Diff of the two buildlogs: -- --- b1/build.log 2023-05-03 14:14:58.202628406 +0000 +++ b2/build.log 2023-05-03 14:17:31.447899045 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed May 3 02:10:08 -12 2023 -I: pbuilder-time-stamp: 1683123008 +I: Current time: Wed Jun 5 10:38:01 +14 2024 +I: pbuilder-time-stamp: 1717533481 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 [./psortb_3.0.6+dfsg.orig.tar.xz] I: copying [./psortb_3.0.6+dfsg-3.debian.tar.xz] I: Extracting source -gpgv: Signature made Sun Apr 24 08:35:50 2022 -12 +gpgv: Signature made Mon Apr 25 10:35:50 2022 +14 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key @@ -33,135 +33,167 @@ dpkg-source: info: applying fix_module_path.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1592463/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3912051/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-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 5 10:38 /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/3912051/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3912051/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=15' - 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=16' + 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='333258bd7c7b42e5ba3474e0b0646382' - 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='1592463' - PS1='# ' - PS2='> ' + INVOCATION_ID=249aee1183c94abfb18ca04a72851ae7 + 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=3912051 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.pSKouvbJ/pbuilderrc_mulj --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.pSKouvbJ/b1 --logfile b1/build.log psortb_3.0.6+dfsg-3.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://78.137.99.97:3128' + 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.pSKouvbJ/pbuilderrc_L5tM --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.pSKouvbJ/b2 --logfile b2/build.log --extrapackages usrmerge psortb_3.0.6+dfsg-3.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://85.184.249.68:3128 I: uname -a - Linux ionos1-amd64 5.10.0-22-amd64 #1 SMP Debian 5.10.178-3 (2023-04-22) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-0.deb11.6-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.15-1~bpo11+1 (2023-03-16) x86_64 GNU/Linux I: ls -l /bin total 5632 - -rwxr-xr-x 1 root root 1265648 Apr 23 09:23 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 01:20 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 22:02 dmesg - lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname - -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep - -rwxr-xr-x 1 root root 35664 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep - -rwxr-xr-x 1 root root 85600 Mar 22 22:02 findmnt - -rwsr-xr-x 1 root root 35128 Mar 22 20:35 fusermount - -rwxr-xr-x 1 root root 203152 Jan 24 02:43 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 01:33 hostname - -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln - -rwxr-xr-x 1 root root 53024 Mar 23 00:40 login - -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls - -rwxr-xr-x 1 root root 207168 Mar 22 22:02 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 22:02 more - -rwsr-xr-x 1 root root 59704 Mar 22 22:02 mount - -rwxr-xr-x 1 root root 18744 Mar 22 22:02 mountpoint - -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv - lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Apr 23 09:23 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 04:31 run-parts - -rwxr-xr-x 1 root root 126424 Jan 5 07:55 sed - lrwxrwxrwx 1 root root 4 Jan 5 01:20 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 22:02 su - -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync - -rwxr-xr-x 1 root root 531984 Apr 6 02:25 tar - -rwxr-xr-x 1 root root 14520 Nov 2 04:31 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 20:35 ulockmgr_server - -rwsr-xr-x 1 root root 35128 Mar 22 22:02 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 22:02 wdctl - lrwxrwxrwx 1 root root 8 Dec 19 01:33 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/1592463/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1265648 Apr 24 2023 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 2023 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 2023 dmesg + lrwxrwxrwx 1 root root 8 Dec 20 2022 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Dec 20 2022 domainname -> hostname + -rwxr-xr-x 1 root root 43856 Sep 21 2022 echo + -rwxr-xr-x 1 root root 41 Jan 25 2023 egrep + -rwxr-xr-x 1 root root 35664 Sep 21 2022 false + -rwxr-xr-x 1 root root 41 Jan 25 2023 fgrep + -rwxr-xr-x 1 root root 85600 Mar 24 2023 findmnt + -rwsr-xr-x 1 root root 35128 Mar 23 2023 fusermount + -rwxr-xr-x 1 root root 203152 Jan 25 2023 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 2022 hostname + -rwxr-xr-x 1 root root 72824 Sep 21 2022 ln + -rwxr-xr-x 1 root root 53024 Mar 24 2023 login + -rwxr-xr-x 1 root root 151344 Sep 21 2022 ls + -rwxr-xr-x 1 root root 207168 Mar 24 2023 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 2023 more + -rwsr-xr-x 1 root root 59704 Mar 24 2023 mount + -rwxr-xr-x 1 root root 18744 Mar 24 2023 mountpoint + -rwxr-xr-x 1 root root 142968 Sep 21 2022 mv + lrwxrwxrwx 1 root root 8 Dec 20 2022 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 3 2023 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43952 Sep 21 2022 pwd + lrwxrwxrwx 1 root root 4 Apr 24 2023 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 2023 sed + lrwxrwxrwx 1 root root 9 Jun 5 10:38 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 2023 su + -rwxr-xr-x 1 root root 39824 Sep 21 2022 sync + -rwxr-xr-x 1 root root 531984 Apr 7 2023 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 2023 ulockmgr_server + -rwsr-xr-x 1 root root 35128 Mar 24 2023 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 2023 wdctl + lrwxrwxrwx 1 root root 8 Dec 20 2022 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/3912051/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -296,7 +328,7 @@ Get: 79 http://deb.debian.org/debian bookworm/main amd64 pkgconf-bin amd64 1.8.1-1 [29.5 kB] Get: 80 http://deb.debian.org/debian bookworm/main amd64 pkgconf amd64 1.8.1-1 [25.9 kB] Get: 81 http://deb.debian.org/debian bookworm/main amd64 pkg-config amd64 1.8.1-1 [13.7 kB] -Fetched 70.8 MB in 3s (23.3 MB/s) +Fetched 70.8 MB in 1s (51.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19596 files and directories currently installed.) @@ -636,8 +668,19 @@ 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/psortb-3.0.6+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 > ../psortb_3.0.6+dfsg-3_source.changes +I: user script /srv/workspace/pbuilder/3912051/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/3912051/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/psortb-3.0.6+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 > ../psortb_3.0.6+dfsg-3_source.changes dpkg-buildpackage: info: source package psortb dpkg-buildpackage: info: source version 3.0.6+dfsg-3 dpkg-buildpackage: info: source distribution unstable @@ -677,14 +720,14 @@ readdir() attempted on invalid dirhandle $dir_fh at /usr/share/perl/5.36/ExtUtils/Liblist.pm line 22. closedir() attempted on invalid dirhandle $dir_fh at /usr/share/perl/5.36/ExtUtils/Liblist.pm line 23. -hmmer was not found in the dynamic linker path, is there somewhere else we should check? [/usr/local/lib] /usr/local/lib +hmmer was not found in the dynamic linker path, is there somewhere else we should check? [/usr/local/lib64] /usr/local/lib64 readdir() attempted on invalid dirhandle $dir_fh at /usr/share/perl/5.36/ExtUtils/Liblist.pm line 22. closedir() attempted on invalid dirhandle $dir_fh at /usr/share/perl/5.36/ExtUtils/Liblist.pm line 23. readdir() attempted on invalid dirhandle $dir_fh at /usr/share/perl/5.36/ExtUtils/Liblist.pm line 22. closedir() attempted on invalid dirhandle $dir_fh at /usr/share/perl/5.36/ExtUtils/Liblist.pm line 23. We're still not finding hmmer either in your dynamic linker path (/etc/ld.so.conf) or -in /usr/local/lib. +in /usr/local/lib64. Do you want to continue anyways? [Y/n] [Y] Y readdir() attempted on invalid dirhandle $dir_fh at /usr/share/perl/5.36/ExtUtils/Liblist.pm line 22. @@ -692,14 +735,14 @@ readdir() attempted on invalid dirhandle $dir_fh at /usr/share/perl/5.36/ExtUtils/Liblist.pm line 22. closedir() attempted on invalid dirhandle $dir_fh at /usr/share/perl/5.36/ExtUtils/Liblist.pm line 23. -squid was not found in the dynamic linker path, is there somewhere else we should check? [/usr/local/lib] /usr/local/lib +squid was not found in the dynamic linker path, is there somewhere else we should check? [/usr/local/lib64] /usr/local/lib64 readdir() attempted on invalid dirhandle $dir_fh at /usr/share/perl/5.36/ExtUtils/Liblist.pm line 22. closedir() attempted on invalid dirhandle $dir_fh at /usr/share/perl/5.36/ExtUtils/Liblist.pm line 23. readdir() attempted on invalid dirhandle $dir_fh at /usr/share/perl/5.36/ExtUtils/Liblist.pm line 22. closedir() attempted on invalid dirhandle $dir_fh at /usr/share/perl/5.36/ExtUtils/Liblist.pm line 23. We're still not finding squid either in your dynamic linker path (/etc/ld.so.conf) or -in /usr/local/lib. +in /usr/local/lib64. Do you want to continue anyways? [Y/n] [Y] Y Checking if your kit is complete... @@ -710,14 +753,14 @@ readdir() attempted on invalid dirhandle $dir_fh at /usr/share/perl/5.36/ExtUtils/Liblist.pm line 22. closedir() attempted on invalid dirhandle $dir_fh at /usr/share/perl/5.36/ExtUtils/Liblist.pm line 23. -svmloc was not found in the dynamic linker path, is there somewhere else we should check? [/usr/local/lib] /usr/local/lib +svmloc was not found in the dynamic linker path, is there somewhere else we should check? [/usr/local/lib64] /usr/local/lib64 readdir() attempted on invalid dirhandle $dir_fh at /usr/share/perl/5.36/ExtUtils/Liblist.pm line 22. closedir() attempted on invalid dirhandle $dir_fh at /usr/share/perl/5.36/ExtUtils/Liblist.pm line 23. readdir() attempted on invalid dirhandle $dir_fh at /usr/share/perl/5.36/ExtUtils/Liblist.pm line 22. closedir() attempted on invalid dirhandle $dir_fh at /usr/share/perl/5.36/ExtUtils/Liblist.pm line 23. We're still not finding svmloc either in your dynamic linker path (/etc/ld.so.conf) or -in /usr/local/lib. +in /usr/local/lib64. Do you want to continue anyways? [Y/n] [Y] Y Checking if your kit is complete... @@ -728,14 +771,14 @@ readdir() attempted on invalid dirhandle $dir_fh at /usr/share/perl/5.36/ExtUtils/Liblist.pm line 22. closedir() attempted on invalid dirhandle $dir_fh at /usr/share/perl/5.36/ExtUtils/Liblist.pm line 23. -modhmm was not found in the dynamic linker path, is there somewhere else we should check? [/usr/local/lib] /usr/local/lib +modhmm was not found in the dynamic linker path, is there somewhere else we should check? [/usr/local/lib64] /usr/local/lib64 readdir() attempted on invalid dirhandle $dir_fh at /usr/share/perl/5.36/ExtUtils/Liblist.pm line 22. closedir() attempted on invalid dirhandle $dir_fh at /usr/share/perl/5.36/ExtUtils/Liblist.pm line 23. readdir() attempted on invalid dirhandle $dir_fh at /usr/share/perl/5.36/ExtUtils/Liblist.pm line 22. closedir() attempted on invalid dirhandle $dir_fh at /usr/share/perl/5.36/ExtUtils/Liblist.pm line 23. We're still not finding modhmm either in your dynamic linker path (/etc/ld.so.conf) or -in /usr/local/lib. +in /usr/local/lib64. Do you want to continue anyways? [Y/n] [Y] Y Writing MYMETA.yml and MYMETA.json @@ -746,7 +789,7 @@ Making sclblast databases -Building a new DB, current time: 05/03/2023 02:11:57 +Building a new DB, current time: 06/05/2024 10:39:30 New DB name: /build/psortb-3.0.6+dfsg/psort/conf/analysis/sclblast/gramneg/sclblast New DB title: sclblast Sequence type: Protein @@ -760,7 +803,7 @@ Program failed, try executing the command manually. -Building a new DB, current time: 05/03/2023 02:11:59 +Building a new DB, current time: 06/05/2024 10:39:31 New DB name: /build/psortb-3.0.6+dfsg/psort/conf/analysis/sclblast/grampos/sclblast New DB title: sclblast Sequence type: Protein @@ -774,7 +817,7 @@ Program failed, try executing the command manually. -Building a new DB, current time: 05/03/2023 02:12:00 +Building a new DB, current time: 06/05/2024 10:39:32 New DB name: /build/psortb-3.0.6+dfsg/psort/conf/analysis/sclblast/archaea/sclblast New DB title: sclblast Sequence type: Protein @@ -807,65 +850,65 @@ # hack around the issue that configure injects wrong root dir /usr/local/psortb mv psort/bin/psort.debsave psort/bin/psort dh_auto_build - make -j15 + make -j16 make[2]: Entering directory '/build/psortb-3.0.6+dfsg' make[3]: Entering directory '/build/psortb-3.0.6+dfsg/algorithm-hmm' Running Mkbootstrap for HMM () -cp lib/Bio/Tools/PSort/Module/Profile.pm blib/lib/Bio/Tools/PSort/Module/Profile.pm -cp lib/Bio/Tools/Motif/Pattern.pm blib/lib/Bio/Tools/Motif/Pattern.pm -cp lib/Bio/Tools/PSort/ModuleI.pm blib/lib/Bio/Tools/PSort/ModuleI.pm -cp lib/Bio/Tools/PSort/Pathway.pm blib/lib/Bio/Tools/PSort/Pathway.pm -cp lib/Bio/Tools/Motif/Match.pm blib/lib/Bio/Tools/Motif/Match.pm -cp lib/Bio/Tools/PSort/Module/SVMLocApache.pm blib/lib/Bio/Tools/PSort/Module/SVMLocApache.pm cp lib/Bio/Tools/PSort/Module/OutputI.pm blib/lib/Bio/Tools/PSort/Module/OutputI.pm +cp lib/Bio/Tools/PSort/Pathway.pm blib/lib/Bio/Tools/PSort/Pathway.pm +cp lib/Bio/Tools/PSort/Profile/Match.pm blib/lib/Bio/Tools/PSort/Profile/Match.pm cp lib/Bio/Tools/PSort.pm blib/lib/Bio/Tools/PSort.pm -cp lib/Bio/Tools/PSort/Report/Formatter/long.pm blib/lib/Bio/Tools/PSort/Report/Formatter/long.pm -cp lib/Bio/Tools/PSort/Module/SCLBlast.pm blib/lib/Bio/Tools/PSort/Module/SCLBlast.pm -cp lib/Bio/Tools/PSort/Module/ModHMM.pm blib/lib/Bio/Tools/PSort/Module/ModHMM.pm -cp lib/Bio/Tools/PSort/Module/Signal.pm blib/lib/Bio/Tools/PSort/Module/Signal.pm -cp lib/Bio/Tools/Motif.pm blib/lib/Bio/Tools/Motif.pm -cp lib/Bio/Tools/PSort/Module/AnalysisI.pm blib/lib/Bio/Tools/PSort/Module/AnalysisI.pm cp lib/Bio/Tools/PSort/Module/InputI.pm blib/lib/Bio/Tools/PSort/Module/InputI.pm -cp lib/Bio/Tools/PSort/Module/SVMLoc.pm blib/lib/Bio/Tools/PSort/Module/SVMLoc.pm +cp lib/Bio/Tools/PSort/Module/OMPMotif.pm blib/lib/Bio/Tools/PSort/Module/OMPMotif.pm +cp lib/Bio/Tools/PSort/ModuleI.pm blib/lib/Bio/Tools/PSort/ModuleI.pm cp lib/Bio/Tools/PSort/Module/Motif.pm blib/lib/Bio/Tools/PSort/Module/Motif.pm -cp lib/Bio/Tools/PSort/Report.pm blib/lib/Bio/Tools/PSort/Report.pm -cp lib/Bio/Tools/PSort/Report/Result.pm blib/lib/Bio/Tools/PSort/Report/Result.pm +cp lib/Bio/Tools/PSort/Module/Profile.pm blib/lib/Bio/Tools/PSort/Module/Profile.pm +cp lib/Bio/Tools/Motif/Match.pm blib/lib/Bio/Tools/Motif/Match.pm cp lib/Bio/Tools/PSort/Module/HMMTOP.pm blib/lib/Bio/Tools/PSort/Module/HMMTOP.pm cp lib/Bio/Tools/PSort/Constants.pm blib/lib/Bio/Tools/PSort/Constants.pm -cp lib/Bio/Tools/PSort/Profile/Match.pm blib/lib/Bio/Tools/PSort/Profile/Match.pm -cp lib/Bio/Tools/PSort/Report/Formatter/terse.pm blib/lib/Bio/Tools/PSort/Report/Formatter/terse.pm +cp lib/Bio/Tools/Motif.pm blib/lib/Bio/Tools/Motif.pm +cp lib/Bio/Tools/PSort/Report.pm blib/lib/Bio/Tools/PSort/Report.pm +cp lib/Bio/Tools/PSort/Module/ModHMM.pm blib/lib/Bio/Tools/PSort/Module/ModHMM.pm cp lib/Bio/Tools/PSort/Install.pm blib/lib/Bio/Tools/PSort/Install.pm -cp lib/Bio/Tools/PSort/Profile.pm blib/lib/Bio/Tools/PSort/Profile.pm -cp lib/Bio/Tools/PSort/Report/Formatter/normal.pm blib/lib/Bio/Tools/PSort/Report/Formatter/normal.pm cp lib/Bio/Tools/PSort/Report/Formatter.pm blib/lib/Bio/Tools/PSort/Report/Formatter.pm -cp lib/Bio/Tools/PSort/Report/Formatter/html.pm blib/lib/Bio/Tools/PSort/Report/Formatter/html.pm cp lib/Bio/Tools/PSort/Module/Bayesian.pm blib/lib/Bio/Tools/PSort/Module/Bayesian.pm -cp lib/Bio/Tools/PSort/Module/Null.pm blib/lib/Bio/Tools/PSort/Module/Null.pm +cp lib/Bio/Tools/PSort/Module/Signal.pm blib/lib/Bio/Tools/PSort/Module/Signal.pm +cp lib/Bio/Tools/PSort/Module/AnalysisI.pm blib/lib/Bio/Tools/PSort/Module/AnalysisI.pm +cp lib/Bio/Tools/PSort/Module/SVMLocApache.pm blib/lib/Bio/Tools/PSort/Module/SVMLocApache.pm cp lib/Bio/Tools/PSort/Module/Rules.pm blib/lib/Bio/Tools/PSort/Module/Rules.pm -cp lib/Bio/Tools/PSort/Module/OMPMotif.pm blib/lib/Bio/Tools/PSort/Module/OMPMotif.pm -chmod 644 "HMM.bs" -"/usr/bin/perl" "/usr/share/perl/5.36.0/ExtUtils/xsubpp" -C++ -typemap '/usr/share/perl/5.36/ExtUtils/typemap' -typemap '/build/psortb-3.0.6+dfsg/algorithm-hmm/typemap' HMM.xs > HMM.xsc -g++ -c -Isrc/include `pkg-config --cflags libsquid` `pkg-config --cflags libhmmer2` -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -ffile-prefix-map=/build/psortb-3.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"0.02\" -DXS_VERSION=\"0.02\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.36/CORE" hmm-binding.cpp +cp lib/Bio/Tools/Motif/Pattern.pm blib/lib/Bio/Tools/Motif/Pattern.pm +cp lib/Bio/Tools/PSort/Module/SCLBlast.pm blib/lib/Bio/Tools/PSort/Module/SCLBlast.pm +cp lib/Bio/Tools/PSort/Profile.pm blib/lib/Bio/Tools/PSort/Profile.pm +cp lib/Bio/Tools/PSort/Module/Null.pm blib/lib/Bio/Tools/PSort/Module/Null.pm +cp lib/Bio/Tools/PSort/Report/Formatter/terse.pm blib/lib/Bio/Tools/PSort/Report/Formatter/terse.pm +cp lib/Bio/Tools/PSort/Report/Formatter/long.pm blib/lib/Bio/Tools/PSort/Report/Formatter/long.pm +cp lib/Bio/Tools/PSort/Report/Formatter/html.pm blib/lib/Bio/Tools/PSort/Report/Formatter/html.pm +cp lib/Bio/Tools/PSort/Module/SVMLoc.pm blib/lib/Bio/Tools/PSort/Module/SVMLoc.pm +cp lib/Bio/Tools/PSort/Report/Formatter/normal.pm blib/lib/Bio/Tools/PSort/Report/Formatter/normal.pm +cp lib/Bio/Tools/PSort/Report/Result.pm blib/lib/Bio/Tools/PSort/Report/Result.pm +cp lib/Algorithm/HMM/Hit.pm ../blib/lib/Algorithm/HMM/Hit.pm +cp lib/Algorithm/HMM/Report.pm ../blib/lib/Algorithm/HMM/Report.pm +cp lib/Algorithm/HMM/Hit/Domain.pm ../blib/lib/Algorithm/HMM/Hit/Domain.pm cp lib/Algorithm/HMM.pm ../blib/lib/Algorithm/HMM.pm AutoSplitting ../blib/lib/Algorithm/HMM.pm (../blib/lib/auto/Algorithm/HMM) cp lib/Algorithm/HMM/Hit/Global.pm ../blib/lib/Algorithm/HMM/Hit/Global.pm -cp lib/Algorithm/HMM/Hit.pm ../blib/lib/Algorithm/HMM/Hit.pm -cp lib/Algorithm/HMM/Hit/Domain.pm ../blib/lib/Algorithm/HMM/Hit/Domain.pm -cp lib/Algorithm/HMM/Report.pm ../blib/lib/Algorithm/HMM/Report.pm -"/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- HMM.bs ../blib/arch/auto/Algorithm/HMM/HMM.bs 644 -cp lib/Bio/Tools/Run/SCLBlastLocal.pm blib/lib/Bio/Tools/Run/SCLBlastLocal.pm -cp lib/Bio/Tools/Run/SCLBlast/Hit.pm blib/lib/Bio/Tools/Run/SCLBlast/Hit.pm -cp lib/Bio/Tools/Run/SCLBlast.pm blib/lib/Bio/Tools/Run/SCLBlast.pm +chmod 644 "HMM.bs" +"/usr/bin/perl" "/usr/share/perl/5.36.0/ExtUtils/xsubpp" -C++ -typemap '/usr/share/perl/5.36/ExtUtils/typemap' -typemap '/build/psortb-3.0.6+dfsg/algorithm-hmm/typemap' HMM.xs > HMM.xsc +g++ -c -Isrc/include `pkg-config --cflags libsquid` `pkg-config --cflags libhmmer2` -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -ffile-prefix-map=/build/psortb-3.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"0.02\" -DXS_VERSION=\"0.02\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.36/CORE" hmm-binding.cpp +cp lib/Bio/Tools/SVMLoc.pm blib/lib/Bio/Tools/SVMLoc.pm cp lib/Bio/Tools/Signal/Report.pm blib/lib/Bio/Tools/Signal/Report.pm cp lib/Bio/Tools/Run/HMMTOP/Report.pm blib/lib/Bio/Tools/Run/HMMTOP/Report.pm +cp lib/Bio/Tools/Run/HMMTOP.pm blib/lib/Bio/Tools/Run/HMMTOP.pm +cp lib/Bio/Tools/Run/SCLBlast/Hit.pm blib/lib/Bio/Tools/Run/SCLBlast/Hit.pm cp lib/Bio/Tools/Signal.pm blib/lib/Bio/Tools/Signal.pm +cp lib/Bio/Tools/Run/SCLBlast/Report.pm blib/lib/Bio/Tools/Run/SCLBlast/Report.pm +cp lib/Bio/Tools/Run/SCLBlastLocal.pm blib/lib/Bio/Tools/Run/SCLBlastLocal.pm cp lib/Bio/Tools/PSort/XMLRPC/Client.pm blib/lib/Bio/Tools/PSort/XMLRPC/Client.pm cp lib/Bio/Tools/Run/HMMTOP/Helix.pm blib/lib/Bio/Tools/Run/HMMTOP/Helix.pm -cp lib/Bio/Tools/SVMLoc.pm blib/lib/Bio/Tools/SVMLoc.pm -cp lib/Bio/Tools/Run/HMMTOP.pm blib/lib/Bio/Tools/Run/HMMTOP.pm -cp lib/Bio/Tools/Run/SCLBlast/Report.pm blib/lib/Bio/Tools/Run/SCLBlast/Report.pm +cp lib/Bio/Tools/Run/SCLBlast.pm blib/lib/Bio/Tools/Run/SCLBlast.pm Please specify prototyping behavior for HMM.xs (see perlxs manual) mv HMM.xsc HMM.c +"/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- HMM.bs ../blib/arch/auto/Algorithm/HMM/HMM.bs 644 g++ -c -Isrc/include `pkg-config --cflags libsquid` `pkg-config --cflags libhmmer2` -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -ffile-prefix-map=/build/psortb-3.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"0.02\" -DXS_VERSION=\"0.02\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.36/CORE" HMM.c hmm-binding.cpp: In member function 'HMMReport* HMM::search(char*)': hmm-binding.cpp:136:71: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] @@ -873,36 +916,36 @@ | ^~~~~ rm -f ../blib/arch/auto/Algorithm/HMM/HMM.so x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/psortb-3.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -shared -L/usr/local/lib -fstack-protector-strong HMM.o hmm-binding.o -o ../blib/arch/auto/Algorithm/HMM/HMM.so \ - -lm -lpthread -lstdc++ -L/usr/local/lib -lhmmer -lsquid \ + -lm -lpthread -lstdc++ -lhmmer -lsquid \ chmod 755 ../blib/arch/auto/Algorithm/HMM/HMM.so Manifying 5 pod documents make[3]: Leaving directory '/build/psortb-3.0.6+dfsg/algorithm-hmm' make[3]: Entering directory '/build/psortb-3.0.6+dfsg/bio-tools-psort-svmloc' Running Mkbootstrap for SVMLoc () -"/usr/bin/perl" "/usr/share/perl/5.36.0/ExtUtils/xsubpp" -C++ -typemap '/usr/share/perl/5.36/ExtUtils/typemap' -typemap '/build/psortb-3.0.6+dfsg/bio-tools-psort-svmloc/typemap' SVMLoc.xs > SVMLoc.xsc chmod 644 "SVMLoc.bs" -cp lib/Bio/Tools/PSort/SVMLoc/DataSet.pm ../blib/lib/Bio/Tools/PSort/SVMLoc/DataSet.pm cp lib/Bio/Tools/PSort/SVMLoc.pm ../blib/lib/Bio/Tools/PSort/SVMLoc.pm AutoSplitting ../blib/lib/Bio/Tools/PSort/SVMLoc.pm (../blib/lib/auto/Bio/Tools/PSort/SVMLoc) +cp lib/Bio/Tools/PSort/SVMLoc/DataSet.pm ../blib/lib/Bio/Tools/PSort/SVMLoc/DataSet.pm +"/usr/bin/perl" "/usr/share/perl/5.36.0/ExtUtils/xsubpp" -C++ -typemap '/usr/share/perl/5.36/ExtUtils/typemap' -typemap '/build/psortb-3.0.6+dfsg/bio-tools-psort-svmloc/typemap' SVMLoc.xs > SVMLoc.xsc "/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- SVMLoc.bs ../blib/arch/auto/Bio/Tools/PSort/SVMLoc/SVMLoc.bs 644 Please specify prototyping behavior for SVMLoc.xs (see perlxs manual) mv SVMLoc.xsc SVMLoc.c g++ -c -Wall -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -ffile-prefix-map=/build/psortb-3.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"0.01\" -DXS_VERSION=\"0.01\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.36/CORE" SVMLoc.c rm -f ../blib/arch/auto/Bio/Tools/PSort/SVMLoc/SVMLoc.so x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/psortb-3.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -shared -L/usr/local/lib -fstack-protector-strong SVMLoc.o -o ../blib/arch/auto/Bio/Tools/PSort/SVMLoc/SVMLoc.so \ - -L/usr/local/lib -lsvmloc -lm -lsvm -lstdc++ \ + -lsvmloc -lm -lsvm -lstdc++ \ chmod 755 ../blib/arch/auto/Bio/Tools/PSort/SVMLoc/SVMLoc.so Manifying 2 pod documents make[3]: Leaving directory '/build/psortb-3.0.6+dfsg/bio-tools-psort-svmloc' make[3]: Entering directory '/build/psortb-3.0.6+dfsg/bio-tools-psort-modhmm' Running Mkbootstrap for ModHMM () -"/usr/bin/perl" "/usr/share/perl/5.36.0/ExtUtils/xsubpp" -typemap '/usr/share/perl/5.36/ExtUtils/typemap' -typemap '/build/psortb-3.0.6+dfsg/bio-tools-psort-modhmm/typemap' modhmm.xs > modhmm.xsc -cc -c -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -ffile-prefix-map=/build/psortb-3.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"0.01\" -DXS_VERSION=\"0.01\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.36/CORE" binding.c -chmod 644 "ModHMM.bs" cp lib/Bio/Tools/PSort/ModHMM.pm ../blib/lib/Bio/Tools/PSort/ModHMM.pm AutoSplitting ../blib/lib/Bio/Tools/PSort/ModHMM.pm (../blib/lib/auto/Bio/Tools/PSort/ModHMM) +chmod 644 "ModHMM.bs" +"/usr/bin/perl" "/usr/share/perl/5.36.0/ExtUtils/xsubpp" -typemap '/usr/share/perl/5.36/ExtUtils/typemap' -typemap '/build/psortb-3.0.6+dfsg/bio-tools-psort-modhmm/typemap' modhmm.xs > modhmm.xsc +cc -c -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -ffile-prefix-map=/build/psortb-3.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"0.01\" -DXS_VERSION=\"0.01\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.36/CORE" binding.c binding.c: In function 'helix_DESTROY': binding.c:52:13: warning: implicit declaration of function 'free' [-Wimplicit-function-declaration] 52 | free(hSites->helix); @@ -929,7 +972,7 @@ | get_helices rm -f ../blib/arch/auto/Bio/Tools/PSort/ModHMM/ModHMM.so x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/psortb-3.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -shared -L/usr/local/lib -fstack-protector-strong modhmm.o binding.o -o ../blib/arch/auto/Bio/Tools/PSort/ModHMM/ModHMM.so \ - -lm -lstdc++ -L/usr/local/lib -lmodhmm \ + -lm -lstdc++ -lmodhmm \ chmod 755 ../blib/arch/auto/Bio/Tools/PSort/ModHMM/ModHMM.so Manifying 1 pod document @@ -938,7 +981,7 @@ make[2]: Leaving directory '/build/psortb-3.0.6+dfsg' make[1]: Leaving directory '/build/psortb-3.0.6+dfsg' dh_auto_test - make -j15 test TEST_VERBOSE=1 + make -j16 test TEST_VERBOSE=1 make[1]: Entering directory '/build/psortb-3.0.6+dfsg' make[2]: Entering directory '/build/psortb-3.0.6+dfsg/algorithm-hmm' "/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- HMM.bs ../blib/arch/auto/Algorithm/HMM/HMM.bs 644 @@ -967,7 +1010,7 @@ ok 5 - Testing reloading a model ok All tests successful. -Files=1, Tests=5, 1 wallclock secs ( 0.05 usr 0.00 sys + 0.15 cusr 0.03 csys = 0.23 CPU) +Files=1, Tests=5, 0 wallclock secs ( 0.03 usr 0.01 sys + 0.11 cusr 0.02 csys = 0.17 CPU) Result: PASS make[2]: Leaving directory '/build/psortb-3.0.6+dfsg/algorithm-hmm' make[2]: Entering directory '/build/psortb-3.0.6+dfsg/bio-tools-psort-svmloc' @@ -999,7 +1042,7 @@ Everything looks ok! ok All tests successful. -Files=1, Tests=15, 1 wallclock secs ( 0.04 usr 0.01 sys + 0.44 cusr 0.02 csys = 0.51 CPU) +Files=1, Tests=15, 0 wallclock secs ( 0.04 usr 0.00 sys + 0.36 cusr 0.05 csys = 0.45 CPU) Result: PASS make[2]: Leaving directory '/build/psortb-3.0.6+dfsg/bio-tools-psort-svmloc' make[2]: Entering directory '/build/psortb-3.0.6+dfsg/bio-tools-psort-modhmm' @@ -1015,7 +1058,7 @@ ok 4 - Retreiving TM helix sites ok All tests successful. -Files=1, Tests=4, 1 wallclock secs ( 0.04 usr 0.01 sys + 0.38 cusr 0.02 csys = 0.45 CPU) +Files=1, Tests=4, 1 wallclock secs ( 0.04 usr 0.00 sys + 0.35 cusr 0.01 csys = 0.40 CPU) Result: PASS make[2]: Leaving directory '/build/psortb-3.0.6+dfsg/bio-tools-psort-modhmm' PERL_DL_NONLAZY=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(1, 'blib/lib', 'blib/arch')" t/*.t @@ -1026,13 +1069,13 @@ ok 2 - PSort object made ok All tests successful. -Files=1, Tests=2, 1 wallclock secs ( 0.04 usr 0.00 sys + 0.20 cusr 0.03 csys = 0.27 CPU) +Files=1, Tests=2, 0 wallclock secs ( 0.03 usr 0.01 sys + 0.13 cusr 0.04 csys = 0.21 CPU) Result: PASS make[1]: Leaving directory '/build/psortb-3.0.6+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/psortb/ - make -j15 install DESTDIR=/build/psortb-3.0.6\+dfsg/debian/psortb AM_UPDATE_INFO_DIR=no PREFIX=/usr + make -j16 install DESTDIR=/build/psortb-3.0.6\+dfsg/debian/psortb AM_UPDATE_INFO_DIR=no PREFIX=/usr make[1]: Entering directory '/build/psortb-3.0.6+dfsg' make[2]: Entering directory '/build/psortb-3.0.6+dfsg/algorithm-hmm' "/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- HMM.bs ../blib/arch/auto/Algorithm/HMM/HMM.bs 644 @@ -1054,57 +1097,57 @@ Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Algorithm/HMM.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Algorithm/HMM/Report.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Algorithm/HMM/Hit.pm -Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Algorithm/HMM/Hit/Domain.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Algorithm/HMM/Hit/Global.pm +Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Algorithm/HMM/Hit/Domain.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/auto/Algorithm/HMM/autosplit.ix Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/auto/Bio/Tools/PSort/ModHMM/autosplit.ix Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/auto/Bio/Tools/PSort/SVMLoc/autosplit.ix -Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/SVMLoc.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/Signal.pm +Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/SVMLoc.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/Motif.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort.pm -Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/Signal/Report.pm -Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/Run/HMMTOP.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/Run/SCLBlast.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/Run/SCLBlastLocal.pm -Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/Run/HMMTOP/Helix.pm -Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/Run/HMMTOP/Report.pm +Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/Run/HMMTOP.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/Run/SCLBlast/Report.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/Run/SCLBlast/Hit.pm -Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/Motif/Match.pm +Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/Run/HMMTOP/Helix.pm +Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/Run/HMMTOP/Report.pm +Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/Signal/Report.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/Motif/Pattern.pm +Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/Motif/Match.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/ModHMM.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/SVMLoc.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Profile.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Install.pm -Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Constants.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Report.pm -Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Pathway.pm +Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Constants.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/ModuleI.pm +Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Pathway.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/SVMLoc/DataSet.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/XMLRPC/Client.pm -Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Profile/Match.pm -Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Report/Formatter.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Report/Result.pm -Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Report/Formatter/html.pm +Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Report/Formatter.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Report/Formatter/normal.pm -Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Report/Formatter/terse.pm +Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Report/Formatter/html.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Report/Formatter/long.pm -Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Module/OMPMotif.pm -Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Module/Rules.pm +Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Report/Formatter/terse.pm +Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Profile/Match.pm +Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Module/SVMLoc.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Module/Null.pm +Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Module/SCLBlast.pm +Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Module/Rules.pm +Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Module/SVMLocApache.pm +Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Module/AnalysisI.pm +Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Module/Signal.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Module/Bayesian.pm +Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Module/ModHMM.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Module/HMMTOP.pm +Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Module/Profile.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Module/Motif.pm -Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Module/SVMLoc.pm +Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Module/OMPMotif.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Module/InputI.pm -Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Module/AnalysisI.pm -Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Module/Signal.pm -Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Module/ModHMM.pm -Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Module/SCLBlast.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Module/OutputI.pm -Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Module/SVMLocApache.pm -Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.36/Bio/Tools/PSort/Module/Profile.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::Signal.3pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::SVMLoc.3pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::Run::HMMTOP.3pm @@ -1155,8 +1198,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'psortb-dbgsym' in '../psortb-dbgsym_3.0.6+dfsg-3_amd64.deb'. dpkg-deb: building package 'psortb' in '../psortb_3.0.6+dfsg-3_amd64.deb'. +dpkg-deb: building package 'psortb-dbgsym' in '../psortb-dbgsym_3.0.6+dfsg-3_amd64.deb'. dpkg-genbuildinfo --build=binary -O../psortb_3.0.6+dfsg-3_amd64.buildinfo dpkg-genchanges --build=binary -O../psortb_3.0.6+dfsg-3_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1164,12 +1207,14 @@ 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/3912051/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3912051/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/1592463 and its subdirectories -I: Current time: Wed May 3 02:14:57 -12 2023 -I: pbuilder-time-stamp: 1683123297 +I: removing directory /srv/workspace/pbuilder/3912051 and its subdirectories +I: Current time: Wed Jun 5 10:40:31 +14 2024 +I: pbuilder-time-stamp: 1717533631