Diff of the two buildlogs: -- --- b1/build.log 2023-06-01 17:02:53.461238218 +0000 +++ b2/build.log 2023-06-01 17:04:07.305999251 +0000 @@ -1,49 +1,8 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Jul 3 11:22:38 -12 2024 -I: pbuilder-time-stamp: 1720048958 +I: Current time: Fri Jun 2 07:02:54 +14 2023 +I: pbuilder-time-stamp: 1685638974 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] -tar: ./usr/share/perl5/Debian: time stamp 2025-08-04 08:27:02 is 34290261.342289657 s in the future -tar: ./usr/share/man/pt/man8: time stamp 2025-08-04 08:27:02 is 34290261.287079393 s in the future -tar: ./usr/share/man/pt/man5: time stamp 2025-08-04 08:27:02 is 34290261.283838274 s in the future -tar: ./usr/share/man/nl/man8: time stamp 2025-08-04 08:27:02 is 34290261.276521906 s in the future -tar: ./usr/share/man/nl/man5: time stamp 2025-08-04 08:27:02 is 34290261.273789454 s in the future -tar: ./usr/share/man/man5: time stamp 2025-08-04 08:27:02 is 34290261.252984434 s in the future -tar: ./usr/share/man/fr/man5: time stamp 2025-08-04 08:27:02 is 34290261.206881487 s in the future -tar: ./usr/share/man/de/man5: time stamp 2025-08-04 08:27:02 is 34290261.192448829 s in the future -tar: ./usr/share/locale/zh_CN/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34290261.031700233 s in the future -tar: ./usr/share/locale/vi/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34290261.007810068 s in the future -tar: ./usr/share/locale/uk/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34290260.964330296 s in the future -tar: ./usr/share/locale/sv/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34290260.901921419 s in the future -tar: ./usr/share/locale/sk/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34290260.882917971 s in the future -tar: ./usr/share/locale/ru/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34290260.843335671 s in the future -tar: ./usr/share/locale/pt_BR/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34290260.806186745 s in the future -tar: ./usr/share/locale/pt/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34290260.779111183 s in the future -tar: ./usr/share/locale/pl/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34290260.75978349 s in the future -tar: ./usr/share/locale/nl/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34290260.735792111 s in the future -tar: ./usr/share/locale/nb/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34290260.718471555 s in the future -tar: ./usr/share/locale/ko/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34290260.694981265 s in the future -tar: ./usr/share/locale/ja/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34290260.666797288 s in the future -tar: ./usr/share/locale/it/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34290260.648928249 s in the future -tar: ./usr/share/locale/hu/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34290260.63550086 s in the future -tar: ./usr/share/locale/gl/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34290260.62545288 s in the future -tar: ./usr/share/locale/fr/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34290260.585088237 s in the future -tar: ./usr/share/locale/eu/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34290260.557314594 s in the future -tar: ./usr/share/locale/es/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34290260.522728551 s in the future -tar: ./usr/share/locale/de/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34290260.484587134 s in the future -tar: ./usr/share/locale/da/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34290260.462500148 s in the future -tar: ./usr/share/locale/cs/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34290260.441907561 s in the future -tar: ./usr/share/locale/ca/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34290260.420254419 s in the future -tar: ./usr/share/doc/adduser/examples/adduser.local.conf.examples/skel.other: time stamp 2025-08-04 08:27:02 is 34290260.353497322 s in the future -tar: ./usr/share/doc/adduser/examples/adduser.local.conf.examples/skel: time stamp 2025-08-04 08:27:02 is 34290260.353340604 s in the future -tar: ./usr/share/doc/adduser/examples/adduser.local.conf.examples: time stamp 2025-08-04 08:27:02 is 34290260.353252654 s in the future -tar: ./usr/share/doc/adduser/examples: time stamp 2025-08-04 08:27:02 is 34290260.351953867 s in the future -tar: ./usr/share/doc/adduser: time stamp 2025-08-04 08:27:02 is 34290260.351701503 s in the future -tar: ./var/lib/dpkg/info/adduser.list: time stamp 2025-08-04 08:27:02 is 34290251.646259301 s in the future -tar: ./usr/share/man/de/man8: time stamp 2025-08-04 08:27:02 is 34290250.447438296 s in the future -tar: ./usr/share/man/fr/man8: time stamp 2025-08-04 08:27:02 is 34290250.447251081 s in the future -tar: ./usr/share/man/man8: time stamp 2025-08-04 08:27:02 is 34290250.447005675 s in the future -tar: ./usr/sbin: time stamp 2025-08-04 08:27:02 is 34290250.437182669 s in the future I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem @@ -57,7 +16,7 @@ I: copying [./libpsortb_1.0+dfsg.orig.tar.xz] I: copying [./libpsortb_1.0+dfsg-5.debian.tar.xz] I: Extracting source -gpgv: Signature made Wed Nov 17 04:51:13 2021 -12 +gpgv: Signature made Thu Nov 18 06:51:13 2021 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -70,135 +29,167 @@ dpkg-source: info: applying use_debian_packaged_libsvm.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3633491/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1094935/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 Jun 2 07:03 /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/1094935/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1094935/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='f61efbac669546348e2e9ee928f50f47' - 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='3633491' - PS1='# ' - PS2='> ' + INVOCATION_ID=26ddee71bf12403c87f05c69e21e642b + 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=1094935 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.AuAiLGY3/pbuilderrc_8sti --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.AuAiLGY3/b1 --logfile b1/build.log libpsortb_1.0+dfsg-5.dsc' - SUDO_GID='110' - SUDO_UID='105' - 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.AuAiLGY3/pbuilderrc_WB5d --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.AuAiLGY3/b2 --logfile b2/build.log --extrapackages usrmerge libpsortb_1.0+dfsg-5.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 ionos5-amd64 6.1.0-0.deb11.7-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.20-2~bpo11+1 (2023-04-23) x86_64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-23-amd64 #1 SMP Debian 5.10.179-1 (2023-05-12) x86_64 GNU/Linux I: ls -l /bin total 5632 - -rwxr-xr-x 1 root root 1265648 Apr 23 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 Apr 23 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/3633491/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1265648 Apr 24 11:23 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 Apr 24 11:23 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 2022 run-parts + -rwxr-xr-x 1 root root 126424 Jan 6 09:55 sed + lrwxrwxrwx 1 root root 9 Jun 2 07:03 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 2022 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/1094935/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -284,7 +275,7 @@ Get: 38 http://deb.debian.org/debian bookworm/main amd64 pkgconf-bin amd64 1.8.1-1 [29.5 kB] Get: 39 http://deb.debian.org/debian bookworm/main amd64 pkgconf amd64 1.8.1-1 [25.9 kB] Get: 40 http://deb.debian.org/debian bookworm/main amd64 pkg-config amd64 1.8.1-1 [13.7 kB] -Fetched 19.3 MB in 1s (31.7 MB/s) +Fetched 19.3 MB in 1s (28.2 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 ... 19591 files and directories currently installed.) @@ -458,8 +449,19 @@ 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/libpsortb-1.0+dfsg/ && 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 > ../libpsortb_1.0+dfsg-5_source.changes +I: user script /srv/workspace/pbuilder/1094935/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/1094935/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/libpsortb-1.0+dfsg/ && 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 > ../libpsortb_1.0+dfsg-5_source.changes dpkg-buildpackage: info: source package libpsortb dpkg-buildpackage: info: source version 1.0+dfsg-5 dpkg-buildpackage: info: source distribution unstable @@ -504,7 +506,7 @@ ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes -checking for a race-free mkdir -p... /bin/mkdir -p +checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes @@ -532,10 +534,10 @@ checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf -checking for a sed that does not truncate output... /bin/sed -checking for grep that handles long lines and -e... /bin/grep -checking for egrep... /bin/grep -E -checking for fgrep... /bin/grep -F +checking for a sed that does not truncate output... /usr/bin/sed +checking for grep that handles long lines and -e... /usr/bin/grep +checking for egrep... /usr/bin/grep -E +checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B @@ -555,8 +557,8 @@ checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no -checking for a working dd... /bin/dd -checking how to truncate binary pipes... /bin/dd bs=4096 count=1 +checking for a working dd... /usr/bin/dd +checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for stdio.h... yes @@ -598,7 +600,7 @@ checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for main in -lm... yes -checking for egrep... (cached) /bin/grep -E +checking for egrep... (cached) /usr/bin/grep -E checking for float.h... yes checking for limits.h... yes checking for memory.h... yes @@ -643,19 +645,19 @@ config.status: executing depfiles commands config.status: executing libtool commands dh_auto_build - make -j16 + make -j15 make[1]: Entering directory '/build/libpsortb-1.0+dfsg' make all-recursive make[2]: Entering directory '/build/libpsortb-1.0+dfsg' Making all in svmloc make[3]: Entering directory '/build/libpsortb-1.0+dfsg/svmloc' -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o binding.lo binding.cpp -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o svmloc.lo svmloc.cpp -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c svmloc.cpp -fPIC -DPIC -o .libs/svmloc.o +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o binding.lo binding.cpp +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o svmloc.lo svmloc.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c binding.cpp -fPIC -DPIC -o .libs/binding.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c svmloc.cpp -fPIC -DPIC -o .libs/svmloc.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c binding.cpp -o binding.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c svmloc.cpp -o svmloc.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 0:0:0 -lsvm -Wl,-z,relro -Wl,-z,now -o libsvmloc.la -rpath /usr/lib/x86_64-linux-gnu binding.lo svmloc.lo -lm +/bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 0:0:0 -lsvm -Wl,-z,relro -Wl,-z,now -o libsvmloc.la -rpath /usr/lib/x86_64-linux-gnu binding.lo svmloc.lo -lm libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/12/crtbeginS.o .libs/binding.o .libs/svmloc.o -lsvm -L/usr/lib/gcc/x86_64-linux-gnu/12 -L/usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/12/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/12/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/12/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/crtn.o -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libsvmloc.so.0 -o .libs/libsvmloc.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libsvmloc.so.0" && ln -s "libsvmloc.so.0.0.0" "libsvmloc.so.0") libtool: link: (cd ".libs" && rm -f "libsvmloc.so" && ln -s "libsvmloc.so.0.0.0" "libsvmloc.so") @@ -665,24 +667,24 @@ make[3]: Leaving directory '/build/libpsortb-1.0+dfsg/svmloc' Making all in modhmm0.92b make[3]: Entering directory '/build/libpsortb-1.0+dfsg/modhmm0.92b' -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o core_algorithms_multialpha.lo core_algorithms_multialpha.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o debug_funcs.lo debug_funcs.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o hmmsearch.lo hmmsearch.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o readhmm.lo readhmm.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o readhmm_multialpha.lo readhmm_multialpha.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o readseqs_multialpha.lo readseqs_multialpha.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o std_calculation_funcs.lo std_calculation_funcs.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o std_funcs.lo std_funcs.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o training_algorithms_multialpha.lo training_algorithms_multialpha.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o core_algorithms_multialpha.lo core_algorithms_multialpha.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o debug_funcs.lo debug_funcs.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o hmmsearch.lo hmmsearch.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o readhmm.lo readhmm.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o readhmm_multialpha.lo readhmm_multialpha.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o readseqs_multialpha.lo readseqs_multialpha.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o std_calculation_funcs.lo std_calculation_funcs.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o std_funcs.lo std_funcs.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o training_algorithms_multialpha.lo training_algorithms_multialpha.c +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c training_algorithms_multialpha.c -fPIC -DPIC -o .libs/training_algorithms_multialpha.o +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c hmmsearch.c -fPIC -DPIC -o .libs/hmmsearch.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c core_algorithms_multialpha.c -fPIC -DPIC -o .libs/core_algorithms_multialpha.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c debug_funcs.c -fPIC -DPIC -o .libs/debug_funcs.o -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c readhmm.c -fPIC -DPIC -o .libs/readhmm.o -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c std_calculation_funcs.c -fPIC -DPIC -o .libs/std_calculation_funcs.o -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c readhmm_multialpha.c -fPIC -DPIC -o .libs/readhmm_multialpha.o -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c hmmsearch.c -fPIC -DPIC -o .libs/hmmsearch.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c readseqs_multialpha.c -fPIC -DPIC -o .libs/readseqs_multialpha.o +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c std_calculation_funcs.c -fPIC -DPIC -o .libs/std_calculation_funcs.o +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c readhmm.c -fPIC -DPIC -o .libs/readhmm.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c std_funcs.c -fPIC -DPIC -o .libs/std_funcs.o -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c training_algorithms_multialpha.c -fPIC -DPIC -o .libs/training_algorithms_multialpha.o +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c readhmm_multialpha.c -fPIC -DPIC -o .libs/readhmm_multialpha.o debug_funcs.c: In function 'dump_viterbi_path': debug_funcs.c:320:38: warning: implicit declaration of function 'get_mtx_index' [-Wimplicit-function-declaration] 320 | dump_viterbi_path(viterbi_mtxp + get_mtx_index(row-1, cur->prev, row_size), hmmp, @@ -722,7 +724,69 @@ readhmm.c:397:28: warning: assignment to 'struct transition_s *' from incompatible pointer type 'int *' [-Wincompatible-pointer-types] 397 | hmmp->trans_tie_groups = (int*)(malloc_or_die((hmmp->nr_t + hmmp->nr_ttg) * sizeof(struct transition_s))); | ^ +std_funcs.c: In function 'get_replacement_letter_index_single': +std_funcs.c:683:62: warning: comparison between pointer and integer + 683 | if(((replacement_letters->letters + a_index)->letter)[0] == c) { + | ^~ +training_algorithms_multialpha.c: In function 'msa_baum_welch_dirichlet_multi': +training_algorithms_multialpha.c:701:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] + 701 | alphabet = hmmp->alphabet; + | ^ +training_algorithms_multialpha.c:710:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] + 710 | alphabet = hmmp->alphabet_2; + | ^ +training_algorithms_multialpha.c:719:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] + 719 | alphabet = hmmp->alphabet_3; + | ^ +training_algorithms_multialpha.c:728:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] + 728 | alphabet = hmmp->alphabet_4; + | ^ +hmmsearch.c: In function 'get_scores': +readseqs_multialpha.c: In function 'get_sequence_fasta_multi': +hmmsearch.c:535:19: warning: assignment to 'struct helix_site *' from incompatible pointer type 'helix_sites *' [-Wincompatible-pointer-types] + 535 | hSites->helix = (helix_sites *) malloc(sizeof (helix_sites) * helices); + | ^ +readseqs_multialpha.c:83:39: warning: assignment to 'char' from 'char *' makes integer from pointer without a cast [-Wint-conversion] + 83 | (seq_infop->seqs + seq_nr)->name[0] = "s"; + | ^ +readseqs_multialpha.c: In function 'get_sequence_std_multi': +readseqs_multialpha.c:121:55: warning: unknown escape sequence: '\s' + 121 | if(line[0] == '<' || line[0] == '#' || line[0] == '\s' || line[0] == '\n' || line[0] == '/') { + | ^~~~ +hmmsearch.c: In function 'get_nullmodel_score_multi': +hmmsearch.c:656:42: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'struct letter_s *' [-Wformat=] + 656 | printf("Could not find letter %s when scoring null model\n", &seq[l]); + | ~^ ~~~~~~~ + | | | + | char * struct letter_s * +hmmsearch.c:674:44: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'struct letter_s *' [-Wformat=] + 674 | printf("Could not find letter %s when scoring null model\n", &seq_2[l]); + | ~^ ~~~~~~~~~ + | | | + | char * struct letter_s * +hmmsearch.c:693:44: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'struct letter_s *' [-Wformat=] + 693 | printf("Could not find letter %s when scoring null model\n", &seq_3[l]); + | ~^ ~~~~~~~~~ + | | | + | char * struct letter_s * +hmmsearch.c:712:44: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'struct letter_s *' [-Wformat=] + 712 | printf("Could not find letter %s when scoring null model\n", &seq[l]); + | ~^ ~~~~~~~ + | | | + | char * struct letter_s * +readseqs_multialpha.c: In function 'get_sequences_msa_std_multi': +readseqs_multialpha.c:372:18: warning: unknown escape sequence: '\s' + 372 | else if(i == '\s' && i == '\n') { + | ^~~~ +readhmm.c: In function 'readhmm': +readhmm.c:69:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 69 | fgets(s, MAX_LINE, file); + | ^~~~~~~~~~~~~~~~~~~~~~~~ core_algorithms_multialpha.c: In function 'msa_forward_multi': +readseqs_multialpha.c:389:22: warning: implicit declaration of function 'read_multi_prior_file_multi'; did you mean 'read_prior_file_multi'? [-Wimplicit-function-declaration] + 389 | read_priorfile = read_multi_prior_file_multi(&em_di_1, hmmp, priorfile_a1, 1); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ + | read_prior_file_multi core_algorithms_multialpha.c:1192:87: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] 1192 | a_index = get_alphabet_index((msa_seq_infop->msa_seq_1 + (c * (hmmp->a_size+1)))->query_letter, hmmp->alphabet, hmmp->a_size); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ @@ -756,9 +820,18 @@ funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ -readhmm.c: In function 'readhmm': -readhmm.c:69:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 69 | fgets(s, MAX_LINE, file); +std_funcs.c: In function 'get_reverse_msa_seq': +readhmm_multialpha.c: In function 'copy_hmm_struct': +std_funcs.c:2076:74: warning: assignment to 'int *' from 'int' makes pointer from integer without a cast [-Wint-conversion] + 2076 | *(reverse_msa_seq_infop->gaps + (msa_seq_infop->msa_seq_length + i)) = END; + | ^ +readhmm_multialpha.c:273:34: warning: assignment to 'struct transition_s *' from incompatible pointer type 'int *' [-Wincompatible-pointer-types] + 273 | retrain_hmmp->trans_tie_groups = (int*)(malloc_or_die((hmmp->nr_t + hmmp->nr_ttg) * sizeof(struct transition_s))); + | ^ +readhmm.c: In function 'readanhmm': +training_algorithms_multialpha.c: In function 'extended_msa_baum_welch_dirichlet_multi': +readhmm.c:345:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 345 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ core_algorithms_multialpha.c: In function 'msa_backward_multi': core_algorithms_multialpha.c:1419:87: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] @@ -766,17 +839,12 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ | | | char * -readseqs_multialpha.c: In function 'get_sequence_fasta_multi': -readseqs_multialpha.c:83:39: warning: assignment to 'char' from 'char *' makes integer from pointer without a cast [-Wint-conversion] - 83 | (seq_infop->seqs + seq_nr)->name[0] = "s"; - | ^ -readseqs_multialpha.c: In function 'get_sequence_std_multi': -readseqs_multialpha.c:121:55: warning: unknown escape sequence: '\s' - 121 | if(line[0] == '<' || line[0] == '#' || line[0] == '\s' || line[0] == '\n' || line[0] == '/') { - | ^~~~ funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ +training_algorithms_multialpha.c:1639:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] + 1639 | alphabet = hmmp->alphabet; + | ^ core_algorithms_multialpha.c:1426:93: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] 1426 | a_index_2 = get_alphabet_index((msa_seq_infop->msa_seq_2 + (c * (hmmp->a_size_2+1)))->query_letter, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ @@ -785,6 +853,7 @@ funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ +std_funcs.c: In function 'get_reverse_msa_seq_multi': core_algorithms_multialpha.c:1435:93: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] 1435 | a_index_3 = get_alphabet_index((msa_seq_infop->msa_seq_3 + (c * (hmmp->a_size_3+1)))->query_letter, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ @@ -793,6 +862,9 @@ funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ +training_algorithms_multialpha.c:1646:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] + 1646 | alphabet = hmmp->alphabet_2; + | ^ core_algorithms_multialpha.c:1444:93: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] 1444 | a_index_4 = get_alphabet_index((msa_seq_infop->msa_seq_4 + (c * (hmmp->a_size_4+1)))->query_letter, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ @@ -801,10 +873,19 @@ funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ -readhmm.c: In function 'readanhmm': -readhmm.c:345:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 345 | fgets(s, MAX_LINE, file); - | ^~~~~~~~~~~~~~~~~~~~~~~~ +std_funcs.c:2184:74: warning: assignment to 'int *' from 'int' makes pointer from integer without a cast [-Wint-conversion] + 2184 | *(reverse_msa_seq_infop->gaps + (msa_seq_infop->msa_seq_length + i)) = END; + | ^ +training_algorithms_multialpha.c:1653:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] + 1653 | alphabet = hmmp->alphabet_3; + | ^ +readhmm_multialpha.c: In function 'readhmm_multialpha': +training_algorithms_multialpha.c:1660:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] + 1660 | alphabet = hmmp->alphabet_4; + | ^ +readhmm_multialpha.c:469:28: warning: assignment to 'struct transition_s *' from incompatible pointer type 'int *' [-Wincompatible-pointer-types] + 469 | hmmp->trans_tie_groups = (int*)(malloc_or_die((hmmp->nr_t + hmmp->nr_ttg) * sizeof(struct transition_s))); + | ^ core_algorithms_multialpha.c: In function 'msa_viterbi_multi': core_algorithms_multialpha.c:1608:87: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] 1608 | a_index = get_alphabet_index((msa_seq_infop->msa_seq_1 + (c * (hmmp->a_size+1)))->query_letter, hmmp->alphabet, hmmp->a_size); @@ -814,6 +895,10 @@ funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ +readhmm.c: In function 'read_module': +readhmm.c:751:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 751 | fgets(s, MAX_LINE, file); + | ^~~~~~~~~~~~~~~~~~~~~~~~ core_algorithms_multialpha.c:1615:93: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] 1615 | a_index_2 = get_alphabet_index((msa_seq_infop->msa_seq_2 + (c * (hmmp->a_size_2+1)))->query_letter, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ @@ -822,6 +907,13 @@ funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ +std_calculation_funcs.c: In function 'update_labelings': +training_algorithms_multialpha.c:1784:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] + 1784 | alphabet = hmmp->alphabet; + | ^ +readhmm.c:786:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 786 | fgets(s, MAX_LINE, file); + | ^~~~~~~~~~~~~~~~~~~~~~~~ core_algorithms_multialpha.c:1624:93: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] 1624 | a_index_3 = get_alphabet_index((msa_seq_infop->msa_seq_3 + (c * (hmmp->a_size_3+1)))->query_letter, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ @@ -830,39 +922,50 @@ funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ +readhmm.c:821:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 821 | fgets(s, MAX_LINE, file); + | ^~~~~~~~~~~~~~~~~~~~~~~~ core_algorithms_multialpha.c:1633:93: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] 1633 | a_index_4 = get_alphabet_index((msa_seq_infop->msa_seq_4 + (c * (hmmp->a_size_4+1)))->query_letter, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ | | | char * -readseqs_multialpha.c: In function 'get_sequences_msa_std_multi': -readseqs_multialpha.c:372:18: warning: unknown escape sequence: '\s' - 372 | else if(i == '\s' && i == '\n') { - | ^~~~ -readseqs_multialpha.c:389:22: warning: implicit declaration of function 'read_multi_prior_file_multi'; did you mean 'read_prior_file_multi'? [-Wimplicit-function-declaration] - 389 | read_priorfile = read_multi_prior_file_multi(&em_di_1, hmmp, priorfile_a1, 1); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ - | read_prior_file_multi funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ -readhmm.c: In function 'read_module': -readhmm.c:751:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 751 | fgets(s, MAX_LINE, file); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -readhmm.c:786:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 786 | fgets(s, MAX_LINE, file); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -readhmm.c:821:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 821 | fgets(s, MAX_LINE, file); - | ^~~~~~~~~~~~~~~~~~~~~~~~ +training_algorithms_multialpha.c:1791:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] + 1791 | alphabet = hmmp->alphabet_2; + | ^ +std_calculation_funcs.c:1295:21: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] + 1295 | cur_address = (int)((cur_rowp+v)->labeling); + | ^ readhmm.c:850:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 850 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ +std_calculation_funcs.c:1309:12: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] + 1309 | if((int)((cur_rowp+w)->labeling) == cur_address && (cur_rowp + w)->is_updated == NO) { + | ^ +training_algorithms_multialpha.c:1798:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] + 1798 | alphabet = hmmp->alphabet_3; + | ^ readhmm.c:854:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 854 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ +training_algorithms_multialpha.c:1805:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] + 1805 | alphabet = hmmp->alphabet_4; + | ^ +std_funcs.c: In function 'update_shares_prior_multi': +std_calculation_funcs.c: In function 'deallocate_row_labelings': +std_calculation_funcs.c:1425:21: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] + 1425 | cur_address = (int)((prev_rowp+v)->labeling); + | ^ +std_calculation_funcs.c:1430:12: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] + 1430 | if((int)((prev_rowp+w)->labeling) == cur_address) { + | ^ core_algorithms_multialpha.c: In function 'msa_one_best_multi': +std_funcs.c:2471:5: warning: 'return' with no value, in function returning non-void + 2471 | return; + | ^~~~~~ core_algorithms_multialpha.c:1892:87: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] 1892 | a_index = get_alphabet_index((msa_seq_infop->msa_seq_1 + (c * (hmmp->a_size+1)))->query_letter, hmmp->alphabet, hmmp->a_size); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ @@ -876,13 +979,12 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ | | | char * +std_funcs.c:2457:5: note: declared here + 2457 | int update_shares_prior_multi(struct emission_dirichlet_s *em_di, struct hmm_multi_s *hmmp, + | ^~~~~~~~~~~~~~~~~~~~~~~~~ funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ -readhmm.c: In function 'read_prior_files': -readhmm.c:1231:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 1231 | fgets(ps, 2048, priorfile); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ core_algorithms_multialpha.c:1908:93: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] 1908 | a_index_3 = get_alphabet_index((msa_seq_infop->msa_seq_3 + (c * (hmmp->a_size_3+1)))->query_letter, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ @@ -899,93 +1001,19 @@ funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ -std_funcs.c: In function 'get_replacement_letter_index_single': -std_funcs.c:683:62: warning: comparison between pointer and integer - 683 | if(((replacement_letters->letters + a_index)->letter)[0] == c) { - | ^~ -readhmm_multialpha.c: In function 'copy_hmm_struct': -readhmm_multialpha.c:273:34: warning: assignment to 'struct transition_s *' from incompatible pointer type 'int *' [-Wincompatible-pointer-types] - 273 | retrain_hmmp->trans_tie_groups = (int*)(malloc_or_die((hmmp->nr_t + hmmp->nr_ttg) * sizeof(struct transition_s))); - | ^ -hmmsearch.c: In function 'get_scores': -hmmsearch.c:535:19: warning: assignment to 'struct helix_site *' from incompatible pointer type 'helix_sites *' [-Wincompatible-pointer-types] - 535 | hSites->helix = (helix_sites *) malloc(sizeof (helix_sites) * helices); - | ^ -hmmsearch.c: In function 'get_nullmodel_score_multi': -hmmsearch.c:656:42: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'struct letter_s *' [-Wformat=] - 656 | printf("Could not find letter %s when scoring null model\n", &seq[l]); - | ~^ ~~~~~~~ - | | | - | char * struct letter_s * -hmmsearch.c:674:44: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'struct letter_s *' [-Wformat=] - 674 | printf("Could not find letter %s when scoring null model\n", &seq_2[l]); - | ~^ ~~~~~~~~~ - | | | - | char * struct letter_s * -hmmsearch.c:693:44: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'struct letter_s *' [-Wformat=] - 693 | printf("Could not find letter %s when scoring null model\n", &seq_3[l]); - | ~^ ~~~~~~~~~ - | | | - | char * struct letter_s * -readhmm_multialpha.c: In function 'readhmm_multialpha': -readhmm_multialpha.c:469:28: warning: assignment to 'struct transition_s *' from incompatible pointer type 'int *' [-Wincompatible-pointer-types] - 469 | hmmp->trans_tie_groups = (int*)(malloc_or_die((hmmp->nr_t + hmmp->nr_ttg) * sizeof(struct transition_s))); - | ^ -hmmsearch.c:712:44: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'struct letter_s *' [-Wformat=] - 712 | printf("Could not find letter %s when scoring null model\n", &seq[l]); - | ~^ ~~~~~~~ - | | | - | char * struct letter_s * +readhmm.c: In function 'read_prior_files': +readhmm.c:1231:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 1231 | fgets(ps, 2048, priorfile); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ readseqs_multialpha.c: In function 'get_sequence_std_multi': readseqs_multialpha.c:286:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 286 | fgets(line, MAX_LINE, seqfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -std_funcs.c: In function 'get_reverse_msa_seq': -std_funcs.c:2076:74: warning: assignment to 'int *' from 'int' makes pointer from integer without a cast [-Wint-conversion] - 2076 | *(reverse_msa_seq_infop->gaps + (msa_seq_infop->msa_seq_length + i)) = END; - | ^ -std_calculation_funcs.c: In function 'update_labelings': -std_calculation_funcs.c:1295:21: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] - 1295 | cur_address = (int)((cur_rowp+v)->labeling); - | ^ -std_calculation_funcs.c:1309:12: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] - 1309 | if((int)((cur_rowp+w)->labeling) == cur_address && (cur_rowp + w)->is_updated == NO) { - | ^ -std_calculation_funcs.c: In function 'deallocate_row_labelings': -std_calculation_funcs.c:1425:21: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] - 1425 | cur_address = (int)((prev_rowp+v)->labeling); - | ^ -std_calculation_funcs.c:1430:12: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] - 1430 | if((int)((prev_rowp+w)->labeling) == cur_address) { - | ^ -std_funcs.c: In function 'get_reverse_msa_seq_multi': -std_funcs.c:2184:74: warning: assignment to 'int *' from 'int' makes pointer from integer without a cast [-Wint-conversion] - 2184 | *(reverse_msa_seq_infop->gaps + (msa_seq_infop->msa_seq_length + i)) = END; - | ^ -readseqs_multialpha.c: In function 'get_sequences_msa_std_multi': -readseqs_multialpha.c:625:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 625 | fgets(line, MAX_LINE, seqfile); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -readseqs_multialpha.c:754:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 754 | fgets(line, MAX_LINE, seqfile); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -readseqs_multialpha.c:874:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 874 | fgets(line, MAX_LINE, seqfile); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -readseqs_multialpha.c:995:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 995 | fgets(line, MAX_LINE, seqfile); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -std_funcs.c: In function 'update_shares_prior_multi': -std_funcs.c:2471:5: warning: 'return' with no value, in function returning non-void - 2471 | return; - | ^~~~~~ -std_funcs.c:2457:5: note: declared here - 2457 | int update_shares_prior_multi(struct emission_dirichlet_s *em_di, struct hmm_multi_s *hmmp, - | ^~~~~~~~~~~~~~~~~~~~~~~~~ readhmm_multialpha.c:326:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 326 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readhmm_multialpha.c: In function 'read_module_multi': +training_algorithms_multialpha.c: In function 'add_to_E_multi': readhmm_multialpha.c:1042:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1042 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ @@ -998,90 +1026,31 @@ readhmm_multialpha.c:1140:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1140 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ +training_algorithms_multialpha.c:3564:5: warning: implicit declaration of function 'add_to_E_continuous' [-Wimplicit-function-declaration] + 3564 | add_to_E_continuous(E, Eka_base, msa_seq, p, k, a_size, emissions); + | ^~~~~~~~~~~~~~~~~~~ readhmm_multialpha.c:1143:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1143 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ +readseqs_multialpha.c: In function 'get_sequences_msa_std_multi': readhmm_multialpha.c:1169:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1169 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ +readseqs_multialpha.c:625:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 625 | fgets(line, MAX_LINE, seqfile); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ readhmm_multialpha.c:1172:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1172 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ +readseqs_multialpha.c:754:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 754 | fgets(line, MAX_LINE, seqfile); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ readhmm_multialpha.c:1198:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1198 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ -readhmm_multialpha.c:1202:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 1202 | fgets(s, MAX_LINE, file); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -training_algorithms_multialpha.c: In function 'msa_baum_welch_dirichlet_multi': -training_algorithms_multialpha.c:701:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] - 701 | alphabet = hmmp->alphabet; - | ^ -training_algorithms_multialpha.c:710:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] - 710 | alphabet = hmmp->alphabet_2; - | ^ -training_algorithms_multialpha.c:719:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] - 719 | alphabet = hmmp->alphabet_3; - | ^ -training_algorithms_multialpha.c:728:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] - 728 | alphabet = hmmp->alphabet_4; - | ^ -readhmm_multialpha.c:1229:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 1229 | fgets(s, MAX_LINE, file); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -readhmm_multialpha.c:1236:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 1236 | fgets(s, MAX_LINE, file); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -training_algorithms_multialpha.c: In function 'extended_msa_baum_welch_dirichlet_multi': -training_algorithms_multialpha.c:1639:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] - 1639 | alphabet = hmmp->alphabet; - | ^ -training_algorithms_multialpha.c:1646:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] - 1646 | alphabet = hmmp->alphabet_2; - | ^ -training_algorithms_multialpha.c:1653:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] - 1653 | alphabet = hmmp->alphabet_3; - | ^ -training_algorithms_multialpha.c:1660:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] - 1660 | alphabet = hmmp->alphabet_4; - | ^ -training_algorithms_multialpha.c:1784:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] - 1784 | alphabet = hmmp->alphabet; - | ^ -training_algorithms_multialpha.c:1791:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] - 1791 | alphabet = hmmp->alphabet_2; - | ^ -training_algorithms_multialpha.c:1798:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] - 1798 | alphabet = hmmp->alphabet_3; - | ^ -training_algorithms_multialpha.c:1805:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] - 1805 | alphabet = hmmp->alphabet_4; - | ^ -std_funcs.c: In function 'get_nr_alphabets': -std_funcs.c:2731:10: warning: 'fgets' writing 4000 bytes into a region of size 1000 overflows the destination [-Wstringop-overflow=] - 2731 | if(fgets(s, MAX_LINE, hmmfile) != NULL) { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -std_funcs.c:2724:8: note: destination object 's' of size 1000 - 2724 | char s[1000]; - | ^ -In file included from /usr/include/stdio.h:906, - from std_funcs.c:1: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:209:1: note: in a call to function 'fgets' declared with attribute 'access (write_only, 1, 2)' - 209 | fgets (char *__restrict __s, int __n, FILE *__restrict __stream) - | ^~~~~ -std_funcs.c:2738:8: warning: 'fgets' writing 4000 bytes into a region of size 1000 overflows the destination [-Wstringop-overflow=] - 2738 | if(fgets(s, MAX_LINE, hmmfile) != NULL) { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -std_funcs.c:2724:8: note: destination object 's' of size 1000 - 2724 | char s[1000]; - | ^ -/usr/include/x86_64-linux-gnu/bits/stdio2.h:209:1: note: in a call to function 'fgets' declared with attribute 'access (write_only, 1, 2)' - 209 | fgets (char *__restrict __s, int __n, FILE *__restrict __stream) - | ^~~~~ -training_algorithms_multialpha.c: In function 'add_to_E_multi': -training_algorithms_multialpha.c:3564:5: warning: implicit declaration of function 'add_to_E_continuous' [-Wimplicit-function-declaration] - 3564 | add_to_E_continuous(E, Eka_base, msa_seq, p, k, a_size, emissions); - | ^~~~~~~~~~~~~~~~~~~ +readseqs_multialpha.c:874:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 874 | fgets(line, MAX_LINE, seqfile); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ training_algorithms_multialpha.c:3589:43: warning: passing argument 9 of 'add_to_E_subst_mtx_dot_product_nr_occ' makes pointer from integer without a cast [-Wint-conversion] 3589 | alphabet); | ^~~~~~~~ @@ -1091,6 +1060,18 @@ funcs.h:257:103: note: expected 'char *' but argument is of type 'int' 257 | int k, int a_size, int normalize, double *subst_mtx, char *alphabet); | ~~~~~~^~~~~~~~ +readhmm_multialpha.c:1202:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 1202 | fgets(s, MAX_LINE, file); + | ^~~~~~~~~~~~~~~~~~~~~~~~ +readseqs_multialpha.c:995:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 995 | fgets(line, MAX_LINE, seqfile); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +readhmm_multialpha.c:1229:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 1229 | fgets(s, MAX_LINE, file); + | ^~~~~~~~~~~~~~~~~~~~~~~~ +readhmm_multialpha.c:1236:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 1236 | fgets(s, MAX_LINE, file); + | ^~~~~~~~~~~~~~~~~~~~~~~~ training_algorithms_multialpha.c:3593:49: warning: passing argument 9 of 'add_to_E_subst_mtx_dot_product_prior_nr_occ' makes pointer from integer without a cast [-Wint-conversion] 3593 | alphabet); | ^~~~~~~~ @@ -1115,12 +1096,33 @@ funcs.h:240:102: note: expected 'char *' but argument is of type 'int' 240 | int k, int a_size, int normalize, double *subst_mtx, char *alphabet); | ~~~~~~^~~~~~~~ +std_funcs.c: In function 'get_nr_alphabets': +std_funcs.c:2731:10: warning: 'fgets' writing 4000 bytes into a region of size 1000 overflows the destination [-Wstringop-overflow=] + 2731 | if(fgets(s, MAX_LINE, hmmfile) != NULL) { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +std_funcs.c:2724:8: note: destination object 's' of size 1000 + 2724 | char s[1000]; + | ^ +In file included from /usr/include/stdio.h:906, + from std_funcs.c:1: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:209:1: note: in a call to function 'fgets' declared with attribute 'access (write_only, 1, 2)' + 209 | fgets (char *__restrict __s, int __n, FILE *__restrict __stream) + | ^~~~~ +std_funcs.c:2738:8: warning: 'fgets' writing 4000 bytes into a region of size 1000 overflows the destination [-Wstringop-overflow=] + 2738 | if(fgets(s, MAX_LINE, hmmfile) != NULL) { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +std_funcs.c:2724:8: note: destination object 's' of size 1000 + 2724 | char s[1000]; + | ^ +/usr/include/x86_64-linux-gnu/bits/stdio2.h:209:1: note: in a call to function 'fgets' declared with attribute 'access (write_only, 1, 2)' + 209 | fgets (char *__restrict __s, int __n, FILE *__restrict __stream) + | ^~~~~ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c hmmsearch.c -o hmmsearch.o >/dev/null 2>&1 -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c debug_funcs.c -o debug_funcs.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c readhmm.c -o readhmm.o >/dev/null 2>&1 +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c debug_funcs.c -o debug_funcs.o >/dev/null 2>&1 +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c readhmm_multialpha.c -o readhmm_multialpha.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c std_calculation_funcs.c -o std_calculation_funcs.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c readseqs_multialpha.c -o readseqs_multialpha.o >/dev/null 2>&1 -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c readhmm_multialpha.c -o readhmm_multialpha.o >/dev/null 2>&1 In function 'fgets', inlined from 'get_nr_alphabets' at std_funcs.c:2731:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:215:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] @@ -1134,7 +1136,7 @@ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c std_funcs.c -o std_funcs.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c core_algorithms_multialpha.c -o core_algorithms_multialpha.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c training_algorithms_multialpha.c -o training_algorithms_multialpha.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 0:0:0 -Wl,-z,relro -Wl,-z,now -o libmodhmm.la -rpath /usr/lib/x86_64-linux-gnu core_algorithms_multialpha.lo debug_funcs.lo hmmsearch.lo readhmm.lo readhmm_multialpha.lo readseqs_multialpha.lo std_calculation_funcs.lo std_funcs.lo training_algorithms_multialpha.lo -lm +/bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 0:0:0 -Wl,-z,relro -Wl,-z,now -o libmodhmm.la -rpath /usr/lib/x86_64-linux-gnu core_algorithms_multialpha.lo debug_funcs.lo hmmsearch.lo readhmm.lo readhmm_multialpha.lo readseqs_multialpha.lo std_calculation_funcs.lo std_funcs.lo training_algorithms_multialpha.lo -lm libtool: link: gcc -shared -fPIC -DPIC .libs/core_algorithms_multialpha.o .libs/debug_funcs.o .libs/hmmsearch.o .libs/readhmm.o .libs/readhmm_multialpha.o .libs/readseqs_multialpha.o .libs/std_calculation_funcs.o .libs/std_funcs.o .libs/training_algorithms_multialpha.o -lm -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libmodhmm.so.0 -o .libs/libmodhmm.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libmodhmm.so.0" && ln -s "libmodhmm.so.0.0.0" "libmodhmm.so.0") libtool: link: (cd ".libs" && rm -f "libmodhmm.so" && ln -s "libmodhmm.so.0.0.0" "libmodhmm.so") @@ -1147,7 +1149,7 @@ make[2]: Leaving directory '/build/libpsortb-1.0+dfsg' make[1]: Leaving directory '/build/libpsortb-1.0+dfsg' dh_auto_test - make -j16 check "TESTSUITEFLAGS=-j16 --verbose" VERBOSE=1 + make -j15 check "TESTSUITEFLAGS=-j15 --verbose" VERBOSE=1 make[1]: Entering directory '/build/libpsortb-1.0+dfsg' Making check in svmloc make[2]: Entering directory '/build/libpsortb-1.0+dfsg/svmloc' @@ -1170,8 +1172,8 @@ Making install in svmloc make[3]: Entering directory '/build/libpsortb-1.0+dfsg/svmloc' make[4]: Entering directory '/build/libpsortb-1.0+dfsg/svmloc' - /bin/mkdir -p '/build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu' - /bin/bash ../libtool --mode=install /usr/bin/install -c libsvmloc.la '/build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu' + /usr/bin/mkdir -p '/build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu' + /bin/sh ../libtool --mode=install /usr/bin/install -c libsvmloc.la '/build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libsvmloc.so.0.0.0 /build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libsvmloc.so.0.0.0 libtool: install: (cd /build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libsvmloc.so.0.0.0 libsvmloc.so.0 || { rm -f libsvmloc.so.0 && ln -s libsvmloc.so.0.0.0 libsvmloc.so.0; }; }) libtool: install: (cd /build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libsvmloc.so.0.0.0 libsvmloc.so || { rm -f libsvmloc.so && ln -s libsvmloc.so.0.0.0 libsvmloc.so; }; }) @@ -1186,8 +1188,8 @@ Making install in modhmm0.92b make[3]: Entering directory '/build/libpsortb-1.0+dfsg/modhmm0.92b' make[4]: Entering directory '/build/libpsortb-1.0+dfsg/modhmm0.92b' - /bin/mkdir -p '/build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu' - /bin/bash ../libtool --mode=install /usr/bin/install -c libmodhmm.la '/build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu' + /usr/bin/mkdir -p '/build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu' + /bin/sh ../libtool --mode=install /usr/bin/install -c libmodhmm.la '/build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libmodhmm.so.0.0.0 /build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libmodhmm.so.0.0.0 libtool: install: (cd /build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libmodhmm.so.0.0.0 libmodhmm.so.0 || { rm -f libmodhmm.so.0 && ln -s libmodhmm.so.0.0.0 libmodhmm.so.0; }; }) libtool: install: (cd /build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libmodhmm.so.0.0.0 libmodhmm.so || { rm -f libmodhmm.so && ln -s libmodhmm.so.0.0.0 libmodhmm.so; }; }) @@ -1255,12 +1257,12 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'libmodhmm0-dbgsym' in '../libmodhmm0-dbgsym_1.0+dfsg-5_amd64.deb'. -dpkg-deb: building package 'libsvmloc-dev' in '../libsvmloc-dev_1.0+dfsg-5_amd64.deb'. dpkg-deb: building package 'libmodhmm0' in '../libmodhmm0_1.0+dfsg-5_amd64.deb'. -dpkg-deb: building package 'libsvmloc0-dbgsym' in '../libsvmloc0-dbgsym_1.0+dfsg-5_amd64.deb'. +dpkg-deb: building package 'libmodhmm0-dbgsym' in '../libmodhmm0-dbgsym_1.0+dfsg-5_amd64.deb'. dpkg-deb: building package 'libmodhmm-dev' in '../libmodhmm-dev_1.0+dfsg-5_amd64.deb'. dpkg-deb: building package 'libsvmloc0' in '../libsvmloc0_1.0+dfsg-5_amd64.deb'. +dpkg-deb: building package 'libsvmloc0-dbgsym' in '../libsvmloc0-dbgsym_1.0+dfsg-5_amd64.deb'. +dpkg-deb: building package 'libsvmloc-dev' in '../libsvmloc-dev_1.0+dfsg-5_amd64.deb'. dpkg-genbuildinfo --build=binary -O../libpsortb_1.0+dfsg-5_amd64.buildinfo dpkg-genchanges --build=binary -O../libpsortb_1.0+dfsg-5_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1268,12 +1270,14 @@ 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/1094935/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1094935/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/3633491 and its subdirectories -I: Current time: Wed Jul 3 11:25:53 -12 2024 -I: pbuilder-time-stamp: 1720049153 +I: removing directory /srv/workspace/pbuilder/1094935 and its subdirectories +I: Current time: Fri Jun 2 07:04:06 +14 2023 +I: pbuilder-time-stamp: 1685639046