Diff of the two buildlogs: -- --- b1/build.log 2023-04-25 03:48:32.129114195 +0000 +++ b2/build.log 2023-04-25 03:51:24.537471555 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun May 26 22:02:01 -12 2024 -I: pbuilder-time-stamp: 1716804121 +I: Current time: Tue Apr 25 17:48:34 +14 2023 +I: pbuilder-time-stamp: 1682394514 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 [./phyx_1.3+ds.orig.tar.xz] I: copying [./phyx_1.3+ds-2.debian.tar.xz] I: Extracting source -gpgv: Signature made Mon Nov 14 19:03:17 2022 -12 +gpgv: Signature made Tue Nov 15 21:03:17 2022 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -30,135 +30,167 @@ dpkg-source: info: applying i386.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3355276/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1131147/tmp/hooks/D01_modify_environment starting +debug: Running on ionos1-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 25 17:48 /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/1131147/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1131147/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='8d6e0262a7f34868a936d0b886568c33' - 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='3355276' - PS1='# ' - PS2='> ' + INVOCATION_ID=dc46685b41b4450fbdfc4bcd95f88b9b + 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=1131147 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.8uJ3JqYC/pbuilderrc_DoGg --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.8uJ3JqYC/b1 --logfile b1/build.log phyx_1.3+ds-2.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.8uJ3JqYC/pbuilderrc_Eog5 --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.8uJ3JqYC/b2 --logfile b2/build.log --extrapackages usrmerge phyx_1.3+ds-2.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://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/3355276/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 25 17:48 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/1131147/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -286,7 +318,7 @@ Get: 80 http://deb.debian.org/debian bookworm/main amd64 libnlopt-dev amd64 2.7.1-4+b4 [46.5 kB] Get: 81 http://deb.debian.org/debian bookworm/main amd64 libnlopt-cxx0 amd64 2.7.1-4+b4 [201 kB] Get: 82 http://deb.debian.org/debian bookworm/main amd64 libnlopt-cxx-dev amd64 2.7.1-4+b4 [13.3 kB] -Fetched 43.7 MB in 1s (29.6 MB/s) +Fetched 43.7 MB in 1s (47.8 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.) @@ -635,8 +667,19 @@ 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/phyx-1.3+ds/ && 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 > ../phyx_1.3+ds-2_source.changes +I: user script /srv/workspace/pbuilder/1131147/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/1131147/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/phyx-1.3+ds/ && 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 > ../phyx_1.3+ds-2_source.changes dpkg-buildpackage: info: source package phyx dpkg-buildpackage: info: source version 1.3+ds-2 dpkg-buildpackage: info: source distribution unstable @@ -704,7 +747,7 @@ config.status: creating Makefile config.status: creating config.h dh_auto_build -O--sourcedirectory=src - cd src && make -j16 + cd src && make -j15 make[1]: Entering directory '/build/phyx-1.3+ds/src' g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "utils.d" -o "utils.o" "utils.cpp" g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "citations.d" -o "citations.o" "citations.cpp" @@ -723,6 +766,7 @@ g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "tree_reader.d" -o "tree_reader.o" "tree_reader.cpp" g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "tree_utils.d" -o "tree_utils.o" "tree_utils.cpp" g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "bd_sim.d" -o "bd_sim.o" "bd_sim.cpp" +g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_bd_sim.d" -o "main_bd_sim.o" "main_bd_sim.cpp" utils.cpp: In function ‘void v_mean_variance(std::vector&, double&, double&)’: utils.cpp:456:21: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 456 | std::bind2nd(std::minus(), mn)); @@ -752,7 +796,6 @@ /usr/include/c++/12/backward/binders.h:136:5: note: declared here 136 | bind1st(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_bd_sim.d" -o "main_bd_sim.o" "main_bd_sim.cpp" g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "seq_sample.d" -o "seq_sample.o" "seq_sample.cpp" g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_boot.d" -o "main_boot.o" "main_boot.cpp" g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_bp.d" -o "main_bp.o" "main_bp.cpp" @@ -795,9 +838,6 @@ g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_rmk.d" -o "main_rmk.o" "main_rmk.cpp" g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_rms.d" -o "main_rms.o" "main_rms.cpp" g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_rmt.d" -o "main_rmt.o" "main_rmt.cpp" -g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_rr.d" -o "main_rr.o" "main_rr.cpp" -g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_s2fa.d" -o "main_s2fa.o" "main_s2fa.cpp" -g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_s2nex.d" -o "main_s2nex.o" "main_s2nex.cpp" nj.cpp: In member function ‘void NJOI::CalcQ(const int&, std::vector >&, std::vector >&, std::vector >&)’: nj.cpp:69:25: warning: ‘std::binder1st<_Operation> std::bind1st(const _Operation&, const _Tp&) [with _Operation = multiplies; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 69 | std::bind1st(std::multiplies(), static_cast(NumbOfSequences - 2))); @@ -809,6 +849,9 @@ /usr/include/c++/12/backward/binders.h:136:5: note: declared here 136 | bind1st(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_rr.d" -o "main_rr.o" "main_rr.cpp" +g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_s2fa.d" -o "main_s2fa.o" "main_s2fa.cpp" +g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_s2nex.d" -o "main_s2nex.o" "main_s2nex.cpp" g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_s2phy.d" -o "main_s2phy.o" "main_s2phy.cpp" g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "rate_model.d" -o "rate_model.o" "rate_model.cpp" g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "state_reconstructor.d" -o "state_reconstructor.o" "state_reconstructor.cpp" @@ -844,14 +887,14 @@ g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxaa2cdn" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math aa2cdn.o main_aa2cdn.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-z,relro -Wl,-z,now building pxbdsim g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxbdsim" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math bd_sim.o main_bd_sim.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now -cat man/pxaa2cdn.1.in > man/pxaa2cdn.1 building pxboot g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxboot" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math seq_sample.o main_boot.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-z,relro -Wl,-z,now +cat man/pxaa2cdn.1.in > man/pxaa2cdn.1 building pxbp g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxbp" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_bp.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now -cat man/pxbdsim.1.in > man/pxbdsim.1 building pxcat g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxcat" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math concat.o main_cat.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-z,relro -Wl,-z,now +cat man/pxbdsim.1.in > man/pxbdsim.1 cat man/pxboot.1.in > man/pxboot.1 building pxclsq g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxclsq" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math clean_seq.o main_clsq.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-z,relro -Wl,-z,now @@ -860,123 +903,123 @@ cat man/pxbp.1.in > man/pxbp.1 building pxcolt g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxcolt" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math collapse_tree.o main_colt.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now +cat man/pxcat.1.in > man/pxcat.1 building pxcomp g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxcomp" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math comp_test.o main_comp.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-z,relro -Wl,-z,now -cat man/pxcat.1.in > man/pxcat.1 -building pxconsq -g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxconsq" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_consq.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-z,relro -Wl,-z,now cat man/pxclsq.1.in > man/pxclsq.1 cat man/pxcltr.1.in > man/pxcltr.1 +building pxconsq +g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxconsq" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_consq.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-z,relro -Wl,-z,now building pxfqfilt g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxfqfilt" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_fqfilt.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-z,relro -Wl,-z,now +cat man/pxcolt.1.in > man/pxcolt.1 +cat man/pxcomp.1.in > man/pxcomp.1 building pxlog g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxlog" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math log_manip.o main_log.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now -cat man/pxcolt.1.in > man/pxcolt.1 bulding pxlssq g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxlssq" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math seq_info.o main_lssq.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-z,relro -Wl,-z,now +cat man/pxconsq.1.in > man/pxconsq.1 building pxlstr g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxlstr" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math tree_info.o main_lstr.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now -cat man/pxconsq.1.in > man/pxconsq.1 +cat man/pxfqfilt.1.in > man/pxfqfilt.1 building pxmono g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxmono" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_mono.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now -cat man/pxcomp.1.in > man/pxcomp.1 +cat man/pxlog.1.in > man/pxlog.1 building pxmrca g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxmrca" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_mrca.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now building pxmrcacut g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxmrcacut" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_mrca_cut.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now -cat man/pxfqfilt.1.in > man/pxfqfilt.1 +cat man/pxlssq.1.in > man/pxlssq.1 building pxmrcaname g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxmrcaname" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_mrca_name.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now -cat man/pxlog.1.in > man/pxlog.1 -building pxnw cat man/pxlstr.1.in > man/pxlstr.1 +building pxnw g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxnw" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_nw.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-z,relro -Wl,-z,now +cat man/pxmono.1.in > man/pxmono.1 building pxpoly g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxpoly" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math polytomy.o main_poly.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now -cat man/pxlssq.1.in > man/pxlssq.1 building pxrecode g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxrecode" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math recode.o main_recode.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-z,relro -Wl,-z,now cat man/pxmrca.1.in > man/pxmrca.1 building pxrevcomp g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxrevcomp" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_revcomp.o edlib.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-z,relro -Wl,-z,now cat man/pxmrcacut.1.in > man/pxmrcacut.1 -cat man/pxmono.1.in > man/pxmono.1 building pxrls g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxrls" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math relabel.o main_rls.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now building pxupgma -g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxupgma" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math upgma.o main_upgma.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now cat man/pxmrcaname.1.in > man/pxmrcaname.1 +g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxupgma" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math upgma.o main_upgma.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now building pxrlt g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxrlt" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math relabel.o main_rlt.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now -cat man/pxpoly.1.in > man/pxpoly.1 +cat man/pxnw.1.in > man/pxnw.1 building pxnj g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxnj" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math nj.o main_nj.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now -cat man/pxnw.1.in > man/pxnw.1 +cat man/pxrecode.1.in > man/pxrecode.1 +cat man/pxrevcomp.1.in > man/pxrevcomp.1 building pxrmk g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxrmk" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_rmk.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now -cat man/pxrecode.1.in > man/pxrecode.1 building pxrms g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxrms" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_rms.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-z,relro -Wl,-z,now +cat man/pxpoly.1.in > man/pxpoly.1 building pxrmt g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxrmt" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_rmt.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now +cat man/pxrls.1.in > man/pxrls.1 cat man/pxupgma.1.in > man/pxupgma.1 building pxrr -cat man/pxrevcomp.1.in > man/pxrevcomp.1 -g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxrr" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_rr.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now building pxs2fa +g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxrr" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_rr.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxs2fa" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_s2fa.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-z,relro -Wl,-z,now -cat man/pxrls.1.in > man/pxrls.1 cat man/pxrlt.1.in > man/pxrlt.1 building pxs2nex +cat man/pxnj.1.in > man/pxnj.1 +cat man/pxrmk.1.in > man/pxrmk.1 g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxs2nex" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_s2nex.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-z,relro -Wl,-z,now building pxs2phy g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxs2phy" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_s2phy.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-z,relro -Wl,-z,now -cat man/pxrmk.1.in > man/pxrmk.1 building pxsstat g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxsstat" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math sstat.o main_sstat.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-z,relro -Wl,-z,now cat man/pxrmt.1.in > man/pxrmt.1 building pxsw -cat man/pxrms.1.in > man/pxrms.1 g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxsw" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_sw.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-z,relro -Wl,-z,now +cat man/pxrms.1.in > man/pxrms.1 +cat man/pxrr.1.in > man/pxrr.1 building pxt2new g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxt2new" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_t2new.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now -cat man/pxnj.1.in > man/pxnj.1 building pxt2nex g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxt2nex" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_t2nex.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now cat man/pxs2fa.1.in > man/pxs2fa.1 building pxtcol g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxtcol" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_tcol.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now -cat man/pxrr.1.in > man/pxrr.1 building pxtcomb g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxtcomb" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_tcomb.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now -cat man/pxs2nex.1.in > man/pxs2nex.1 +cat man/pxs2phy.1.in > man/pxs2phy.1 +cat man/pxt2nex.1.in > man/pxt2nex.1 +cat man/pxsw.1.in > man/pxsw.1 building pxtgen g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxtgen" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math tgen.o main_tgen.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now -cat man/pxs2phy.1.in > man/pxs2phy.1 building pxtlate +cat man/pxsstat.1.in > man/pxsstat.1 g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxtlate" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math tlate.o main_tlate.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-z,relro -Wl,-z,now -cat man/pxt2new.1.in > man/pxt2new.1 -cat man/pxsw.1.in > man/pxsw.1 building pxtrt g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxtrt" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_trt.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now +cat man/pxs2nex.1.in > man/pxs2nex.1 building pxtscale g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxtscale" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math tscale.o main_tscale.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now -cat man/pxsstat.1.in > man/pxsstat.1 building pxvcf2fa g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxvcf2fa" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math vcf_reader.o main_vcf2fa.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-z,relro -Wl,-z,now -cat man/pxt2nex.1.in > man/pxt2nex.1 +cat man/pxt2new.1.in > man/pxt2new.1 +cat man/pxtcol.1.in > man/pxtcol.1 building pxbdfit g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -o "pxbdfit" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math bd_fit.o main_bd_fit.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -llapack -lblas -lpthread -lm -lnlopt -larmadillo -cat man/pxtcol.1.in > man/pxtcol.1 +building pxssort +g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxssort" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_ssort.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-z,relro -Wl,-z,now cat man/pxtcomb.1.in > man/pxtcomb.1 -cat man/pxtlate.1.in > man/pxtlate.1 cat man/pxtgen.1.in > man/pxtgen.1 +cat man/pxtlate.1.in > man/pxtlate.1 +cat man/pxtrt.1.in > man/pxtrt.1 cat man/pxtscale.1.in > man/pxtscale.1 cat man/pxvcf2fa.1.in > man/pxvcf2fa.1 -cat man/pxtrt.1.in > man/pxtrt.1 cat man/pxbdfit.1.in > man/pxbdfit.1 -building pxssort -g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxssort" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_ssort.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-z,relro -Wl,-z,now cat man/pxssort.1.in > man/pxssort.1 building pxseqgen g++ -g -O2 -ffile-prefix-map=/build/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -o "pxseqgen" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_seqgen.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./rate_model.o ./state_reconstructor.o ./optimize_state_reconstructor_nlopt.o ./optimize_state_reconstructor_periods_nlopt.o ./branch_segment.o ./cont_models.o ./seq_gen.o -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -llapack -lblas -lpthread -lm -lnlopt -larmadillo @@ -1218,7 +1261,7 @@ make[1]: Entering directory '/build/phyx-1.3+ds' mkdir -p /build/phyx-1.3+ds/debian/phyx/usr/bin dh_auto_install -- PREFIX=/build/phyx-1.3+ds/debian/phyx/usr - cd src && make -j16 install DESTDIR=/build/phyx-1.3\+ds/debian/phyx AM_UPDATE_INFO_DIR=no PREFIX=/build/phyx-1.3\+ds/debian/phyx/usr + cd src && make -j15 install DESTDIR=/build/phyx-1.3\+ds/debian/phyx AM_UPDATE_INFO_DIR=no PREFIX=/build/phyx-1.3\+ds/debian/phyx/usr make[2]: Entering directory '/build/phyx-1.3+ds/src' mkdir -p /build/phyx-1.3+ds/debian/phyx/usr/bin && install -m 0755 px* /build/phyx-1.3+ds/debian/phyx/usr/bin mkdir -p /build/phyx-1.3+ds/debian/phyx/usr/share/man/man1 && install -m 0755 man/px*.1 /build/phyx-1.3+ds/debian/phyx/usr/share/man/man1 @@ -1257,12 +1300,14 @@ 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/1131147/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1131147/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/3355276 and its subdirectories -I: Current time: Sun May 26 22:11:33 -12 2024 -I: pbuilder-time-stamp: 1716804693 +I: removing directory /srv/workspace/pbuilder/1131147 and its subdirectories +I: Current time: Tue Apr 25 17:51:24 +14 2023 +I: pbuilder-time-stamp: 1682394684