DC-Build-Header: libpsortb 1.0+dfsg-3 / 2020-05-03 05:00:41 +0000 DC-Task: type:rebuild-binarch-only source:libpsortb version:1.0+dfsg-3 chroot:unstable esttime:93 logfile:/tmp/libpsortb_1.0+dfsg-3_unstable_clang10.log modes:clang10:binarch-only DC-Sbuild-call: su user42 -c 'sbuild -n --arch-any --apt-update -d unstable -v --no-run-lintian --chroot-setup-commands=/tmp/clang10 libpsortb_1.0+dfsg-3' sbuild (Debian sbuild) 0.78.1 (09 February 2019) on ip-172-31-7-28.eu-central-1.compute.internal +==============================================================================+ | libpsortb 1.0+dfsg-3 (amd64) Sun, 03 May 2020 05:00:41 +0000 | +==============================================================================+ Package: libpsortb Version: 1.0+dfsg-3 Source Version: 1.0+dfsg-3 Distribution: unstable Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: binary I: NOTICE: Log filtering will replace 'var/run/schroot/mount/sid-amd64-sbuild-7721d8f7-0296-4838-8e00-8da72747c2ff' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /tmp/clang10 ------------ + echo 'Entering customization script...' Entering customization script... + CLANG_VERSION=10 + echo 'Install of clang-10' Install of clang-10 + apt-get update Get:1 http://127.0.0.1:12990/debian sid InRelease [146 kB] Get:2 http://127.0.0.1:12990/debian sid/main Sources.diff/Index [27.9 kB] Get:3 http://127.0.0.1:12990/debian sid/main amd64 Packages.diff/Index [27.9 kB] Get:4 http://127.0.0.1:12990/debian sid/main Sources 2020-05-02-0208.16.pdiff [3982 B] Get:5 http://127.0.0.1:12990/debian sid/main Sources 2020-05-02-0807.49.pdiff [10.9 kB] Get:6 http://127.0.0.1:12990/debian sid/main Sources 2020-05-02-1412.30.pdiff [12.9 kB] Get:7 http://127.0.0.1:12990/debian sid/main Sources 2020-05-02-2007.10.pdiff [13.4 kB] Get:8 http://127.0.0.1:12990/debian sid/main Sources 2020-05-03-0208.39.pdiff [9476 B] Get:8 http://127.0.0.1:12990/debian sid/main Sources 2020-05-03-0208.39.pdiff [9476 B] Get:9 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-05-02-0208.16.pdiff [2772 B] Get:10 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-05-02-0807.49.pdiff [3238 B] Get:11 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-05-02-1412.30.pdiff [7641 B] Get:12 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-05-02-2007.10.pdiff [10.5 kB] Get:13 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-05-03-0208.39.pdiff [18.4 kB] Get:13 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-05-03-0208.39.pdiff [18.4 kB] Get:14 http://127.0.0.1:12990/debian sid/main Translation-en [6185 kB] Fetched 6480 kB in 2s (4017 kB/s) Reading package lists... + apt-get install --yes --no-install-recommends --force-yes clang-10 libomp-10-dev libobjc-9-dev Reading package lists... Building dependency tree... The following additional packages will be installed: gcc-10-base lib32gcc-s1 lib32gcc1 lib32stdc++6 libatomic1 libbsd0 libc6-i386 libcc1-0 libclang-common-10-dev libclang-cpp10 libclang1-10 libedit2 libgc1c2 libgcc-s1 libgomp1 libitm1 libllvm10 liblsan0 libobjc4 libomp5-10 libquadmath0 libstdc++6 libtsan0 libubsan1 libz3-4 Suggested packages: clang-10-doc libomp-10-doc Recommended packages: llvm-10-dev python3 The following NEW packages will be installed: clang-10 lib32gcc-s1 lib32gcc1 lib32stdc++6 libbsd0 libc6-i386 libclang-common-10-dev libclang-cpp10 libclang1-10 libedit2 libgc1c2 libllvm10 libobjc-9-dev libobjc4 libomp-10-dev libomp5-10 libz3-4 The following packages will be upgraded: gcc-10-base libatomic1 libcc1-0 libgcc-s1 libgomp1 libitm1 liblsan0 libquadmath0 libstdc++6 libtsan0 libubsan1 11 upgraded, 17 newly installed, 0 to remove and 0 not upgraded. Need to get 51.4 MB of archives. After this operation, 259 MB of additional disk space will be used. Get:1 http://127.0.0.1:12990/debian sid/main amd64 libatomic1 amd64 10-20200502-1 [9048 B] Get:2 http://127.0.0.1:12990/debian sid/main amd64 libubsan1 amd64 10-20200502-1 [134 kB] Get:3 http://127.0.0.1:12990/debian sid/main amd64 libtsan0 amd64 10-20200502-1 [313 kB] Get:4 http://127.0.0.1:12990/debian sid/main amd64 gcc-10-base amd64 10-20200502-1 [197 kB] Get:5 http://127.0.0.1:12990/debian sid/main amd64 libstdc++6 amd64 10-20200502-1 [492 kB] Get:6 http://127.0.0.1:12990/debian sid/main amd64 libquadmath0 amd64 10-20200502-1 [145 kB] Get:7 http://127.0.0.1:12990/debian sid/main amd64 liblsan0 amd64 10-20200502-1 [141 kB] Get:8 http://127.0.0.1:12990/debian sid/main amd64 libitm1 amd64 10-20200502-1 [25.7 kB] Get:9 http://127.0.0.1:12990/debian sid/main amd64 libgomp1 amd64 10-20200502-1 [99.3 kB] Get:10 http://127.0.0.1:12990/debian sid/main amd64 libcc1-0 amd64 10-20200502-1 [39.7 kB] Get:11 http://127.0.0.1:12990/debian sid/main amd64 libgcc-s1 amd64 10-20200502-1 [41.2 kB] Get:12 http://127.0.0.1:12990/debian sid/main amd64 libbsd0 amd64 0.10.0-1 [107 kB] Get:13 http://127.0.0.1:12990/debian sid/main amd64 libedit2 amd64 3.1-20191231-1 [95.4 kB] Get:14 http://127.0.0.1:12990/debian sid/main amd64 libz3-4 amd64 4.8.7-4 [6790 kB] Get:15 http://127.0.0.1:12990/debian sid/main amd64 libllvm10 amd64 1:10.0.0-4 [15.5 MB] Get:16 http://127.0.0.1:12990/debian sid/main amd64 libclang-cpp10 amd64 1:10.0.0-4 [10.1 MB] Get:17 http://127.0.0.1:12990/debian sid/main amd64 libgc1c2 amd64 1:7.6.4-0.4 [224 kB] Get:18 http://127.0.0.1:12990/debian sid/main amd64 libobjc4 amd64 10-20200502-1 [41.6 kB] Get:19 http://127.0.0.1:12990/debian sid/main amd64 libobjc-9-dev amd64 9.3.0-11 [218 kB] Get:20 http://127.0.0.1:12990/debian sid/main amd64 libc6-i386 amd64 2.30-4 [2926 kB] Get:21 http://127.0.0.1:12990/debian sid/main amd64 lib32gcc-s1 amd64 10-20200502-1 [49.4 kB] Get:22 http://127.0.0.1:12990/debian sid/main amd64 lib32gcc1 amd64 1:10-20200502-1 [1100 B] Get:23 http://127.0.0.1:12990/debian sid/main amd64 lib32stdc++6 amd64 10-20200502-1 [510 kB] Get:24 http://127.0.0.1:12990/debian sid/main amd64 libclang-common-10-dev amd64 1:10.0.0-4 [5062 kB] Get:25 http://127.0.0.1:12990/debian sid/main amd64 libclang1-10 amd64 1:10.0.0-4 [7609 kB] Get:26 http://127.0.0.1:12990/debian sid/main amd64 clang-10 amd64 1:10.0.0-4 [105 kB] Get:27 http://127.0.0.1:12990/debian sid/main amd64 libomp5-10 amd64 1:10.0.0-4 [338 kB] Get:28 http://127.0.0.1:12990/debian sid/main amd64 libomp-10-dev amd64 1:10.0.0-4 [85.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 51.4 MB in 0s (142 MB/s) (Reading database ... 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W: --force-yes is deprecated, use one of the options starting with --allow instead. + echo 'Replace gcc, g++ & cpp by clang' Replace gcc, g++ & cpp by clang + VERSIONS='4.6 4.7 4.8 4.9 5 6 7 8 9 10' + cd /usr/bin + for VERSION in $VERSIONS + rm -f g++-4.6 gcc-4.6 cpp-4.6 gcc + ln -s clang++-10 g++-4.6 + ln -s clang-10 gcc-4.6 + ln -s clang-10 cpp-4.6 + ln -s clang-10 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++-10 g++-4.7 + ln -s clang-10 gcc-4.7 + ln -s clang-10 cpp-4.7 + ln -s clang-10 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++-10 g++-4.8 + ln -s clang-10 gcc-4.8 + ln -s clang-10 cpp-4.8 + ln -s clang-10 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++-10 g++-4.9 + ln -s clang-10 gcc-4.9 + ln -s clang-10 cpp-4.9 + ln -s clang-10 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++-10 g++-5 + ln -s clang-10 gcc-5 + ln -s clang-10 cpp-5 + ln -s clang-10 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++-10 g++-6 + ln -s clang-10 gcc-6 + ln -s clang-10 cpp-6 + ln -s clang-10 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++-10 g++-7 + ln -s clang-10 gcc-7 + ln -s clang-10 cpp-7 + ln -s clang-10 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++-10 g++-8 + ln -s clang-10 gcc-8 + ln -s clang-10 cpp-8 + ln -s clang-10 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++-10 g++-9 + ln -s clang-10 gcc-9 + ln -s clang-10 cpp-9 + ln -s clang-10 gcc + echo 'gcc-9 hold' + dpkg --set-selections + echo 'g++-9 hold' + dpkg --set-selections + for VERSION in $VERSIONS + rm -f g++-10 gcc-10 cpp-10 gcc + ln -s clang++-10 g++-10 + ln -s clang-10 gcc-10 + ln -s clang-10 cpp-10 + ln -s clang-10 gcc + echo 'gcc-10 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-10 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-10 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-10 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + cd - /build/libpsortb-DMBGvt + 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-10 clang++ + ln -s clang-10 clang + clang++ --version clang version 10.0.0-4 Target: x86_64-pc-linux-gnu Thread model: posix InstalledDir: /usr/bin + clang --version clang version 10.0.0-4 Target: x86_64-pc-linux-gnu Thread model: posix InstalledDir: /usr/bin + cd - /build/libpsortb-DMBGvt + 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 1270 kB of archives. After this operation, 4788 kB of additional disk space will be used. Get:1 http://127.0.0.1:12990/debian sid/main amd64 qt5-qmake-bin amd64 5.12.5+dfsg-10 [1015 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 5.12.5+dfsg-10 [229 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 1270 kB in 0s (20.4 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 ... 12968 files and directories currently installed.) Preparing to unpack .../qt5-qmake-bin_5.12.5+dfsg-10_amd64.deb ... Unpacking qt5-qmake-bin (5.12.5+dfsg-10) ... 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_5.12.5+dfsg-10_amd64.deb ... Unpacking qt5-qmake:amd64 (5.12.5+dfsg-10) ... Setting up qt5-qmake-bin (5.12.5+dfsg-10) ... Setting up qtchooser (66-2) ... Setting up qt5-qmake:amd64 (5.12.5+dfsg-10) ... 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 May 3 05:00 . drwxr-xr-x 75 root root 4096 May 3 05:00 .. -rw-r--r-- 1 root root 276 May 3 05:00 qmake.conf -rw-r--r-- 1 root root 3218 May 3 05:00 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/clang10'. Finished processing commands. -------------------------------------------------------------------------------- I: NOTICE: Log filtering will replace 'build/libpsortb-DMBGvt/resolver-xnxLgD' 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-3 (dsc) [2157 B] Get:2 http://127.0.0.1:12990/debian sid/main libpsortb 1.0+dfsg-3 (tar) [95.6 kB] Get:3 http://127.0.0.1:12990/debian sid/main libpsortb 1.0+dfsg-3 (diff) [4956 B] Fetched 103 kB in 0s (1324 kB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/libpsortb-DMBGvt/libpsortb-1.0+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/libpsortb-DMBGvt' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper (>= 11~), d-shlibs, libsvm-dev, libsquid-dev, libhmmer2-dev, pkg-config, build-essential, fakeroot Filtered Build-Depends: debhelper (>= 11~), 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 [486 B] Fetched 1846 B in 0s (0 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils d-shlibs debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libcroco3 libdebhelper-perl libelf1 libfile-stripnondeterminism-perl libglib2.0-0 libhmmer2-dev libicu63 libmagic-mgc libmagic1 libpipeline1 libpvm3 libsigsegv2 libsquid-dev libsquid1 libsub-override-perl libsvm-dev libsvm3 libtool libuchardet0 libxml2 m4 man-db pkg-config po-debconf sensible-utils Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation 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 pvm libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils d-shlibs debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libcroco3 libdebhelper-perl libelf1 libfile-stripnondeterminism-perl libglib2.0-0 libhmmer2-dev libicu63 libmagic-mgc libmagic1 libpipeline1 libpvm3 libsigsegv2 libsquid-dev libsquid1 libsub-override-perl libsvm-dev libsvm3 libtool libuchardet0 libxml2 m4 man-db pkg-config po-debconf sbuild-build-depends-main-dummy sensible-utils 0 upgraded, 42 newly installed, 0 to remove and 0 not upgraded. Need to get 20.1 MB of archives. After this operation, 72.6 MB of additional disk space will be used. 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(Reading database ... 13685 files and directories currently installed.) Preparing to unpack .../00-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../01-libuchardet0_0.0.6-3_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-4_amd64.deb ... Unpacking groff-base (1.22.4-4) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../03-libpipeline1_1.5.2-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.2-2) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.1-1_amd64.deb ... Unpacking man-db (2.9.1-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../05-sensible-utils_0.0.12+nmu1_all.deb ... Unpacking sensible-utils (0.0.12+nmu1) ... 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Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:amd64 (2.64.2-1) ... No schema files found: doing nothing. Setting up libdebhelper-perl (13) ... Setting up libmagic1:amd64 (1:5.38-4) ... Setting up gettext-base (0.19.8.1-10) ... Setting up file (1:5.38-4) ... Setting up libicu63:amd64 (63.2-3) ... Setting up autotools-dev (20180224.1) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up autopoint (0.19.8.1-10) ... Setting up pkg-config (0.29.2-1) ... Setting up d-shlibs (0.91) ... Setting up libsquid1 (1.9g+cvs20050121-11) ... Setting up sensible-utils (0.0.12+nmu1) ... Setting up libuchardet0:amd64 (0.0.6-3) ... Setting up libsub-override-perl (0.09-2) ... Setting up libhmmer2-dev (2.3.2+dfsg-6) ... Setting up libelf1:amd64 (0.176-1.1) ... Setting up libxml2:amd64 (2.9.10+dfsg-5) ... Setting up libsvm3 (3.24+ds-4) ... Setting up libfile-stripnondeterminism-perl (1.8.0-1) ... Setting up libtool (2.4.6-14) ... Setting up m4 (1.4.18-4) ... Setting up libsquid-dev (1.9g+cvs20050121-11) ... Setting up libsvm-dev (3.24+ds-4) ... Setting up libcroco3:amd64 (0.6.13-1) ... Setting up autoconf (2.69-11.1) ... Setting up dh-strip-nondeterminism (1.8.0-1) ... Setting up dwz (0.13-5) ... Setting up groff-base (1.22.4-4) ... Setting up automake (1:1.16.2-1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.19.8.1-10) ... Setting up man-db (2.9.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up po-debconf (1.0.21) ... Setting up dh-autoreconf (19) ... Setting up debhelper (13) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.30-4) ... +------------------------------------------------------------------------------+ | 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_2.34-6 dpkg-dev_1.19.7 g++-9_9.3.0-11 gcc-9_9.3.0-11 libc6-dev_2.30-4 libstdc++-9-dev_9.3.0-11 libstdc++6_10-20200502-1 linux-libc-dev_5.6.7-1 Package versions: adduser_3.118 apt_2.0.2 autoconf_2.69-11.1 automake_1:1.16.2-1 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11 base-passwd_3.5.47 bash_5.0-6 binutils_2.34-6 binutils-common_2.34-6 binutils-x86-64-linux-gnu_2.34-6 bsdmainutils_11.1.2+b1 bsdutils_1:2.34-0.1 build-essential_12.8 bzip2_1.0.8-2 clang-10_1:10.0.0-4 coreutils_8.30-3+b1 cpp_4:9.2.1-3.1 cpp-9_9.3.0-11 d-shlibs_0.91 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13 debian-archive-keyring_2019.1 debianutils_4.9.1 dh-autoreconf_19 dh-strip-nondeterminism_1.8.0-1 diffutils_1:3.7-3 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.6-1 fakeroot_1.24-1 fdisk_2.34-0.1 file_1:5.38-4 findutils_4.7.0-1 g++_4:9.2.1-3.1 g++-9_9.3.0-11 gcc_4:9.2.1-3.1 gcc-10-base_10-20200502-1 gcc-9_9.3.0-11 gcc-9-base_9.3.0-11 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gpgv_2.2.20-1 grep_3.4-1 groff-base_1.22.4-4 gzip_1.10-2 hostname_3.23 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 lib32gcc-s1_10-20200502-1 lib32gcc1_1:10-20200502-1 lib32stdc++6_10-20200502-1 libacl1_2.2.53-8 libapt-pkg6.0_2.0.2 libarchive-zip-perl_1.68-1 libasan5_9.3.0-11 libatomic1_10-20200502-1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3 libaudit1_1:2.8.5-3+b1 libbinutils_2.34-6 libblkid1_2.34-0.1 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.30-4 libc-dev-bin_2.30-4 libc6_2.30-4 libc6-dev_2.30-4 libc6-i386_2.30-4 libcap-ng0_0.7.9-2.1+b2 libcc1-0_10-20200502-1 libclang-common-10-dev_1:10.0.0-4 libclang-cpp10_1:10.0.0-4 libclang1-10_1:10.0.0-4 libcom-err2_1.45.6-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.16-1 libcrypt1_1:4.4.16-1 libctf-nobfd0_2.34-6 libctf0_2.34-6 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.251 libdebhelper-perl_13 libdpkg-perl_1.19.7 libedit2_3.1-20191231-1 libelf1_0.176-1.1 libext2fs2_1.45.6-1 libfakeroot_1.24-1 libfdisk1_2.34-0.1 libffi7_3.3-4 libfile-stripnondeterminism-perl_1.8.0-1 libgc1c2_1:7.6.4-0.4 libgcc-9-dev_9.3.0-11 libgcc-s1_10-20200502-1 libgcrypt20_1.8.5-5 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.64.2-1 libgmp10_2:6.2.0+dfsg-4 libgnutls30_3.6.13-2 libgomp1_10-20200502-1 libgpg-error0_1.37-1 libhmmer2-dev_2.3.2+dfsg-6 libhogweed5_3.5.1+really3.5.1-2 libicu63_63.2-3 libidn2-0_2.3.0-1 libisl22_0.22.1-1 libitm1_10-20200502-1 libllvm10_1:10.0.0-4 liblsan0_10-20200502-1 liblz4-1_1.9.2-2 liblzma5_5.2.4-1+b1 libmagic-mgc_1:5.38-4 libmagic1_1:5.38-4 libmount1_2.34-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libncursesw6_6.2-1 libnettle7_3.5.1+really3.5.1-2 libobjc-9-dev_9.3.0-11 libobjc4_10-20200502-1 libomp-10-dev_1:10.0.0-4 libomp5-10_1:10.0.0-4 libp11-kit0_0.23.20-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.34-7 libpcre3_2:8.39-12+b1 libperl5.30_5.30.0-10 libpipeline1_1.5.2-2 libpvm3_3.4.6-2+b1 libquadmath0_10-20200502-1 libseccomp2_2.4.3-1+b1 libselinux1_3.0-1+b3 libsemanage-common_3.0-1 libsemanage1_3.0-1+b3 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1 libsquid-dev_1.9g+cvs20050121-11 libsquid1_1.9g+cvs20050121-11 libss2_1.45.6-1 libstdc++-9-dev_9.3.0-11 libstdc++6_10-20200502-1 libsub-override-perl_0.09-2 libsvm-dev_3.24+ds-4 libsvm3_3.24+ds-4 libsystemd0_245.5-2 libtasn1-6_4.16.0-2 libtinfo6_6.2-1 libtool_2.4.6-14 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MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: libpsortb Binary: libmodhmm0, libmodhmm-dev, libsvmloc0, libsvmloc-dev Architecture: any Version: 1.0+dfsg-3 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: http://www.psort.org/ Standards-Version: 4.3.0 Vcs-Browser: https://salsa.debian.org/med-team/libpsortb Vcs-Git: https://salsa.debian.org/med-team/libpsortb.git Build-Depends: debhelper (>= 11~), 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 9581ed83240d7e44651767b9035807e8e1eda53e 4956 libpsortb_1.0+dfsg-3.debian.tar.xz Checksums-Sha256: 5021b7ac656b33b8f0aa8c2e0403056a5459e1b92c17008b3ff442e262b3e2e5 95644 libpsortb_1.0+dfsg.orig.tar.xz c9dc56178e2cc354432463ca370716d879031412a0d01bd4636349e696053c19 4956 libpsortb_1.0+dfsg-3.debian.tar.xz Files: f9c6cf32032da4c9e88b609fba9bb02d 95644 libpsortb_1.0+dfsg.orig.tar.xz 16ac9a3c62655d61a2a274551465224e 4956 libpsortb_1.0+dfsg-3.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAlwwp9EACgkQPCZ2P2xn 5uJzaBAAoqn9fmd3ekBpzVbP0/8Wg6Zqn3GepMhvecTmbzPGHlT/GBpL22miX86z 6nTJG0tATGr9haxfXcYhZrErGb0CJwpooG8juHytoJCO34lKB+KHAMSY1ZzPIiJL FxWePp4JXkTHSrBvwdEYdhlbQBpEQp9r1klnAGxfYU5L4P7eNFR/WIsiEGzBtaq1 D7ZZUkxvHbDZcMypWPaDHw8R9x70bRXswDVT6Gu6s2jnaKRhLaASjlmQkJ2+Bd+x tDHhuntPxD/EIP5XvGdY746Tb6tRGwHThkWFKZ8gLJHnlmwP9VML8zRdgoYvKvf9 CkkIl4r+XGectQVo6U+gVAado2qiYQJwi/XUa2R48huNJ+XMpgNIefaReS/ymMSF 3UFDvcbJ6KH1Q9+dOxVh1tP0vYohlNZTm5mzZdHg3pJGajZSUd+rl8MkeuoH5TjF /pylAZuewfQdi2QdJJceDUWgv/DESUG2tJD4YlG8iYfaQDGsjNDI1EOizegaMJIh CStYWkjoQkTFOXhIwBBR1vnkmwzIfosGDZC+bfTJsnNoGmhHp1gl8eV74WSpgW4Q uFQKdpiRRj2ZDsDvIeVC0aExDdoKxRk1NCyJJ6xkB2nkN9a3A21oADih3G0QvKY/ FiQ93oOZLigcvqon+RwJP2N0yiArRhzSeSWlJ0CgLiyK2RTZf1Y= =MPeV -----END PGP SIGNATURE----- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Sat Jan 5 12:49:21 2019 UTC gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./libpsortb_1.0+dfsg-3.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-3.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-7721d8f7-0296-4838-8e00-8da72747c2ff 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-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean dh_clean debian/rules build dh build 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: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-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --libexecdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking configure: WARNING: unrecognized options: --disable-maintainer-mode checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe 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 we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... none checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... 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 ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.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 ANSI C header files... (cached) yes checking float.h usability... yes checking float.h presence... yes checking for float.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking for memory.h... (cached) yes checking netinet/in.h usability... yes checking netinet/in.h presence... 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 stdbool.h that conforms to C99... yes checking for _Bool... yes checking for an ANSI C-conforming const... yes checking for inline... inline checking for size_t... yes checking whether time.h and sys/time.h may both be included... 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 stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for stdlib.h... (cached) 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 _doprnt... no 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 configure: WARNING: unrecognized options: --disable-maintainer-mode 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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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/bin/../lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/crti.o /usr/bin/../lib/gcc/x86_64-linux-gnu/9/crtbeginS.o .libs/binding.o .libs/svmloc.o -lsvm -L/usr/bin/../lib/gcc/x86_64-linux-gnu/9 -L/usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu -L/lib/x86_64-linux-gnu -L/lib/../lib64 -L/usr/lib/x86_64-linux-gnu -L/usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../.. -L/usr/lib/llvm-10/bin/../lib -L/lib -L/usr/lib -lstdc++ -lm -lc -lgcc_s -lgcc /usr/bin/../lib/gcc/x86_64-linux-gnu/9/crtendS.o /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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] fgets(s, MAX_LINE, file); ^~~~~ ~~~~~~~~~~~~~~~~~ debug_funcs.creadhmm.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))); :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); ^ 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); ^ 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); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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))); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ readhmm.c:580:1: warning: non-void function does not return a value in all control paths [-Wreturn-type] } ^ 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: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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c hmmsearch.c -o hmmsearch.o >/dev/null 2>&1 11 warnings generated. libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c readhmm.c -o readhmm.o >/dev/null 2>&1 8 warnings generated. libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c debug_funcs.c -o debug_funcs.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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~ 16 warnings generated. readseqs_multialpha.c:372:19: warning: unknown escape sequence '\s' [-Wunknown-escape-sequence] else if(i == '\s' && i == '\n') { ^~ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-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: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); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~ 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); ^ 15 warnings generated. libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c readhmm_multialpha.c -o readhmm_multialpha.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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] } ^ /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o training_algorithms_multialpha.lo training_algorithms_multialpha.c 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:477: std_funcs.lo] Error 1 make[3]: *** Waiting for unfinished jobs.... libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c training_algorithms_multialpha.c -fPIC -DPIC -o .libs/training_algorithms_multialpha.o training_algorithms_multialpha.c:701:12: warning: incompatible pointer to integer conversion assigning to 'int' from 'char [1000]' [-Wint-conversion] alphabet = hmmp->alphabet; ^ ~~~~~~~~~~~~~~ training_algorithms_multialpha.c:710:12: warning: incompatible pointer to integer conversion assigning to 'int' from 'char [1000]' [-Wint-conversion] alphabet = hmmp->alphabet_2; ^ ~~~~~~~~~~~~~~~~ training_algorithms_multialpha.c:719:12: warning: incompatible pointer to integer conversion assigning to 'int' from 'char [1000]' [-Wint-conversion] alphabet = hmmp->alphabet_3; ^ ~~~~~~~~~~~~~~~~ training_algorithms_multialpha.c:728:12: warning: incompatible pointer to integer conversion assigning to 'int' from 'char [1000]' [-Wint-conversion] alphabet = hmmp->alphabet_4; ^ ~~~~~~~~~~~~~~~~ training_algorithms_multialpha.c:1639:12: warning: incompatible pointer to integer conversion assigning to 'int' from 'char [1000]' [-Wint-conversion] alphabet = hmmp->alphabet; ^ ~~~~~~~~~~~~~~ training_algorithms_multialpha.c:1646:12: warning: incompatible pointer to integer conversion assigning to 'int' from 'char [1000]' [-Wint-conversion] alphabet = hmmp->alphabet_2; ^ ~~~~~~~~~~~~~~~~ training_algorithms_multialpha.c:1653:12: warning: incompatible pointer to integer conversion assigning to 'int' from 'char [1000]' [-Wint-conversion] alphabet = hmmp->alphabet_3; ^ ~~~~~~~~~~~~~~~~ training_algorithms_multialpha.c:1660:12: warning: incompatible pointer to integer conversion assigning to 'int' from 'char [1000]' [-Wint-conversion] alphabet = hmmp->alphabet_4; ^ ~~~~~~~~~~~~~~~~ training_algorithms_multialpha.c:1784:12: warning: incompatible pointer to integer conversion assigning to 'int' from 'char [1000]' [-Wint-conversion] alphabet = hmmp->alphabet; ^ ~~~~~~~~~~~~~~ training_algorithms_multialpha.c:1791:12: warning: incompatible pointer to integer conversion assigning to 'int' from 'char [1000]' [-Wint-conversion] alphabet = hmmp->alphabet_2; ^ ~~~~~~~~~~~~~~~~ training_algorithms_multialpha.c:1798:12: warning: incompatible pointer to integer conversion assigning to 'int' from 'char [1000]' [-Wint-conversion] alphabet = hmmp->alphabet_3; ^ ~~~~~~~~~~~~~~~~ training_algorithms_multialpha.c:1805:12: warning: incompatible pointer to integer conversion assigning to 'int' from 'char [1000]' [-Wint-conversion] alphabet = hmmp->alphabet_4; ^ ~~~~~~~~~~~~~~~~ training_algorithms_multialpha.c:2626:1: warning: non-void function does not return a value in all control paths [-Wreturn-type] } ^ training_algorithms_multialpha.c:3564:5: warning: implicit declaration of function 'add_to_E_continuous' is invalid in C99 [-Wimplicit-function-declaration] add_to_E_continuous(E, Eka_base, msa_seq, p, k, a_size, emissions); ^ training_algorithms_multialpha.c:3589:8: warning: incompatible integer to pointer conversion passing 'int' to parameter of type 'char *' [-Wint-conversion] alphabet); ^~~~~~~~ ./funcs.h:257:68: note: passing argument to parameter 'alphabet' here int k, int a_size, int normalize, double *subst_mtx, char *alphabet); ^ training_algorithms_multialpha.c:3593:7: warning: incompatible integer to pointer conversion passing 'int' to parameter of type 'char *' [-Wint-conversion] alphabet); ^~~~~~~~ ./funcs.h:259:67: note: passing argument to parameter 'alphabet' here int k, int a_size, int normalize, double *subst_mtx, char *alphabet); ^ training_algorithms_multialpha.c:3618:8: warning: incompatible integer to pointer conversion passing 'int' to parameter of type 'char *' [-Wint-conversion] alphabet); ^~~~~~~~ ./funcs.h:238:68: note: passing argument to parameter 'alphabet' here int k, int a_size, int normalize, double *subst_mtx, char *alphabet); ^ training_algorithms_multialpha.c:3622:7: warning: incompatible integer to pointer conversion passing 'int' to parameter of type 'char *' [-Wint-conversion] alphabet); ^~~~~~~~ ./funcs.h:240:67: note: passing argument to parameter 'alphabet' here int k, int a_size, int normalize, double *subst_mtx, char *alphabet); ^ 18 warnings generated. libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c training_algorithms_multialpha.c -o training_algorithms_multialpha.o >/dev/null 2>&1 make[3]: Leaving directory '/<>/modhmm0.92b' make[2]: *** [Makefile:405: all-recursive] Error 1 make[2]: Leaving directory '/<>' make[1]: *** [Makefile:337: all] Error 2 make[1]: Leaving directory '/<>' dh_auto_build: error: make -j4 returned exit code 2 make: *** [debian/rules:8: build] Error 25 dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2020-05-03T05:01:18Z 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: 7708 Build-Time: 17 Distribution: unstable Fail-Stage: build Host Architecture: amd64 Install-Time: 5 Job: libpsortb_1.0+dfsg-3 Machine Architecture: amd64 Package: libpsortb Package-Time: 37 Source-Version: 1.0+dfsg-3 Space: 7708 Status: attempted Version: 1.0+dfsg-3 -------------------------------------------------------------------------------- Finished at 2020-05-03T05:01:18Z Build needed 00:00:37, 7708k disk space E: Build failure (dpkg-buildpackage died) DC-Status: Failed 37.688871387s DC-Time-Estimation: 37.688871387 versus expected 93 (r/m: 1.4675719006029573 ; m: 37.688871387)