Diff of the two buildlogs: -- --- b1/build.log 2023-04-19 15:37:09.742458745 +0000 +++ b2/build.log 2023-04-19 15:38:22.411235269 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue May 21 09:59:16 -12 2024 -I: pbuilder-time-stamp: 1716328756 +I: Current time: Thu Apr 20 05:37:12 +14 2023 +I: pbuilder-time-stamp: 1681918632 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ 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: Signature made Tue Nov 24 10:10:25 2020 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -33,135 +33,167 @@ dpkg-source: info: applying hardening.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/427718/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3986795/tmp/hooks/D01_modify_environment starting +debug: Running on ionos11-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Apr 20 05:37 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/3986795/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3986795/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='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='45502a3b06ad41f2a05a05d072431801' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - 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='427718' - PS1='# ' - PS2='> ' + INVOCATION_ID=5f40f771a6bb43e8bce1d60bcd85b72b + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=3986795 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.FW02bibi/pbuilderrc_qBwi --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.FW02bibi/b1 --logfile b1/build.log proda_1.0-13.dsc' - SUDO_GID='111' - SUDO_UID='106' - 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' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.FW02bibi/pbuilderrc_cJnd --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.FW02bibi/b2 --logfile b2/build.log --extrapackages usrmerge proda_1.0-13.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://78.137.99.97:3128 I: uname -a - Linux ionos15-amd64 6.1.0-0.deb11.5-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.12-1~bpo11+1 (2023-03-05) x86_64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 GNU/Linux I: ls -l /bin total 5632 - -rwxr-xr-x 1 root root 1265648 Feb 12 2023 bash - -rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2 - -rwxr-xr-x 3 root root 39224 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 39224 Sep 18 2022 bzip2 - -rwxr-xr-x 1 root root 14568 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 44016 Sep 20 2022 cat - -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp - -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod - -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown - -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp - -rwxr-xr-x 1 root root 125640 Jan 5 2023 dash - -rwxr-xr-x 1 root root 121904 Sep 20 2022 date - -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd - -rwxr-xr-x 1 root root 102200 Sep 20 2022 df - -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir - -rwxr-xr-x 1 root root 88656 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 43856 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep - -rwxr-xr-x 1 root root 35664 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep - -rwxr-xr-x 1 root root 85600 Mar 22 2023 findmnt - -rwsr-xr-x 1 root root 35128 Mar 22 2023 fusermount - -rwxr-xr-x 1 root root 203152 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 98136 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 22680 Dec 19 2022 hostname - -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln - -rwxr-xr-x 1 root root 53024 Mar 23 2023 login - -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls - -rwxr-xr-x 1 root root 207168 Mar 22 2023 lsblk - -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir - -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod - -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp - -rwxr-xr-x 1 root root 59712 Mar 22 2023 more - -rwsr-xr-x 1 root root 59704 Mar 22 2023 mount - -rwxr-xr-x 1 root root 18744 Mar 22 2023 mountpoint - -rwxr-xr-x 1 root root 142968 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 43952 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Feb 12 2023 rbash -> bash - -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink - -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm - -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 27560 Nov 2 2022 run-parts - -rwxr-xr-x 1 root root 126424 Jan 5 2023 sed - lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash - -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep - -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty - -rwsr-xr-x 1 root root 72000 Mar 22 2023 su - -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync - -rwxr-xr-x 1 root root 531984 Apr 6 2023 tar - -rwxr-xr-x 1 root root 14520 Nov 2 2022 tempfile - -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch - -rwxr-xr-x 1 root root 35664 Sep 20 2022 true - -rwxr-xr-x 1 root root 14568 Mar 22 2023 ulockmgr_server - -rwsr-xr-x 1 root root 35128 Mar 22 2023 umount - -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir - -rwxr-xr-x 1 root root 72024 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/427718/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1265648 Feb 13 10:05 bash + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bunzip2 + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzcat + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzip2 + -rwxr-xr-x 1 root root 14568 Sep 19 2022 bzip2recover + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore + -rwxr-xr-x 1 root root 44016 Sep 21 2022 cat + -rwxr-xr-x 1 root root 68656 Sep 21 2022 chgrp + -rwxr-xr-x 1 root root 64496 Sep 21 2022 chmod + -rwxr-xr-x 1 root root 72752 Sep 21 2022 chown + -rwxr-xr-x 1 root root 151152 Sep 21 2022 cp + -rwxr-xr-x 1 root root 125640 Jan 6 03:20 dash + -rwxr-xr-x 1 root root 121904 Sep 21 2022 date + -rwxr-xr-x 1 root root 89240 Sep 21 2022 dd + -rwxr-xr-x 1 root root 102200 Sep 21 2022 df + -rwxr-xr-x 1 root root 151344 Sep 21 2022 dir + -rwxr-xr-x 1 root root 88656 Mar 24 00:02 dmesg + lrwxrwxrwx 1 root root 8 Dec 20 03:33 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Dec 20 03:33 domainname -> hostname + -rwxr-xr-x 1 root root 43856 Sep 21 2022 echo + -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep + -rwxr-xr-x 1 root root 35664 Sep 21 2022 false + -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep + -rwxr-xr-x 1 root root 85600 Mar 24 00:02 findmnt + -rwsr-xr-x 1 root root 35128 Mar 23 22:35 fusermount + -rwxr-xr-x 1 root root 203152 Jan 25 04:43 grep + -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip + -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe + -rwxr-xr-x 1 root root 98136 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 22680 Dec 20 03:33 hostname + -rwxr-xr-x 1 root root 72824 Sep 21 2022 ln + -rwxr-xr-x 1 root root 53024 Mar 24 02:40 login + -rwxr-xr-x 1 root root 151344 Sep 21 2022 ls + -rwxr-xr-x 1 root root 207168 Mar 24 00:02 lsblk + -rwxr-xr-x 1 root root 97552 Sep 21 2022 mkdir + -rwxr-xr-x 1 root root 72912 Sep 21 2022 mknod + -rwxr-xr-x 1 root root 43952 Sep 21 2022 mktemp + -rwxr-xr-x 1 root root 59712 Mar 24 00:02 more + -rwsr-xr-x 1 root root 59704 Mar 24 00:02 mount + -rwxr-xr-x 1 root root 18744 Mar 24 00:02 mountpoint + -rwxr-xr-x 1 root root 142968 Sep 21 2022 mv + lrwxrwxrwx 1 root root 8 Dec 20 03:33 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43952 Sep 21 2022 pwd + lrwxrwxrwx 1 root root 4 Feb 13 10:05 rbash -> bash + -rwxr-xr-x 1 root root 52112 Sep 21 2022 readlink + -rwxr-xr-x 1 root root 72752 Sep 21 2022 rm + -rwxr-xr-x 1 root root 56240 Sep 21 2022 rmdir + -rwxr-xr-x 1 root root 27560 Nov 3 06:31 run-parts + -rwxr-xr-x 1 root root 126424 Jan 6 09:55 sed + lrwxrwxrwx 1 root root 9 Apr 20 05:37 sh -> /bin/bash + -rwxr-xr-x 1 root root 43888 Sep 21 2022 sleep + -rwxr-xr-x 1 root root 85008 Sep 21 2022 stty + -rwsr-xr-x 1 root root 72000 Mar 24 00:02 su + -rwxr-xr-x 1 root root 39824 Sep 21 2022 sync + -rwxr-xr-x 1 root root 531984 Apr 7 04:25 tar + -rwxr-xr-x 1 root root 14520 Nov 3 06:31 tempfile + -rwxr-xr-x 1 root root 109616 Sep 21 2022 touch + -rwxr-xr-x 1 root root 35664 Sep 21 2022 true + -rwxr-xr-x 1 root root 14568 Mar 23 22:35 ulockmgr_server + -rwsr-xr-x 1 root root 35128 Mar 24 00:02 umount + -rwxr-xr-x 1 root root 43888 Sep 21 2022 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 151344 Sep 21 2022 vdir + -rwxr-xr-x 1 root root 72024 Mar 24 00:02 wdctl + lrwxrwxrwx 1 root root 8 Dec 20 03:33 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat + -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp + -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff + -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep + -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep + -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce + -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep + -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless + -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore + -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew +I: user script /srv/workspace/pbuilder/3986795/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -227,7 +259,7 @@ Get: 28 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] -Fetched 18.7 MB in 0s (42.2 MB/s) +Fetched 18.7 MB in 0s (66.3 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 ... 19596 files and directories currently installed.) @@ -361,8 +393,19 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 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 +I: user script /srv/workspace/pbuilder/3986795/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +removed '/etc/unsupported-skip-usrmerge-conversion' +The system has been successfully converted. +I: user script /srv/workspace/pbuilder/3986795/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/proda-1.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-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 @@ -372,7 +415,7 @@ debian/rules clean dh clean dh_auto_clean - make -j16 clean + make -j15 clean make[1]: Entering directory '/build/proda-1.0' rm -f *.o make[1]: Leaving directory '/build/proda-1.0' @@ -383,7 +426,7 @@ dh_autoreconf dh_auto_configure dh_auto_build - make -j16 "INSTALL=install --strip-program=true" + make -j15 "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 @@ -401,7 +444,6 @@ 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 LocalAlign.h:12, from LocalAlign.cc:5: @@ -432,6 +474,7 @@ SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 62 | const int GetNumCols() const; | ^~~~~ +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 Matrix.cc:7: SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] @@ -493,79 +536,6 @@ SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 62 | const int GetNumCols() const; | ^~~~~ -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 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; - | ^~~~~ -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; - | ^~~~~ -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 MultiSequence.h:12, from Main.cc:12: Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] @@ -626,23 +596,6 @@ 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 { - | ^~~~~ 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; @@ -656,54 +609,6 @@ MultiSequence.h:49:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 49 | const int GetLength() 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 { - | ^~~~~ -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; - | ^~~~~ 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; @@ -717,12 +622,6 @@ 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; - | ^~~~~ 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] @@ -731,54 +630,22 @@ Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 52 | const int GetID () 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 { | ^~~~~ -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 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 { - | ^~~~~ -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; - | ^~~~~ -ScoreMatrix.h:96:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 96 | const int GetNumRows() const { - | ^~~~~ -SparseMatrix.h:60:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 60 | const int GetNumLayers() const; - | ^~~~~ -ScoreMatrix.h:104:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 104 | const int GetNumCols() 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, from SparseMatrix.h:12, - from Consistency.h:10, - from Consistency.cc:5: + from SparseMatrix.cc:6: Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 51 | const int GetLength () const; | ^~~~~ @@ -803,34 +670,6 @@ 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 { - | ^~~~~ -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; | ^~~~~ @@ -843,6 +682,18 @@ SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 62 | 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: Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] @@ -869,19 +720,24 @@ 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 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 ScoreMatrix.h:12, - from ScoreMatrix.cc:7: + 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; | ^~~~~ @@ -897,6 +753,15 @@ 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 Matrix.h:12, from Types.h:12, from Block.h:10, @@ -923,6 +788,18 @@ ScoreMatrix.h:104:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 104 | 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; + | ^~~~~ Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 100 | const int GetNumLayers() const { | ^~~~~ @@ -951,10 +828,18 @@ Tree.h:45:5: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 45 | const int GetNumSequences() 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; + | ^~~~~ In file included from Matrix.h:12, from Types.h:12, from ProbModel.h:11, - from ScoreMatrix.cc:8: + 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; | ^~~~~ @@ -967,6 +852,16 @@ 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 { + | ^~~~~ Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 100 | const int GetNumLayers() const { | ^~~~~ @@ -976,6 +871,114 @@ Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 116 | const int GetNumCols() const { | ^~~~~ +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]; + | ^ +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]; + | ^ +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 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; + | ^~~~~ +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 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; + | ^~~ +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]; + | ^ In file included from Matrix.h:12, from Types.h:12, from Block.h:10, @@ -1002,6 +1005,32 @@ 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.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 100 | const int GetNumLayers() const { | ^~~~~ @@ -1035,45 +1064,32 @@ 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 { | ^~~~~ -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]; - | ^ -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)]; - | ^ +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 { + | ^~~~~ 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); @@ -1087,32 +1103,66 @@ Main.cc:284:48: note: returned from 'void* operator new [](std::size_t)' 284 | int *used = new int[m]; | ^ -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]; - | ^ -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]; - | ^ +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 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 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 { + | ^~~~~ +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: @@ -1183,13 +1233,6 @@ 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 | ^ -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]; - | ^ 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; @@ -1197,13 +1240,6 @@ MultiSequence.cc:702:40: note: returned from 'void* operator new [](std::size_t)' 702 | int *map = new int[numSequences]; | ^ -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; - | ^~~~ -Block.cc:331:34: note: returned from 'void* operator new [](std::size_t)' - 331 | int *used = new int[asize]; - | ^ 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; @@ -1217,12 +1253,12 @@ MultiSequence.cc:513:51: note: returned from 'void* operator new [](std::size_t)' 513 | const char **data = new pchar[numSequences]; | ^ -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]; +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; + | ^~~~ +Block.cc:331:34: note: returned from 'void* operator new [](std::size_t)' + 331 | int *used = new int[asize]; | ^ 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] @@ -1231,6 +1267,13 @@ 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; @@ -1278,12 +1321,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/3986795/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3986795/tmp/hooks/B01_cleanup finished 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/427718 and its subdirectories -I: Current time: Tue May 21 10:00:09 -12 2024 -I: pbuilder-time-stamp: 1716328809 +I: removing directory /srv/workspace/pbuilder/3986795 and its subdirectories +I: Current time: Thu Apr 20 05:38:21 +14 2023 +I: pbuilder-time-stamp: 1681918701