DC-Build-Header: libpsortb 1.0+dfsg-4 / 2021-10-26 23:01:34 +0000 DC-Task: type:rebuild-binarch-only source:libpsortb version:1.0+dfsg-4 chroot:unstable esttime:70 logfile:/tmp/libpsortb_1.0+dfsg-4_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 libpsortb_1.0+dfsg-4' sbuild (Debian sbuild) 0.78.1 (09 February 2019) on ip-172-31-12-73.eu-central-1.compute.internal +==============================================================================+ | libpsortb 1.0+dfsg-4 (amd64) Tue, 26 Oct 2021 23:01:35 +0000 | +==============================================================================+ Package: libpsortb Version: 1.0+dfsg-4 Source Version: 1.0+dfsg-4 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-45d0c29d-9d9b-4143-a6f1-c82ce4f8da6e' 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 (2721 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 (156 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/libpsortb-afNFKI + 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/libpsortb-afNFKI + 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 (58.3 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 23:01 . drwxr-xr-x 76 root root 4096 Oct 26 23:01 .. -rw-r--r-- 1 root root 276 Oct 26 23:01 qmake.conf -rw-r--r-- 1 root root 3218 Oct 26 23:01 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/libpsortb-afNFKI/resolver-R5hVDB' 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: 'libpsortb' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/libpsortb.git Please use: git clone https://salsa.debian.org/med-team/libpsortb.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 103 kB of source archives. Get:1 http://127.0.0.1:12990/debian sid/main libpsortb 1.0+dfsg-4 (dsc) [2188 B] Get:2 http://127.0.0.1:12990/debian sid/main libpsortb 1.0+dfsg-4 (tar) [95.6 kB] Get:3 http://127.0.0.1:12990/debian sid/main libpsortb 1.0+dfsg-4 (diff) [5124 B] Fetched 103 kB in 0s (1350 kB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/libpsortb-afNFKI/libpsortb-1.0+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/libpsortb-afNFKI' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), d-shlibs, libsvm-dev, libsquid-dev, libhmmer2-dev, pkg-config, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), d-shlibs, libsvm-dev, libsquid-dev, libhmmer2-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 [403 B] Get:5 copy:/<>/apt_archive ./ Packages [482 B] Fetched 1842 B in 0s (181 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 d-shlibs debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libdebhelper-perl libelf1 libfile-stripnondeterminism-perl libglib2.0-0 libhmmer2-dev libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libsquid-dev libsquid1 libsub-override-perl libsvm-dev libsvm3 libtool libuchardet0 m4 man-db pkg-config po-debconf sensible-utils Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff biosquid libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils d-shlibs debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libdebhelper-perl libelf1 libfile-stripnondeterminism-perl libglib2.0-0 libhmmer2-dev libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libsquid-dev libsquid1 libsub-override-perl libsvm-dev libsvm3 libtool libuchardet0 m4 man-db pkg-config po-debconf sbuild-build-depends-main-dummy sensible-utils 0 upgraded, 38 newly installed, 0 to remove and 0 not upgraded. Need to get 10.9 MB of archives. After this operation, 37.7 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [908 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 sensible-utils all 0.0.17 [21.5 kB] Get:8 http://127.0.0.1:12990/debian sid/main amd64 libmagic-mgc amd64 1:5.39-3 [273 kB] Get:9 http://127.0.0.1:12990/debian sid/main amd64 libmagic1 amd64 1:5.39-3 [126 kB] Get:10 http://127.0.0.1:12990/debian sid/main amd64 file amd64 1:5.39-3 [69.1 kB] Get:11 http://127.0.0.1:12990/debian sid/main amd64 gettext-base amd64 0.21-4 [175 kB] Get:12 http://127.0.0.1:12990/debian sid/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get:13 http://127.0.0.1:12990/debian sid/main amd64 m4 amd64 1.4.18-5 [204 kB] Get:14 http://127.0.0.1:12990/debian sid/main amd64 autoconf all 2.71-2 [343 kB] Get:15 http://127.0.0.1:12990/debian sid/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get:16 http://127.0.0.1:12990/debian sid/main amd64 automake all 1:1.16.5-1 [823 kB] Get:17 http://127.0.0.1:12990/debian sid/main amd64 autopoint all 0.21-4 [510 kB] Get:18 http://127.0.0.1:12990/debian sid/main amd64 d-shlibs all 0.103 [18.2 kB] Get:19 http://127.0.0.1:12990/debian sid/main amd64 libdebhelper-perl all 13.5.2 [192 kB] Get:20 http://127.0.0.1:12990/debian sid/main amd64 libtool all 2.4.6-15 [513 kB] Get:21 http://127.0.0.1:12990/debian sid/main amd64 dh-autoreconf all 20 [17.1 kB] Get:22 http://127.0.0.1:12990/debian sid/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:23 http://127.0.0.1:12990/debian sid/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get:24 http://127.0.0.1:12990/debian sid/main amd64 libfile-stripnondeterminism-perl all 1.12.0-2 [26.3 kB] Get:25 http://127.0.0.1:12990/debian sid/main amd64 dh-strip-nondeterminism all 1.12.0-2 [15.5 kB] Get:26 http://127.0.0.1:12990/debian sid/main amd64 libelf1 amd64 0.185-2 [172 kB] Get:27 http://127.0.0.1:12990/debian sid/main amd64 dwz amd64 0.14-1 [98.3 kB] Get:28 http://127.0.0.1:12990/debian sid/main amd64 gettext amd64 0.21-4 [1311 kB] Get:29 http://127.0.0.1:12990/debian sid/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:30 http://127.0.0.1:12990/debian sid/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:31 http://127.0.0.1:12990/debian sid/main amd64 debhelper all 13.5.2 [1056 kB] Get:32 http://127.0.0.1:12990/debian sid/main amd64 libglib2.0-0 amd64 2.70.0-3 [1401 kB] Get:33 http://127.0.0.1:12990/debian sid/main amd64 libhmmer2-dev amd64 2.3.2+dfsg-7 [99.2 kB] Get:34 http://127.0.0.1:12990/debian sid/main amd64 libsquid1 amd64 1.9g+cvs20050121-12 [76.6 kB] Get:35 http://127.0.0.1:12990/debian sid/main amd64 libsquid-dev amd64 1.9g+cvs20050121-12 [145 kB] Get:36 http://127.0.0.1:12990/debian sid/main amd64 libsvm3 amd64 3.24+ds-6 [43.6 kB] Get:37 http://127.0.0.1:12990/debian sid/main amd64 libsvm-dev amd64 3.24+ds-6 [64.2 kB] Get:38 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 10.9 MB in 0s (117 MB/s) Selecting previously unselected package bsdextrautils. (Reading database ... 14273 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.37.2-4_amd64.deb ... Unpacking bsdextrautils (2.37.2-4) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../01-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-7_amd64.deb ... Unpacking groff-base (1.22.4-7) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../03-libpipeline1_1.5.3-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2_amd64.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../05-sensible-utils_0.0.17_all.deb ... Unpacking sensible-utils (0.0.17) ... Selecting previously unselected package libmagic-mgc. 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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) +------------------------------------------------------------------------------+ | 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-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 clang-13_1:13.0.0-8 coreutils_8.32-4+b1 cpp_4:11.2.0-2 cpp-11_11.2.0-10 d-shlibs_0.103 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-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 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-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 gpgv_2.2.27-2 grep_3.7-1 groff-base_1.22.4-7 gzip_1.10-4 hostname_3.23 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 libarchive-zip-perl_1.68-1 libasan5_9.4.0-3 libasan6_11.2.0-10 libatomic1_11.2.0-10 libattr1_1:2.5.1-1 libaudit-common_1:3.0.6-1 libaudit1_1:3.0.6-1 libbinutils_2.37-7 libblkid1_2.37.2-4 libbsd0_0.11.3-1 libbz2-1.0_1.0.8-4 libc-bin_2.32-4 libc-dev-bin_2.32-4 libc6_2.32-4 libc6-dev_2.32-4 libc6-i386_2.32-4 libcap-ng0_0.7.9-2.2+b1 libcap2_1:2.44-1 libcc1-0_11.2.0-10 libclang-common-13-dev_1:13.0.0-8 libclang-cpp13_1:13.0.0-8 libclang1-13_1:13.0.0-8 libcom-err2_1.46.4-1 libcrypt-dev_1:4.4.25-2 libcrypt1_1:4.4.25-2 libctf-nobfd0_2.37-7 libctf0_2.37-7 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.260 libdebhelper-perl_13.5.2 libdpkg-perl_1.20.9 libedit2_3.1-20210910-1 libelf1_0.185-2 libext2fs2_1.46.4-1 libfakeroot_1.26-1 libffi8_3.4.2-3 libfile-stripnondeterminism-perl_1.12.0-2 libgc1_1:8.0.4-3 libgcc-11-dev_11.2.0-10 libgcc-9-dev_9.4.0-3 libgcc-s1_11.2.0-10 libgcrypt20_1.9.4-3+b1 libgdbm-compat4_1.22-1 libgdbm6_1.22-1 libglib2.0-0_2.70.0-3 libgmp10_2:6.2.1+dfsg-2 libgnutls30_3.7.2-2 libgomp1_11.2.0-10 libgpg-error0_1.42-3 libgssapi-krb5-2_1.18.3-7 libhmmer2-dev_2.3.2+dfsg-7 libhogweed6_3.7.3-1 libicu67_67.1-7 libidn2-0_2.3.2-2 libisl23_0.24-2 libitm1_11.2.0-10 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libsvm3_3.24+ds-6 libsystemd0_249.5-1 libtasn1-6_4.17.0-2 libtinfo6_6.2+20210905-1 libtirpc-common_1.3.2-2 libtirpc-dev_1.3.2-2 libtirpc3_1.3.2-2 libtool_2.4.6-15 libtsan0_11.2.0-10 libubsan1_11.2.0-10 libuchardet0_0.0.7-1 libudev1_249.5-1 libunistring2_0.9.10-6 libuuid1_2.37.2-4 libxml2_2.9.12+dfsg-5 libxxhash0_0.8.0-2 libz3-4_4.8.12-1+b1 libzstd1_1.4.8+dfsg-3 linux-libc-dev_5.14.12-1 login_1:4.8.1-1 logsave_1.46.4-1 lsb-base_11.1.0 m4_1.4.18-5 make_4.3-4.1 man-db_2.9.4-2 mawk_1.3.4.20200120-2 mount_2.37.2-4 ncurses-base_6.2+20210905-1 ncurses-bin_6.2+20210905-1 passwd_1:4.8.1-1 patch_2.7.6-7 perl_5.32.1-6 perl-base_5.32.1-6 perl-modules-5.32_5.32.1-6 pkg-config_0.29.2-1 po-debconf_1.0.21+nmu1 qt5-qmake_5.15.2+dfsg-12 qt5-qmake-bin_5.15.2+dfsg-12 qtchooser_66-2 rpcsvc-proto_1.4.2-4 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sysvinit-utils_3.00-1 tar_1.34+dfsg-1 tzdata_2021e-1 util-linux_2.37.2-4 xz-utils_5.2.5-2 zlib1g_1:1.2.11.dfsg-2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: libpsortb Binary: libmodhmm0, libmodhmm-dev, libsvmloc0, libsvmloc-dev Architecture: any Version: 1.0+dfsg-4 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://www.psort.org/ Standards-Version: 4.5.1 Vcs-Browser: https://salsa.debian.org/med-team/libpsortb Vcs-Git: https://salsa.debian.org/med-team/libpsortb.git Build-Depends: debhelper-compat (= 13), d-shlibs, libsvm-dev, libsquid-dev, libhmmer2-dev, pkg-config Package-List: libmodhmm-dev deb libdevel optional arch=any libmodhmm0 deb libs optional arch=any libsvmloc-dev deb libdevel optional arch=any libsvmloc0 deb libs optional arch=any Checksums-Sha1: 44d3705f46372837f5ecdf8fa2ad0273a6c38433 95644 libpsortb_1.0+dfsg.orig.tar.xz 58416b4a31e5e91311e6e2182ab877c1760b738c 5124 libpsortb_1.0+dfsg-4.debian.tar.xz Checksums-Sha256: 5021b7ac656b33b8f0aa8c2e0403056a5459e1b92c17008b3ff442e262b3e2e5 95644 libpsortb_1.0+dfsg.orig.tar.xz 85492138c8999ff80b53e9563e2b6b710be9526a62da2eb1a64edc7aa998c0f6 5124 libpsortb_1.0+dfsg-4.debian.tar.xz Files: f9c6cf32032da4c9e88b609fba9bb02d 95644 libpsortb_1.0+dfsg.orig.tar.xz 5f16611eb342d7c8fc78b0e548bbd3a2 5124 libpsortb_1.0+dfsg-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl/JVdURHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtGKZBAAkWjLia+dlwHxR+rk8uNGNiaRUy7cXyoE S1og8+jjKGDdChbd/XwJu542s7nN6Vp+iCwGFj8TnW8Uva0fJK0p9cqr80lRroTL YiXeSjcjDnvM+d/r7N0feb4/D7gnP3qsxeE7mhmIzIVCMefDzijsAqjMt316/hrx 3dTzEdOHuZtW/Gk1TOy0W1BexEfmPERJFZg9Gj8OED/esN3NFqp8RINVM9H9Adiw q5RXf+ohf6tO6VfN3WY7dqhPRU3YM5pnO2KVPRZMHknDKFuf2KZzOSW6HrYHR/sy fTFuCcrOMagHNb/oezg0mjqerTGX5HZt+b8h6EvjJq33Ck8fHLDnwo/5Io1c/tEy +9CeB+CyS4yCetAndSs5jygx1p84usFwG2BhuZbld48+iEHZ1342rbuJ463Ja+Ft G2EB3F+Jjb0RxCpBV8uuegX9fxOLAi2t7qFHE3ImRGviV1IA03M0S7HbitKkUwbQ 7cj+8QbB9QIobOuL4XqnuO1GirSTwXj13LbHPFjV8AGkWjbjYJUGVdv/oNYlsBcM 7GnVC5FT6OaB4f9xMPlLhudeU90ccRBwugVLmtbJbAJYrbTvb4HjipLHUvlISYMj UJVzVA1j6YAik5/RxIH57MDCMEg7I0OonEbVjkLVItGxvBHOGHRV/sUyXCEGvZ3S mfY1VY0qSEE= =K8Pu -----END PGP SIGNATURE----- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.51JNAUjS/trustedkeys.kbx': General error gpgv: Signature made Thu Dec 3 21:17:09 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 ./libpsortb_1.0+dfsg-4.dsc dpkg-source: info: extracting libpsortb in /<> dpkg-source: info: unpacking libpsortb_1.0+dfsg.orig.tar.xz dpkg-source: info: unpacking libpsortb_1.0+dfsg-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_packaged_libs.patch dpkg-source: info: applying use_debian_packaged_libsvm.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-45d0c29d-9d9b-4143-a6f1-c82ce4f8da6e 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 libpsortb dpkg-buildpackage: info: source version 1.0+dfsg-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: Consider adding 'AC_CONFIG_MACRO_DIRS([m4])' to configure.ac, libtoolize: and rerunning libtoolize and aclocal. libtoolize: Consider adding '-I m4' to ACLOCAL_AMFLAGS in Makefile.am. configure.ac:7: warning: The macro `AC_CONFIG_HEADER' is obsolete. configure.ac:7: You should run autoupdate. ./lib/autoconf/status.m4:719: AC_CONFIG_HEADER is expanded from... configure.ac:7: the top level configure.ac:17: warning: The macro `AC_PROG_LIBTOOL' is obsolete. configure.ac:17: You should run autoupdate. aclocal.m4:121: AC_PROG_LIBTOOL is expanded from... configure.ac:17: the top level configure.ac:47: warning: The macro `AC_HEADER_STDC' is obsolete. configure.ac:47: You should run autoupdate. ./lib/autoconf/headers.m4:704: AC_HEADER_STDC is expanded from... configure.ac:47: the top level configure.ac:55: warning: The macro `AC_HEADER_TIME' is obsolete. configure.ac:55: You should run autoupdate. ./lib/autoconf/headers.m4:743: AC_HEADER_TIME is expanded from... configure.ac:55: the top level configure.ac:12: installing './compile' configure.ac:17: installing './config.guess' configure.ac:17: installing './config.sub' configure.ac:8: installing './install-sh' configure.ac:8: installing './missing' modhmm0.92b/Makefile.am: installing './depcomp' dh_auto_configure ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for g++... g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... none checking for gcc... gcc checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking how to run the C preprocessor... gcc -E checking whether ln -s works... yes checking whether make sets $(MAKE)... (cached) yes checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for sys/time.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... yes checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for main in -lm... yes checking for egrep... (cached) /bin/grep -E checking for float.h... yes checking for limits.h... yes checking for memory.h... yes checking for netinet/in.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking for _Bool... yes checking for stdbool.h that conforms to C99... yes checking for an ANSI C-conforming const... yes checking for inline... inline checking for size_t... yes checking whether struct tm is in sys/time.h or time.h... time.h checking for _LARGEFILE_SOURCE value needed for large files... no checking for GNU libc compatible malloc... yes checking for GNU libc compatible realloc... yes checking whether lstat correctly handles trailing slash... yes checking whether stat accepts an empty string... no checking for strftime... yes checking for vprintf... yes checking for working strtod... yes checking for atexit... yes checking for floor... yes checking for memmove... yes checking for memset... yes checking for pow... yes checking for sqrt... yes checking for strchr... yes checking for strcspn... yes checking for strerror... yes checking for strpbrk... yes checking for strrchr... yes checking for strspn... yes checking for strstr... yes checking for strtol... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating svmloc/Makefile config.status: creating modhmm0.92b/Makefile config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands dh_auto_build make -j4 make[1]: Entering directory '/<>' make all-recursive make[2]: Entering directory '/<>' Making all in svmloc make[3]: Entering directory '/<>/svmloc' /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o binding.lo binding.cpp /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o svmloc.lo svmloc.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c binding.cpp -fPIC -DPIC -o .libs/binding.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c svmloc.cpp -fPIC -DPIC -o .libs/svmloc.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c binding.cpp -o binding.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c svmloc.cpp -o svmloc.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 0:0:0 -lsvm -Wl,-z,relro -Wl,-z,now -o libsvmloc.la -rpath /usr/lib/x86_64-linux-gnu binding.lo svmloc.lo -lm libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/x86_64-linux-gnu/crti.o /usr/bin/../lib/gcc/x86_64-linux-gnu/11/crtbeginS.o .libs/binding.o .libs/svmloc.o -lsvm -L/usr/bin/../lib/gcc/x86_64-linux-gnu/11 -L/lib/x86_64-linux-gnu -L/lib/../lib64 -L/usr/lib/x86_64-linux-gnu -L/usr/lib/llvm-13/bin/../lib -L/lib -L/usr/lib -lstdc++ -lm -lc -lgcc_s -lgcc /usr/bin/../lib/gcc/x86_64-linux-gnu/11/crtendS.o /usr/lib/x86_64-linux-gnu/crtn.o -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libsvmloc.so.0 -o .libs/libsvmloc.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libsvmloc.so.0" && ln -s "libsvmloc.so.0.0.0" "libsvmloc.so.0") libtool: link: (cd ".libs" && rm -f "libsvmloc.so" && ln -s "libsvmloc.so.0.0.0" "libsvmloc.so") libtool: link: ar cr .libs/libsvmloc.a binding.o svmloc.o libtool: link: ranlib .libs/libsvmloc.a libtool: link: ( cd ".libs" && rm -f "libsvmloc.la" && ln -s "../libsvmloc.la" "libsvmloc.la" ) make[3]: Leaving directory '/<>/svmloc' Making all in modhmm0.92b make[3]: Entering directory '/<>/modhmm0.92b' /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o core_algorithms_multialpha.lo core_algorithms_multialpha.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o debug_funcs.lo debug_funcs.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o hmmsearch.lo hmmsearch.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o readhmm.lo readhmm.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c debug_funcs.c -fPIC -DPIC -o .libs/debug_funcs.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c core_algorithms_multialpha.c -fPIC -DPIC -o .libs/core_algorithms_multialpha.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c hmmsearch.c -fPIC -DPIC -o .libs/hmmsearch.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c readhmm.c -fPIC -DPIC -o .libs/readhmm.o debug_funcs.c:320:38: warning: implicit declaration of function 'get_mtx_index' is invalid in C99 [-Wimplicit-function-declaration] dump_viterbi_path(viterbi_mtxp + get_mtx_index(row-1, cur->prev, row_size), hmmp, ^ debug_funcs.c:345:44: warning: implicit declaration of function 'get_mtx_index' is invalid in C99 [-Wimplicit-function-declaration] dump_viterbi_label_path(viterbi_mtxp + get_mtx_index(row-1, cur->prev, row_size), hmmp, ^ debug_funcs.c:677:53: warning: implicit declaration of function 'get_mtx_index' is invalid in C99 [-Wimplicit-function-declaration] printf("label: %c\n", (msa_seq_infop->msa_seq + get_mtx_index(i,0,a_size+1))->label); ^ readhmm.c:69:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] debug_funcs.c fgets(s, MAX_LINE, file); ^~~~~ ~~~~~~~~~~~~~~~~~ :734:55: warning: implicit declaration of function 'get_mtx_index' is invalid in C99 [-Wimplicit-function-declaration] printf("label: %c\n", (msa_seq_infop->msa_seq_1 + get_mtx_index(i,0,hmmp->a_size+1))->label); ^ debug_funcs.c:755:57: warning: implicit declaration of function 'get_mtx_index' is invalid in C99 [-Wimplicit-function-declaration] printf("label: %c\n", (msa_seq_infop->msa_seq_2 + get_mtx_index(i,0,hmmp->a_size_2+1))->label); ^ readhmm.c:121:28: warning: incompatible pointer types assigning to 'struct transition_s *' from 'int *' [-Wincompatible-pointer-types] hmmp->trans_tie_groups = (int*)(malloc_or_die((hmmp->nr_t + hmmp->nr_ttg) * sizeof(struct transition_s))); debug_funcs.c:777:57: warning: implicit declaration of function 'get_mtx_index' is invalid in C99 [-Wimplicit-function-declaration] printf("label: %c\n", (msa_seq_infop->msa_seq_3 + get_mtx_index(i,0,hmmp->a_size_3+1))->label); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ debug_funcs.c:799:57: warning: implicit declaration of function 'get_mtx_index' is invalid in C99 [-Wimplicit-function-declaration] printf("label: %c\n", (msa_seq_infop->msa_seq_4 + get_mtx_index(i,0,hmmp->a_size_4+1))->label); ^ readhmm.c:345:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(s, MAX_LINE, file); ^~~~~ ~~~~~~~~~~~~~~~~~ readhmm.c:397:28: warning: incompatible pointer types assigning to 'struct transition_s *' from 'int *' [-Wincompatible-pointer-types] hmmp->trans_tie_groups = (int*)(malloc_or_die((hmmp->nr_t + hmmp->nr_ttg) * sizeof(struct transition_s))); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hmmsearch.c:535:19: warning: incompatible pointer types assigning to 'struct helix_site *' from 'helix_sites *' [-Wincompatible-pointer-types] hSites->helix = (helix_sites *) malloc(sizeof (helix_sites) * helices); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ debug_funcs.c:1047:11: warning: implicit declaration of function 'get_mtx_index' is invalid in C99 [-Wimplicit-function-declaration] x = get_mtx_index(v,w,nr_cols); ^ readhmm.c:580:1: warning: non-void function does not return a value in all control paths [-Wreturn-type] } ^ readhmm.c:751:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(s, MAX_LINE, file); ^~~~~ ~~~~~~~~~~~~~~~~~ readhmm.c:786:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(s, MAX_LINE, file); ^~~~~ ~~~~~~~~~~~~~~~~~ readhmm.c:821:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(s, MAX_LINE, file); ^~~~~ ~~~~~~~~~~~~~~~~~ readhmm.c:850:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(s, MAX_LINE, file); ^~~~~ ~~~~~~~~~~~~~~~~~ readhmm.c:854:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(s, MAX_LINE, file); ^~~~~ ~~~~~~~~~~~~~~~~~ core_algorithms_multialpha.c:1192:36: warning: incompatible pointer types passing 'char [5]' to parameter of type 'struct letter_s *' [-Wincompatible-pointer-types] a_index = get_alphabet_index((msa_seq_infop->msa_seq_1 + (c * (hmmp->a_size+1)))->query_letter, hmmp->alphabet, hmmp->a_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./funcs.h:136:40: note: passing argument to parameter here int get_alphabet_index(struct letter_s*, char*, int); ^ core_algorithms_multialpha.c:1199:33: warning: incompatible pointer types passing 'char [5]' to parameter of type 'struct letter_s *' [-Wincompatible-pointer-types] a_index_2 = get_alphabet_index((msa_seq_infop->msa_seq_2 + (c * (hmmp->a_size_2+1)))->query_letter, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./funcs.h:136:40: note: passing argument to parameter here int get_alphabet_index(struct letter_s*, char*, int); ^ core_algorithms_multialpha.c:1208:33: warning: incompatible pointer types passing 'char [5]' to parameter of type 'struct letter_s *' [-Wincompatible-pointer-types] a_index_3 = get_alphabet_index((msa_seq_infop->msa_seq_3 + (c * (hmmp->a_size_3+1)))->query_letter, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./funcs.h:136:40: note: passing argument to parameter here int get_alphabet_index(struct letter_s*, char*, int); ^ core_algorithms_multialpha.c:1217:33: warning: incompatible pointer types passing 'char [5]' to parameter of type 'struct letter_s *' [-Wincompatible-pointer-types] a_index_4 = get_alphabet_index((msa_seq_infop->msa_seq_4 + (c * (hmmp->a_size_4+1)))->query_letter, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./funcs.h:136:40: note: passing argument to parameter here int get_alphabet_index(struct letter_s*, char*, int); ^ core_algorithms_multialpha.c:1419:36: warning: incompatible pointer types passing 'char [5]' to parameter of type 'struct letter_s *' [-Wincompatible-pointer-types] a_index = get_alphabet_index((msa_seq_infop->msa_seq_1 + (c * (hmmp->a_size+1)))->query_letter, hmmp->alphabet, hmmp->a_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./funcs.h:136:40: note: passing argument to parameter here int get_alphabet_index(struct letter_s*, char*, int); ^ core_algorithms_multialpha.c:1426:33: warning: incompatible pointer types passing 'char [5]' to parameter of type 'struct letter_s *' [-Wincompatible-pointer-types] a_index_2 = get_alphabet_index((msa_seq_infop->msa_seq_2 + (c * (hmmp->a_size_2+1)))->query_letter, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./funcs.h:136:40: note: passing argument to parameter here int get_alphabet_index(struct letter_s*, char*, int); ^ core_algorithms_multialpha.c:1435:33: warning: incompatible pointer types passing 'char [5]' to parameter of type 'struct letter_s *' [-Wincompatible-pointer-types] a_index_3 = get_alphabet_index((msa_seq_infop->msa_seq_3 + (c * (hmmp->a_size_3+1)))->query_letter, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./funcs.h:136:40: note: passing argument to parameter here int get_alphabet_index(struct letter_s*, char*, int); ^ core_algorithms_multialpha.c:1444:33: warning: incompatible pointer types passing 'char [5]' to parameter of type 'struct letter_s *' [-Wincompatible-pointer-types] a_index_4 = get_alphabet_index((msa_seq_infop->msa_seq_4 + (c * (hmmp->a_size_4+1)))->query_letter, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./funcs.h:136:40: note: passing argument to parameter here int get_alphabet_index(struct letter_s*, char*, int); ^ readhmm.c:1231:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(ps, 2048, priorfile); ^~~~~ ~~~~~~~~~~~~~~~~~~~ core_algorithms_multialpha.c:1608:36: warning: incompatible pointer types passing 'char [5]' to parameter of type 'struct letter_s *' [-Wincompatible-pointer-types] a_index = get_alphabet_index((msa_seq_infop->msa_seq_1 + (c * (hmmp->a_size+1)))->query_letter, hmmp->alphabet, hmmp->a_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./funcs.h:136:40: note: passing argument to parameter here int get_alphabet_index(struct letter_s*, char*, int); ^ core_algorithms_multialpha.c:1615:33: warning: incompatible pointer types passing 'char [5]' to parameter of type 'struct letter_s *' [-Wincompatible-pointer-types] a_index_2 = get_alphabet_index((msa_seq_infop->msa_seq_2 + (c * (hmmp->a_size_2+1)))->query_letter, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./funcs.h:136:40: note: passing argument to parameter here int get_alphabet_index(struct letter_s*, char*, int); ^ core_algorithms_multialpha.c:1624:33: warning: incompatible pointer types passing 'char [5]' to parameter of type 'struct letter_s *' [-Wincompatible-pointer-types] a_index_3 = get_alphabet_index((msa_seq_infop->msa_seq_3 + (c * (hmmp->a_size_3+1)))->query_letter, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./funcs.h:136:40: note: passing argument to parameter here int get_alphabet_index(struct letter_s*, char*, int); ^ core_algorithms_multialpha.c:1633:33: warning: incompatible pointer types passing 'char [5]' to parameter of type 'struct letter_s *' [-Wincompatible-pointer-types] a_index_4 = get_alphabet_index((msa_seq_infop->msa_seq_4 + (c * (hmmp->a_size_4+1)))->query_letter, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./funcs.h:136:40: note: passing argument to parameter here int get_alphabet_index(struct letter_s*, char*, int); ^ core_algorithms_multialpha.c:1892:36: warning: incompatible pointer types passing 'char [5]' to parameter of type 'struct letter_s *' [-Wincompatible-pointer-types] a_index = get_alphabet_index((msa_seq_infop->msa_seq_1 + (c * (hmmp->a_size+1)))->query_letter, hmmp->alphabet, hmmp->a_size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./funcs.h:136:40: note: passing argument to parameter here int get_alphabet_index(struct letter_s*, char*, int); ^ core_algorithms_multialpha.c:1899:33: warning: incompatible pointer types passing 'char [5]' to parameter of type 'struct letter_s *' [-Wincompatible-pointer-types] a_index_2 = get_alphabet_index((msa_seq_infop->msa_seq_2 + (c * (hmmp->a_size_2+1)))->query_letter, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./funcs.h:136:40: note: passing argument to parameter here int get_alphabet_index(struct letter_s*, char*, int); ^ core_algorithms_multialpha.c:1908:33: warning: incompatible pointer types passing 'char [5]' to parameter of type 'struct letter_s *' [-Wincompatible-pointer-types] a_index_3 = get_alphabet_index((msa_seq_infop->msa_seq_3 + (c * (hmmp->a_size_3+1)))->query_letter, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./funcs.h:136:40: note: passing argument to parameter here int get_alphabet_index(struct letter_s*, char*, int); ^ core_algorithms_multialpha.c:1917:33: warning: incompatible pointer types passing 'char [5]' to parameter of type 'struct letter_s *' [-Wincompatible-pointer-types] a_index_4 = get_alphabet_index((msa_seq_infop->msa_seq_4 + (c * (hmmp->a_size_4+1)))->query_letter, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./funcs.h:136:40: note: passing argument to parameter here int get_alphabet_index(struct letter_s*, char*, int); ^ 1 warning generated. libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c hmmsearch.c -o hmmsearch.o >/dev/null 2>&1 8 warnings generated. libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c debug_funcs.c -o debug_funcs.o >/dev/null 2>&1 11 warnings generated. libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c readhmm.c -o readhmm.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o readhmm_multialpha.lo readhmm_multialpha.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c readhmm_multialpha.c -fPIC -DPIC -o .libs/readhmm_multialpha.o readhmm_multialpha.c:273:34: warning: incompatible pointer types assigning to 'struct transition_s *' from 'int *' [-Wincompatible-pointer-types] retrain_hmmp->trans_tie_groups = (int*)(malloc_or_die((hmmp->nr_t + hmmp->nr_ttg) * sizeof(struct transition_s))); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ readhmm_multialpha.c:326:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(s, MAX_LINE, file); ^~~~~ ~~~~~~~~~~~~~~~~~ readhmm_multialpha.c:469:28: warning: incompatible pointer types assigning to 'struct transition_s *' from 'int *' [-Wincompatible-pointer-types] hmmp->trans_tie_groups = (int*)(malloc_or_die((hmmp->nr_t + hmmp->nr_ttg) * sizeof(struct transition_s))); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ readhmm_multialpha.c:701:1: warning: non-void function does not return a value in all control paths [-Wreturn-type] } ^ readhmm_multialpha.c:1042:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(s, MAX_LINE, file); ^~~~~ ~~~~~~~~~~~~~~~~~ readhmm_multialpha.c:1077:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(s, MAX_LINE, file); ^~~~~ ~~~~~~~~~~~~~~~~~ readhmm_multialpha.c:1111:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(s, MAX_LINE, file); ^~~~~ ~~~~~~~~~~~~~~~~~ readhmm_multialpha.c:1140:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(s, MAX_LINE, file); ^~~~~ ~~~~~~~~~~~~~~~~~ readhmm_multialpha.c:1143:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(s, MAX_LINE, file); ^~~~~ ~~~~~~~~~~~~~~~~~ readhmm_multialpha.c:1169:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(s, MAX_LINE, file); ^~~~~ ~~~~~~~~~~~~~~~~~ readhmm_multialpha.c:1172:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(s, MAX_LINE, file); ^~~~~ ~~~~~~~~~~~~~~~~~ readhmm_multialpha.c:1198:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(s, MAX_LINE, file); ^~~~~ ~~~~~~~~~~~~~~~~~ readhmm_multialpha.c:1202:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(s, MAX_LINE, file); ^~~~~ ~~~~~~~~~~~~~~~~~ readhmm_multialpha.c:1229:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(s, MAX_LINE, file); ^~~~~ ~~~~~~~~~~~~~~~~~ readhmm_multialpha.c:1236:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(s, MAX_LINE, file); ^~~~~ ~~~~~~~~~~~~~~~~~ /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o readseqs_multialpha.lo readseqs_multialpha.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o std_calculation_funcs.lo std_calculation_funcs.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c readseqs_multialpha.c -fPIC -DPIC -o .libs/readseqs_multialpha.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c std_calculation_funcs.c -fPIC -DPIC -o .libs/std_calculation_funcs.o readseqs_multialpha.c:83:39: warning: incompatible pointer to integer conversion assigning to 'char' from 'char [2]' [-Wint-conversion] (seq_infop->seqs + seq_nr)->name[0] = "s"; ^ ~~~ readseqs_multialpha.c:121:56: warning: unknown escape sequence '\s' [-Wunknown-escape-sequence] if(line[0] == '<' || line[0] == '#' || line[0] == '\s' || line[0] == '\n' || line[0] == '/') { ^~ readseqs_multialpha.c:286:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, MAX_LINE, seqfile); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~ readseqs_multialpha.c:372:19: warning: unknown escape sequence '\s' [-Wunknown-escape-sequence] else if(i == '\s' && i == '\n') { ^~ readseqs_multialpha.c:389:22: warning: implicit declaration of function 'read_multi_prior_file_multi' is invalid in C99 [-Wimplicit-function-declaration] read_priorfile = read_multi_prior_file_multi(&em_di_1, hmmp, priorfile_a1, 1); ^ readseqs_multialpha.c:625:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, MAX_LINE, seqfile); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~ readseqs_multialpha.c:754:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, MAX_LINE, seqfile); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~ readseqs_multialpha.c:874:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, MAX_LINE, seqfile); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~ readseqs_multialpha.c:995:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, MAX_LINE, seqfile); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~ 16 warnings generated. libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c core_algorithms_multialpha.c -o core_algorithms_multialpha.o >/dev/null 2>&1 readseqs_multialpha.c:1380:22: warning: implicit declaration of function 'read_multi_prior_file_multi' is invalid in C99 [-Wimplicit-function-declaration] read_priorfile = read_multi_prior_file_multi(&em_di, hmmp, priorfile, 1); ^ std_calculation_funcs.c:1295:21: warning: cast to smaller integer type 'int' from 'char *' [-Wpointer-to-int-cast] cur_address = (int)((cur_rowp+v)->labeling); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ std_calculation_funcs.c:1309:5: warning: cast to smaller integer type 'int' from 'char *' [-Wpointer-to-int-cast] if((int)((cur_rowp+w)->labeling) == cur_address && (cur_rowp + w)->is_updated == NO) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ std_calculation_funcs.c:1425:21: warning: cast to smaller integer type 'int' from 'char *' [-Wpointer-to-int-cast] cur_address = (int)((prev_rowp+v)->labeling); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ std_calculation_funcs.c:1430:5: warning: cast to smaller integer type 'int' from 'char *' [-Wpointer-to-int-cast] if((int)((prev_rowp+w)->labeling) == cur_address) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 15 warnings generated. libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c readhmm_multialpha.c -o readhmm_multialpha.o >/dev/null 2>&1 4 warnings generated. libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c std_calculation_funcs.c -o std_calculation_funcs.o >/dev/null 2>&1 10 warnings generated. libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c readseqs_multialpha.c -o readseqs_multialpha.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o std_funcs.lo std_funcs.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c std_funcs.c -fPIC -DPIC -o .libs/std_funcs.o std_funcs.c:683:62: warning: comparison between pointer and integer ('char' and 'char *') [-Wpointer-integer-compare] if(((replacement_letters->letters + a_index)->letter)[0] == c) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~ std_funcs.c:1214:1: warning: non-void function does not return a value in all control paths [-Wreturn-type] } ^ std_funcs.c:1318:21: warning: equality comparison result unused [-Wunused-comparison] aa_freqs_temp == aa_freqs_2; ~~~~~~~~~~~~~~^~~~~~~~~~~~~ std_funcs.c:1318:21: note: use '=' to turn this equality comparison into an assignment aa_freqs_temp == aa_freqs_2; ^~ = std_funcs.c:1323:21: warning: equality comparison result unused [-Wunused-comparison] aa_freqs_temp == aa_freqs_3; ~~~~~~~~~~~~~~^~~~~~~~~~~~~ std_funcs.c:1323:21: note: use '=' to turn this equality comparison into an assignment aa_freqs_temp == aa_freqs_3; ^~ = std_funcs.c:1328:21: warning: equality comparison result unused [-Wunused-comparison] aa_freqs_temp == aa_freqs_4; ~~~~~~~~~~~~~~^~~~~~~~~~~~~ std_funcs.c:1328:21: note: use '=' to turn this equality comparison into an assignment aa_freqs_temp == aa_freqs_4; ^~ = std_funcs.c:1496:1: warning: non-void function does not return a value in all control paths [-Wreturn-type] } ^ std_funcs.c:2076:74: warning: incompatible integer to pointer conversion assigning to 'int *' from 'int' [-Wint-conversion] *(reverse_msa_seq_infop->gaps + (msa_seq_infop->msa_seq_length + i)) = END; ^ ~~~ std_funcs.c:2184:74: warning: incompatible integer to pointer conversion assigning to 'int *' from 'int' [-Wint-conversion] *(reverse_msa_seq_infop->gaps + (msa_seq_infop->msa_seq_length + i)) = END; ^ ~~~ std_funcs.c:2325:1: warning: non-void function does not return a value [-Wreturn-type] } ^ std_funcs.c:2471:5: error: non-void function 'update_shares_prior_multi' should return a value [-Wreturn-type] return; ^ 9 warnings and 1 error generated. make[3]: *** [Makefile:478: std_funcs.lo] Error 1 make[3]: *** Waiting for unfinished jobs.... make[3]: Leaving directory '/<>/modhmm0.92b' make[2]: *** [Makefile:407: all-recursive] Error 1 make[2]: Leaving directory '/<>' make[1]: *** [Makefile:339: all] Error 2 make[1]: Leaving directory '/<>' dh_auto_build: error: make -j4 returned exit code 2 make: *** [debian/rules:8: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2021-10-26T23:02:14Z 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: 7880 Build-Time: 14 Distribution: unstable Fail-Stage: build Host Architecture: amd64 Install-Time: 4 Job: libpsortb_1.0+dfsg-4 Machine Architecture: amd64 Package: libpsortb Package-Time: 39 Source-Version: 1.0+dfsg-4 Space: 7880 Status: attempted Version: 1.0+dfsg-4 -------------------------------------------------------------------------------- Finished at 2021-10-26T23:02:14Z Build needed 00:00:39, 7880k disk space E: Build failure (dpkg-buildpackage died) DC-Status: Failed 40.327118468s