Diff of the two buildlogs: -- --- b1/build.log 2023-04-16 05:31:05.230241037 +0000 +++ b2/build.log 2023-04-16 05:42:32.791714318 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri May 17 23:52:01 -12 2024 -I: pbuilder-time-stamp: 1716033121 +I: Current time: Sun Apr 16 19:31:08 +14 2023 +I: pbuilder-time-stamp: 1681623068 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 [./gubbins_2.4.1.orig.tar.gz] I: copying [./gubbins_2.4.1-5.debian.tar.xz] I: Extracting source -gpgv: Signature made Sun Feb 13 02:24:30 2022 -12 +gpgv: Signature made Mon Feb 14 04:24:30 2022 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -32,135 +32,167 @@ dpkg-source: info: applying iqtree2.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3484544/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2321909/tmp/hooks/D01_modify_environment starting +debug: Running on ionos11-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Apr 16 19:31 /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/2321909/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2321909/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='5373289701624ec1906743a90ba91073' - 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='3484544' - PS1='# ' - PS2='> ' + INVOCATION_ID=98b9c45ffff34b42905dac5e6105e005 + 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=2321909 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.whOOMsYZ/pbuilderrc_vUxK --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.whOOMsYZ/b1 --logfile b1/build.log gubbins_2.4.1-5.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.whOOMsYZ/pbuilderrc_H3GA --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.whOOMsYZ/b2 --logfile b2/build.log --extrapackages usrmerge gubbins_2.4.1-5.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.deb11.5-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.12-1~bpo11+1 (2023-03-05) x86_64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 GNU/Linux I: ls -l /bin total 5632 - -rwxr-xr-x 1 root root 1265648 Feb 12 2023 bash - -rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2 - -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzcat - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep - -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzip2 - -rwxr-xr-x 1 root root 14568 Sep 18 2022 bzip2recover - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore - -rwxr-xr-x 1 root root 44016 Sep 20 2022 cat - -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp - -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod - -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown - -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp - -rwxr-xr-x 1 root root 125640 Jan 5 2023 dash - -rwxr-xr-x 1 root root 121904 Sep 20 2022 date - -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd - -rwxr-xr-x 1 root root 102200 Sep 20 2022 df - -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir - -rwxr-xr-x 1 root root 88656 Mar 22 2023 dmesg - lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname - -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep - -rwxr-xr-x 1 root root 35664 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep - -rwxr-xr-x 1 root root 85600 Mar 22 2023 findmnt - -rwsr-xr-x 1 root root 35128 Mar 22 2023 fusermount - -rwxr-xr-x 1 root root 203152 Jan 24 2023 grep - -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip - -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe - -rwxr-xr-x 1 root root 98136 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 22680 Dec 19 2022 hostname - -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln - -rwxr-xr-x 1 root root 53024 Mar 23 2023 login - -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls - -rwxr-xr-x 1 root root 207168 Mar 22 2023 lsblk - -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir - -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod - -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp - -rwxr-xr-x 1 root root 59712 Mar 22 2023 more - -rwsr-xr-x 1 root root 59704 Mar 22 2023 mount - -rwxr-xr-x 1 root root 18744 Mar 22 2023 mountpoint - -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv - lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 2 2023 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Feb 12 2023 rbash -> bash - -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink - -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm - -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 27560 Nov 2 2022 run-parts - -rwxr-xr-x 1 root root 126424 Jan 5 2023 sed - lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash - -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep - -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty - -rwsr-xr-x 1 root root 72000 Mar 22 2023 su - -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync - -rwxr-xr-x 1 root root 531984 Apr 6 2023 tar - -rwxr-xr-x 1 root root 14520 Nov 2 2022 tempfile - -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch - -rwxr-xr-x 1 root root 35664 Sep 20 2022 true - -rwxr-xr-x 1 root root 14568 Mar 22 2023 ulockmgr_server - -rwsr-xr-x 1 root root 35128 Mar 22 2023 umount - -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir - -rwxr-xr-x 1 root root 72024 Mar 22 2023 wdctl - lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/3484544/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1265648 Feb 13 10:05 bash + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bunzip2 + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzcat + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzip2 + -rwxr-xr-x 1 root root 14568 Sep 19 2022 bzip2recover + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore + -rwxr-xr-x 1 root root 44016 Sep 21 2022 cat + -rwxr-xr-x 1 root root 68656 Sep 21 2022 chgrp + -rwxr-xr-x 1 root root 64496 Sep 21 2022 chmod + -rwxr-xr-x 1 root root 72752 Sep 21 2022 chown + -rwxr-xr-x 1 root root 151152 Sep 21 2022 cp + -rwxr-xr-x 1 root root 125640 Jan 6 03:20 dash + -rwxr-xr-x 1 root root 121904 Sep 21 2022 date + -rwxr-xr-x 1 root root 89240 Sep 21 2022 dd + -rwxr-xr-x 1 root root 102200 Sep 21 2022 df + -rwxr-xr-x 1 root root 151344 Sep 21 2022 dir + -rwxr-xr-x 1 root root 88656 Mar 24 00:02 dmesg + lrwxrwxrwx 1 root root 8 Dec 20 03:33 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Dec 20 03:33 domainname -> hostname + -rwxr-xr-x 1 root root 43856 Sep 21 2022 echo + -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep + -rwxr-xr-x 1 root root 35664 Sep 21 2022 false + -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep + -rwxr-xr-x 1 root root 85600 Mar 24 00:02 findmnt + -rwsr-xr-x 1 root root 35128 Mar 23 22:35 fusermount + -rwxr-xr-x 1 root root 203152 Jan 25 04:43 grep + -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip + -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe + -rwxr-xr-x 1 root root 98136 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 22680 Dec 20 03:33 hostname + -rwxr-xr-x 1 root root 72824 Sep 21 2022 ln + -rwxr-xr-x 1 root root 53024 Mar 24 02:40 login + -rwxr-xr-x 1 root root 151344 Sep 21 2022 ls + -rwxr-xr-x 1 root root 207168 Mar 24 00:02 lsblk + -rwxr-xr-x 1 root root 97552 Sep 21 2022 mkdir + -rwxr-xr-x 1 root root 72912 Sep 21 2022 mknod + -rwxr-xr-x 1 root root 43952 Sep 21 2022 mktemp + -rwxr-xr-x 1 root root 59712 Mar 24 00:02 more + -rwsr-xr-x 1 root root 59704 Mar 24 00:02 mount + -rwxr-xr-x 1 root root 18744 Mar 24 00:02 mountpoint + -rwxr-xr-x 1 root root 142968 Sep 21 2022 mv + lrwxrwxrwx 1 root root 8 Dec 20 03:33 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43952 Sep 21 2022 pwd + lrwxrwxrwx 1 root root 4 Feb 13 10:05 rbash -> bash + -rwxr-xr-x 1 root root 52112 Sep 21 2022 readlink + -rwxr-xr-x 1 root root 72752 Sep 21 2022 rm + -rwxr-xr-x 1 root root 56240 Sep 21 2022 rmdir + -rwxr-xr-x 1 root root 27560 Nov 3 06:31 run-parts + -rwxr-xr-x 1 root root 126424 Jan 6 09:55 sed + lrwxrwxrwx 1 root root 9 Apr 16 19:31 sh -> /bin/bash + -rwxr-xr-x 1 root root 43888 Sep 21 2022 sleep + -rwxr-xr-x 1 root root 85008 Sep 21 2022 stty + -rwsr-xr-x 1 root root 72000 Mar 24 00:02 su + -rwxr-xr-x 1 root root 39824 Sep 21 2022 sync + -rwxr-xr-x 1 root root 531984 Apr 7 04:25 tar + -rwxr-xr-x 1 root root 14520 Nov 3 06:31 tempfile + -rwxr-xr-x 1 root root 109616 Sep 21 2022 touch + -rwxr-xr-x 1 root root 35664 Sep 21 2022 true + -rwxr-xr-x 1 root root 14568 Mar 23 22:35 ulockmgr_server + -rwsr-xr-x 1 root root 35128 Mar 24 00:02 umount + -rwxr-xr-x 1 root root 43888 Sep 21 2022 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 151344 Sep 21 2022 vdir + -rwxr-xr-x 1 root root 72024 Mar 24 00:02 wdctl + lrwxrwxrwx 1 root root 8 Dec 20 03:33 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat + -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp + -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff + -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep + -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep + -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce + -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep + -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless + -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore + -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew +I: user script /srv/workspace/pbuilder/2321909/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -387,7 +419,7 @@ Get: 157 http://deb.debian.org/debian bookworm/main amd64 python3-setuptools all 66.1.1-1 [521 kB] Get: 158 http://deb.debian.org/debian bookworm/main amd64 python3-wheel all 0.38.4-1 [30.8 kB] Get: 159 http://deb.debian.org/debian bookworm/main amd64 raxml amd64 8.2.12+dfsg-8+b2 [1481 kB] -Fetched 115 MB in 1s (98.9 MB/s) +Fetched 115 MB in 7s (15.9 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.) @@ -1052,8 +1084,19 @@ 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/gubbins-2.4.1/ && 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 > ../gubbins_2.4.1-5_source.changes +I: user script /srv/workspace/pbuilder/2321909/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/2321909/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/gubbins-2.4.1/ && 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 > ../gubbins_2.4.1-5_source.changes dpkg-buildpackage: info: source package gubbins dpkg-buildpackage: info: source version 2.4.1-5 dpkg-buildpackage: info: source distribution unstable @@ -1097,7 +1140,7 @@ ./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 @@ -1118,10 +1161,10 @@ checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none -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 @@ -1142,8 +1185,8 @@ 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 @@ -1223,72 +1266,72 @@ config.status: executing depfiles commands config.status: executing libtool commands dh_auto_build - make -j16 + make -j15 make[1]: Entering directory '/build/gubbins-2.4.1' make all-recursive make[2]: Entering directory '/build/gubbins-2.4.1' Making all in src make[3]: Entering directory '/build/gubbins-2.4.1/src' gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o main.o main.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/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Newickform.lo Newickform.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/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o alignment_file.lo alignment_file.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/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o block_tab_file.lo block_tab_file.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/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o branch_sequences.lo branch_sequences.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/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o string_cat.lo string_cat.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 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-ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snp_sites.lo snp_sites.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/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o tree_statistics.lo tree_statistics.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c string_cat.c -fPIC -DPIC -o .libs/string_cat.o -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c Newickform.c -fPIC -DPIC -o .libs/Newickform.o +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c gff_file.c -fPIC -DPIC -o .libs/gff_file.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c block_tab_file.c -fPIC -DPIC -o .libs/block_tab_file.o +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c Newickform.c -fPIC -DPIC -o .libs/Newickform.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c gubbins.c -fPIC -DPIC -o .libs/gubbins.o +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c alignment_file.c -fPIC -DPIC -o .libs/alignment_file.o +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c fasta_of_snp_sites.c -fPIC -DPIC -o .libs/fasta_of_snp_sites.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c branch_sequences.c -fPIC -DPIC -o .libs/branch_sequences.o -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c gff_file.c -fPIC -DPIC -o .libs/gff_file.o -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c parse_phylip.c -fPIC -DPIC -o .libs/parse_phylip.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c parse_vcf.c -fPIC -DPIC -o .libs/parse_vcf.o +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c parse_phylip.c -fPIC -DPIC -o .libs/parse_phylip.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c phylip_of_snp_sites.c -fPIC -DPIC -o .libs/phylip_of_snp_sites.o -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c fasta_of_snp_sites.c -fPIC -DPIC -o .libs/fasta_of_snp_sites.o -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c seqUtil.c -fPIC -DPIC -o .libs/seqUtil.o -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c snp_searching.c -fPIC -DPIC -o .libs/snp_searching.o -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c tree_statistics.c -fPIC -DPIC -o .libs/tree_statistics.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c snp_sites.c -fPIC -DPIC -o .libs/snp_sites.o -/bin/bash ../libtool 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snp_sites.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/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c Newickform.c -o Newickform.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/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c snp_searching.c -o snp_searching.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/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c tree_scaling.c -fPIC -DPIC -o .libs/tree_scaling.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c vcf.c -fPIC -DPIC -o .libs/vcf.o -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c tree_scaling.c -o tree_scaling.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/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c alignment_file.c -o alignment_file.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/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c vcf.c -o vcf.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/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c tree_scaling.c -o tree_scaling.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/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c parse_phylip.c -o parse_phylip.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/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c vcf.c -o vcf.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/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c branch_sequences.c -o branch_sequences.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 0:1 -Wl,-z,relro -Wl,-z,now -o libgubbins.la -rpath /usr/lib/x86_64-linux-gnu Newickform.lo alignment_file.lo block_tab_file.lo branch_sequences.lo string_cat.lo fasta_of_snp_sites.lo gff_file.lo gubbins.lo parse_phylip.lo parse_vcf.lo phylip_of_snp_sites.lo seqUtil.lo snp_searching.lo snp_sites.lo tree_statistics.lo tree_scaling.lo vcf.lo -lm +/bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 0:1 -Wl,-z,relro -Wl,-z,now -o libgubbins.la -rpath /usr/lib/x86_64-linux-gnu Newickform.lo alignment_file.lo block_tab_file.lo branch_sequences.lo string_cat.lo fasta_of_snp_sites.lo gff_file.lo gubbins.lo parse_phylip.lo parse_vcf.lo phylip_of_snp_sites.lo seqUtil.lo snp_searching.lo snp_sites.lo tree_statistics.lo tree_scaling.lo vcf.lo -lm libtool: link: gcc -shared -fPIC -DPIC .libs/Newickform.o .libs/alignment_file.o .libs/block_tab_file.o .libs/branch_sequences.o .libs/string_cat.o .libs/fasta_of_snp_sites.o .libs/gff_file.o .libs/gubbins.o .libs/parse_phylip.o .libs/parse_vcf.o .libs/phylip_of_snp_sites.o .libs/seqUtil.o .libs/snp_searching.o .libs/snp_sites.o .libs/tree_statistics.o .libs/tree_scaling.o .libs/vcf.o -lm -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libgubbins.so.0 -o .libs/libgubbins.so.0.0.1 libtool: link: (cd ".libs" && rm -f "libgubbins.so.0" && ln -s "libgubbins.so.0.0.1" "libgubbins.so.0") libtool: link: (cd ".libs" && rm -f "libgubbins.so" && ln -s "libgubbins.so.0.0.1" "libgubbins.so") libtool: link: ar cr .libs/libgubbins.a Newickform.o alignment_file.o block_tab_file.o branch_sequences.o string_cat.o fasta_of_snp_sites.o gff_file.o gubbins.o parse_phylip.o parse_vcf.o phylip_of_snp_sites.o seqUtil.o snp_searching.o snp_sites.o tree_statistics.o tree_scaling.o vcf.o libtool: link: ranlib .libs/libgubbins.a libtool: link: ( cd ".libs" && rm -f "libgubbins.la" && ln -s "../libgubbins.la" "libgubbins.la" ) -/bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o gubbins main.o libgubbins.la -lz -lm +/bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o gubbins main.o libgubbins.la -lz -lm libtool: link: gcc -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/gubbins main.o ./.libs/libgubbins.so -lz -lm make[3]: Leaving directory '/build/gubbins-2.4.1/src' Making all in release @@ -1302,7 +1345,7 @@ debian/rules override_dh_auto_test make[1]: Entering directory '/build/gubbins-2.4.1' dh_auto_test - make -j16 check "TESTSUITEFLAGS=-j16 --verbose" VERBOSE=1 + make -j15 check "TESTSUITEFLAGS=-j15 --verbose" VERBOSE=1 make[2]: Entering directory '/build/gubbins-2.4.1' Making check in src make[3]: Entering directory '/build/gubbins-2.4.1/src' @@ -1316,18 +1359,16 @@ gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ../tests/run_all_tests-check_vcf_parsing.o `test -f '../tests/check_vcf_parsing.c' || echo './'`../tests/check_vcf_parsing.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ../tests/run_all_tests-helper_methods.o `test -f '../tests/helper_methods.c' || echo './'`../tests/helper_methods.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ../tests/run_all_tests-run_all_tests.o `test -f '../tests/run_all_tests.c' || echo './'`../tests/run_all_tests.c -../tests/helper_methods.c: In function 'compare_files': -../tests/helper_methods.c:27:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 27 | fread(expected_buffer, sizeof(char), numbytes, expected_output_fh); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../tests/helper_methods.c:34:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 34 | fread(actual_buffer, sizeof(char), numbytes, actual_output_fh); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check_branch_sequences.c: In function 'check_copy_and_concat_2d_integer_arrays_fn': ../tests/check_branch_sequences.c:67:23: warning: implicit declaration of function 'copy_and_concat_2d_integer_arrays'; did you mean 'copy_and_concat_integer_arrays'? [-Wimplicit-function-declaration] 67 | output_size = copy_and_concat_2d_integer_arrays(block_coords, 3, block_coords_2, 2, block_coords_out) ; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | copy_and_concat_integer_arrays +In file included from ../tests/check_gubbins.c:4: +../tests/check_gubbins.c: In function 'check_gubbins_no_recombinations_fn': +../tests/check_gubbins.c:21:15: warning: implicit declaration of function 'number_of_recombinations_in_file' [-Wimplicit-function-declaration] + 21 | fail_unless(number_of_recombinations_in_file("../tests/data/no_recombinations.tre.tab") == 0); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../tests/check_snp_sites.c:5: ../tests/check_snp_sites.c: In function 'valid_alignment_with_large_numbers_of_snps_fn': ../tests/check_snp_sites.c:16:155: warning: too many arguments for format [-Wformat-extra-args] @@ -1339,12 +1380,7 @@ ../tests/check_snp_sites.c:18:175: warning: too many arguments for format [-Wformat-extra-args] 18 | fail_unless( compare_files("../tests/data/alignment_file_with_large_number_of_snps.aln.snp_sites.aln","alignment_file_with_large_number_of_snps.aln.snp_sites.aln" ) == 1 , "Invalid ALN file for 1 line per seq"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from ../tests/check_gubbins.c:4: -../tests/check_gubbins.c: In function 'check_gubbins_no_recombinations_fn': ../tests/check_snp_sites.c: In function 'valid_alignment_with_one_line_per_sequence_fn': -../tests/check_gubbins.c:21:15: warning: implicit declaration of function 'number_of_recombinations_in_file' [-Wimplicit-function-declaration] - 21 | fail_unless(number_of_recombinations_in_file("../tests/data/no_recombinations.tre.tab") == 0); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check_snp_sites.c:29:153: warning: too many arguments for format [-Wformat-extra-args] 29 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.phylip", "alignment_file_one_line_per_sequence.aln.phylip" ) == 1, "Invalid Phylip file for 1 line per seq" ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1394,7 +1430,14 @@ ../tests/check_snp_sites.c:85:122: warning: too many arguments for format [-Wformat-extra-args] 85 | fail_unless( compare_files("../tests/data/two_sequences.aln.snp_sites.aln","two_sequences.aln.snp_sites.aln" ) == 1 ,"Invalid ALN file for multiple lines per seq"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/bin/bash ../libtool --tag=CC --mode=link gcc -I../tests -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o run_all_tests ../tests/run_all_tests-check_branch_sequences.o ../tests/run_all_tests-check_gubbins.o ../tests/run_all_tests-check_parse_phylip.o ../tests/run_all_tests-check_snp_searching.o ../tests/run_all_tests-check_snp_sites.o ../tests/run_all_tests-check_vcf_parsing.o ../tests/run_all_tests-helper_methods.o ../tests/run_all_tests-run_all_tests.o -lcheck libgubbins.la -lz -lm -lrt -lsubunit +../tests/helper_methods.c: In function 'compare_files': +../tests/helper_methods.c:27:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 27 | fread(expected_buffer, sizeof(char), numbytes, expected_output_fh); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../tests/helper_methods.c:34:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 34 | fread(actual_buffer, sizeof(char), numbytes, actual_output_fh); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/bin/sh ../libtool --tag=CC --mode=link gcc -I../tests -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o run_all_tests ../tests/run_all_tests-check_branch_sequences.o ../tests/run_all_tests-check_gubbins.o ../tests/run_all_tests-check_parse_phylip.o ../tests/run_all_tests-check_snp_searching.o ../tests/run_all_tests-check_snp_sites.o ../tests/run_all_tests-check_vcf_parsing.o ../tests/run_all_tests-helper_methods.o ../tests/run_all_tests-run_all_tests.o -lcheck libgubbins.la -lz -lm -lrt -lsubunit libtool: link: gcc -I../tests -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/run_all_tests ../tests/run_all_tests-check_branch_sequences.o ../tests/run_all_tests-check_gubbins.o ../tests/run_all_tests-check_parse_phylip.o ../tests/run_all_tests-check_snp_searching.o ../tests/run_all_tests-check_snp_sites.o ../tests/run_all_tests-check_vcf_parsing.o ../tests/run_all_tests-helper_methods.o ../tests/run_all_tests-run_all_tests.o -lcheck ./.libs/libgubbins.so -lz -lm -lrt -lsubunit make[4]: Leaving directory '/build/gubbins-2.4.1/src' make check-TESTS @@ -1543,17 +1586,17 @@ Checking dependencies... -...done. Run time: 0.00 s +...done. Run time: 0.02 s Checking input files... -...done. Run time: 0.00 s +...done. Run time: 0.02 s Filtering input alignment... -...done. Run time: 0.01 s +...done. Run time: 0.03 s Running Gubbins to detect SNPs... -gubbins /build/gubbins-2.4.1/python/tmpgsreag7f/multiple_recombinations.aln -...done. Run time: 0.02 s +gubbins /build/gubbins-2.4.1/python/tmph9cyhd7o/multiple_recombinations.aln +...done. Run time: 0.21 s Entering the main loop. @@ -1561,81 +1604,81 @@ Constructing the phylogenetic tree with raxmlHPC... raxmlHPC -f d -p 1 -m GTRCAT -V -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_1 > /dev/null 2>&1 -...done. Run time: 0.28 s +...done. Run time: 1.94 s Reconstructing ancestral sequences with raxmlHPC... -raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_1.internal -t /build/gubbins-2.4.1/python/tmpgsreag7f/multiple_recombinations.iteration_1.tre.rooted > /dev/null 2>&1 -...done. Run time: 0.35 s +raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_1.internal -t /build/gubbins-2.4.1/python/tmph9cyhd7o/multiple_recombinations.iteration_1.tre.rooted > /dev/null 2>&1 +...done. Run time: 2.38 s Reinserting gaps into the alignment... -...done. Run time: 0.36 s +...done. Run time: 2.39 s Running Gubbins to detect recombinations... -gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpgsreag7f/multiple_recombinations.aln -t multiple_recombinations.iteration_1.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln -...done. Run time: 0.38 s +gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmph9cyhd7o/multiple_recombinations.aln -t multiple_recombinations.iteration_1.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln +...done. Run time: 2.59 s Checking for convergence... -...done. Run time: 0.38 s +...done. Run time: 2.59 s *** Iteration 2 *** Constructing the phylogenetic tree with raxmlHPC... raxmlHPC -f d -p 1 -m GTRCAT -V -s /build/gubbins-2.4.1/python/multiple_recombinations.iteration_1.tre.phylip -n multiple_recombinations.iteration_2 -t /build/gubbins-2.4.1/python/multiple_recombinations.iteration_1.tre > /dev/null 2>&1 -...done. Run time: 0.54 s +...done. Run time: 3.70 s Reconstructing ancestral sequences with raxmlHPC... -raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_2.internal -t /build/gubbins-2.4.1/python/tmpgsreag7f/multiple_recombinations.iteration_2.tre.rooted > /dev/null 2>&1 -...done. Run time: 0.68 s +raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_2.internal -t /build/gubbins-2.4.1/python/tmph9cyhd7o/multiple_recombinations.iteration_2.tre.rooted > /dev/null 2>&1 +...done. Run time: 4.76 s Reinserting gaps into the alignment... -...done. Run time: 0.68 s +...done. Run time: 4.78 s Running Gubbins to detect recombinations... -gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpgsreag7f/multiple_recombinations.aln -t multiple_recombinations.iteration_2.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln -...done. Run time: 0.71 s +gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmph9cyhd7o/multiple_recombinations.aln -t multiple_recombinations.iteration_2.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln +...done. Run time: 4.98 s Checking for convergence... -...done. Run time: 0.71 s +...done. Run time: 4.98 s *** Iteration 3 *** Constructing the phylogenetic tree with raxmlHPC... raxmlHPC -f d -p 1 -m GTRCAT -V -s /build/gubbins-2.4.1/python/multiple_recombinations.iteration_2.tre.phylip -n multiple_recombinations.iteration_3 -t /build/gubbins-2.4.1/python/multiple_recombinations.iteration_2.tre > /dev/null 2>&1 -...done. Run time: 0.86 s +...done. Run time: 5.73 s Reconstructing ancestral sequences with raxmlHPC... -raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_3.internal -t /build/gubbins-2.4.1/python/tmpgsreag7f/multiple_recombinations.iteration_3.tre.rooted > /dev/null 2>&1 -...done. Run time: 0.92 s +raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_3.internal -t /build/gubbins-2.4.1/python/tmph9cyhd7o/multiple_recombinations.iteration_3.tre.rooted > /dev/null 2>&1 +...done. Run time: 6.83 s Reinserting gaps into the alignment... -...done. Run time: 0.93 s +...done. Run time: 6.84 s Running Gubbins to detect recombinations... -gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpgsreag7f/multiple_recombinations.aln -t multiple_recombinations.iteration_3.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln -...done. Run time: 0.95 s +gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmph9cyhd7o/multiple_recombinations.aln -t multiple_recombinations.iteration_3.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln +...done. Run time: 7.01 s Checking for convergence... -...done. Run time: 0.96 s +...done. Run time: 7.03 s *** Iteration 4 *** Constructing the phylogenetic tree with raxmlHPC... raxmlHPC -f d -p 1 -m GTRCAT -V -s /build/gubbins-2.4.1/python/multiple_recombinations.iteration_3.tre.phylip -n multiple_recombinations.iteration_4 -t /build/gubbins-2.4.1/python/multiple_recombinations.iteration_3.tre > /dev/null 2>&1 -...done. Run time: 1.23 s +...done. Run time: 9.69 s Reconstructing ancestral sequences with raxmlHPC... -raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_4.internal -t /build/gubbins-2.4.1/python/tmpgsreag7f/multiple_recombinations.iteration_4.tre.rooted > /dev/null 2>&1 -...done. Run time: 1.29 s +raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_4.internal -t /build/gubbins-2.4.1/python/tmph9cyhd7o/multiple_recombinations.iteration_4.tre.rooted > /dev/null 2>&1 +...done. Run time: 10.15 s Reinserting gaps into the alignment... -...done. Run time: 1.29 s +...done. Run time: 10.17 s Running Gubbins to detect recombinations... -gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpgsreag7f/multiple_recombinations.aln -t multiple_recombinations.iteration_4.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln -...done. Run time: 1.31 s +gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmph9cyhd7o/multiple_recombinations.aln -t multiple_recombinations.iteration_4.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln +...done. Run time: 10.33 s Checking for convergence... -...done. Run time: 1.32 s +...done. Run time: 10.36 s *** Iteration 5 *** @@ -1643,44 +1686,44 @@ ok test_fasttree (gubbins.tests.test_dependencies.TestExternalDependencies.test_fasttree) ... ok test_hybrid (gubbins.tests.test_dependencies.TestExternalDependencies.test_hybrid) ... raxmlHPC -f d -p 1 -m GTRCAT -V -s /build/gubbins-2.4.1/python/multiple_recombinations.iteration_4.tre.phylip -n multiple_recombinations.iteration_5 -t /build/gubbins-2.4.1/python/multiple_recombinations.iteration_4.tre > /dev/null 2>&1 -...done. Run time: 1.61 s +...done. Run time: 13.71 s Reconstructing ancestral sequences with raxmlHPC... -raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_5.internal -t /build/gubbins-2.4.1/python/tmpgsreag7f/multiple_recombinations.iteration_5.tre.rooted > /dev/null 2>&1 -...done. Run time: 1.67 s +raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_5.internal -t /build/gubbins-2.4.1/python/tmph9cyhd7o/multiple_recombinations.iteration_5.tre.rooted > /dev/null 2>&1 +...done. Run time: 14.42 s Reinserting gaps into the alignment... -...done. Run time: 1.67 s +...done. Run time: 14.43 s Running Gubbins to detect recombinations... -gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpgsreag7f/multiple_recombinations.aln -t multiple_recombinations.iteration_5.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln -...done. Run time: 1.69 s +gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmph9cyhd7o/multiple_recombinations.aln -t multiple_recombinations.iteration_5.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln +...done. Run time: 14.69 s Checking for convergence... -...done. Run time: 1.70 s +...done. Run time: 14.71 s Maximum number of iterations (5) reached. Exiting the main loop. Creating the final output... -...finished. Total run time: 1.71 s +...finished. Total run time: 14.73 s --- Gubbins 2.4.1 --- Checking dependencies... -...done. Run time: 0.00 s +...done. Run time: 0.02 s Checking input files... -...done. Run time: 0.00 s +...done. Run time: 0.02 s Filtering input alignment... -...done. Run time: 0.01 s +...done. Run time: 0.02 s Running Gubbins to detect SNPs... -gubbins /build/gubbins-2.4.1/python/tmpsuo7cx_b/multiple_recombinations.aln -...done. Run time: 0.02 s +gubbins /build/gubbins-2.4.1/python/tmpn511btj3/multiple_recombinations.aln +...done. Run time: 0.25 s Entering the main loop. @@ -1688,98 +1731,98 @@ Constructing the phylogenetic tree with FastTree... FastTree -nosupport -gtr -gamma -nt -out multiple_recombinations.iteration_1.tre /build/gubbins-2.4.1/python/multiple_recombinations.aln.snp_sites.aln > /dev/null 2>&1 -...done. Run time: 0.13 s +...done. Run time: 0.47 s Reconstructing ancestral sequences with raxmlHPC... -raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.snp_sites.aln -n multiple_recombinations.iteration_1.internal -t /build/gubbins-2.4.1/python/tmpsuo7cx_b/multiple_recombinations.iteration_1.tre.rooted > /dev/null 2>&1 -...done. Run time: 0.19 s +raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.snp_sites.aln -n multiple_recombinations.iteration_1.internal -t /build/gubbins-2.4.1/python/tmpn511btj3/multiple_recombinations.iteration_1.tre.rooted > /dev/null 2>&1 +...done. Run time: 0.87 s Reinserting gaps into the alignment... -...done. Run time: 0.19 s +...done. Run time: 0.88 s Running Gubbins to detect recombinations... -gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpsuo7cx_b/multiple_recombinations.aln -t multiple_recombinations.iteration_1.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln -...done. Run time: 0.21 s +gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpn511btj3/multiple_recombinations.aln -t multiple_recombinations.iteration_1.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln +...done. Run time: 1.09 s Checking for convergence... -...done. Run time: 0.21 s +...done. Run time: 1.09 s *** Iteration 2 *** Constructing the phylogenetic tree with FastTree... FastTree -nosupport -gtr -gamma -nt -intree /build/gubbins-2.4.1/python/multiple_recombinations.iteration_1.tre -out multiple_recombinations.iteration_2.tre /build/gubbins-2.4.1/python/multiple_recombinations.iteration_1.tre.snp_sites.aln > /dev/null 2>&1 -...done. Run time: 0.25 s +...done. Run time: 1.21 s Reconstructing ancestral sequences with raxmlHPC... -raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.snp_sites.aln -n multiple_recombinations.iteration_2.internal -t /build/gubbins-2.4.1/python/tmpsuo7cx_b/multiple_recombinations.iteration_2.tre.rooted > /dev/null 2>&1 -...done. Run time: 0.31 s +raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.snp_sites.aln -n multiple_recombinations.iteration_2.internal -t /build/gubbins-2.4.1/python/tmpn511btj3/multiple_recombinations.iteration_2.tre.rooted > /dev/null 2>&1 +...done. Run time: 1.64 s Reinserting gaps into the alignment... -...done. Run time: 0.31 s +...done. Run time: 1.64 s Running Gubbins to detect recombinations... -gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpsuo7cx_b/multiple_recombinations.aln -t multiple_recombinations.iteration_2.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln -...done. Run time: 0.33 s +gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpn511btj3/multiple_recombinations.aln -t multiple_recombinations.iteration_2.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln +...done. Run time: 1.88 s Checking for convergence... -...done. Run time: 0.33 s +...done. Run time: 1.88 s *** Iteration 3 *** Constructing the phylogenetic tree with FastTree... FastTree -nosupport -gtr -gamma -nt -intree /build/gubbins-2.4.1/python/multiple_recombinations.iteration_2.tre -out multiple_recombinations.iteration_3.tre /build/gubbins-2.4.1/python/multiple_recombinations.iteration_2.tre.snp_sites.aln > /dev/null 2>&1 -...done. Run time: 0.39 s +...done. Run time: 2.06 s Reconstructing ancestral sequences with raxmlHPC... -raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.snp_sites.aln -n multiple_recombinations.iteration_3.internal -t /build/gubbins-2.4.1/python/tmpsuo7cx_b/multiple_recombinations.iteration_3.tre.rooted > /dev/null 2>&1 -...done. Run time: 0.44 s +raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.snp_sites.aln -n multiple_recombinations.iteration_3.internal -t /build/gubbins-2.4.1/python/tmpn511btj3/multiple_recombinations.iteration_3.tre.rooted > /dev/null 2>&1 +...done. Run time: 2.47 s Reinserting gaps into the alignment... -...done. Run time: 0.45 s +...done. Run time: 2.48 s Running Gubbins to detect recombinations... -gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpsuo7cx_b/multiple_recombinations.aln -t multiple_recombinations.iteration_3.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln -...done. Run time: 0.47 s +gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpn511btj3/multiple_recombinations.aln -t multiple_recombinations.iteration_3.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln +...done. Run time: 2.68 s Checking for convergence... -...done. Run time: 0.47 s +...done. Run time: 2.69 s *** Iteration 4 *** Constructing the phylogenetic tree with FastTree... FastTree -nosupport -gtr -gamma -nt -intree /build/gubbins-2.4.1/python/multiple_recombinations.iteration_3.tre -out multiple_recombinations.iteration_4.tre /build/gubbins-2.4.1/python/multiple_recombinations.iteration_3.tre.snp_sites.aln > /dev/null 2>&1 -...done. Run time: 0.54 s +...done. Run time: 2.94 s Reconstructing ancestral sequences with raxmlHPC... -raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.snp_sites.aln -n multiple_recombinations.iteration_4.internal -t /build/gubbins-2.4.1/python/tmpsuo7cx_b/multiple_recombinations.iteration_4.tre.rooted > /dev/null 2>&1 -...done. Run time: 0.60 s +raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.snp_sites.aln -n multiple_recombinations.iteration_4.internal -t /build/gubbins-2.4.1/python/tmpn511btj3/multiple_recombinations.iteration_4.tre.rooted > /dev/null 2>&1 +...done. Run time: 3.41 s Reinserting gaps into the alignment... -...done. Run time: 0.60 s +...done. Run time: 3.41 s Running Gubbins to detect recombinations... -gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpsuo7cx_b/multiple_recombinations.aln -t multiple_recombinations.iteration_4.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln -...done. Run time: 0.62 s +gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpn511btj3/multiple_recombinations.aln -t multiple_recombinations.iteration_4.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln +...done. Run time: 3.69 s Checking for convergence... -...done. Run time: 0.63 s +...done. Run time: 3.71 s *** Iteration 5 *** Constructing the phylogenetic tree with FastTree... FastTree -nosupport -gtr -gamma -nt -intree /build/gubbins-2.4.1/python/multiple_recombinations.iteration_4.tre -out multiple_recombinations.iteration_5.tre /build/gubbins-2.4.1/python/multiple_recombinations.iteration_4.tre.snp_sites.aln > /dev/null 2>&1 -...done. Run time: 0.69 s +...done. Run time: 3.95 s Reconstructing ancestral sequences with raxmlHPC... -raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.snp_sites.aln -n multiple_recombinations.iteration_5.internal -t /build/gubbins-2.4.1/python/tmpsuo7cx_b/multiple_recombinations.iteration_5.tre.rooted > /dev/null 2>&1 -...done. Run time: 0.74 s +raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.snp_sites.aln -n multiple_recombinations.iteration_5.internal -t /build/gubbins-2.4.1/python/tmpn511btj3/multiple_recombinations.iteration_5.tre.rooted > /dev/null 2>&1 +...done. Run time: 4.46 s Reinserting gaps into the alignment... -...done. Run time: 0.74 s +...done. Run time: 4.47 s Running Gubbins to detect recombinations... -gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpsuo7cx_b/multiple_recombinations.aln -t multiple_recombinations.iteration_5.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln -...done. Run time: 0.76 s +gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpn511btj3/multiple_recombinations.aln -t multiple_recombinations.iteration_5.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln +...done. Run time: 4.66 s Checking for convergence... Convergence after 5 iterations: Tree observed before. @@ -1787,24 +1830,24 @@ Exiting the main loop. Creating the final output... -...finished. Total run time: 0.77 s +...finished. Total run time: 4.67 s --- Gubbins 2.4.1 --- Checking dependencies... -...done. Run time: 0.00 s +...done. Run time: 0.01 s Checking input files... -...done. Run time: 0.00 s +...done. Run time: 0.02 s Filtering input alignment... -...done. Run time: 0.01 s +...done. Run time: 0.02 s Running Gubbins to detect SNPs... -gubbins /build/gubbins-2.4.1/python/tmpj586geap/multiple_recombinations.aln -...done. Run time: 0.02 s +gubbins /build/gubbins-2.4.1/python/tmpr4z627t1/multiple_recombinations.aln +...done. Run time: 0.19 s Entering the main loop. @@ -1812,108 +1855,108 @@ Constructing the phylogenetic tree with FastTree... FastTree -nosupport -gtr -gamma -nt -out multiple_recombinations.iteration_1.tre /build/gubbins-2.4.1/python/multiple_recombinations.aln.snp_sites.aln > /dev/null 2>&1 -...done. Run time: 0.12 s +...done. Run time: 0.51 s Reconstructing ancestral sequences with raxmlHPC... -raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.snp_sites.aln -n multiple_recombinations.iteration_1.internal -t /build/gubbins-2.4.1/python/tmpj586geap/multiple_recombinations.iteration_1.tre.rooted > /dev/null 2>&1 -...done. Run time: 0.18 s +raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.snp_sites.aln -n multiple_recombinations.iteration_1.internal -t /build/gubbins-2.4.1/python/tmpr4z627t1/multiple_recombinations.iteration_1.tre.rooted > /dev/null 2>&1 +...done. Run time: 0.96 s Reinserting gaps into the alignment... -...done. Run time: 0.18 s +...done. Run time: 0.97 s Running Gubbins to detect recombinations... ok -test_iqtree (gubbins.tests.test_dependencies.TestExternalDependencies.test_iqtree) ... gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpj586geap/multiple_recombinations.aln -t multiple_recombinations.iteration_1.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln -...done. Run time: 0.20 s +test_iqtree (gubbins.tests.test_dependencies.TestExternalDependencies.test_iqtree) ... gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpr4z627t1/multiple_recombinations.aln -t multiple_recombinations.iteration_1.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln +...done. Run time: 1.17 s Checking for convergence... -...done. Run time: 0.21 s +...done. Run time: 1.17 s *** Iteration 2 *** Constructing the phylogenetic tree with raxmlHPC... raxmlHPC -f d -p 1 -m GTRCAT -V -s /build/gubbins-2.4.1/python/multiple_recombinations.iteration_1.tre.phylip -n multiple_recombinations.iteration_2 -t /build/gubbins-2.4.1/python/multiple_recombinations.iteration_1.tre > /dev/null 2>&1 -...done. Run time: 0.33 s +...done. Run time: 1.82 s Reconstructing ancestral sequences with raxmlHPC... -raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_2.internal -t /build/gubbins-2.4.1/python/tmpj586geap/multiple_recombinations.iteration_2.tre.rooted > /dev/null 2>&1 -...done. Run time: 0.39 s +raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_2.internal -t /build/gubbins-2.4.1/python/tmpr4z627t1/multiple_recombinations.iteration_2.tre.rooted > /dev/null 2>&1 +...done. Run time: 2.56 s Reinserting gaps into the alignment... -...done. Run time: 0.39 s +...done. Run time: 2.57 s Running Gubbins to detect recombinations... -gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpj586geap/multiple_recombinations.aln -t multiple_recombinations.iteration_2.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln -...done. Run time: 0.42 s +gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpr4z627t1/multiple_recombinations.aln -t multiple_recombinations.iteration_2.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln +...done. Run time: 2.76 s Checking for convergence... -...done. Run time: 0.42 s +...done. Run time: 2.76 s *** Iteration 3 *** Constructing the phylogenetic tree with raxmlHPC... raxmlHPC -f d -p 1 -m GTRCAT -V -s /build/gubbins-2.4.1/python/multiple_recombinations.iteration_2.tre.phylip -n multiple_recombinations.iteration_3 -t /build/gubbins-2.4.1/python/multiple_recombinations.iteration_2.tre > /dev/null 2>&1 -...done. Run time: 0.60 s +...done. Run time: 4.39 s Reconstructing ancestral sequences with raxmlHPC... -raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_3.internal -t /build/gubbins-2.4.1/python/tmpj586geap/multiple_recombinations.iteration_3.tre.rooted > /dev/null 2>&1 -...done. Run time: 0.67 s +raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_3.internal -t /build/gubbins-2.4.1/python/tmpr4z627t1/multiple_recombinations.iteration_3.tre.rooted > /dev/null 2>&1 +...done. Run time: 5.11 s Reinserting gaps into the alignment... -...done. Run time: 0.67 s +...done. Run time: 5.12 s Running Gubbins to detect recombinations... -gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpj586geap/multiple_recombinations.aln -t multiple_recombinations.iteration_3.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln -...done. Run time: 0.69 s +gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpr4z627t1/multiple_recombinations.aln -t multiple_recombinations.iteration_3.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln +...done. Run time: 5.31 s Checking for convergence... -...done. Run time: 0.70 s +...done. Run time: 5.32 s *** Iteration 4 *** Constructing the phylogenetic tree with raxmlHPC... raxmlHPC -f d -p 1 -m GTRCAT -V -s /build/gubbins-2.4.1/python/multiple_recombinations.iteration_3.tre.phylip -n multiple_recombinations.iteration_4 -t /build/gubbins-2.4.1/python/multiple_recombinations.iteration_3.tre > /dev/null 2>&1 -...done. Run time: 0.94 s +...done. Run time: 7.28 s Reconstructing ancestral sequences with raxmlHPC... -raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_4.internal -t /build/gubbins-2.4.1/python/tmpj586geap/multiple_recombinations.iteration_4.tre.rooted > /dev/null 2>&1 -...done. Run time: 1.00 s +raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_4.internal -t /build/gubbins-2.4.1/python/tmpr4z627t1/multiple_recombinations.iteration_4.tre.rooted > /dev/null 2>&1 +...done. Run time: 7.81 s Reinserting gaps into the alignment... -...done. Run time: 1.00 s +...done. Run time: 7.82 s Running Gubbins to detect recombinations... -gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpj586geap/multiple_recombinations.aln -t multiple_recombinations.iteration_4.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln -...done. Run time: 1.02 s +gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpr4z627t1/multiple_recombinations.aln -t multiple_recombinations.iteration_4.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln +...done. Run time: 8.03 s Checking for convergence... -...done. Run time: 1.03 s +...done. Run time: 8.06 s *** Iteration 5 *** Constructing the phylogenetic tree with raxmlHPC... raxmlHPC -f d -p 1 -m GTRCAT -V -s /build/gubbins-2.4.1/python/multiple_recombinations.iteration_4.tre.phylip -n multiple_recombinations.iteration_5 -t /build/gubbins-2.4.1/python/multiple_recombinations.iteration_4.tre > /dev/null 2>&1 -...done. Run time: 1.12 s +...done. Run time: 8.75 s Reconstructing ancestral sequences with raxmlHPC... -raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_5.internal -t /build/gubbins-2.4.1/python/tmpj586geap/multiple_recombinations.iteration_5.tre.rooted > /dev/null 2>&1 -...done. Run time: 1.17 s +raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_5.internal -t /build/gubbins-2.4.1/python/tmpr4z627t1/multiple_recombinations.iteration_5.tre.rooted > /dev/null 2>&1 +...done. Run time: 9.19 s Reinserting gaps into the alignment... -...done. Run time: 1.17 s +...done. Run time: 9.21 s Running Gubbins to detect recombinations... -gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpj586geap/multiple_recombinations.aln -t multiple_recombinations.iteration_5.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln -...done. Run time: 1.19 s +gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpr4z627t1/multiple_recombinations.aln -t multiple_recombinations.iteration_5.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln +...done. Run time: 9.43 s Checking for convergence... -...done. Run time: 1.20 s +...done. Run time: 9.46 s Maximum number of iterations (5) reached. Exiting the main loop. Creating the final output... -...finished. Total run time: 1.20 s +...finished. Total run time: 9.47 s --- Gubbins 2.4.1 --- @@ -1929,8 +1972,8 @@ ...done. Run time: 0.00 s Running Gubbins to detect SNPs... -gubbins /build/gubbins-2.4.1/python/tmpr6__2_cl/multiple_recombinations.aln -...done. Run time: 0.02 s +gubbins /build/gubbins-2.4.1/python/tmp7q57zhgz/multiple_recombinations.aln +...done. Run time: 0.17 s Entering the main loop. @@ -1938,125 +1981,125 @@ Constructing the phylogenetic tree with iqtree2... iqtree2 -safe -m GTR+G4 -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -pre multiple_recombinations.iteration_1 -nt 1 -quiet -...done. Run time: 0.96 s +...done. Run time: 1.51 s Reconstructing ancestral sequences with iqtree2... -iqtree2 -safe -asr -m GTR+G4 -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -pre multiple_recombinations.iteration_1.internal -nt 1 -te /build/gubbins-2.4.1/python/tmpr6__2_cl/multiple_recombinations.iteration_1.tre.rooted -quiet -...done. Run time: 1.02 s +iqtree2 -safe -asr -m GTR+G4 -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -pre multiple_recombinations.iteration_1.internal -nt 1 -te /build/gubbins-2.4.1/python/tmp7q57zhgz/multiple_recombinations.iteration_1.tre.rooted -quiet +...done. Run time: 1.69 s Reinserting gaps into the alignment... -...done. Run time: 1.03 s +...done. Run time: 1.70 s Running Gubbins to detect recombinations... -gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpr6__2_cl/multiple_recombinations.aln -t multiple_recombinations.iteration_1.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln -...done. Run time: 1.05 s +gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmp7q57zhgz/multiple_recombinations.aln -t multiple_recombinations.iteration_1.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln +...done. Run time: 1.90 s Checking for convergence... -...done. Run time: 1.05 s +...done. Run time: 1.90 s *** Iteration 2 *** Constructing the phylogenetic tree with iqtree2... iqtree2 -safe -m GTR+G4 -s /build/gubbins-2.4.1/python/multiple_recombinations.iteration_1.tre.phylip -pre multiple_recombinations.iteration_2 -nt 1 -t /build/gubbins-2.4.1/python/multiple_recombinations.iteration_1.tre -quiet -...done. Run time: 1.42 s +...done. Run time: 3.68 s Reconstructing ancestral sequences with iqtree2... -iqtree2 -safe -asr -m GTR+G4 -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -pre multiple_recombinations.iteration_2.internal -nt 1 -te /build/gubbins-2.4.1/python/tmpr6__2_cl/multiple_recombinations.iteration_2.tre.rooted -quiet -...done. Run time: 1.47 s +iqtree2 -safe -asr -m GTR+G4 -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -pre multiple_recombinations.iteration_2.internal -nt 1 -te /build/gubbins-2.4.1/python/tmp7q57zhgz/multiple_recombinations.iteration_2.tre.rooted -quiet +...done. Run time: 3.94 s Reinserting gaps into the alignment... -...done. Run time: 1.48 s +...done. Run time: 3.97 s Running Gubbins to detect recombinations... -gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpr6__2_cl/multiple_recombinations.aln -t multiple_recombinations.iteration_2.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln -...done. Run time: 1.50 s +gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmp7q57zhgz/multiple_recombinations.aln -t multiple_recombinations.iteration_2.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln +...done. Run time: 4.16 s Checking for convergence... -...done. Run time: 1.50 s +...done. Run time: 4.16 s *** Iteration 3 *** Constructing the phylogenetic tree with iqtree2... iqtree2 -safe -m GTR+G4 -s /build/gubbins-2.4.1/python/multiple_recombinations.iteration_2.tre.phylip -pre multiple_recombinations.iteration_3 -nt 1 -t /build/gubbins-2.4.1/python/multiple_recombinations.iteration_2.tre -quiet -...done. Run time: 1.60 s +...done. Run time: 5.28 s Reconstructing ancestral sequences with iqtree2... -iqtree2 -safe -asr -m GTR+G4 -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -pre multiple_recombinations.iteration_3.internal -nt 1 -te /build/gubbins-2.4.1/python/tmpr6__2_cl/multiple_recombinations.iteration_3.tre.rooted -quiet -...done. Run time: 1.65 s +iqtree2 -safe -asr -m GTR+G4 -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -pre multiple_recombinations.iteration_3.internal -nt 1 -te /build/gubbins-2.4.1/python/tmp7q57zhgz/multiple_recombinations.iteration_3.tre.rooted -quiet +...done. Run time: 5.51 s Reinserting gaps into the alignment... -...done. Run time: 1.65 s +...done. Run time: 5.53 s Running Gubbins to detect recombinations... ok -test_raxml (gubbins.tests.test_dependencies.TestExternalDependencies.test_raxml) ... gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpr6__2_cl/multiple_recombinations.aln -t multiple_recombinations.iteration_3.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln -...done. Run time: 1.68 s +test_raxml (gubbins.tests.test_dependencies.TestExternalDependencies.test_raxml) ... gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmp7q57zhgz/multiple_recombinations.aln -t multiple_recombinations.iteration_3.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln +...done. Run time: 5.72 s Checking for convergence... -...done. Run time: 1.68 s +...done. Run time: 5.73 s *** Iteration 4 *** Constructing the phylogenetic tree with iqtree2... iqtree2 -safe -m GTR+G4 -s /build/gubbins-2.4.1/python/multiple_recombinations.iteration_3.tre.phylip -pre multiple_recombinations.iteration_4 -nt 1 -t /build/gubbins-2.4.1/python/multiple_recombinations.iteration_3.tre -quiet -...done. Run time: 2.13 s +...done. Run time: 6.74 s Reconstructing ancestral sequences with iqtree2... -iqtree2 -safe -asr -m GTR+G4 -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -pre multiple_recombinations.iteration_4.internal -nt 1 -te /build/gubbins-2.4.1/python/tmpr6__2_cl/multiple_recombinations.iteration_4.tre.rooted -quiet -...done. Run time: 2.24 s +iqtree2 -safe -asr -m GTR+G4 -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -pre multiple_recombinations.iteration_4.internal -nt 1 -te /build/gubbins-2.4.1/python/tmp7q57zhgz/multiple_recombinations.iteration_4.tre.rooted -quiet +...done. Run time: 6.98 s Reinserting gaps into the alignment... -...done. Run time: 2.24 s +...done. Run time: 6.99 s Running Gubbins to detect recombinations... -gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpr6__2_cl/multiple_recombinations.aln -t multiple_recombinations.iteration_4.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln -...done. Run time: 2.26 s +gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmp7q57zhgz/multiple_recombinations.aln -t multiple_recombinations.iteration_4.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln +...done. Run time: 7.19 s Checking for convergence... -...done. Run time: 2.27 s +...done. Run time: 7.20 s *** Iteration 5 *** Constructing the phylogenetic tree with iqtree2... iqtree2 -safe -m GTR+G4 -s /build/gubbins-2.4.1/python/multiple_recombinations.iteration_4.tre.phylip -pre multiple_recombinations.iteration_5 -nt 1 -t /build/gubbins-2.4.1/python/multiple_recombinations.iteration_4.tre -quiet -...done. Run time: 3.28 s +...done. Run time: 8.31 s Reconstructing ancestral sequences with iqtree2... -iqtree2 -safe -asr -m GTR+G4 -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -pre multiple_recombinations.iteration_5.internal -nt 1 -te /build/gubbins-2.4.1/python/tmpr6__2_cl/multiple_recombinations.iteration_5.tre.rooted -quiet -...done. Run time: 3.33 s +iqtree2 -safe -asr -m GTR+G4 -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -pre multiple_recombinations.iteration_5.internal -nt 1 -te /build/gubbins-2.4.1/python/tmp7q57zhgz/multiple_recombinations.iteration_5.tre.rooted -quiet +...done. Run time: 8.55 s Reinserting gaps into the alignment... -...done. Run time: 3.33 s +...done. Run time: 8.56 s Running Gubbins to detect recombinations... -gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpr6__2_cl/multiple_recombinations.aln -t multiple_recombinations.iteration_5.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln -...done. Run time: 3.35 s +gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmp7q57zhgz/multiple_recombinations.aln -t multiple_recombinations.iteration_5.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln +...done. Run time: 8.77 s Checking for convergence... -...done. Run time: 3.36 s +...done. Run time: 8.79 s Maximum number of iterations (5) reached. Exiting the main loop. Creating the final output... -...finished. Total run time: 3.36 s +...finished. Total run time: 8.80 s --- Gubbins 2.4.1 --- Checking dependencies... -...done. Run time: 0.00 s +...done. Run time: 0.02 s Checking input files... -...done. Run time: 0.01 s +...done. Run time: 0.02 s Filtering input alignment... -...done. Run time: 0.01 s +...done. Run time: 0.02 s Running Gubbins to detect SNPs... -gubbins /build/gubbins-2.4.1/python/tmppy_1dwz8/multiple_recombinations.aln -...done. Run time: 0.03 s +gubbins /build/gubbins-2.4.1/python/tmp4gxirj5d/multiple_recombinations.aln +...done. Run time: 0.22 s Entering the main loop. @@ -2064,94 +2107,94 @@ Constructing the phylogenetic tree with raxmlHPC... raxmlHPC -f d -p 1 -m GTRCAT -V -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_1 > /dev/null 2>&1 -...done. Run time: 0.28 s +...done. Run time: 1.56 s Reconstructing ancestral sequences with raxmlHPC... -raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_1.internal -t /build/gubbins-2.4.1/python/tmppy_1dwz8/multiple_recombinations.iteration_1.tre.rooted > /dev/null 2>&1 -...done. Run time: 0.36 s +raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_1.internal -t /build/gubbins-2.4.1/python/tmp4gxirj5d/multiple_recombinations.iteration_1.tre.rooted > /dev/null 2>&1 +...done. Run time: 2.05 s Reinserting gaps into the alignment... -...done. Run time: 0.37 s +...done. Run time: 2.06 s Running Gubbins to detect recombinations... -gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmppy_1dwz8/multiple_recombinations.aln -t multiple_recombinations.iteration_1.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln -...done. Run time: 0.39 s +gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmp4gxirj5d/multiple_recombinations.aln -t multiple_recombinations.iteration_1.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln +...done. Run time: 2.25 s Checking for convergence... -...done. Run time: 0.39 s +...done. Run time: 2.26 s *** Iteration 2 *** Constructing the phylogenetic tree with raxmlHPC... raxmlHPC -f d -p 1 -m GTRCAT -V -s /build/gubbins-2.4.1/python/multiple_recombinations.iteration_1.tre.phylip -n multiple_recombinations.iteration_2 -t /build/gubbins-2.4.1/python/multiple_recombinations.iteration_1.tre > /dev/null 2>&1 -...done. Run time: 0.54 s +...done. Run time: 2.91 s Reconstructing ancestral sequences with raxmlHPC... -raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_2.internal -t /build/gubbins-2.4.1/python/tmppy_1dwz8/multiple_recombinations.iteration_2.tre.rooted > /dev/null 2>&1 -...done. Run time: 0.67 s +raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_2.internal -t /build/gubbins-2.4.1/python/tmp4gxirj5d/multiple_recombinations.iteration_2.tre.rooted > /dev/null 2>&1 +...done. Run time: 3.64 s Reinserting gaps into the alignment... -...done. Run time: 0.68 s +...done. Run time: 3.65 s Running Gubbins to detect recombinations... -gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmppy_1dwz8/multiple_recombinations.aln -t multiple_recombinations.iteration_2.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln -...done. Run time: 0.70 s +gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmp4gxirj5d/multiple_recombinations.aln -t multiple_recombinations.iteration_2.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln +...done. Run time: 3.84 s Checking for convergence... -...done. Run time: 0.70 s +...done. Run time: 3.84 s *** Iteration 3 *** Constructing the phylogenetic tree with raxmlHPC... raxmlHPC -f d -p 1 -m GTRCAT -V -s /build/gubbins-2.4.1/python/multiple_recombinations.iteration_2.tre.phylip -n multiple_recombinations.iteration_3 -t /build/gubbins-2.4.1/python/multiple_recombinations.iteration_2.tre > /dev/null 2>&1 -...done. Run time: 0.81 s +...done. Run time: 5.07 s Reconstructing ancestral sequences with raxmlHPC... -raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_3.internal -t /build/gubbins-2.4.1/python/tmppy_1dwz8/multiple_recombinations.iteration_3.tre.rooted > /dev/null 2>&1 -...done. Run time: 0.87 s +raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_3.internal -t /build/gubbins-2.4.1/python/tmp4gxirj5d/multiple_recombinations.iteration_3.tre.rooted > /dev/null 2>&1 +...done. Run time: 5.36 s Reinserting gaps into the alignment... -...done. Run time: 0.88 s +...done. Run time: 5.37 s Running Gubbins to detect recombinations... -gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmppy_1dwz8/multiple_recombinations.aln -t multiple_recombinations.iteration_3.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln -...done. Run time: 0.90 s +gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmp4gxirj5d/multiple_recombinations.aln -t multiple_recombinations.iteration_3.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln +...done. Run time: 5.59 s Checking for convergence... -...done. Run time: 0.91 s +...done. Run time: 5.60 s *** Iteration 4 *** Constructing the phylogenetic tree with raxmlHPC... raxmlHPC -f d -p 1 -m GTRCAT -V -s /build/gubbins-2.4.1/python/multiple_recombinations.iteration_3.tre.phylip -n multiple_recombinations.iteration_4 -t /build/gubbins-2.4.1/python/multiple_recombinations.iteration_3.tre > /dev/null 2>&1 -...done. Run time: 1.17 s +...done. Run time: 7.18 s Reconstructing ancestral sequences with raxmlHPC... -raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_4.internal -t /build/gubbins-2.4.1/python/tmppy_1dwz8/multiple_recombinations.iteration_4.tre.rooted > /dev/null 2>&1 -...done. Run time: 1.23 s +raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_4.internal -t /build/gubbins-2.4.1/python/tmp4gxirj5d/multiple_recombinations.iteration_4.tre.rooted > /dev/null 2>&1 +...done. Run time: 7.68 s Reinserting gaps into the alignment... -...done. Run time: 1.24 s +...done. Run time: 7.70 s Running Gubbins to detect recombinations... -gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmppy_1dwz8/multiple_recombinations.aln -t multiple_recombinations.iteration_4.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln -...done. Run time: 1.26 s +gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmp4gxirj5d/multiple_recombinations.aln -t multiple_recombinations.iteration_4.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln +...done. Run time: 7.88 s Checking for convergence... -...done. Run time: 1.27 s +...done. Run time: 7.90 s *** Iteration 5 *** Constructing the phylogenetic tree with raxmlHPC... raxmlHPC -f d -p 1 -m GTRCAT -V -s /build/gubbins-2.4.1/python/multiple_recombinations.iteration_4.tre.phylip -n multiple_recombinations.iteration_5 -t /build/gubbins-2.4.1/python/multiple_recombinations.iteration_4.tre > /dev/null 2>&1 -...done. Run time: 1.55 s +...done. Run time: 9.09 s Reconstructing ancestral sequences with raxmlHPC... -raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_5.internal -t /build/gubbins-2.4.1/python/tmppy_1dwz8/multiple_recombinations.iteration_5.tre.rooted > /dev/null 2>&1 -...done. Run time: 1.62 s +raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_5.internal -t /build/gubbins-2.4.1/python/tmp4gxirj5d/multiple_recombinations.iteration_5.tre.rooted > /dev/null 2>&1 +...done. Run time: 9.46 s Reinserting gaps into the alignment... -...done. Run time: 1.63 s +...done. Run time: 9.47 s Running Gubbins to detect recombinations... ok @@ -2168,37 +2211,37 @@ test_reinsert_gaps_into_fasta_file (gubbins.tests.test_alignment_python_methods.TestAlignmentMethods.test_reinsert_gaps_into_fasta_file) ... ok ---------------------------------------------------------------------- -Ran 67 tests in 10.475s +Ran 67 tests in 57.769s OK -gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmppy_1dwz8/multiple_recombinations.aln -t multiple_recombinations.iteration_5.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln -...done. Run time: 1.65 s +gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmp4gxirj5d/multiple_recombinations.aln -t multiple_recombinations.iteration_5.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln +...done. Run time: 9.67 s Checking for convergence... -...done. Run time: 1.66 s +...done. Run time: 9.70 s Maximum number of iterations (5) reached. Exiting the main loop. Creating the final output... -...finished. Total run time: 1.66 s +...finished. Total run time: 9.71 s --- Gubbins 2.4.1 --- Checking dependencies... -...done. Run time: 0.00 s +...done. Run time: 0.03 s Checking input files... -...done. Run time: 0.00 s +...done. Run time: 0.03 s Filtering input alignment... -...done. Run time: 0.01 s +...done. Run time: 0.03 s Running Gubbins to detect SNPs... -gubbins /build/gubbins-2.4.1/python/tmpokvpx6vk/multiple_recombinations.aln -...done. Run time: 0.02 s +gubbins /build/gubbins-2.4.1/python/tmph3s7thlr/multiple_recombinations.aln +...done. Run time: 0.21 s Entering the main loop. @@ -2206,107 +2249,107 @@ Constructing the phylogenetic tree with raxmlHPC... raxmlHPC -f d -p 1 -m GTRCAT -V -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_1 > /dev/null 2>&1 -...done. Run time: 0.29 s +...done. Run time: 1.39 s Reconstructing ancestral sequences with raxmlHPC... -raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_1.internal -t /build/gubbins-2.4.1/python/tmpokvpx6vk/multiple_recombinations.iteration_1.tre.rooted > /dev/null 2>&1 -...done. Run time: 0.37 s +raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_1.internal -t /build/gubbins-2.4.1/python/tmph3s7thlr/multiple_recombinations.iteration_1.tre.rooted > /dev/null 2>&1 +...done. Run time: 1.95 s Reinserting gaps into the alignment... -...done. Run time: 0.37 s +...done. Run time: 1.96 s Running Gubbins to detect recombinations... -gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpokvpx6vk/multiple_recombinations.aln -t multiple_recombinations.iteration_1.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln -...done. Run time: 0.40 s +gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmph3s7thlr/multiple_recombinations.aln -t multiple_recombinations.iteration_1.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln +...done. Run time: 2.16 s Checking for convergence... -...done. Run time: 0.40 s +...done. Run time: 2.16 s *** Iteration 2 *** Constructing the phylogenetic tree with raxmlHPC... raxmlHPC -f d -p 1 -m GTRCAT -V -s /build/gubbins-2.4.1/python/multiple_recombinations.iteration_1.tre.phylip -n multiple_recombinations.iteration_2 -t /build/gubbins-2.4.1/python/multiple_recombinations.iteration_1.tre > /dev/null 2>&1 -...done. Run time: 0.56 s +...done. Run time: 2.92 s Reconstructing ancestral sequences with raxmlHPC... -raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_2.internal -t /build/gubbins-2.4.1/python/tmpokvpx6vk/multiple_recombinations.iteration_2.tre.rooted > /dev/null 2>&1 -...done. Run time: 0.72 s +raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_2.internal -t /build/gubbins-2.4.1/python/tmph3s7thlr/multiple_recombinations.iteration_2.tre.rooted > /dev/null 2>&1 +...done. Run time: 3.77 s Reinserting gaps into the alignment... -...done. Run time: 0.72 s +...done. Run time: 3.78 s Running Gubbins to detect recombinations... -gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpokvpx6vk/multiple_recombinations.aln -t multiple_recombinations.iteration_2.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln -...done. Run time: 0.74 s +gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmph3s7thlr/multiple_recombinations.aln -t multiple_recombinations.iteration_2.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln +...done. Run time: 3.98 s Checking for convergence... -...done. Run time: 0.75 s +...done. Run time: 3.98 s *** Iteration 3 *** Constructing the phylogenetic tree with raxmlHPC... raxmlHPC -f d -p 1 -m GTRCAT -V -s /build/gubbins-2.4.1/python/multiple_recombinations.iteration_2.tre.phylip -n multiple_recombinations.iteration_3 -t /build/gubbins-2.4.1/python/multiple_recombinations.iteration_2.tre > /dev/null 2>&1 -...done. Run time: 0.91 s +...done. Run time: 4.72 s Reconstructing ancestral sequences with raxmlHPC... -raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_3.internal -t /build/gubbins-2.4.1/python/tmpokvpx6vk/multiple_recombinations.iteration_3.tre.rooted > /dev/null 2>&1 -...done. Run time: 0.97 s +raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_3.internal -t /build/gubbins-2.4.1/python/tmph3s7thlr/multiple_recombinations.iteration_3.tre.rooted > /dev/null 2>&1 +...done. Run time: 5.33 s Reinserting gaps into the alignment... -...done. Run time: 0.97 s +...done. Run time: 5.34 s Running Gubbins to detect recombinations... -gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpokvpx6vk/multiple_recombinations.aln -t multiple_recombinations.iteration_3.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln -...done. Run time: 1.00 s +gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmph3s7thlr/multiple_recombinations.aln -t multiple_recombinations.iteration_3.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln +...done. Run time: 5.49 s Checking for convergence... -...done. Run time: 1.00 s +...done. Run time: 5.51 s *** Iteration 4 *** Constructing the phylogenetic tree with raxmlHPC... raxmlHPC -f d -p 1 -m GTRCAT -V -s /build/gubbins-2.4.1/python/multiple_recombinations.iteration_3.tre.phylip -n multiple_recombinations.iteration_4 -t /build/gubbins-2.4.1/python/multiple_recombinations.iteration_3.tre > /dev/null 2>&1 -...done. Run time: 1.27 s +...done. Run time: 6.84 s Reconstructing ancestral sequences with raxmlHPC... -raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_4.internal -t /build/gubbins-2.4.1/python/tmpokvpx6vk/multiple_recombinations.iteration_4.tre.rooted > /dev/null 2>&1 -...done. Run time: 1.33 s +raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_4.internal -t /build/gubbins-2.4.1/python/tmph3s7thlr/multiple_recombinations.iteration_4.tre.rooted > /dev/null 2>&1 +...done. Run time: 7.37 s Reinserting gaps into the alignment... -...done. Run time: 1.33 s +...done. Run time: 7.38 s Running Gubbins to detect recombinations... -gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpokvpx6vk/multiple_recombinations.aln -t multiple_recombinations.iteration_4.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln -...done. Run time: 1.36 s +gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmph3s7thlr/multiple_recombinations.aln -t multiple_recombinations.iteration_4.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln +...done. Run time: 7.58 s Checking for convergence... -...done. Run time: 1.37 s +...done. Run time: 7.61 s *** Iteration 5 *** Constructing the phylogenetic tree with raxmlHPC... raxmlHPC -f d -p 1 -m GTRCAT -V -s /build/gubbins-2.4.1/python/multiple_recombinations.iteration_4.tre.phylip -n multiple_recombinations.iteration_5 -t /build/gubbins-2.4.1/python/multiple_recombinations.iteration_4.tre > /dev/null 2>&1 -...done. Run time: 1.57 s +...done. Run time: 9.35 s Reconstructing ancestral sequences with raxmlHPC... -raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_5.internal -t /build/gubbins-2.4.1/python/tmpokvpx6vk/multiple_recombinations.iteration_5.tre.rooted > /dev/null 2>&1 -...done. Run time: 1.63 s +raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_5.internal -t /build/gubbins-2.4.1/python/tmph3s7thlr/multiple_recombinations.iteration_5.tre.rooted > /dev/null 2>&1 +...done. Run time: 9.73 s Reinserting gaps into the alignment... -...done. Run time: 1.63 s +...done. Run time: 9.75 s Running Gubbins to detect recombinations... -gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpokvpx6vk/multiple_recombinations.aln -t multiple_recombinations.iteration_5.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln -...done. Run time: 1.66 s +gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmph3s7thlr/multiple_recombinations.aln -t multiple_recombinations.iteration_5.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln +...done. Run time: 9.94 s Checking for convergence... -...done. Run time: 1.67 s +...done. Run time: 9.99 s Maximum number of iterations (5) reached. Exiting the main loop. Creating the final output... -...finished. Total run time: 1.67 s +...finished. Total run time: 10.00 s make[1]: Leaving directory '/build/gubbins-2.4.1' create-stamp debian/debhelper-build-stamp dh_prep @@ -2318,8 +2361,8 @@ Making install in src make[3]: Entering directory '/build/gubbins-2.4.1/src' make[4]: Entering directory '/build/gubbins-2.4.1/src' - /bin/mkdir -p '/build/gubbins-2.4.1/debian/gubbins/usr/lib/x86_64-linux-gnu' - /bin/bash ../libtool --mode=install /usr/bin/install -c libgubbins.la '/build/gubbins-2.4.1/debian/gubbins/usr/lib/x86_64-linux-gnu' + /usr/bin/mkdir -p '/build/gubbins-2.4.1/debian/gubbins/usr/lib/x86_64-linux-gnu' + /bin/sh ../libtool --mode=install /usr/bin/install -c libgubbins.la '/build/gubbins-2.4.1/debian/gubbins/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libgubbins.so.0.0.1 /build/gubbins-2.4.1/debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.so.0.0.1 libtool: install: (cd /build/gubbins-2.4.1/debian/gubbins/usr/lib/x86_64-linux-gnu && { ln -s -f libgubbins.so.0.0.1 libgubbins.so.0 || { rm -f libgubbins.so.0 && ln -s libgubbins.so.0.0.1 libgubbins.so.0; }; }) libtool: install: (cd /build/gubbins-2.4.1/debian/gubbins/usr/lib/x86_64-linux-gnu && { ln -s -f libgubbins.so.0.0.1 libgubbins.so || { rm -f libgubbins.so && ln -s libgubbins.so.0.0.1 libgubbins.so; }; }) @@ -2328,8 +2371,8 @@ libtool: install: chmod 644 /build/gubbins-2.4.1/debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.a libtool: install: ranlib /build/gubbins-2.4.1/debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.a libtool: warning: remember to run 'libtool --finish /usr/lib/x86_64-linux-gnu' - /bin/mkdir -p '/build/gubbins-2.4.1/debian/gubbins/usr/bin' - /bin/bash ../libtool --mode=install /usr/bin/install -c gubbins '/build/gubbins-2.4.1/debian/gubbins/usr/bin' + /usr/bin/mkdir -p '/build/gubbins-2.4.1/debian/gubbins/usr/bin' + /bin/sh ../libtool --mode=install /usr/bin/install -c gubbins '/build/gubbins-2.4.1/debian/gubbins/usr/bin' libtool: warning: 'libgubbins.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/gubbins /build/gubbins-2.4.1/debian/gubbins/usr/bin/gubbins make[4]: Nothing to be done for 'install-data-am'. @@ -2464,16 +2507,16 @@ dh_strip -a dh_makeshlibs -a dh_shlibdeps -a -dpkg-shlibdeps: warning: symbol gzread used by debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzclose used by debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.so.0.0.1 found in none of the libraries +dpkg-shlibdeps: warning: symbol gzread used by debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzopen used by debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/gubbins/usr/lib/gubbins/gubbins was not linked against libz.so.1 (it uses none of the library's symbols) dh_installdeb dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'gubbins-dbgsym' in '../gubbins-dbgsym_2.4.1-5_amd64.deb'. dpkg-deb: building package 'gubbins' in '../gubbins_2.4.1-5_amd64.deb'. +dpkg-deb: building package 'gubbins-dbgsym' in '../gubbins-dbgsym_2.4.1-5_amd64.deb'. dpkg-genbuildinfo --build=binary -O../gubbins_2.4.1-5_amd64.buildinfo dpkg-genchanges --build=binary -O../gubbins_2.4.1-5_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -2481,12 +2524,14 @@ 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/2321909/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2321909/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/3484544 and its subdirectories -I: Current time: Fri May 17 23:54:06 -12 2024 -I: pbuilder-time-stamp: 1716033246 +I: removing directory /srv/workspace/pbuilder/2321909 and its subdirectories +I: Current time: Sun Apr 16 19:42:32 +14 2023 +I: pbuilder-time-stamp: 1681623752