Fri Jun 9 18:02:47 UTC 2023 I: starting to build proda/bookworm/i386 on jenkins on '2023-06-09 18:02' Fri Jun 9 18:02:47 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_12/295/console.log Fri Jun 9 18:02:47 UTC 2023 I: Downloading source for bookworm/proda=1.0-13 --2023-06-09 18:02:47-- http://cdn-fastly.deb.debian.org/debian/pool/main/p/proda/proda_1.0-13.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 1981 (1.9K) [text/prs.lines.tag] Saving to: ‘proda_1.0-13.dsc’ 0K . 100% 217M=0s 2023-06-09 18:02:47 (217 MB/s) - ‘proda_1.0-13.dsc’ saved [1981/1981] Fri Jun 9 18:02:47 UTC 2023 I: proda_1.0-13.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: proda Binary: proda Architecture: any Version: 1.0-13 Maintainer: Debian Med Packaging Team Uploaders: David Paleino , Charles Plessy , Andreas Tille Homepage: http://proda.stanford.edu/ Standards-Version: 4.5.1 Vcs-Browser: https://salsa.debian.org/med-team/proda Vcs-Git: https://salsa.debian.org/med-team/proda.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13) Package-List: proda deb science optional arch=any Checksums-Sha1: 44303e1639b5c52278758d23d149ef1c434593a4 38868 proda_1.0.orig.tar.gz 9b6d0d967470f1d70e763ccf9837635202bda2fc 10176 proda_1.0-13.debian.tar.xz Checksums-Sha256: 439a93bf35e1a29ac1d5dde51e61f2cb174618596afaaaaa27d33a8ea1868a08 38868 proda_1.0.orig.tar.gz ae92f92a8eb307e637b88ad6c70a2eabee251ef9bc5584ebd1ccea67c93d7419 10176 proda_1.0-13.debian.tar.xz Files: 99a0c04983d043f70e74b33ba6f38018 38868 proda_1.0.orig.tar.gz 4883534eaf8f913925a6e946012bf38a 10176 proda_1.0-13.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl+8FzERHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtGGYxAAhEs4uCYRb4lCIxBt06rAc1Ktws5gHFkS DA6UJI4blWPJFDKYJHrQO9cD62bfemSln7nFTtP9GIZN42VKMvZuQ7C5tgSTYYle /uXISDstczzzo0BelFW2HWm3fl3qmWiOKpmIL57pqRpmnN4DqAc+rR9x8REbqUFB xReOO0vPjVG/Lg84+aftveTOv7h46RhUV5IO3ksLa6C0bsmefzzKBiPXqlTXAl95 Cn8CeKq9SH3BM1YtGDU7CIYEAMZCIXOyzIkMuX8uimuKjkivxrFVi+RKylg007A+ 3VsrFK4WV4GJpj1N+7oPds/wCoi4t8XQe+noGXaW0O+LjrgK4j/ZohMWrPd3Xe4D Rb5PfI5K6mB+/gcGoIzYcQY+myAFq6y2sprNeyFxWlKknektflsyezPJneXgv4o/ OJmckr3KCh+npRjFcXw6TYt9VOlABE/uE6lamfE/hii9Tv/ygjNpgLXMiPecKSOJ TYQfaX5DLwC3kn7fct0RiFs0oRZsc46qca8omDVllk+yv8Im1+i3gRXase6gKF8B SsGD1y1Js7AWLUgwQ/imc4RHQ5moVbcTrHnErdQxdUaOFvC/DFiiEDltxlayfRFq fJZwfCtITmsKhsBt+Usk7aPLNGfdvmPGxxeTHe/Nww1VuLJQvesk0Ni3ktWnYxbe 9JInbflVU18= =zKRD -----END PGP SIGNATURE----- Fri Jun 9 18:02:47 UTC 2023 I: Checking whether the package is not for us Fri Jun 9 18:02:47 UTC 2023 I: Starting 1st build on remote node ionos16-i386.debian.net. Fri Jun 9 18:02:47 UTC 2023 I: Preparing to do remote build '1' on ionos16-i386.debian.net. Fri Jun 9 18:03:11 UTC 2023 I: Deleting $TMPDIR on ionos16-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Jul 11 12:25:46 -12 2024 I: pbuilder-time-stamp: 1720743946 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: using eatmydata during job I: Copying source file I: copying [proda_1.0-13.dsc] I: copying [./proda_1.0.orig.tar.gz] I: copying [./proda_1.0-13.debian.tar.xz] I: Extracting source gpgv: Signature made Mon Nov 23 08:10:25 2020 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./proda_1.0-13.dsc: no acceptable signature found dpkg-source: info: extracting proda in proda-1.0 dpkg-source: info: unpacking proda_1.0.orig.tar.gz dpkg-source: info: unpacking proda_1.0-13.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 01-fix_gcc4.3_warnings.patch dpkg-source: info: applying 02-fix_CXXFLAGS.patch dpkg-source: info: applying 03-fix_FTBFS_gcc4.3_missing_includes.patch dpkg-source: info: applying 04-honour_CXX.patch dpkg-source: info: applying 05-fix_FTBFS_with_GCC6.patch dpkg-source: info: applying hardening.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/99431/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16 ' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='2df450ae786647a69dd162be730c0c48' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='99431' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.dMTu6ITm/pbuilderrc_mPbl --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.dMTu6ITm/b1 --logfile b1/build.log proda_1.0-13.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://85.184.249.68:3128' I: uname -a Linux ionos16-i386 5.10.0-23-amd64 #1 SMP Debian 5.10.179-1 (2023-05-12) x86_64 GNU/Linux I: ls -l /bin total 6036 -rwxr-xr-x 1 root root 1408088 Apr 23 2023 bash -rwxr-xr-x 3 root root 38404 Sep 18 2022 bunzip2 -rwxr-xr-x 3 root root 38404 Sep 18 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep -rwxr-xr-x 3 root root 38404 Sep 18 2022 bzip2 -rwxr-xr-x 1 root root 17892 Sep 18 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore -rwxr-xr-x 1 root root 42920 Sep 20 2022 cat -rwxr-xr-x 1 root root 79816 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 67496 Sep 20 2022 chmod -rwxr-xr-x 1 root root 79816 Sep 20 2022 chown -rwxr-xr-x 1 root root 162024 Sep 20 2022 cp -rwxr-xr-x 1 root root 136916 Jan 5 2023 dash -rwxr-xr-x 1 root root 137160 Sep 20 2022 date -rwxr-xr-x 1 root root 100364 Sep 20 2022 dd -rwxr-xr-x 1 root root 108940 Sep 20 2022 df -rwxr-xr-x 1 root root 162152 Sep 20 2022 dir -rwxr-xr-x 1 root root 87760 Mar 22 2023 dmesg lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname -rwxr-xr-x 1 root root 38760 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep -rwxr-xr-x 1 root root 34664 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep -rwxr-xr-x 1 root root 84272 Mar 22 2023 findmnt -rwsr-xr-x 1 root root 30240 Mar 22 2023 fusermount -rwxr-xr-x 1 root root 218680 Jan 24 2023 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 100952 Apr 9 2022 gzip -rwxr-xr-x 1 root root 21916 Dec 19 2022 hostname -rwxr-xr-x 1 root root 75756 Sep 20 2022 ln -rwxr-xr-x 1 root root 55600 Mar 22 2023 login -rwxr-xr-x 1 root root 162152 Sep 20 2022 ls -rwxr-xr-x 1 root root 214568 Mar 22 2023 lsblk -rwxr-xr-x 1 root root 96328 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 84008 Sep 20 2022 mknod -rwxr-xr-x 1 root root 38792 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 63016 Mar 22 2023 more -rwsr-xr-x 1 root root 58912 Mar 22 2023 mount -rwxr-xr-x 1 root root 13856 Mar 22 2023 mountpoint -rwxr-xr-x 1 root root 157932 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 2 2023 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 38792 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 2023 rbash -> bash -rwxr-xr-x 1 root root 51080 Sep 20 2022 readlink -rwxr-xr-x 1 root root 75720 Sep 20 2022 rm -rwxr-xr-x 1 root root 51080 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 22308 Nov 2 2022 run-parts -rwxr-xr-x 1 root root 133224 Jan 5 2023 sed lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash -rwxr-xr-x 1 root root 38760 Sep 20 2022 sleep -rwxr-xr-x 1 root root 87976 Sep 20 2022 stty -rwsr-xr-x 1 root root 83492 Mar 22 2023 su -rwxr-xr-x 1 root root 38792 Sep 20 2022 sync -rwxr-xr-x 1 root root 598456 Apr 6 2023 tar -rwxr-xr-x 1 root root 13860 Nov 2 2022 tempfile -rwxr-xr-x 1 root root 120776 Sep 20 2022 touch -rwxr-xr-x 1 root root 34664 Sep 20 2022 true -rwxr-xr-x 1 root root 17892 Mar 22 2023 ulockmgr_server -rwsr-xr-x 1 root root 30236 Mar 22 2023 umount -rwxr-xr-x 1 root root 38760 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 162152 Sep 20 2022 vdir -rwxr-xr-x 1 root root 71216 Mar 22 2023 wdctl lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/99431/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: i386 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19599 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 30 newly installed, 0 to remove and 0 not upgraded. Need to get 19.0 MB of archives. After unpacking 72.7 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main i386 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 2 http://deb.debian.org/debian bookworm/main i386 libmagic-mgc i386 1:5.44-3 [305 kB] Get: 3 http://deb.debian.org/debian bookworm/main i386 libmagic1 i386 1:5.44-3 [114 kB] Get: 4 http://deb.debian.org/debian bookworm/main i386 file i386 1:5.44-3 [42.5 kB] Get: 5 http://deb.debian.org/debian bookworm/main i386 gettext-base i386 0.21-12 [162 kB] Get: 6 http://deb.debian.org/debian bookworm/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB] Get: 7 http://deb.debian.org/debian bookworm/main i386 groff-base i386 1.22.4-10 [932 kB] Get: 8 http://deb.debian.org/debian bookworm/main i386 bsdextrautils i386 2.38.1-5+b1 [90.3 kB] Get: 9 http://deb.debian.org/debian bookworm/main i386 libpipeline1 i386 1.5.7-1 [40.0 kB] Get: 10 http://deb.debian.org/debian bookworm/main i386 man-db i386 2.11.2-2 [1397 kB] Get: 11 http://deb.debian.org/debian bookworm/main i386 m4 i386 1.4.19-3 [294 kB] Get: 12 http://deb.debian.org/debian bookworm/main i386 autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian bookworm/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian bookworm/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian bookworm/main i386 autopoint all 0.21-12 [495 kB] Get: 16 http://deb.debian.org/debian bookworm/main i386 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 17 http://deb.debian.org/debian bookworm/main i386 libtool all 2.4.7-5 [517 kB] Get: 18 http://deb.debian.org/debian bookworm/main i386 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian bookworm/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian bookworm/main i386 libsub-override-perl all 0.09-4 [9304 B] Get: 21 http://deb.debian.org/debian bookworm/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian bookworm/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian bookworm/main i386 libelf1 i386 0.188-2.1 [179 kB] Get: 24 http://deb.debian.org/debian bookworm/main i386 dwz i386 0.15-1 [118 kB] Get: 25 http://deb.debian.org/debian bookworm/main i386 libicu72 i386 72.1-3 [9541 kB] Get: 26 http://deb.debian.org/debian bookworm/main i386 libxml2 i386 2.9.14+dfsg-1.2 [720 kB] Get: 27 http://deb.debian.org/debian bookworm/main i386 gettext i386 0.21-12 [1311 kB] Get: 28 http://deb.debian.org/debian bookworm/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian bookworm/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian bookworm/main i386 debhelper all 13.11.4 [942 kB] Fetched 19.0 MB in 1s (14.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (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 ... 19599 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.44-3_i386.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../02-libmagic1_1%3a5.44-3_i386.deb ... Unpacking libmagic1:i386 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.44-3_i386.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-12_i386.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../05-libuchardet0_0.0.7-1_i386.deb ... Unpacking libuchardet0:i386 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.22.4-10_i386.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.38.1-5+b1_i386.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../08-libpipeline1_1.5.7-1_i386.deb ... Unpacking libpipeline1:i386 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.11.2-2_i386.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-3_i386.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.11.4_all.deb ... Unpacking libdebhelper-perl (13.11.4) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-5_all.deb ... Unpacking libtool (2.4.7-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../19-libsub-override-perl_0.09-4_all.deb ... Unpacking libsub-override-perl (0.09-4) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:i386. Preparing to unpack .../22-libelf1_0.188-2.1_i386.deb ... Unpacking libelf1:i386 (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1_i386.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:i386. Preparing to unpack .../24-libicu72_72.1-3_i386.deb ... Unpacking libicu72:i386 (72.1-3) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../25-libxml2_2.9.14+dfsg-1.2_i386.deb ... Unpacking libxml2:i386 (2.9.14+dfsg-1.2) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.21-12_i386.deb ... Unpacking gettext (0.21-12) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-intltool-debian_0.35.0+20060710.6_all.deb ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/proda-1.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../proda_1.0-13_source.changes dpkg-buildpackage: info: source package proda dpkg-buildpackage: info: source version 1.0-13 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean dh_auto_clean make -j16 clean make[1]: Entering directory '/build/proda-1.0' rm -f *.o make[1]: Leaving directory '/build/proda-1.0' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j16 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/proda-1.0' g++ -g -O2 -ffile-prefix-map=/build/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o AlignedFragment.o AlignedFragment.cc g++ -g -O2 -ffile-prefix-map=/build/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Assert.o Assert.cc g++ -g -O2 -ffile-prefix-map=/build/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Block.o Block.cc g++ -g -O2 -ffile-prefix-map=/build/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Consistency.o Consistency.cc g++ -g -O2 -ffile-prefix-map=/build/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o GlobalAlign.o GlobalAlign.cc g++ -g -O2 -ffile-prefix-map=/build/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o LocalAlign.o LocalAlign.cc g++ -g -O2 -ffile-prefix-map=/build/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Main.o Main.cc g++ -g -O2 -ffile-prefix-map=/build/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o PairAligner.o PairAligner.cc g++ -g -O2 -ffile-prefix-map=/build/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Matrix.o Matrix.cc g++ -g -O2 -ffile-prefix-map=/build/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o MultiSequence.o MultiSequence.cc g++ -g -O2 -ffile-prefix-map=/build/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o ProbModel.o ProbModel.cc g++ -g -O2 -ffile-prefix-map=/build/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Score.o Score.cc g++ -g -O2 -ffile-prefix-map=/build/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o ScoreMatrix.o ScoreMatrix.cc g++ -g -O2 -ffile-prefix-map=/build/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Sequence.o Sequence.cc g++ -g -O2 -ffile-prefix-map=/build/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o SparseMatrix.o SparseMatrix.cc g++ -g -O2 -ffile-prefix-map=/build/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Tree.o Tree.cc g++ -g -O2 -ffile-prefix-map=/build/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Utilities.o Utilities.cc In file included from Matrix.h:12, from Tree.h:9, from Tree.cc:6: SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 57 | const int GetRowSize (int layer, int row) const; | ^~~~~ SparseMatrix.h:60:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 60 | const int GetNumLayers() const; | ^~~~~ SparseMatrix.h:61:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 61 | const int GetNumRows() const; | ^~~~~ SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 62 | const int GetNumCols() const; | ^~~~~ In file included from Matrix.h:12, from LocalAlign.h:12, from LocalAlign.cc:5: SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 57 | const int GetRowSize (int layer, int row) const; | ^~~~~ SparseMatrix.h:60:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 60 | const int GetNumLayers() const; | ^~~~~ SparseMatrix.h:61:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 61 | const int GetNumRows() const; | ^~~~~ SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 62 | const int GetNumCols() const; | ^~~~~ In file included from Matrix.h:12, from GlobalAlign.h:11, from GlobalAlign.cc:7: SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 57 | const int GetRowSize (int layer, int row) const; | ^~~~~ In file included from Matrix.h:12, from Matrix.cc:7: SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 57 | const int GetRowSize (int layer, int row) const; | ^~~~~ SparseMatrix.h:60:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 60 | const int GetNumLayers() const; | ^~~~~ SparseMatrix.h:60:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 60 | const int GetNumLayers() const; | ^~~~~ SparseMatrix.h:61:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 61 | const int GetNumRows() const; | ^~~~~ SparseMatrix.h:61:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 61 | const int GetNumRows() const; | ^~~~~ SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 62 | const int GetNumCols() const; | ^~~~~ SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 62 | const int GetNumCols() const; | ^~~~~ In file included from Matrix.h:12, from Types.h:12, from Block.h:10, from Block.cc:6: SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 57 | const int GetRowSize (int layer, int row) const; | ^~~~~ SparseMatrix.h:60:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 60 | const int GetNumLayers() const; | ^~~~~ SparseMatrix.h:61:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 61 | const int GetNumRows() const; | ^~~~~ SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 62 | const int GetNumCols() const; | ^~~~~ In file included from Matrix.h:12, from Types.h:12, from ProbModel.h:11, from ProbModel.cc:8: SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 57 | const int GetRowSize (int layer, int row) const; | ^~~~~ SparseMatrix.h:60:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 60 | const int GetNumLayers() const; | ^~~~~ SparseMatrix.h:61:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 61 | const int GetNumRows() const; | ^~~~~ SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 62 | const int GetNumCols() const; | ^~~~~ In file included from ScoreMatrix.h:12, from Matrix.h:13: Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 51 | const int GetLength () const; | ^~~~~ Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 52 | const int GetID () const; | ^~~~~ ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 88 | const int GetNumLayers() const { | ^~~~~ ScoreMatrix.h:96:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 96 | const int GetNumRows() const { | ^~~~~ ScoreMatrix.h:104:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 104 | const int GetNumCols() const { | ^~~~~ Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 100 | const int GetNumLayers() const { | ^~~~~ Matrix.h:108:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 108 | const int GetNumRows() const { | ^~~~~ Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 116 | const int GetNumCols() const { | ^~~~~ In file included from Tree.h:10: MultiSequence.h:24:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 24 | const int AutoDetectFileFormat (const char *filename) const; | ^~~~~ MultiSequence.h:28:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 28 | const char ComputeAnnotation (const char *data, const int size) const; | ^~~~~ MultiSequence.h:48:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 48 | const int GetNumSequences() const; | ^~~~~ MultiSequence.h:49:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 49 | const int GetLength() const; | ^~~~~ Tree.h:44:5: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 44 | const bool GetIsLeaf() const; | ^~~~~ Tree.h:45:5: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 45 | const int GetNumSequences() const; | ^~~~~ Tree.cc:34:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 34 | const bool Tree::TreeNode::GetIsLeaf() const { | ^~~~~ Tree.cc:42:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 42 | const int Tree::TreeNode::GetNumSequences() const { | ^~~~~ In file included from ScoreMatrix.h:12, from Matrix.h:13: Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 51 | const int GetLength () const; | ^~~~~ Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 52 | const int GetID () const; | ^~~~~ ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 88 | const int GetNumLayers() const { | ^~~~~ ScoreMatrix.h:96:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 96 | const int GetNumRows() const { | ^~~~~ ScoreMatrix.h:104:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 104 | const int GetNumCols() const { | ^~~~~ Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 100 | const int GetNumLayers() const { | ^~~~~ Matrix.h:108:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 108 | const int GetNumRows() const { | ^~~~~ Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 116 | const int GetNumCols() const { | ^~~~~ In file included from MultiSequence.h:12, from Main.cc:12: Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 51 | const int GetLength () const; | ^~~~~ Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 52 | const int GetID () const; | ^~~~~ In file included from Block.cc:9: MultiSequence.h:24:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 24 | const int AutoDetectFileFormat (const char *filename) const; | ^~~~~ MultiSequence.h:28:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 28 | const char ComputeAnnotation (const char *data, const int size) const; | ^~~~~ MultiSequence.h:48:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 48 | const int GetNumSequences() const; | ^~~~~ MultiSequence.h:49:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 49 | const int GetLength() const; | ^~~~~ Block.cc: In constructor 'Block::Block(std::vector&, MultiSequence*, bool, Block*)': Block.cc:58:43: warning: variable 'end' set but not used [-Wunused-but-set-variable] 58 | int best,best_id, best_pos, multi,end,bfrag,bk,best_end; | ^~~ In file included from Sequence.cc:8: Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 51 | const int GetLength () const; | ^~~~~ Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 52 | const int GetID () const; | ^~~~~ Sequence.cc:121:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 121 | const int Sequence::GetLength () const { | ^~~~~ Sequence.cc:129:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 129 | const int Sequence::GetID () const { | ^~~~~ In file included from Matrix.h:12, from Types.h:12, from Block.h:10, from MultiSequence.h:13: SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 57 | const int GetRowSize (int layer, int row) const; | ^~~~~ SparseMatrix.h:60:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 60 | const int GetNumLayers() const; | ^~~~~ SparseMatrix.h:61:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 61 | const int GetNumRows() const; | ^~~~~ SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 62 | const int GetNumCols() const; | ^~~~~ In file included from Matrix.h:13: ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 88 | const int GetNumLayers() const { | ^~~~~ ScoreMatrix.h:96:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 96 | const int GetNumRows() const { | ^~~~~ ScoreMatrix.h:104:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 104 | const int GetNumCols() const { | ^~~~~ In file included from MultiSequence.h:12, from MultiSequence.cc:10: Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 51 | const int GetLength () const; | ^~~~~ Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 52 | const int GetID () const; | ^~~~~ Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 100 | const int GetNumLayers() const { | ^~~~~ Matrix.h:108:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 108 | const int GetNumRows() const { | ^~~~~ Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 116 | const int GetNumCols() const { | ^~~~~ In file included from PairAligner.h:10, from PairAligner.cc:9: Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 51 | const int GetLength () const; | ^~~~~ Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 52 | const int GetID () const; | ^~~~~ MultiSequence.h:24:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 24 | const int AutoDetectFileFormat (const char *filename) const; | ^~~~~ MultiSequence.h:28:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 28 | const char ComputeAnnotation (const char *data, const int size) const; | ^~~~~ MultiSequence.h:48:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 48 | const int GetNumSequences() const; | ^~~~~ MultiSequence.h:49:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 49 | const int GetLength() const; | ^~~~~ In file included from Main.cc:18: Tree.h:44:5: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 44 | const bool GetIsLeaf() const; | ^~~~~ Tree.h:45:5: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 45 | const int GetNumSequences() const; | ^~~~~ In file included from ScoreMatrix.h:12, from Matrix.h:13: Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 51 | const int GetLength () const; | ^~~~~ Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 52 | const int GetID () const; | ^~~~~ ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 88 | const int GetNumLayers() const { | ^~~~~ ScoreMatrix.h:96:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 96 | const int GetNumRows() const { | ^~~~~ ScoreMatrix.h:104:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 104 | const int GetNumCols() const { | ^~~~~ Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 100 | const int GetNumLayers() const { | ^~~~~ Matrix.h:108:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 108 | const int GetNumRows() const { | ^~~~~ Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 116 | const int GetNumCols() const { | ^~~~~ In file included from GlobalAlign.h:12: MultiSequence.h:24:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 24 | const int AutoDetectFileFormat (const char *filename) const; | ^~~~~ MultiSequence.h:28:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 28 | const char ComputeAnnotation (const char *data, const int size) const; | ^~~~~ MultiSequence.h:48:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 48 | const int GetNumSequences() const; | ^~~~~ MultiSequence.h:49:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 49 | const int GetLength() const; | ^~~~~ In file included from ScoreMatrix.h:12, from Matrix.h:13, from SparseMatrix.h:12, from SparseMatrix.cc:6: Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 51 | const int GetLength () const; | ^~~~~ Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 52 | const int GetID () const; | ^~~~~ ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 88 | const int GetNumLayers() const { | ^~~~~ ScoreMatrix.h:96:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 96 | const int GetNumRows() const { | ^~~~~ ScoreMatrix.h:104:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 104 | const int GetNumCols() const { | ^~~~~ Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 100 | const int GetNumLayers() const { | ^~~~~ Matrix.h:108:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 108 | const int GetNumRows() const { | ^~~~~ Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 116 | const int GetNumCols() const { | ^~~~~ SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 57 | const int GetRowSize (int layer, int row) const; | ^~~~~ SparseMatrix.h:60:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 60 | const int GetNumLayers() const; | ^~~~~ SparseMatrix.h:61:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 61 | const int GetNumRows() const; | ^~~~~ SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 62 | const int GetNumCols() const; | ^~~~~ In file included from ScoreMatrix.h:12, from Matrix.h:13: Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 51 | const int GetLength () const; | ^~~~~ Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 52 | const int GetID () const; | ^~~~~ ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 88 | const int GetNumLayers() const { | ^~~~~ ScoreMatrix.h:96:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 96 | const int GetNumRows() const { | ^~~~~ ScoreMatrix.h:104:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 104 | const int GetNumCols() const { | ^~~~~ Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 100 | const int GetNumLayers() const { | ^~~~~ Matrix.h:108:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 108 | const int GetNumRows() const { | ^~~~~ Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 116 | const int GetNumCols() const { | ^~~~~ SparseMatrix.cc:199:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 199 | const int SparseMatrix::GetRowSize (int layer, int row) const { | ^~~~~ SparseMatrix.cc:209:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 209 | const int SparseMatrix::GetNumLayers() const { | ^~~~~ SparseMatrix.cc:217:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 217 | const int SparseMatrix::GetNumRows() const { | ^~~~~ SparseMatrix.cc:225:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 225 | const int SparseMatrix::GetNumCols() const { | ^~~~~ In file included from ScoreMatrix.h:12, from Matrix.h:13, from SparseMatrix.h:12, from Consistency.h:10, from Consistency.cc:5: Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 51 | const int GetLength () const; | ^~~~~ Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 52 | const int GetID () const; | ^~~~~ ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 88 | const int GetNumLayers() const { | ^~~~~ ScoreMatrix.h:96:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 96 | const int GetNumRows() const { | ^~~~~ ScoreMatrix.h:104:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 104 | const int GetNumCols() const { | ^~~~~ Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 100 | const int GetNumLayers() const { | ^~~~~ Matrix.h:108:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 108 | const int GetNumRows() const { | ^~~~~ Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 116 | const int GetNumCols() const { | ^~~~~ SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 57 | const int GetRowSize (int layer, int row) const; | ^~~~~ SparseMatrix.h:60:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 60 | const int GetNumLayers() const; | ^~~~~ SparseMatrix.h:61:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 61 | const int GetNumRows() const; | ^~~~~ SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 62 | const int GetNumCols() const; | ^~~~~ In file included from ScoreMatrix.h:12, from ScoreMatrix.cc:7: Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 51 | const int GetLength () const; | ^~~~~ Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 52 | const int GetID () const; | ^~~~~ ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 88 | const int GetNumLayers() const { | ^~~~~ ScoreMatrix.h:96:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 96 | const int GetNumRows() const { | ^~~~~ ScoreMatrix.h:104:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 104 | const int GetNumCols() const { | ^~~~~ In file included from ScoreMatrix.h:12, from Matrix.h:13: Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 51 | const int GetLength () const; | ^~~~~ Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 52 | const int GetID () const; | ^~~~~ ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 88 | const int GetNumLayers() const { | ^~~~~ ScoreMatrix.h:96:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 96 | const int GetNumRows() const { | ^~~~~ ScoreMatrix.h:104:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 104 | const int GetNumCols() const { | ^~~~~ Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 100 | const int GetNumLayers() const { | ^~~~~ Matrix.h:108:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 108 | const int GetNumRows() const { | ^~~~~ Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 116 | const int GetNumCols() const { | ^~~~~ Matrix.cc: In member function 'float Matrix::SumOfRow(int, int) const': Matrix.cc:165:13: warning: variable 'pos' set but not used [-Wunused-but-set-variable] 165 | int pos = 0; | ^~~ Matrix.cc:166:16: warning: variable 'ptr' set but not used [-Wunused-but-set-variable] 166 | float *ptr; | ^~~ Matrix.cc: In member function 'float Matrix::SumOfColumn(int, int) const': Matrix.cc:186:13: warning: variable 'pos' set but not used [-Wunused-but-set-variable] 186 | int pos = 0; | ^~~ In file included from Matrix.h:12, from Types.h:12, from ProbModel.h:11, from ScoreMatrix.cc:8: SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 57 | const int GetRowSize (int layer, int row) const; | ^~~~~ SparseMatrix.h:60:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 60 | const int GetNumLayers() const; | ^~~~~ SparseMatrix.h:61:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 61 | const int GetNumRows() const; | ^~~~~ SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 62 | const int GetNumCols() const; | ^~~~~ Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 100 | const int GetNumLayers() const { | ^~~~~ Matrix.h:108:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 108 | const int GetNumRows() const { | ^~~~~ Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 116 | const int GetNumCols() const { | ^~~~~ In file included from Matrix.h:12, from Types.h:12, from Block.h:10, from MultiSequence.h:13: SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 57 | const int GetRowSize (int layer, int row) const; | ^~~~~ SparseMatrix.h:60:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 60 | const int GetNumLayers() const; | ^~~~~ SparseMatrix.h:61:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 61 | const int GetNumRows() const; | ^~~~~ SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 62 | const int GetNumCols() const; | ^~~~~ In file included from Matrix.h:13: ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 88 | const int GetNumLayers() const { | ^~~~~ ScoreMatrix.h:96:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 96 | const int GetNumRows() const { | ^~~~~ ScoreMatrix.h:104:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 104 | const int GetNumCols() const { | ^~~~~ In file included from Matrix.h:12, from Types.h:12, from ProbModel.h:11, from PairAligner.h:11: SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 57 | const int GetRowSize (int layer, int row) const; | ^~~~~ SparseMatrix.h:60:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 60 | const int GetNumLayers() const; | ^~~~~ SparseMatrix.h:61:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 61 | const int GetNumRows() const; | ^~~~~ SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 62 | const int GetNumCols() const; | ^~~~~ Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 100 | const int GetNumLayers() const { | ^~~~~ Matrix.h:108:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 108 | const int GetNumRows() const { | ^~~~~ Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 116 | const int GetNumCols() const { | ^~~~~ In file included from Matrix.h:13: ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 88 | const int GetNumLayers() const { | ^~~~~ ScoreMatrix.h:96:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 96 | const int GetNumRows() const { | ^~~~~ ScoreMatrix.h:104:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 104 | const int GetNumCols() const { | ^~~~~ Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 100 | const int GetNumLayers() const { | ^~~~~ Matrix.h:108:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 108 | const int GetNumRows() const { | ^~~~~ Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 116 | const int GetNumCols() const { | ^~~~~ In file included from ScoreMatrix.h:12, from Matrix.h:13: Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 51 | const int GetLength () const; | ^~~~~ Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 52 | const int GetID () const; | ^~~~~ ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 88 | const int GetNumLayers() const { | ^~~~~ ScoreMatrix.h:96:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 96 | const int GetNumRows() const { | ^~~~~ ScoreMatrix.h:104:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 104 | const int GetNumCols() const { | ^~~~~ Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 100 | const int GetNumLayers() const { | ^~~~~ Matrix.h:108:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 108 | const int GetNumRows() const { | ^~~~~ Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 116 | const int GetNumCols() const { | ^~~~~ MultiSequence.h:24:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 24 | const int AutoDetectFileFormat (const char *filename) const; | ^~~~~ MultiSequence.h:28:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 28 | const char ComputeAnnotation (const char *data, const int size) const; | ^~~~~ MultiSequence.h:48:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 48 | const int GetNumSequences() const; | ^~~~~ MultiSequence.h:49:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 49 | const int GetLength() const; | ^~~~~ MultiSequence.cc:86:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 86 | const int MultiSequence::GetNumSequences() const { | ^~~~~ MultiSequence.cc:94:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 94 | const int MultiSequence::GetLength() const { | ^~~~~ MultiSequence.cc:130:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 130 | const int MultiSequence::AutoDetectFileFormat (const char *filename) const { | ^~~~~ MultiSequence.cc:388:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 388 | const char MultiSequence::ComputeAnnotation (const char *data, const int size) const { | ^~~~~ Main.cc: In function 'void RunLocalAligner(int, char**)': Main.cc:339:57: warning: 'fasta' may be used uninitialized [-Wmaybe-uninitialized] 339 | seqs->WriteFASTA(fasta,block,result,start,end); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Main.cc:214:9: note: 'fasta' was declared here 214 | FILE *fasta; | ^~~~~ Main.cc:291:34: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 291 | delete used; | ^~~~ Main.cc:284:48: note: returned from 'void* operator new [](std::size_t)' 284 | int *used = new int[m]; | ^ LocalAlign.cc: In static member function 'static AlignedFragment* LocalAlign::ComputeLocalAlignment(const Sequence&, const Sequence&, const Matrix&, float*)': LocalAlign.cc:68:17: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 68 | delete nullX; | ^~~~~ LocalAlign.cc:22:38: note: returned from 'void* operator new [](std::size_t)' 22 | float *nullX = new float[rows]; | ^ LocalAlign.cc:69:17: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 69 | delete nullY; | ^~~~~ LocalAlign.cc:23:38: note: returned from 'void* operator new [](std::size_t)' 23 | float *nullY = new float[cols]; | ^ LocalAlign.cc:73:25: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 73 | delete traceback; | ^~~~~~~~~ LocalAlign.cc:19:65: note: returned from 'void* operator new [](std::size_t)' 19 | TracebackType *traceback = new TracebackType[rows * cols]; | ^ LocalAlign.cc:121:10: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 121 | delete s2; | ^~ LocalAlign.cc:99:34: note: returned from 'void* operator new [](std::size_t)' 99 | int *s2 = new int[besty - c + 1]; | ^ GlobalAlign.cc: In static member function 'static float GlobalAlign::ComputeAlignmentScore(const MultiSequence&, int, SparseMatrix**)': GlobalAlign.cc:226:10: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 226 | delete scores; | ^~~~~~ GlobalAlign.cc:191:35: note: returned from 'void* operator new [](std::size_t)' 191 | float *scores = new float[length]; | ^ Main.cc: In function 'int main(int, char**)': Main.cc:111:10: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 111 | delete filenames; | ^~~~~~~~~ Main.cc:61:38: note: returned from 'void* operator new [](std::size_t)' 61 | string *filenames = new string[argc]; | ^ In file included from Sequence.h:11: In member function 'Fragment& Fragment::operator=(Fragment)', inlined from 'Block::Block(std::vector&, MultiSequence*, bool, Block*)' at Block.cc:105:9: AlignedFragment.h:66:80: warning: 'best_end' may be used uninitialized [-Wmaybe-uninitialized] 66 | {begin = f.begin; length = f.length; multiply = f.multiply;end = f.end;id = f.id;return *this;} | ~~~~^~~~~~~ Block.cc: In constructor 'Block::Block(std::vector&, MultiSequence*, bool, Block*)': Block.cc:58:56: note: 'best_end' was declared here 58 | int best,best_id, best_pos, multi,end,bfrag,bk,best_end; | ^~~~~~~~ Block.cc:130:27: warning: 'bk' may be used uninitialized [-Wmaybe-uninitialized] 130 | bad[bfrag]=bk; | ~~~~~~~~~~^~~ Block.cc:58:53: note: 'bk' was declared here 58 | int best,best_id, best_pos, multi,end,bfrag,bk,best_end; | ^~ Block.cc:130:21: warning: 'bfrag' may be used uninitialized [-Wmaybe-uninitialized] 130 | bad[bfrag]=bk; | ^~~~~ Block.cc:58:47: note: 'bfrag' was declared here 58 | int best,best_id, best_pos, multi,end,bfrag,bk,best_end; | ^~~~~ In member function 'Fragment& Fragment::operator=(Fragment)', inlined from 'Block::Block(std::vector&, MultiSequence*, bool, Block*)' at Block.cc:105:9: AlignedFragment.h:66:24: warning: 'best_pos' may be used uninitialized [-Wmaybe-uninitialized] 66 | {begin = f.begin; length = f.length; multiply = f.multiply;end = f.end;id = f.id;return *this;} | ~~~~~~^~~~~~~~~ Block.cc: In constructor 'Block::Block(std::vector&, MultiSequence*, bool, Block*)': Block.cc:58:27: note: 'best_pos' was declared here 58 | int best,best_id, best_pos, multi,end,bfrag,bk,best_end; | ^~~~~~~~ In member function 'Fragment& Fragment::operator=(Fragment)', inlined from 'Block::Block(std::vector&, MultiSequence*, bool, Block*)' at Block.cc:105:9: AlignedFragment.h:66:91: warning: 'best_id' may be used uninitialized [-Wmaybe-uninitialized] 66 | {begin = f.begin; length = f.length; multiply = f.multiply;end = f.end;id = f.id;return *this;} | ~~~^~~~~~ Block.cc: In constructor 'Block::Block(std::vector&, MultiSequence*, bool, Block*)': Block.cc:58:18: note: 'best_id' was declared here 58 | int best,best_id, best_pos, multi,end,bfrag,bk,best_end; | ^~~~~~~ Block.cc:131:24: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 131 | delete frs; | ^~~ Block.cc:108:35: note: returned from 'void* operator new [](std::size_t)' 108 | frs = new Fragment[multi+1]; | ^ Block.cc:182:16: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 182 | delete frs; | ^~~ Block.cc:108:35: note: returned from 'void* operator new [](std::size_t)' 108 | frs = new Fragment[multi+1]; | ^ Block.cc:263:16: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 263 | delete frs; | ^~~ Block.cc:228:42: note: returned from 'void* operator new [](std::size_t)' 228 | frs = new Fragment[t_frags.size()]; | ^ Block.cc:264:16: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 264 | delete used; | ^~~~ Block.cc:59:42: note: returned from 'void* operator new [](std::size_t)' 59 | int *used = new int[afrags.size()]; //indicators of used fragmentsem | ^ Block.cc:265:16: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 265 | delete bad; | ^~~ Block.cc:60:41: note: returned from 'void* operator new [](std::size_t)' 60 | int *bad = new int[afrags.size()];//fragments that cannot be a seed | ^ PairAligner.cc: In member function 'void PairAligner::ConsistencyCheck(AVECT&)': PairAligner.cc:178:64: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 178 | delete l_map; | ^~~~~ PairAligner.cc:169:98: note: returned from 'void* operator new [](std::size_t)' 169 | int *l_map = new int[(xLen+1)* (yLen + 1)]; | ^ PairAligner.cc: In member function 'void PairAligner::FastPairAlign(AVECT&)': PairAligner.cc:206:24: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 206 | delete s1;delete s2; | ^~ PairAligner.cc:200:39: note: returned from 'void* operator new [](std::size_t)' 200 | int *s1 = new int[xLen]; | ^ PairAligner.cc:206:34: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 206 | delete s1;delete s2; | ^~ PairAligner.cc:201:39: note: returned from 'void* operator new [](std::size_t)' 201 | int *s2 = new int[xLen]; | ^ MultiSequence.cc: In member function 'void MultiSequence::WriteFASTA(FILE*, Block*, MultiSequence*, int, int)': MultiSequence.cc:757:16: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 757 | delete map; | ^~~ MultiSequence.cc:702:40: note: returned from 'void* operator new [](std::size_t)' 702 | int *map = new int[numSequences]; | ^ PairAligner.cc: In member function 'void PairAligner::PairAlign(AVECT&)': PairAligner.cc:281:24: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 281 | delete s1;delete s2; | ^~ PairAligner.cc:275:39: note: returned from 'void* operator new [](std::size_t)' 275 | int *s1 = new int[xLen]; | ^ PairAligner.cc:281:34: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 281 | delete s1;delete s2; | ^~ PairAligner.cc:276:39: note: returned from 'void* operator new [](std::size_t)' 276 | int *s2 = new int[xLen]; | ^ Block.cc: In member function 'int Block::AdjustAFragmentList(AVECT&, Matrix*, float)': Block.cc:369:16: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 369 | delete used; | ^~~~ MultiSequence.cc: In member function 'void MultiSequence::FindBlock(Block&, int&, int&, int)': MultiSequence.cc:633:16: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 633 | delete map; | ^~~ MultiSequence.cc:534:50: note: returned from 'void* operator new [](std::size_t)' 534 | int **map = new pint[numSequences]; | ^ Block.cc:331:34: note: returned from 'void* operator new [](std::size_t)' 331 | int *used = new int[asize]; | ^ MultiSequence.cc:634:16: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 634 | delete data; | ^~~~ MultiSequence.cc:513:51: note: returned from 'void* operator new [](std::size_t)' 513 | const char **data = new pchar[numSequences]; | ^ Block.cc: In member function 'int Block::AdjustAFragmentList(AVECT&, int, Matrix*, float)': Block.cc:426:16: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 426 | delete used; | ^~~~ Block.cc:387:34: note: returned from 'void* operator new [](std::size_t)' 387 | int *used = new int[asize]; | ^ ProbModel.cc: In member function 'AlignedFragment* ProbModel::Viterbi(const Sequence&, const Sequence&, int*)': ProbModel.cc:866:10: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 866 | delete s2; | ^~ ProbModel.cc:843:34: note: returned from 'void* operator new [](std::size_t)' 843 | int *s2 = new int[besty - c + 1]; | ^ ProbModel.cc: In member function 'void ProbModel::ViterbiUpdate(ScoreMatrix*, Matrix*, const Sequence&, const Sequence&, int*, AlignedFragment*, int)': ProbModel.cc:1239:10: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 1239 | delete buf; | ^~~ ProbModel.cc:969:42: note: returned from 'void* operator new [](std::size_t)' 969 | SCORE *buf = new SCORE[NUM_STATES]; | ^ ProbModel.cc: In member function 'AlignedFragment* ProbModel::OneAligment(const Sequence&, const Sequence&, Matrix&, ScoreMatrix&)': ProbModel.cc:1311:10: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 1311 | delete s2; | ^~ ProbModel.cc:1289:34: note: returned from 'void* operator new [](std::size_t)' 1289 | int *s2 = new int[besty - c + 1]; | ^ g++ -g -O2 -ffile-prefix-map=/build/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -lm AlignedFragment.o Assert.o Block.o Consistency.o GlobalAlign.o LocalAlign.o Main.o PairAligner.o Matrix.o MultiSequence.o ProbModel.o Score.o ScoreMatrix.o Sequence.o SparseMatrix.o Tree.o Utilities.o -o proda -Wl,-z,relro -Wl,-z,now make[1]: Leaving directory '/build/proda-1.0' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/proda/ dh_install dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'proda' in '../proda_1.0-13_i386.deb'. dpkg-deb: building package 'proda-dbgsym' in '../proda-dbgsym_1.0-13_i386.deb'. dpkg-genbuildinfo --build=binary -O../proda_1.0-13_i386.buildinfo dpkg-genchanges --build=binary -O../proda_1.0-13_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/99431 and its subdirectories I: Current time: Thu Jul 11 12:26:08 -12 2024 I: pbuilder-time-stamp: 1720743968 Fri Jun 9 18:03:11 UTC 2023 I: 1st build successful. Starting 2nd build on remote node ionos2-i386.debian.net. Fri Jun 9 18:03:11 UTC 2023 I: Preparing to do remote build '2' on ionos2-i386.debian.net. Fri Jun 9 18:05:01 UTC 2023 I: Deleting $TMPDIR on ionos2-i386.debian.net. Fri Jun 9 18:05:01 UTC 2023 I: proda_1.0-13_i386.changes: Format: 1.8 Date: Mon, 23 Nov 2020 20:57:38 +0100 Source: proda Binary: proda proda-dbgsym Architecture: i386 Version: 1.0-13 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: proda - multiple alignment of protein sequences Changes: proda (1.0-13) unstable; urgency=medium . * Standards-Version: 4.5.1 (routine-update) * debhelper-compat 13 (routine-update) * Secure URI in copyright format (routine-update) * Remove trailing whitespace in debian/changelog (routine-update) * autopkgtest: s/ADTTMP/AUTOPKGTEST_TMP/g (routine-update) * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) * Trim trailing whitespace. * Set field Upstream-Name in debian/copyright. * Remove obsolete field Name from debian/upstream/metadata (already present in machine-readable debian/copyright). Checksums-Sha1: cc605c0b621a460d5ca4440177d2812f49299901 260508 proda-dbgsym_1.0-13_i386.deb a8cc889159b2f7773e23a8ac0e25e2e7a106925f 5024 proda_1.0-13_i386.buildinfo 54649f1ba15f1d6178785ab8330b5c3f0bc0de0f 64380 proda_1.0-13_i386.deb Checksums-Sha256: 111f1c90604ac70251a4cb0c6643de285c1a5c182545b890a55a23b99b6f860d 260508 proda-dbgsym_1.0-13_i386.deb c7e958382178a2aa10b63465beb3bafc17872b48d7ab7b022cfd54e5cfb6696b 5024 proda_1.0-13_i386.buildinfo 0319ac892ea7a4834a4f960d3fb37a3c5df1a5c5205015898c271cbd392857af 64380 proda_1.0-13_i386.deb Files: 3accc4c7603c7b4601841ec803ee9798 260508 debug optional proda-dbgsym_1.0-13_i386.deb 3e7a41703dc20ac48aadff0fe8cdc035 5024 science optional proda_1.0-13_i386.buildinfo c5a6397f770eb19b582ff599b5211883 64380 science optional proda_1.0-13_i386.deb Fri Jun 9 18:05:02 UTC 2023 I: diffoscope 242 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.dMTu6ITm/proda_1.0-13.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.dMTu6ITm/proda_1.0-13.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.dMTu6ITm/proda_1.0-13.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.dMTu6ITm/b1/proda_1.0-13_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.dMTu6ITm/b2/proda_1.0-13_i386.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.444s) 0.444s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.024s) 0.024s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Fri Jun 9 18:05:04 UTC 2023 I: diffoscope 242 found no differences in the changes files, and a .buildinfo file also exists. Fri Jun 9 18:05:04 UTC 2023 I: proda from bookworm built successfully and reproducibly on i386. Fri Jun 9 18:05:06 UTC 2023 I: Submitting .buildinfo files to external archives: Fri Jun 9 18:05:06 UTC 2023 I: Submitting 8.0K b1/proda_1.0-13_i386.buildinfo.asc Fri Jun 9 18:05:06 UTC 2023 I: Submitting 8.0K b2/proda_1.0-13_i386.buildinfo.asc Fri Jun 9 18:05:07 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri Jun 9 18:05:07 UTC 2023 I: Done submitting .buildinfo files. Fri Jun 9 18:05:07 UTC 2023 I: Removing signed proda_1.0-13_i386.buildinfo.asc files: removed './b1/proda_1.0-13_i386.buildinfo.asc' removed './b2/proda_1.0-13_i386.buildinfo.asc'