21 http://127.0.0.1:12990/debian sid/main amd64 autoconf all 2.71-2 [343 kB] Get:22 http://127.0.0.1:12990/debian sid/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get:23 http://127.0.0.1:12990/debian sid/main amd64 automake all 1:1.16.5-1 [823 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1.10.0-2 [178 kB] Get:35 http://127.0.0.1:12990/debian sid/main amd64 libcurl4 amd64 7.74.0-1.3+b1 [341 kB] Get:36 http://127.0.0.1:12990/debian sid/main amd64 libexpat1 amd64 2.4.1-3 [104 kB] Get:37 http://127.0.0.1:12990/debian sid/main amd64 libjsoncpp24 amd64 1.9.4-5 [78.8 kB] Get:38 http://127.0.0.1:12990/debian sid/main amd64 librhash0 amd64 1.4.2-1 [129 kB] Get:39 http://127.0.0.1:12990/debian sid/main amd64 libuv1 amd64 1.42.0-1 [135 kB] Get:40 http://127.0.0.1:12990/debian sid/main amd64 dh-elpa-helper all 2.0.9 [11.2 kB] Get:41 http://127.0.0.1:12990/debian sid/main amd64 emacsen-common all 3.0.4 [19.3 kB] Get:42 http://127.0.0.1:12990/debian sid/main amd64 cmake-data all 3.21.3-5 [1878 kB] Get:43 http://127.0.0.1:12990/debian sid/main amd64 cmake amd64 3.21.3-5 [7907 kB] Get:44 http://127.0.0.1:12990/debian sid/main amd64 cpp-10 amd64 10.3.0-11 [8569 kB] Get:45 http://127.0.0.1:12990/debian sid/main amd64 libdebhelper-perl all 13.5.2 [192 kB] Get:46 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http://127.0.0.1:12990/debian sid/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:58 http://127.0.0.1:12990/debian sid/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:59 http://127.0.0.1:12990/debian sid/main amd64 debhelper all 13.5.2 [1056 kB] Get:60 http://127.0.0.1:12990/debian sid/main amd64 libgfortran5 amd64 11.2.0-10 [710 kB] Get:61 http://127.0.0.1:12990/debian sid/main amd64 libgfortran-10-dev amd64 10.3.0-11 [769 kB] Get:62 http://127.0.0.1:12990/debian sid/main amd64 gfortran-10 amd64 10.3.0-11 [9491 kB] Get:63 http://127.0.0.1:12990/debian sid/main amd64 libnl-3-200 amd64 3.4.0-1+b1 [63.6 kB] Get:64 http://127.0.0.1:12990/debian sid/main amd64 libnl-route-3-200 amd64 3.4.0-1+b1 [161 kB] Get:65 http://127.0.0.1:12990/debian sid/main amd64 libibverbs1 amd64 36.0-1 [60.3 kB] Get:66 http://127.0.0.1:12990/debian sid/main amd64 ibverbs-providers amd64 36.0-1 [275 kB] Get:67 http://127.0.0.1:12990/debian sid/main amd64 libcurl3-gnutls amd64 7.74.0-1.3+b1 [338 kB] Get:68 http://127.0.0.1:12990/debian sid/main amd64 libcurl4-gnutls-dev amd64 7.74.0-1.3+b1 [429 kB] Get:69 http://127.0.0.1:12990/debian sid/main amd64 libevent-2.1-7 amd64 2.1.12-stable-1 [188 kB] Get:70 http://127.0.0.1:12990/debian sid/main amd64 libevent-core-2.1-7 amd64 2.1.12-stable-1 [139 kB] Get:71 http://127.0.0.1:12990/debian sid/main amd64 libevent-extra-2.1-7 amd64 2.1.12-stable-1 [110 kB] Get:72 http://127.0.0.1:12990/debian sid/main amd64 libevent-pthreads-2.1-7 amd64 2.1.12-stable-1 [57.1 kB] Get:73 http://127.0.0.1:12990/debian sid/main amd64 libevent-openssl-2.1-7 amd64 2.1.12-stable-1 [64.1 kB] Get:74 http://127.0.0.1:12990/debian sid/main amd64 libevent-dev amd64 2.1.12-stable-1 [311 kB] Get:75 http://127.0.0.1:12990/debian sid/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.1 [169 kB] Get:76 http://127.0.0.1:12990/debian sid/main amd64 libnuma1 amd64 2.0.14-3 [24.4 kB] Get:77 http://127.0.0.1:12990/debian sid/main amd64 libpsm2-2 amd64 11.2.185-1 [181 kB] Get:78 http://127.0.0.1:12990/debian sid/main amd64 librdmacm1 amd64 36.0-1 [69.1 kB] Get:79 http://127.0.0.1:12990/debian sid/main amd64 libfabric1 amd64 1.11.0-2 [521 kB] Get:80 http://127.0.0.1:12990/debian sid/main amd64 libglib2.0-0 amd64 2.70.0-3 [1401 kB] Get:81 http://127.0.0.1:12990/debian sid/main amd64 libhwloc15 amd64 2.5.0+dfsg-2 [154 kB] Get:82 http://127.0.0.1:12990/debian sid/main amd64 libnuma-dev amd64 2.0.14-3 [37.8 kB] Get:83 http://127.0.0.1:12990/debian sid/main amd64 libltdl7 amd64 2.4.6-15 [391 kB] Get:84 http://127.0.0.1:12990/debian sid/main amd64 libltdl-dev amd64 2.4.6-15 [162 kB] Get:85 http://127.0.0.1:12990/debian sid/main amd64 libhwloc-dev amd64 2.5.0+dfsg-2 [239 kB] Get:86 http://127.0.0.1:12990/debian sid/main amd64 libpciaccess0 amd64 0.16-1 [53.6 kB] Get:87 http://127.0.0.1:12990/debian sid/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get:88 http://127.0.0.1:12990/debian sid/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:89 http://127.0.0.1:12990/debian sid/main amd64 libxcb1 amd64 1.14-3 [140 kB] Get:90 http://127.0.0.1:12990/debian sid/main amd64 libx11-data all 2:1.7.2-2 [311 kB] Get:91 http://127.0.0.1:12990/debian sid/main amd64 libx11-6 amd64 2:1.7.2-2+b1 [772 kB] Get:92 http://127.0.0.1:12990/debian sid/main amd64 libxext6 amd64 2:1.3.4-1 [53.1 kB] Get:93 http://127.0.0.1:12990/debian sid/main amd64 libxnvctrl0 amd64 470.57.02-2 [27.1 kB] Get:94 http://127.0.0.1:12990/debian sid/main amd64 ocl-icd-libopencl1 amd64 2.2.14-3 [42.6 kB] Get:95 http://127.0.0.1:12990/debian sid/main amd64 libhwloc-plugins amd64 2.5.0+dfsg-2 [21.6 kB] Get:96 http://127.0.0.1:12990/debian sid/main amd64 libnl-3-dev amd64 3.4.0-1+b1 [102 kB] Get:97 http://127.0.0.1:12990/debian sid/main amd64 libnl-route-3-dev amd64 3.4.0-1+b1 [176 kB] Get:98 http://127.0.0.1:12990/debian sid/main amd64 libibverbs-dev amd64 36.0-1 [533 kB] Get:99 http://127.0.0.1:12990/debian sid/main amd64 libjs-jquery all 3.5.1+dfsg+~3.5.5-8 [315 kB] Get:100 http://127.0.0.1:12990/debian sid/main amd64 libjs-jquery-ui all 1.12.1+dfsg-8 [232 kB] Get:101 http://127.0.0.1:12990/debian sid/main amd64 libpmix2 amd64 4.1.1~rc4-1 [572 kB] Get:102 http://127.0.0.1:12990/debian sid/main amd64 libucx0 amd64 1.11.2-1 [765 kB] Get:103 http://127.0.0.1:12990/debian sid/main amd64 libopenmpi3 amd64 4.1.2~rc1-4 [2388 kB] Get:104 http://127.0.0.1:12990/debian sid/main amd64 openmpi-common all 4.1.2~rc1-4 [183 kB] Get:105 http://127.0.0.1:12990/debian sid/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2 [190 kB] Get:106 http://127.0.0.1:12990/debian sid/main amd64 libpmix-dev amd64 4.1.1~rc4-1 [715 kB] Get:107 http://127.0.0.1:12990/debian sid/main amd64 openmpi-bin amd64 4.1.2~rc1-4 [241 kB] Get:108 http://127.0.0.1:12990/debian sid/main amd64 libopenmpi-dev amd64 4.1.2~rc1-4 [986 kB] Get:109 http://127.0.0.1:12990/debian sid/main amd64 libsqlite3-0 amd64 3.36.0-2 [815 kB] Get:110 http://127.0.0.1:12990/debian sid/main amd64 libsqlite3-dev amd64 3.36.0-2 [984 kB] Get:111 http://127.0.0.1:12990/debian sid/main amd64 libssl-dev amd64 1.1.1l-1 [1809 kB] Get:112 http://127.0.0.1:12990/debian sid/main amd64 mpi-default-dev amd64 1.14 [5548 B] Get:113 http://127.0.0.1:12990/debian sid/main amd64 pkg-config amd64 0.29.2-1 [65.1 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 79.9 MB in 1s (145 MB/s) Selecting previously unselected package bsdextrautils. 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Setting up libgcc-10-dev:amd64 (10.3.0-11) ... Setting up libdebhelper-perl (13.5.2) ... Setting up libbrotli1:amd64 (1.0.9-2+b2) ... Setting up libsqlite3-0:amd64 (3.36.0-2) ... Setting up libnghttp2-14:amd64 (1.43.0-1) ... Setting up libmagic1:amd64 (1:5.39-3) ... Setting up gettext-base (0.21-4) ... Setting up file (1:5.39-3) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-2.1) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libuv1:amd64 (1.42.0-1) ... Setting up emacsen-common (3.0.4) ... Setting up libsqlite3-dev:amd64 (3.36.0-2) ... Setting up libx11-data (2:1.7.2-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up dh-elpa-helper (2.0.9) ... Setting up libncurses6:amd64 (6.2+20210905-1) ... Setting up libsigsegv2:amd64 (2.13-1) ... Setting up libssl-dev:amd64 (1.1.1l-1) ... Setting up libhwloc15:amd64 (2.5.0+dfsg-2) ... Setting up libevent-core-2.1-7:amd64 (2.1.12-stable-1) ... Setting up libevent-2.1-7:amd64 (2.1.12-stable-1) ... Setting up autopoint (0.21-4) ... Setting up pkg-config (0.29.2-1) ... Setting up libncursesw6:amd64 (6.2+20210905-1) ... Setting up libltdl7:amd64 (2.4.6-15) ... Setting up libsasl2-2:amd64 (2.1.27+dfsg-2.1) ... Setting up libgfortran5:amd64 (11.2.0-10) ... Setting up libjsoncpp24:amd64 (1.9.4-5) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-2) ... Setting up libnuma1:amd64 (2.0.14-3) ... Setting up sensible-utils (0.0.17) ... Setting up ocl-icd-libopencl1:amd64 (2.2.14-3) ... Setting up librhash0:amd64 (1.4.2-1) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libnl-3-200:amd64 (3.4.0-1+b1) ... Setting up libpsm2-2 (11.2.185-1) ... Setting up openmpi-common (4.1.2~rc1-4) ... Setting up libsub-override-perl (0.09-2) ... Setting up libx11-6:amd64 (2:1.7.2-2+b1) ... Setting up libgfortran-10-dev:amd64 (10.3.0-11) ... Setting up libssh2-1:amd64 (1.10.0-2) ... Setting up cmake-data (3.21.3-5) ... Setting up libpsm-infinipath1 (3.3+20.604758e7-6.1) ... 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 libjs-jquery (3.5.1+dfsg+~3.5.5-8) ... Setting up libfido2-1:amd64 (1.8.0-1+b1) ... Setting up libelf1:amd64 (0.185-2) ... Setting up chrpath (0.16-2+b1) ... Setting up libprocps8:amd64 (2:3.3.17-5) ... Setting up cpp-10 (10.3.0-11) ... Setting up libevent-pthreads-2.1-7:amd64 (2.1.12-stable-1) ... Setting up libfile-stripnondeterminism-perl (1.12.0-2) ... Setting up libevent-extra-2.1-7:amd64 (2.1.12-stable-1) ... Setting up gettext (0.21-4) ... Setting up libtool (2.4.6-15) ... Setting up openssh-client (1:8.4p1-6) ... Setting up libxext6:amd64 (2:1.3.4-1) ... Setting up libevent-openssl-2.1-7:amd64 (2.1.12-stable-1) ... Setting up libldap-2.4-2:amd64 (2.4.59+dfsg-1) ... Setting up m4 (1.4.18-5) ... Setting up libcurl3-gnutls:amd64 (7.74.0-1.3+b1) ... Setting up libcurl4-gnutls-dev:amd64 (7.74.0-1.3+b1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libnuma-dev:amd64 (2.0.14-3) ... Setting up libnl-route-3-200:amd64 (3.4.0-1+b1) ... Setting up libxnvctrl0:amd64 (470.57.02-2) ... Setting up libjs-jquery-ui (1.12.1+dfsg-8) ... Setting up libevent-dev (2.1.12-stable-1) ... Setting up gcc-10 (10.3.0-11) ... Setting up autoconf (2.71-2) ... Setting up dh-strip-nondeterminism (1.12.0-2) ... Setting up dwz (0.14-1) ... Setting up libnl-3-dev:amd64 (3.4.0-1+b1) ... Setting up groff-base (1.22.4-7) ... Setting up procps (2:3.3.17-5) ... Setting up libcurl4:amd64 (7.74.0-1.3+b1) ... Setting up automake (1:1.16.5-1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libibverbs1:amd64 (36.0-1) ... Setting up ibverbs-providers:amd64 (36.0-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhwloc-plugins:amd64 (2.5.0+dfsg-2) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up dh-autoreconf (20) ... Setting up libnl-route-3-dev:amd64 (3.4.0-1+b1) ... Setting up libltdl-dev:amd64 (2.4.6-15) ... Setting up gfortran-10 (10.3.0-11) ... Setting up cmake (3.21.3-5) ... Setting up libhwloc-dev:amd64 (2.5.0+dfsg-2) ... Setting up librdmacm1:amd64 (36.0-1) ... Setting up libucx0:amd64 (1.11.2-1) ... Setting up libpmix2:amd64 (4.1.1~rc4-1) ... Setting up debhelper (13.5.2) ... Setting up libibverbs-dev:amd64 (36.0-1) ... Setting up libpmix-dev:amd64 (4.1.1~rc4-1) ... Setting up libfabric1 (1.11.0-2) ... Setting up libopenmpi3:amd64 (4.1.2~rc1-4) ... Setting up openmpi-bin (4.1.2~rc1-4) ... 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 (4.1.2~rc1-4) ... 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 (1.14) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.32-4) ... +------------------------------------------------------------------------------+ | 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_2.37-7 dpkg-dev_1.20.9 g++-11_11.2.0-10 gcc-10_10.3.0-11 gcc-11_11.2.0-10 libc6-dev_2.32-4 libstdc++-11-dev_11.2.0-10 libstdc++6_11.2.0-10 linux-libc-dev_5.14.12-1 Package versions: adduser_3.118 apt_2.3.11 autoconf_2.71-2 automake_1:1.16.5-1 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_12 base-passwd_3.5.52 bash_5.1-3+b2 binutils_2.37-7 binutils-common_2.37-7 binutils-x86-64-linux-gnu_2.37-7 bsdextrautils_2.37.2-4 bsdutils_1:2.37.2-4 build-essential_12.9 bzip2_1.0.8-4 chrpath_0.16-2+b1 clang-13_1:13.0.0-8 cmake_3.21.3-5 cmake-data_3.21.3-5 coreutils_8.32-4+b1 cpp_4:11.2.0-2 cpp-10_10.3.0-11 cpp-11_11.2.0-10 dash_0.5.11+git20210120+802ebd4-2 debconf_1.5.78 debhelper_13.5.2 debian-archive-keyring_2021.1.1 debianutils_5.5-1 dh-autoreconf_20 dh-elpa-helper_2.0.9 dh-strip-nondeterminism_1.12.0-2 diffutils_1:3.7-5 dpkg_1.20.9 dpkg-dev_1.20.9 dwz_0.14-1 e2fsprogs_1.46.4-1 emacsen-common_3.0.4 fakeroot_1.26-1 file_1:5.39-3 findutils_4.8.0-1 g++_4:11.2.0-2 g++-11_11.2.0-10 gcc_4:11.2.0-2 gcc-10_10.3.0-11 gcc-10-base_10.3.0-11 gcc-11_11.2.0-10 gcc-11-base_11.2.0-10 gcc-9-base_9.4.0-3 gettext_0.21-4 gettext-base_0.21-4 gfortran-10_10.3.0-11 gpgv_2.2.27-2 grep_3.7-1 groff-base_1.22.4-7 gzip_1.10-4 hostname_3.23 ibverbs-providers_36.0-1 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 lib32gcc-s1_11.2.0-10 lib32stdc++6_11.2.0-10 libacl1_2.3.1-1 libapt-pkg6.0_2.3.11 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+------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: hyphy Binary: hyphy-pt, hyphy-mpi, hyphy-common Architecture: any all Version: 2.5.33+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Étienne Mollier , Nilesh Patra Homepage: https://hyphy.org/ Standards-Version: 4.6.0 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 (= 13), cmake, mpi-default-dev, libcurl4-gnutls-dev | libcurl4-dev, libssl-dev, libsqlite3-dev, pkg-config, chrpath 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: bad30acd91f44cd1a73a9f26f7a069eb52dfaaf4 2479656 hyphy_2.5.33+dfsg.orig.tar.xz 956dbe9a669465b555a490a8b8a8ab80af7bc4e3 16484 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dpkg-source: info: applying rm_arch_specific_flags.patch dpkg-source: info: applying set-zlib-after-setting-default-libs.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-fa31d336-3089-413b-beec-07aff9fab658 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 2.5.33+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --buildsystem=cmake debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' dh_auto_clean --builddirectory obj-avx dh_auto_clean --builddirectory obj-sse3 dh_auto_clean make[1]: Leaving directory '/<>' dh_autoreconf_clean -O--buildsystem=cmake dh_clean -O--buildsystem=cmake debian/rules binary dh binary --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 -DNOAVX=ON -DNOSSE3=ON 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_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DINSTALL_PREFIX=/usr -DNOAVX=ON -DNOSSE3=ON .. -- The C compiler identification is Clang 13.0.0 -- The CXX compiler identification is Clang 13.0.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Performing Test HAVE_NEON_EXTENSIONS -- Performing Test HAVE_NEON_EXTENSIONS - Failed Set compiler flags to -fsigned-char -O3 -- Found OpenMP_C: -fopenmp=libomp (found version "5.0") -- Found OpenMP_CXX: -fopenmp=libomp (found version "5.0") -- Found OpenMP: TRUE (found version "5.0") -- Found CURL: /usr/lib/x86_64-linux-gnu/libcurl.so (found version "7.74.0") /usr/lib/x86_64-linux-gnu/libcurl.so Node not installed; API documentation will not be generated -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.2") -- Checking for module 'sqlite3' -- Found sqlite3, version 3.36.0 -- Found SQLITE3: /usr/lib/x86_64-linux-gnu/libsqlite3.so -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found suitable version "1.2.11", minimum required is "1.2.9") CMake Warning (dev) at /usr/share/cmake-3.21/Modules/FindPackageHandleStandardArgs.cmake:438 (message): The package name passed to `find_package_handle_standard_args` (PkgConfig) does not match the name of the calling package (MPI). This can lead to problems in calling code that expects `find_package` result variables (e.g., `_FOUND`) to follow a certain pattern. Call Stack (most recent call first): /usr/share/cmake-3.21/Modules/FindPkgConfig.cmake:70 (find_package_handle_standard_args) /usr/share/cmake-3.21/Modules/FindMPI.cmake:270 (include) CMakeLists.txt:438 (find_package) This warning is for project developers. Use -Wno-dev to suppress it. -- 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_FIND_PACKAGE_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 dh_auto_configure --builddirectory obj-avx -- -DINSTALL_PREFIX=/usr -DNOAVX=OFF -DNOSSE3=OFF cd obj-avx && 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_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DINSTALL_PREFIX=/usr -DNOAVX=OFF -DNOSSE3=OFF .. -- The C compiler identification is Clang 13.0.0 -- The CXX compiler identification is Clang 13.0.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Performing Test HAVE_AVX_EXTENSIONS -- Performing Test HAVE_AVX_EXTENSIONS - Success -- Performing Test HAVE_FMA3 -- Performing Test HAVE_FMA3 - Success -- Performing Test HAVE_NEON_EXTENSIONS -- Performing Test HAVE_NEON_EXTENSIONS - Failed Set compiler flags to -fsigned-char -O3 -mavx -mfma -- Found OpenMP_C: -fopenmp=libomp (found version "5.0") -- Found OpenMP_CXX: -fopenmp=libomp (found version "5.0") -- Found OpenMP: TRUE (found version "5.0") -- Found CURL: /usr/lib/x86_64-linux-gnu/libcurl.so (found version "7.74.0") /usr/lib/x86_64-linux-gnu/libcurl.so Node not installed; API documentation will not be generated -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.2") -- Checking for module 'sqlite3' -- Found sqlite3, version 3.36.0 -- Found SQLITE3: /usr/lib/x86_64-linux-gnu/libsqlite3.so -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found suitable version "1.2.11", minimum required is "1.2.9") CMake Warning (dev) at /usr/share/cmake-3.21/Modules/FindPackageHandleStandardArgs.cmake:438 (message): The package name passed to `find_package_handle_standard_args` (PkgConfig) does not match the name of the calling package (MPI). This can lead to problems in calling code that expects `find_package` result variables (e.g., `_FOUND`) to follow a certain pattern. Call Stack (most recent call first): /usr/share/cmake-3.21/Modules/FindPkgConfig.cmake:70 (find_package_handle_standard_args) /usr/share/cmake-3.21/Modules/FindMPI.cmake:270 (include) CMakeLists.txt:438 (find_package) This warning is for project developers. Use -Wno-dev to suppress it. -- 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_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR INSTALL_PREFIX -- Build files have been written to: /<>/obj-avx dh_auto_configure --builddirectory obj-sse3 -- -DINSTALL_PREFIX=/usr -DNOAVX=ON -DNOSSE3=OFF cd obj-sse3 && 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_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DINSTALL_PREFIX=/usr -DNOAVX=ON -DNOSSE3=OFF .. -- The C compiler identification is Clang 13.0.0 -- The CXX compiler identification is Clang 13.0.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Performing Test HAVE_SSE3_EXTENSIONS -- Performing Test HAVE_SSE3_EXTENSIONS - Success -- Performing Test HAVE_NEON_EXTENSIONS -- Performing Test HAVE_NEON_EXTENSIONS - Failed Set compiler flags to -fsigned-char -O3 -msse3 -- Found OpenMP_C: -fopenmp=libomp (found version "5.0") -- Found OpenMP_CXX: -fopenmp=libomp (found version "5.0") -- Found OpenMP: TRUE (found version "5.0") -- Found CURL: /usr/lib/x86_64-linux-gnu/libcurl.so (found version "7.74.0") /usr/lib/x86_64-linux-gnu/libcurl.so Node not installed; API documentation will not be generated -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.2") -- Checking for module 'sqlite3' -- Found sqlite3, version 3.36.0 -- Found SQLITE3: /usr/lib/x86_64-linux-gnu/libsqlite3.so -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found suitable version "1.2.11", minimum required is "1.2.9") CMake Warning (dev) at /usr/share/cmake-3.21/Modules/FindPackageHandleStandardArgs.cmake:438 (message): The package name passed to `find_package_handle_standard_args` (PkgConfig) does not match the name of the calling package (MPI). This can lead to problems in calling code that expects `find_package` result variables (e.g., `_FOUND`) to follow a certain pattern. Call Stack (most recent call first): /usr/share/cmake-3.21/Modules/FindPkgConfig.cmake:70 (find_package_handle_standard_args) /usr/share/cmake-3.21/Modules/FindMPI.cmake:270 (include) CMakeLists.txt:438 (find_package) This warning is for project developers. Use -Wno-dev to suppress it. -- 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_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR INSTALL_PREFIX -- Build files have been written to: /<>/obj-sse3 make[1]: Leaving directory '/<>' debian/rules override_dh_auto_build make[1]: Entering directory '/<>' # convert a few ISO-8859-1 files to address national-encoding set -e \ ; for file in res/TemplateBatchFiles/PARRIS.bf res/TemplateBatchFiles/TemplateModels/MEC.mdl res/TemplateBatchFiles/TemplateModels/models.lst \ ; do iconv -f ISO-8859-1 -t UTF-8 < ${file} > "${file}.new" \ ; mv "${file}.new" "${file}" \ ; done dh_auto_build -- MP MPI cd obj-x86_64-linux-gnu && make -j4 "INSTALL=install --strip-program=true" MP MPI VERBOSE=1 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 20 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= 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/alignment.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/avllist.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/<>/src/core/include -I/<>/src/contrib -I/<>/src/lib/Link -I/<>/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -w -g -fopenmp=libomp -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/_hyExecutionContext.cpp.o -MF CMakeFiles/hyphy.dir/src/core/_hyExecutionContext.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/_hyExecutionContext.cpp.o -c /<>/src/core/_hyExecutionContext.cpp /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/<>/src/core/include -I/<>/src/contrib -I/<>/src/lib/Link -I/<>/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -w -g -fopenmp=libomp -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/alignment.cpp.o -MF CMakeFiles/hyphy.dir/src/core/alignment.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/alignment.cpp.o -c /<>/src/core/alignment.cpp /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/<>/src/core/include -I/<>/src/contrib -I/<>/src/lib/Link -I/<>/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -w -g -fopenmp=libomp -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/associative_list.cpp.o -MF CMakeFiles/hyphy.dir/src/core/associative_list.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/associative_list.cpp.o -c /<>/src/core/associative_list.cpp /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/<>/src/core/include -I/<>/src/contrib -I/<>/src/lib/Link -I/<>/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -w -g -fopenmp=libomp -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/avllist.cpp.o -MF CMakeFiles/hyphy.dir/src/core/avllist.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/avllist.cpp.o -c /<>/src/core/avllist.cpp In file included from /<>/src/core/associative_list.cpp:62: In file included from /<>/src/core/include/global_object_lists.h:42: In file included from /<>/src/core/include/dataset_filter.h:44: In file included from /<>/src/core/include/dataset.h:47: /<>/src/core/include/function_templates.h:160:15: error: duplicate directives 'unroll_count(8)' and '#pragma unroll(4)' #pragma GCC unroll 4 ^ In file included from /<>/src/core/alignment.cpp:44: In file included from /<>/src/core/include/alignment.h:44: In file included from /<>/src/core/include/likefunc.h:44: In file included from /<>/src/core/include/category.h:44: In file included from /<>/src/core/include/batchlan.h:47: In file included from /<>/src/core/include/dataset.h:47: /<>/src/core/include/function_templates.h:160:15: error: duplicate directives 'unroll_count(8)' and '#pragma unroll(4)' #pragma GCC unroll 4 ^ [ 5%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllistx.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/<>/src/core/include -I/<>/src/contrib -I/<>/src/lib/Link -I/<>/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -w -g -fopenmp=libomp -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/avllistx.cpp.o -MF CMakeFiles/hyphy.dir/src/core/avllistx.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/avllistx.cpp.o -c /<>/src/core/avllistx.cpp 1 error generated. make[5]: *** [CMakeFiles/hyphy.dir/build.make:107: CMakeFiles/hyphy.dir/src/core/associative_list.cpp.o] Error 1 make[5]: *** Waiting for unfinished jobs.... 1 error generated. make[5]: *** [CMakeFiles/hyphy.dir/build.make:93: CMakeFiles/hyphy.dir/src/core/alignment.cpp.o] Error 1 make[5]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[4]: *** [CMakeFiles/Makefile2:122: CMakeFiles/hyphy.dir/all] Error 2 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: *** [CMakeFiles/Makefile2:363: CMakeFiles/MP.dir/rule] Error 2 make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[2]: *** [Makefile:312: 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 VERBOSE=1 returned exit code 2 make[1]: *** [debian/rules:37: override_dh_auto_build] Error 25 make[1]: Leaving directory '/<>' make: *** [debian/rules:16: binary] Error 2 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2021-10-26T21:45:12Z 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: 30436 Build-Time: 11 Distribution: unstable Fail-Stage: build Host Architecture: amd64 Install-Time: 21 Job: hyphy_2.5.33+dfsg-1 Machine Architecture: amd64 Package: hyphy Package-Time: 53 Source-Version: 2.5.33+dfsg-1 Space: 30436 Status: attempted Version: 2.5.33+dfsg-1 -------------------------------------------------------------------------------- Finished at 2021-10-26T21:45:12Z Build needed 00:00:53, 30436k disk space E: Build failure (dpkg-buildpackage died) DC-Status: Failed 54.59456631s DC-Time-Estimation: 54.59456631 versus expected 312 (r/m: 4.714854445924071 ; m: 54.59456631)