Diff of the two buildlogs: -- --- b1/build.log 2023-05-19 23:24:18.581022163 +0000 +++ b2/build.log 2023-05-19 23:28:02.719158016 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri May 19 11:18:36 -12 2023 -I: pbuilder-time-stamp: 1684538316 +I: Current time: Sat May 20 13:24:26 +14 2023 +I: pbuilder-time-stamp: 1684538666 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 [./bppsuite_2.4.1.orig.tar.gz] I: copying [./bppsuite_2.4.1-6.debian.tar.xz] I: Extracting source -gpgv: Signature made Tue Jan 10 06:12:35 2023 -12 +gpgv: Signature made Wed Jan 11 08:12:35 2023 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -26,135 +26,167 @@ dpkg-source: info: unpacking bppsuite_2.4.1-6.debian.tar.xz I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/26617/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/19176/tmp/hooks/D01_modify_environment starting +debug: Running on jtx1c. +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 May 20 13:24 /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/19176/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/19176/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='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='armhf' + 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]="arm-unknown-linux-gnueabihf") + 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=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='678a5428ee004d18a8150fe101300539' - 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='26617' - PS1='# ' - PS2='> ' + INVOCATION_ID=9ced1f32d0c144a7b0ee651068326fcb + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + 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=19176 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.r6saZbFE/pbuilderrc_qaUI --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.r6saZbFE/b1 --logfile b1/build.log bppsuite_2.4.1-6.dsc' - SUDO_GID='112' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + 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.r6saZbFE/pbuilderrc_2Ov4 --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.r6saZbFE/b2 --logfile b2/build.log --extrapackages usrmerge bppsuite_2.4.1-6.dsc' + SUDO_GID=114 + SUDO_UID=108 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux virt32b 5.10.0-23-armmp-lpae #1 SMP Debian 5.10.179-1 (2023-05-12) armv7l GNU/Linux + Linux i-capture-the-hostname 5.10.0-23-arm64 #1 SMP Debian 5.10.179-1 (2023-05-12) aarch64 GNU/Linux I: ls -l /bin total 5072 - -rwxr-xr-x 1 root root 838488 Apr 23 09:24 bash - -rwxr-xr-x 3 root root 67144 Sep 18 2022 bunzip2 - -rwxr-xr-x 3 root root 67144 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 67144 Sep 18 2022 bzip2 - -rwxr-xr-x 1 root root 67112 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 67632 Sep 20 2022 cat - -rwxr-xr-x 1 root root 67676 Sep 20 2022 chgrp - -rwxr-xr-x 1 root root 67644 Sep 20 2022 chmod - -rwxr-xr-x 1 root root 67684 Sep 20 2022 chown - -rwxr-xr-x 1 root root 133532 Sep 20 2022 cp - -rwxr-xr-x 1 root root 132868 Jan 5 01:20 dash - -rwxr-xr-x 1 root root 133220 Sep 20 2022 date - -rwxr-xr-x 1 root root 67732 Sep 20 2022 dd - -rwxr-xr-x 1 root root 68104 Sep 20 2022 df - -rwxr-xr-x 1 root root 133632 Sep 20 2022 dir - -rwxr-xr-x 1 root root 59128 Mar 22 21:02 dmesg - lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname - -rwxr-xr-x 1 root root 67560 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep - -rwxr-xr-x 1 root root 67548 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep - -rwxr-xr-x 1 root root 55748 Mar 22 21:02 findmnt - -rwsr-xr-x 1 root root 26208 Mar 22 20:15 fusermount - -rwxr-xr-x 1 root root 128608 Jan 24 02:43 grep - -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip - -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe - -rwxr-xr-x 1 root root 64220 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 67032 Dec 19 01:33 hostname - -rwxr-xr-x 1 root root 67720 Sep 20 2022 ln - -rwxr-xr-x 1 root root 35132 Mar 22 21:51 login - -rwxr-xr-x 1 root root 133632 Sep 20 2022 ls - -rwxr-xr-x 1 root root 136808 Mar 22 21:02 lsblk - -rwxr-xr-x 1 root root 67800 Sep 20 2022 mkdir - -rwxr-xr-x 1 root root 67764 Sep 20 2022 mknod - -rwxr-xr-x 1 root root 67596 Sep 20 2022 mktemp - -rwxr-xr-x 1 root root 38504 Mar 22 21:02 more - -rwsr-xr-x 1 root root 38496 Mar 22 21:02 mount - -rwxr-xr-x 1 root root 9824 Mar 22 21:02 mountpoint - -rwxr-xr-x 1 root root 133532 Sep 20 2022 mv - lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 67608 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Apr 23 09:24 rbash -> bash - -rwxr-xr-x 1 root root 67600 Sep 20 2022 readlink - -rwxr-xr-x 1 root root 67672 Sep 20 2022 rm - -rwxr-xr-x 1 root root 67600 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 67400 Nov 2 2022 run-parts - -rwxr-xr-x 1 root root 133372 Jan 5 07:55 sed - lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash - -rwxr-xr-x 1 root root 67584 Sep 20 2022 sleep - -rwxr-xr-x 1 root root 67644 Sep 20 2022 stty - -rwsr-xr-x 1 root root 50800 Mar 22 21:02 su - -rwxr-xr-x 1 root root 67584 Sep 20 2022 sync - -rwxr-xr-x 1 root root 336764 Apr 6 02:25 tar - -rwxr-xr-x 1 root root 67144 Nov 2 2022 tempfile - -rwxr-xr-x 1 root root 133224 Sep 20 2022 touch - -rwxr-xr-x 1 root root 67548 Sep 20 2022 true - -rwxr-xr-x 1 root root 9768 Mar 22 20:15 ulockmgr_server - -rwsr-xr-x 1 root root 22108 Mar 22 21:02 umount - -rwxr-xr-x 1 root root 67572 Sep 20 2022 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 133632 Sep 20 2022 vdir - -rwxr-xr-x 1 root root 42608 Mar 22 21:02 wdctl - lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/26617/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 838488 Apr 24 11:24 bash + -rwxr-xr-x 3 root root 67144 Sep 19 2022 bunzip2 + -rwxr-xr-x 3 root root 67144 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 67144 Sep 19 2022 bzip2 + -rwxr-xr-x 1 root root 67112 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 67632 Sep 21 2022 cat + -rwxr-xr-x 1 root root 67676 Sep 21 2022 chgrp + -rwxr-xr-x 1 root root 67644 Sep 21 2022 chmod + -rwxr-xr-x 1 root root 67684 Sep 21 2022 chown + -rwxr-xr-x 1 root root 133532 Sep 21 2022 cp + -rwxr-xr-x 1 root root 132868 Jan 6 03:20 dash + -rwxr-xr-x 1 root root 133220 Sep 21 2022 date + -rwxr-xr-x 1 root root 67732 Sep 21 2022 dd + -rwxr-xr-x 1 root root 68104 Sep 21 2022 df + -rwxr-xr-x 1 root root 133632 Sep 21 2022 dir + -rwxr-xr-x 1 root root 59128 Mar 23 23:02 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 67560 Sep 21 2022 echo + -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep + -rwxr-xr-x 1 root root 67548 Sep 21 2022 false + -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep + -rwxr-xr-x 1 root root 55748 Mar 23 23:02 findmnt + -rwsr-xr-x 1 root root 26208 Mar 23 22:15 fusermount + -rwxr-xr-x 1 root root 128608 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 64220 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 67032 Dec 20 03:33 hostname + -rwxr-xr-x 1 root root 67720 Sep 21 2022 ln + -rwxr-xr-x 1 root root 35132 Mar 23 23:51 login + -rwxr-xr-x 1 root root 133632 Sep 21 2022 ls + -rwxr-xr-x 1 root root 136808 Mar 23 23:02 lsblk + -rwxr-xr-x 1 root root 67800 Sep 21 2022 mkdir + -rwxr-xr-x 1 root root 67764 Sep 21 2022 mknod + -rwxr-xr-x 1 root root 67596 Sep 21 2022 mktemp + -rwxr-xr-x 1 root root 38504 Mar 23 23:02 more + -rwsr-xr-x 1 root root 38496 Mar 23 23:02 mount + -rwxr-xr-x 1 root root 9824 Mar 23 23:02 mountpoint + -rwxr-xr-x 1 root root 133532 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 67608 Sep 21 2022 pwd + lrwxrwxrwx 1 root root 4 Apr 24 11:24 rbash -> bash + -rwxr-xr-x 1 root root 67600 Sep 21 2022 readlink + -rwxr-xr-x 1 root root 67672 Sep 21 2022 rm + -rwxr-xr-x 1 root root 67600 Sep 21 2022 rmdir + -rwxr-xr-x 1 root root 67400 Nov 3 2022 run-parts + -rwxr-xr-x 1 root root 133372 Jan 6 09:55 sed + lrwxrwxrwx 1 root root 9 May 20 13:24 sh -> /bin/bash + -rwxr-xr-x 1 root root 67584 Sep 21 2022 sleep + -rwxr-xr-x 1 root root 67644 Sep 21 2022 stty + -rwsr-xr-x 1 root root 50800 Mar 23 23:02 su + -rwxr-xr-x 1 root root 67584 Sep 21 2022 sync + -rwxr-xr-x 1 root root 336764 Apr 7 04:25 tar + -rwxr-xr-x 1 root root 67144 Nov 3 2022 tempfile + -rwxr-xr-x 1 root root 133224 Sep 21 2022 touch + -rwxr-xr-x 1 root root 67548 Sep 21 2022 true + -rwxr-xr-x 1 root root 9768 Mar 23 22:15 ulockmgr_server + -rwsr-xr-x 1 root root 22108 Mar 23 23:02 umount + -rwxr-xr-x 1 root root 67572 Sep 21 2022 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 133632 Sep 21 2022 vdir + -rwxr-xr-x 1 root root 42608 Mar 23 23:02 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/19176/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -269,7 +301,7 @@ Get: 67 http://deb.debian.org/debian bookworm/main armhf libxml-libxml-perl armhf 2.0207+dfsg+really+2.0134-1+b1 [307 kB] Get: 68 http://deb.debian.org/debian bookworm/main armhf tex-common all 6.18 [32.5 kB] Get: 69 http://deb.debian.org/debian bookworm/main armhf texinfo armhf 6.8-6+b1 [1803 kB] -Fetched 38.1 MB in 5s (7040 kB/s) +Fetched 38.1 MB in 3s (11.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libproc2-0:armhf. (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 ... 19329 files and directories currently installed.) @@ -569,8 +601,19 @@ 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/bppsuite-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 > ../bppsuite_2.4.1-6_source.changes +I: user script /srv/workspace/pbuilder/19176/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/19176/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/bppsuite-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 > ../bppsuite_2.4.1-6_source.changes dpkg-buildpackage: info: source package bppsuite dpkg-buildpackage: info: source version 2.4.1-6 dpkg-buildpackage: info: source distribution unstable @@ -602,7 +645,7 @@ -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done --- Found /bin/gzip compression program, using file extension .gz +-- Found /usr/bin/gzip compression program, using file extension .gz -- bpp-core 4.1.0 found: -- static lib: /usr/lib/arm-linux-gnueabihf/libbpp-core.a -- shared lib: /usr/lib/arm-linux-gnueabihf/libbpp-core.so.4.1.0 @@ -634,7 +677,7 @@ -- Build files have been written to: /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf make[1]: Leaving directory '/build/bppsuite-2.4.1' dh_auto_build - cd obj-arm-linux-gnueabihf && make -j3 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-arm-linux-gnueabihf && make -j4 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/bppsuite-2.4.1/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/build/bppsuite-2.4.1 -B/build/bppsuite-2.4.1/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/CMakeFiles /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf//CMakeFiles/progress.marks @@ -643,26 +686,34 @@ make -f bppSuite/CMakeFiles/bppml.dir/build.make bppSuite/CMakeFiles/bppml.dir/depend make -f bppSuite/CMakeFiles/bppseqgen.dir/build.make bppSuite/CMakeFiles/bppseqgen.dir/depend make -f bppSuite/CMakeFiles/bppdist.dir/build.make bppSuite/CMakeFiles/bppdist.dir/depend +make -f bppSuite/CMakeFiles/bpppars.dir/build.make bppSuite/CMakeFiles/bpppars.dir/depend make[3]: Entering directory '/build/bppsuite-2.4.1/obj-arm-linux-gnueabihf' cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/bppsuite-2.4.1 /build/bppsuite-2.4.1/bppSuite /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/bppSuite /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/bppSuite/CMakeFiles/bppml.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/bppsuite-2.4.1/obj-arm-linux-gnueabihf' cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/bppsuite-2.4.1 /build/bppsuite-2.4.1/bppSuite /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/bppSuite /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/bppSuite/CMakeFiles/bppseqgen.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/bppsuite-2.4.1/obj-arm-linux-gnueabihf' cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/bppsuite-2.4.1 /build/bppsuite-2.4.1/bppSuite /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/bppSuite /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/bppSuite/CMakeFiles/bppdist.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/bppsuite-2.4.1/obj-arm-linux-gnueabihf' +cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/bppsuite-2.4.1 /build/bppsuite-2.4.1/bppSuite /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/bppSuite /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/bppSuite/CMakeFiles/bpppars.dir/DependInfo.cmake --color= +make[3]: Leaving directory '/build/bppsuite-2.4.1/obj-arm-linux-gnueabihf' +make[3]: Leaving directory '/build/bppsuite-2.4.1/obj-arm-linux-gnueabihf' make[3]: Leaving directory '/build/bppsuite-2.4.1/obj-arm-linux-gnueabihf' make[3]: Leaving directory '/build/bppsuite-2.4.1/obj-arm-linux-gnueabihf' make -f bppSuite/CMakeFiles/bppml.dir/build.make bppSuite/CMakeFiles/bppml.dir/build -make[3]: Entering directory '/build/bppsuite-2.4.1/obj-arm-linux-gnueabihf' make -f bppSuite/CMakeFiles/bppseqgen.dir/build.make bppSuite/CMakeFiles/bppseqgen.dir/build -make[3]: Entering directory '/build/bppsuite-2.4.1/obj-arm-linux-gnueabihf' -make[3]: Leaving directory '/build/bppsuite-2.4.1/obj-arm-linux-gnueabihf' make -f bppSuite/CMakeFiles/bppdist.dir/build.make bppSuite/CMakeFiles/bppdist.dir/build +make -f bppSuite/CMakeFiles/bpppars.dir/build.make bppSuite/CMakeFiles/bpppars.dir/build make[3]: Entering directory '/build/bppsuite-2.4.1/obj-arm-linux-gnueabihf' -[ 2%] Building CXX object bppSuite/CMakeFiles/bppml.dir/bppML.cpp.o -cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/bppSuite && /usr/bin/c++ -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -O2 -g -DNDEBUG -fPIE -MD -MT bppSuite/CMakeFiles/bppml.dir/bppML.cpp.o -MF CMakeFiles/bppml.dir/bppML.cpp.o.d -o CMakeFiles/bppml.dir/bppML.cpp.o -c /build/bppsuite-2.4.1/bppSuite/bppML.cpp -[ 7%] Building CXX object bppSuite/CMakeFiles/bppdist.dir/bppDist.cpp.o +make[3]: Entering directory '/build/bppsuite-2.4.1/obj-arm-linux-gnueabihf' +make[3]: Entering directory '/build/bppsuite-2.4.1/obj-arm-linux-gnueabihf' +make[3]: Entering directory '/build/bppsuite-2.4.1/obj-arm-linux-gnueabihf' +[ 7%] Building CXX object bppSuite/CMakeFiles/bpppars.dir/bppPars.cpp.o +[ 7%] Building CXX object bppSuite/CMakeFiles/bppml.dir/bppML.cpp.o [ 7%] Building CXX object bppSuite/CMakeFiles/bppseqgen.dir/bppSeqGen.cpp.o cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/bppSuite && /usr/bin/c++ -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -O2 -g -DNDEBUG -fPIE -MD -MT bppSuite/CMakeFiles/bppseqgen.dir/bppSeqGen.cpp.o -MF CMakeFiles/bppseqgen.dir/bppSeqGen.cpp.o.d -o CMakeFiles/bppseqgen.dir/bppSeqGen.cpp.o -c /build/bppsuite-2.4.1/bppSuite/bppSeqGen.cpp +cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/bppSuite && /usr/bin/c++ -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -O2 -g -DNDEBUG -fPIE -MD -MT bppSuite/CMakeFiles/bppml.dir/bppML.cpp.o -MF CMakeFiles/bppml.dir/bppML.cpp.o.d -o CMakeFiles/bppml.dir/bppML.cpp.o -c /build/bppsuite-2.4.1/bppSuite/bppML.cpp +cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/bppSuite && /usr/bin/c++ -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -O2 -g -DNDEBUG -fPIE -MD -MT bppSuite/CMakeFiles/bpppars.dir/bppPars.cpp.o -MF CMakeFiles/bpppars.dir/bppPars.cpp.o.d -o CMakeFiles/bpppars.dir/bppPars.cpp.o -c /build/bppsuite-2.4.1/bppSuite/bppPars.cpp +[ 10%] Building CXX object bppSuite/CMakeFiles/bppdist.dir/bppDist.cpp.o cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/bppSuite && /usr/bin/c++ -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -O2 -g -DNDEBUG -fPIE -MD -MT bppSuite/CMakeFiles/bppdist.dir/bppDist.cpp.o -MF CMakeFiles/bppdist.dir/bppDist.cpp.o.d -o CMakeFiles/bppdist.dir/bppDist.cpp.o -c /build/bppsuite-2.4.1/bppSuite/bppDist.cpp In file included from /usr/include/c++/12/vector:64, from /usr/include/Bpp/Io/FileTools.h:46, @@ -683,11 +734,38 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:70, + from /usr/include/Bpp/Io/FileTools.h:46, + from /usr/include/Bpp/App/ApplicationTools.h:44, + from /build/bppsuite-2.4.1/bppSuite/bppPars.cpp:51: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'std::vector > bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /usr/include/Bpp/Phyl/TreeTemplate.h:351:69: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void readTreesCoaSim(std::ifstream&, std::vector&, std::vector >&)' at /build/bppsuite-2.4.1/bppSuite/bppSeqGen.cpp:171:18: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 13%] Linking CXX executable bpppars +cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/bppSuite && /usr/bin/cmake -E cmake_link_script CMakeFiles/bpppars.dir/link.txt --verbose=1 +/usr/bin/c++ -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/bpppars.dir/bppPars.cpp.o -o bpppars /usr/lib/arm-linux-gnueabihf/libbpp-phyl.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-popgen.so.8.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-seq.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.4.1.0 +make[3]: Leaving directory '/build/bppsuite-2.4.1/obj-arm-linux-gnueabihf' +[ 13%] Built target bpppars +make -f bppSuite/CMakeFiles/bppseqman.dir/build.make bppSuite/CMakeFiles/bppseqman.dir/depend +make[3]: Entering directory '/build/bppsuite-2.4.1/obj-arm-linux-gnueabihf' +cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/bppsuite-2.4.1 /build/bppsuite-2.4.1/bppSuite /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/bppSuite /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/bppSuite/CMakeFiles/bppseqman.dir/DependInfo.cmake --color= +make[3]: Leaving directory '/build/bppsuite-2.4.1/obj-arm-linux-gnueabihf' +make -f bppSuite/CMakeFiles/bppseqman.dir/build.make bppSuite/CMakeFiles/bppseqman.dir/build +make[3]: Entering directory '/build/bppsuite-2.4.1/obj-arm-linux-gnueabihf' +[ 15%] Building CXX object bppSuite/CMakeFiles/bppseqman.dir/bppSeqMan.cpp.o +cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/bppSuite && /usr/bin/c++ -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -O2 -g -DNDEBUG -fPIE -MD -MT bppSuite/CMakeFiles/bppseqman.dir/bppSeqMan.cpp.o -MF CMakeFiles/bppseqman.dir/bppSeqMan.cpp.o.d -o CMakeFiles/bppseqman.dir/bppSeqMan.cpp.o -c /build/bppsuite-2.4.1/bppSuite/bppSeqMan.cpp /build/bppsuite-2.4.1/bppSuite/bppSeqGen.cpp: In function 'int main(int, char**)': /build/bppsuite-2.4.1/bppSuite/bppSeqGen.cpp:550:20: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 550 | tmpRates = vector(rates.begin() + previousPos, rates.begin() + currentPos); @@ -725,72 +803,58 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 10%] Linking CXX executable bppseqgen +[ 18%] Linking CXX executable bppseqgen cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/bppSuite && /usr/bin/cmake -E cmake_link_script CMakeFiles/bppseqgen.dir/link.txt --verbose=1 /usr/bin/c++ -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/bppseqgen.dir/bppSeqGen.cpp.o -o bppseqgen /usr/lib/arm-linux-gnueabihf/libbpp-phyl.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-popgen.so.8.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-seq.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.4.1.0 -[ 13%] Linking CXX executable bppdist -cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/bppSuite && /usr/bin/cmake -E cmake_link_script CMakeFiles/bppdist.dir/link.txt --verbose=1 -/usr/bin/c++ -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/bppdist.dir/bppDist.cpp.o -o bppdist /usr/lib/arm-linux-gnueabihf/libbpp-phyl.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-popgen.so.8.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-seq.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.4.1.0 make[3]: Leaving directory '/build/bppsuite-2.4.1/obj-arm-linux-gnueabihf' -[ 13%] Built target bppseqgen -make -f bppSuite/CMakeFiles/bpppars.dir/build.make bppSuite/CMakeFiles/bpppars.dir/depend +[ 18%] Built target bppseqgen +make -f bppSuite/CMakeFiles/bppconsense.dir/build.make bppSuite/CMakeFiles/bppconsense.dir/depend make[3]: Entering directory '/build/bppsuite-2.4.1/obj-arm-linux-gnueabihf' -cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/bppsuite-2.4.1 /build/bppsuite-2.4.1/bppSuite /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/bppSuite /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/bppSuite/CMakeFiles/bpppars.dir/DependInfo.cmake --color= +cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/bppsuite-2.4.1 /build/bppsuite-2.4.1/bppSuite /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/bppSuite /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/bppSuite/CMakeFiles/bppconsense.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/bppsuite-2.4.1/obj-arm-linux-gnueabihf' -make -f bppSuite/CMakeFiles/bpppars.dir/build.make bppSuite/CMakeFiles/bpppars.dir/build +make -f bppSuite/CMakeFiles/bppconsense.dir/build.make bppSuite/CMakeFiles/bppconsense.dir/build make[3]: Entering directory '/build/bppsuite-2.4.1/obj-arm-linux-gnueabihf' -[ 15%] Building CXX object bppSuite/CMakeFiles/bpppars.dir/bppPars.cpp.o -cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/bppSuite && /usr/bin/c++ -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -O2 -g -DNDEBUG -fPIE -MD -MT bppSuite/CMakeFiles/bpppars.dir/bppPars.cpp.o -MF CMakeFiles/bpppars.dir/bppPars.cpp.o.d -o CMakeFiles/bpppars.dir/bppPars.cpp.o -c /build/bppsuite-2.4.1/bppSuite/bppPars.cpp +[ 21%] Building CXX object bppSuite/CMakeFiles/bppconsense.dir/bppConsense.cpp.o +cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/bppSuite && /usr/bin/c++ -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -O2 -g -DNDEBUG -fPIE -MD -MT bppSuite/CMakeFiles/bppconsense.dir/bppConsense.cpp.o -MF CMakeFiles/bppconsense.dir/bppConsense.cpp.o.d -o CMakeFiles/bppconsense.dir/bppConsense.cpp.o -c /build/bppsuite-2.4.1/bppSuite/bppConsense.cpp +[ 23%] Linking CXX executable bppdist +cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/bppSuite && /usr/bin/cmake -E cmake_link_script CMakeFiles/bppdist.dir/link.txt --verbose=1 +/usr/bin/c++ -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/bppdist.dir/bppDist.cpp.o -o bppdist /usr/lib/arm-linux-gnueabihf/libbpp-phyl.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-popgen.so.8.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-seq.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.4.1.0 make[3]: Leaving directory '/build/bppsuite-2.4.1/obj-arm-linux-gnueabihf' -[ 15%] Built target bppdist -make -f bppSuite/CMakeFiles/bppseqman.dir/build.make bppSuite/CMakeFiles/bppseqman.dir/depend +[ 23%] Built target bppdist +make -f bppSuite/CMakeFiles/bppancestor.dir/build.make bppSuite/CMakeFiles/bppancestor.dir/depend make[3]: Entering directory '/build/bppsuite-2.4.1/obj-arm-linux-gnueabihf' -cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/bppsuite-2.4.1 /build/bppsuite-2.4.1/bppSuite /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/bppSuite /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/bppSuite/CMakeFiles/bppseqman.dir/DependInfo.cmake --color= +cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/bppsuite-2.4.1 /build/bppsuite-2.4.1/bppSuite /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/bppSuite /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/bppSuite/CMakeFiles/bppancestor.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/bppsuite-2.4.1/obj-arm-linux-gnueabihf' -make -f bppSuite/CMakeFiles/bppseqman.dir/build.make bppSuite/CMakeFiles/bppseqman.dir/build +make -f bppSuite/CMakeFiles/bppancestor.dir/build.make bppSuite/CMakeFiles/bppancestor.dir/build make[3]: Entering directory '/build/bppsuite-2.4.1/obj-arm-linux-gnueabihf' -[ 18%] Building CXX object bppSuite/CMakeFiles/bppseqman.dir/bppSeqMan.cpp.o -cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/bppSuite && /usr/bin/c++ -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -O2 -g -DNDEBUG -fPIE -MD -MT bppSuite/CMakeFiles/bppseqman.dir/bppSeqMan.cpp.o -MF CMakeFiles/bppseqman.dir/bppSeqMan.cpp.o.d -o CMakeFiles/bppseqman.dir/bppSeqMan.cpp.o -c /build/bppsuite-2.4.1/bppSuite/bppSeqMan.cpp -[ 21%] Linking CXX executable bppml +[ 26%] Building CXX object bppSuite/CMakeFiles/bppancestor.dir/bppAncestor.cpp.o +cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/bppSuite && /usr/bin/c++ -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -O2 -g -DNDEBUG -fPIE -MD -MT bppSuite/CMakeFiles/bppancestor.dir/bppAncestor.cpp.o -MF CMakeFiles/bppancestor.dir/bppAncestor.cpp.o.d -o CMakeFiles/bppancestor.dir/bppAncestor.cpp.o -c /build/bppsuite-2.4.1/bppSuite/bppAncestor.cpp +[ 28%] Linking CXX executable bppml cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/bppSuite && /usr/bin/cmake -E cmake_link_script CMakeFiles/bppml.dir/link.txt --verbose=1 /usr/bin/c++ -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/bppml.dir/bppML.cpp.o -o bppml /usr/lib/arm-linux-gnueabihf/libbpp-phyl.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-popgen.so.8.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-seq.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.4.1.0 make[3]: Leaving directory '/build/bppsuite-2.4.1/obj-arm-linux-gnueabihf' -[ 21%] Built target bppml -make -f bppSuite/CMakeFiles/bppconsense.dir/build.make bppSuite/CMakeFiles/bppconsense.dir/depend +[ 28%] Built target bppml +make -f bppSuite/CMakeFiles/bppmixedlikelihoods.dir/build.make bppSuite/CMakeFiles/bppmixedlikelihoods.dir/depend make[3]: Entering directory '/build/bppsuite-2.4.1/obj-arm-linux-gnueabihf' -cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/bppsuite-2.4.1 /build/bppsuite-2.4.1/bppSuite /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/bppSuite /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/bppSuite/CMakeFiles/bppconsense.dir/DependInfo.cmake --color= +cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/bppsuite-2.4.1 /build/bppsuite-2.4.1/bppSuite /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/bppSuite /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/bppSuite/CMakeFiles/bppmixedlikelihoods.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/bppsuite-2.4.1/obj-arm-linux-gnueabihf' -make 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-fPIE -MD -MT bppSuite/CMakeFiles/bppmixedlikelihoods.dir/bppMixedLikelihoods.cpp.o -MF CMakeFiles/bppmixedlikelihoods.dir/bppMixedLikelihoods.cpp.o.d -o CMakeFiles/bppmixedlikelihoods.dir/bppMixedLikelihoods.cpp.o -c /build/bppsuite-2.4.1/bppSuite/bppMixedLikelihoods.cpp +[ 34%] Linking CXX executable bppseqman cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/bppSuite && /usr/bin/cmake -E cmake_link_script CMakeFiles/bppseqman.dir/link.txt --verbose=1 /usr/bin/c++ -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/bppseqman.dir/bppSeqMan.cpp.o -o bppseqman /usr/lib/arm-linux-gnueabihf/libbpp-phyl.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-popgen.so.8.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-seq.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.4.1.0 make[3]: Leaving directory '/build/bppsuite-2.4.1/obj-arm-linux-gnueabihf' -[ 26%] Built target bppseqman -make -f bppSuite/CMakeFiles/bppancestor.dir/build.make 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'/build/bppsuite-2.4.1/obj-arm-linux-gnueabihf' -make -f bppSuite/CMakeFiles/bppancestor.dir/build.make bppSuite/CMakeFiles/bppancestor.dir/build +make -f bppSuite/CMakeFiles/bppreroot.dir/build.make bppSuite/CMakeFiles/bppreroot.dir/build make[3]: Entering directory '/build/bppsuite-2.4.1/obj-arm-linux-gnueabihf' -[ 28%] Building CXX object bppSuite/CMakeFiles/bppancestor.dir/bppAncestor.cpp.o -cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/bppSuite && /usr/bin/c++ -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -O2 -g -DNDEBUG -fPIE -MD -MT bppSuite/CMakeFiles/bppancestor.dir/bppAncestor.cpp.o -MF CMakeFiles/bppancestor.dir/bppAncestor.cpp.o.d -o CMakeFiles/bppancestor.dir/bppAncestor.cpp.o -c /build/bppsuite-2.4.1/bppSuite/bppAncestor.cpp -In file included from /usr/include/c++/12/vector:70, - from /usr/include/Bpp/Io/FileTools.h:46, - from /usr/include/Bpp/App/ApplicationTools.h:44, - from /build/bppsuite-2.4.1/bppSuite/bppPars.cpp:51: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'std::vector > bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /usr/include/Bpp/Phyl/TreeTemplate.h:351:69: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 36%] Building CXX object bppSuite/CMakeFiles/bppreroot.dir/bppReRoot.cpp.o +cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/bppSuite && /usr/bin/c++ -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -O2 -g -DNDEBUG -fPIE -MD -MT bppSuite/CMakeFiles/bppreroot.dir/bppReRoot.cpp.o -MF CMakeFiles/bppreroot.dir/bppReRoot.cpp.o.d -o CMakeFiles/bppreroot.dir/bppReRoot.cpp.o -c /build/bppsuite-2.4.1/bppSuite/bppReRoot.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Io/FileTools.h:46, from /usr/include/Bpp/App/ApplicationTools.h:44, @@ -805,32 +869,19 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 31%] Linking CXX executable bpppars -cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/bppSuite && /usr/bin/cmake -E cmake_link_script CMakeFiles/bpppars.dir/link.txt --verbose=1 -/usr/bin/c++ -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/bpppars.dir/bppPars.cpp.o -o bpppars /usr/lib/arm-linux-gnueabihf/libbpp-phyl.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-popgen.so.8.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-seq.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.4.1.0 -[ 34%] Linking CXX executable bppconsense +[ 39%] Linking CXX executable bppconsense cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/bppSuite && /usr/bin/cmake -E cmake_link_script CMakeFiles/bppconsense.dir/link.txt --verbose=1 /usr/bin/c++ -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/bppconsense.dir/bppConsense.cpp.o -o bppconsense /usr/lib/arm-linux-gnueabihf/libbpp-phyl.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-popgen.so.8.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-seq.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.4.1.0 make[3]: Leaving directory '/build/bppsuite-2.4.1/obj-arm-linux-gnueabihf' -[ 34%] Built target bpppars -make -f bppSuite/CMakeFiles/bppmixedlikelihoods.dir/build.make 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-DNDEBUG -fPIE -MD -MT bppSuite/CMakeFiles/bppmixedlikelihoods.dir/bppMixedLikelihoods.cpp.o -MF CMakeFiles/bppmixedlikelihoods.dir/bppMixedLikelihoods.cpp.o.d -o CMakeFiles/bppmixedlikelihoods.dir/bppMixedLikelihoods.cpp.o -c /build/bppsuite-2.4.1/bppSuite/bppMixedLikelihoods.cpp -make[3]: Leaving directory '/build/bppsuite-2.4.1/obj-arm-linux-gnueabihf' -[ 36%] Built target bppconsense -make -f bppSuite/CMakeFiles/bppreroot.dir/build.make bppSuite/CMakeFiles/bppreroot.dir/depend +[ 39%] Built target bppconsense +make -f bppSuite/CMakeFiles/bpptreedraw.dir/build.make bppSuite/CMakeFiles/bpptreedraw.dir/depend make[3]: Entering directory '/build/bppsuite-2.4.1/obj-arm-linux-gnueabihf' -cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/bppsuite-2.4.1 /build/bppsuite-2.4.1/bppSuite /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/bppSuite 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-Wconversion -O2 -g -DNDEBUG -fPIE -MD -MT bppSuite/CMakeFiles/bppreroot.dir/bppReRoot.cpp.o -MF CMakeFiles/bppreroot.dir/bppReRoot.cpp.o.d -o CMakeFiles/bppreroot.dir/bppReRoot.cpp.o -c /build/bppsuite-2.4.1/bppSuite/bppReRoot.cpp +[ 42%] Building CXX object bppSuite/CMakeFiles/bpptreedraw.dir/bppTreeDraw.cpp.o +cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/bppSuite && /usr/bin/c++ -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -O2 -g -DNDEBUG -fPIE -MD -MT bppSuite/CMakeFiles/bpptreedraw.dir/bppTreeDraw.cpp.o -MF CMakeFiles/bpptreedraw.dir/bppTreeDraw.cpp.o.d -o CMakeFiles/bpptreedraw.dir/bppTreeDraw.cpp.o -c /build/bppsuite-2.4.1/bppSuite/bppTreeDraw.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Io/FileTools.h:46, from /usr/include/Bpp/App/ApplicationTools.h:44, @@ -891,99 +942,91 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 42%] Linking CXX executable bppreroot +[ 44%] Linking CXX executable bppreroot cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/bppSuite && /usr/bin/cmake -E cmake_link_script CMakeFiles/bppreroot.dir/link.txt --verbose=1 /usr/bin/c++ -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/bppreroot.dir/bppReRoot.cpp.o -o bppreroot /usr/lib/arm-linux-gnueabihf/libbpp-phyl.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-popgen.so.8.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-seq.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.4.1.0 make[3]: Leaving directory '/build/bppsuite-2.4.1/obj-arm-linux-gnueabihf' -[ 42%] Built target bppreroot -make -f bppSuite/CMakeFiles/bpptreedraw.dir/build.make bppSuite/CMakeFiles/bpptreedraw.dir/depend -make[3]: Entering directory '/build/bppsuite-2.4.1/obj-arm-linux-gnueabihf' -cd 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-c /build/bppsuite-2.4.1/bppSuite/bppTreeDraw.cpp -[ 47%] Linking CXX executable bppancestor -cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/bppSuite && /usr/bin/cmake -E cmake_link_script CMakeFiles/bppancestor.dir/link.txt --verbose=1 -/usr/bin/c++ -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/bppancestor.dir/bppAncestor.cpp.o -o bppancestor /usr/lib/arm-linux-gnueabihf/libbpp-phyl.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-popgen.so.8.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-seq.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.4.1.0 -make[3]: Leaving directory '/build/bppsuite-2.4.1/obj-arm-linux-gnueabihf' -[ 47%] Built target bppancestor +[ 44%] Built target bppreroot make -f bppSuite/CMakeFiles/bppalnscore.dir/build.make bppSuite/CMakeFiles/bppalnscore.dir/depend make[3]: Entering directory '/build/bppsuite-2.4.1/obj-arm-linux-gnueabihf' cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/bppsuite-2.4.1 /build/bppsuite-2.4.1/bppSuite /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/bppSuite /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/bppSuite/CMakeFiles/bppalnscore.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/bppsuite-2.4.1/obj-arm-linux-gnueabihf' make -f bppSuite/CMakeFiles/bppalnscore.dir/build.make bppSuite/CMakeFiles/bppalnscore.dir/build make[3]: Entering directory '/build/bppsuite-2.4.1/obj-arm-linux-gnueabihf' -[ 50%] Building CXX object bppSuite/CMakeFiles/bppalnscore.dir/bppAlnScore.cpp.o +[ 47%] Building CXX object bppSuite/CMakeFiles/bppalnscore.dir/bppAlnScore.cpp.o cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/bppSuite && /usr/bin/c++ -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -O2 -g -DNDEBUG -fPIE -MD -MT bppSuite/CMakeFiles/bppalnscore.dir/bppAlnScore.cpp.o -MF CMakeFiles/bppalnscore.dir/bppAlnScore.cpp.o.d -o CMakeFiles/bppalnscore.dir/bppAlnScore.cpp.o -c /build/bppsuite-2.4.1/bppSuite/bppAlnScore.cpp -[ 52%] Linking CXX executable bppmixedlikelihoods -cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/bppSuite && /usr/bin/cmake -E cmake_link_script CMakeFiles/bppmixedlikelihoods.dir/link.txt --verbose=1 -/usr/bin/c++ -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/bppmixedlikelihoods.dir/bppMixedLikelihoods.cpp.o -o bppmixedlikelihoods /usr/lib/arm-linux-gnueabihf/libbpp-phyl.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-popgen.so.8.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-seq.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.4.1.0 +[ 50%] Linking CXX executable bppancestor +cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/bppSuite && /usr/bin/cmake -E cmake_link_script CMakeFiles/bppancestor.dir/link.txt --verbose=1 +/usr/bin/c++ -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/bppancestor.dir/bppAncestor.cpp.o -o bppancestor /usr/lib/arm-linux-gnueabihf/libbpp-phyl.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-popgen.so.8.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-seq.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.4.1.0 make[3]: Leaving directory '/build/bppsuite-2.4.1/obj-arm-linux-gnueabihf' -[ 52%] Built target bppmixedlikelihoods +[ 50%] Built target bppancestor make -f bppSuite/CMakeFiles/bpppopstats.dir/build.make bppSuite/CMakeFiles/bpppopstats.dir/depend make[3]: Entering directory '/build/bppsuite-2.4.1/obj-arm-linux-gnueabihf' cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/bppsuite-2.4.1 /build/bppsuite-2.4.1/bppSuite /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/bppSuite /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/bppSuite/CMakeFiles/bpppopstats.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/bppsuite-2.4.1/obj-arm-linux-gnueabihf' make -f bppSuite/CMakeFiles/bpppopstats.dir/build.make bppSuite/CMakeFiles/bpppopstats.dir/build make[3]: Entering directory '/build/bppsuite-2.4.1/obj-arm-linux-gnueabihf' -[ 55%] Building CXX object bppSuite/CMakeFiles/bpppopstats.dir/bppPopStats.cpp.o +[ 52%] Building CXX object bppSuite/CMakeFiles/bpppopstats.dir/bppPopStats.cpp.o cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/bppSuite && /usr/bin/c++ -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -O2 -g -DNDEBUG -fPIE -MD -MT bppSuite/CMakeFiles/bpppopstats.dir/bppPopStats.cpp.o -MF CMakeFiles/bpppopstats.dir/bppPopStats.cpp.o.d -o CMakeFiles/bpppopstats.dir/bppPopStats.cpp.o -c /build/bppsuite-2.4.1/bppSuite/bppPopStats.cpp -[ 57%] Linking CXX executable bppalnscore -cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/bppSuite && /usr/bin/cmake -E cmake_link_script CMakeFiles/bppalnscore.dir/link.txt --verbose=1 -/usr/bin/c++ -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/bppalnscore.dir/bppAlnScore.cpp.o -o bppalnscore /usr/lib/arm-linux-gnueabihf/libbpp-phyl.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-popgen.so.8.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-seq.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.4.1.0 +[ 55%] Linking CXX executable bppmixedlikelihoods +cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/bppSuite && /usr/bin/cmake -E cmake_link_script CMakeFiles/bppmixedlikelihoods.dir/link.txt --verbose=1 +/usr/bin/c++ -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/bppmixedlikelihoods.dir/bppMixedLikelihoods.cpp.o -o bppmixedlikelihoods /usr/lib/arm-linux-gnueabihf/libbpp-phyl.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-popgen.so.8.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-seq.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.4.1.0 make[3]: Leaving directory '/build/bppsuite-2.4.1/obj-arm-linux-gnueabihf' -[ 57%] Built target bppalnscore +[ 55%] Built target bppmixedlikelihoods make -f doc/CMakeFiles/info.dir/build.make doc/CMakeFiles/info.dir/depend make[3]: Entering directory '/build/bppsuite-2.4.1/obj-arm-linux-gnueabihf' cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/bppsuite-2.4.1 /build/bppsuite-2.4.1/doc /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/doc /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/doc/CMakeFiles/info.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/bppsuite-2.4.1/obj-arm-linux-gnueabihf' make -f doc/CMakeFiles/info.dir/build.make doc/CMakeFiles/info.dir/build make[3]: Entering directory '/build/bppsuite-2.4.1/obj-arm-linux-gnueabihf' -[ 60%] Generating info page +[ 57%] Generating info page cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/doc && /usr/bin/makeinfo --no-split -o /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/doc/bppsuite.info /build/bppsuite-2.4.1/doc/bppsuite.texi -[ 63%] Compressing info page -cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/doc && /bin/gzip -c -n -9 /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/doc/bppsuite.info > /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/doc/bppsuite.info.gz +[ 60%] Compressing info page +cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/doc && /usr/bin/gzip -c -n -9 /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/doc/bppsuite.info > /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/doc/bppsuite.info.gz make[3]: Leaving directory '/build/bppsuite-2.4.1/obj-arm-linux-gnueabihf' -[ 63%] Built target info +[ 60%] Built target info make -f man/CMakeFiles/man.dir/build.make man/CMakeFiles/man.dir/depend make[3]: Entering directory '/build/bppsuite-2.4.1/obj-arm-linux-gnueabihf' cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/bppsuite-2.4.1 /build/bppsuite-2.4.1/man /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/man /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/man/CMakeFiles/man.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/bppsuite-2.4.1/obj-arm-linux-gnueabihf' make -f man/CMakeFiles/man.dir/build.make man/CMakeFiles/man.dir/build make[3]: Entering directory '/build/bppsuite-2.4.1/obj-arm-linux-gnueabihf' -[ 65%] Compressing manpage bppalnscore.1 -cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/man && /bin/gzip -c -n -9 /build/bppsuite-2.4.1/man/bppalnscore.1 > /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/man/bppalnscore.1.gz -[ 68%] Compressing manpage bppancestor.1 -cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/man && /bin/gzip -c -n -9 /build/bppsuite-2.4.1/man/bppancestor.1 > /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/man/bppancestor.1.gz -[ 71%] Compressing manpage bppconsense.1 -cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/man && /bin/gzip -c -n -9 /build/bppsuite-2.4.1/man/bppconsense.1 > /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/man/bppconsense.1.gz -[ 73%] Compressing manpage bppdist.1 -cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/man && /bin/gzip -c -n -9 /build/bppsuite-2.4.1/man/bppdist.1 > /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/man/bppdist.1.gz -[ 76%] Compressing manpage bppmixedlikelihoods.1 -cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/man && /bin/gzip -c -n -9 /build/bppsuite-2.4.1/man/bppmixedlikelihoods.1 > /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/man/bppmixedlikelihoods.1.gz -[ 78%] Compressing manpage bppml.1 -cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/man && /bin/gzip -c -n -9 /build/bppsuite-2.4.1/man/bppml.1 > /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/man/bppml.1.gz -[ 81%] Compressing manpage bpppars.1 -cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/man && /bin/gzip -c -n -9 /build/bppsuite-2.4.1/man/bpppars.1 > /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/man/bpppars.1.gz -[ 84%] Compressing manpage bpppopstats.1 -cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/man && /bin/gzip -c -n -9 /build/bppsuite-2.4.1/man/bpppopstats.1 > /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/man/bpppopstats.1.gz -[ 86%] Compressing manpage bppreroot.1 -cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/man && /bin/gzip -c -n -9 /build/bppsuite-2.4.1/man/bppreroot.1 > /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/man/bppreroot.1.gz -[ 89%] Compressing manpage bppseqgen.1 -cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/man && /bin/gzip -c -n -9 /build/bppsuite-2.4.1/man/bppseqgen.1 > /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/man/bppseqgen.1.gz -[ 92%] Compressing manpage bppseqman.1 -cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/man && /bin/gzip -c -n -9 /build/bppsuite-2.4.1/man/bppseqman.1 > /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/man/bppseqman.1.gz -[ 94%] Compressing manpage bpptreedraw.1 -cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/man && /bin/gzip -c -n -9 /build/bppsuite-2.4.1/man/bpptreedraw.1 > /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/man/bpptreedraw.1.gz +[ 63%] Compressing manpage bppalnscore.1 +cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/man && /usr/bin/gzip -c -n -9 /build/bppsuite-2.4.1/man/bppalnscore.1 > /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/man/bppalnscore.1.gz +[ 65%] Compressing manpage bppancestor.1 +cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/man && /usr/bin/gzip -c -n -9 /build/bppsuite-2.4.1/man/bppancestor.1 > /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/man/bppancestor.1.gz +[ 68%] Compressing manpage bppconsense.1 +cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/man && /usr/bin/gzip -c -n -9 /build/bppsuite-2.4.1/man/bppconsense.1 > /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/man/bppconsense.1.gz +[ 71%] Compressing manpage bppdist.1 +cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/man && /usr/bin/gzip -c -n -9 /build/bppsuite-2.4.1/man/bppdist.1 > /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/man/bppdist.1.gz +[ 73%] Compressing manpage bppmixedlikelihoods.1 +cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/man && /usr/bin/gzip -c -n -9 /build/bppsuite-2.4.1/man/bppmixedlikelihoods.1 > /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/man/bppmixedlikelihoods.1.gz +[ 76%] Compressing manpage bppml.1 +cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/man && /usr/bin/gzip -c -n -9 /build/bppsuite-2.4.1/man/bppml.1 > /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/man/bppml.1.gz +[ 78%] Compressing manpage bpppars.1 +cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/man && /usr/bin/gzip -c -n -9 /build/bppsuite-2.4.1/man/bpppars.1 > /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/man/bpppars.1.gz +[ 81%] Compressing manpage bpppopstats.1 +cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/man && /usr/bin/gzip -c -n -9 /build/bppsuite-2.4.1/man/bpppopstats.1 > /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/man/bpppopstats.1.gz +[ 84%] Compressing manpage bppreroot.1 +cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/man && /usr/bin/gzip -c -n -9 /build/bppsuite-2.4.1/man/bppreroot.1 > /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/man/bppreroot.1.gz +[ 86%] Compressing manpage bppseqgen.1 +cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/man && /usr/bin/gzip -c -n -9 /build/bppsuite-2.4.1/man/bppseqgen.1 > /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/man/bppseqgen.1.gz +[ 89%] Compressing manpage bppseqman.1 +cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/man && /usr/bin/gzip -c -n -9 /build/bppsuite-2.4.1/man/bppseqman.1 > /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/man/bppseqman.1.gz +[ 92%] Compressing manpage bpptreedraw.1 +cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/man && /usr/bin/gzip -c -n -9 /build/bppsuite-2.4.1/man/bpptreedraw.1 > /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/man/bpptreedraw.1.gz make[3]: Leaving directory '/build/bppsuite-2.4.1/obj-arm-linux-gnueabihf' -[ 94%] Built target man -[ 97%] Linking CXX executable bpptreedraw +[ 92%] Built target man +[ 94%] Linking CXX executable bpptreedraw cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/bppSuite && /usr/bin/cmake -E cmake_link_script CMakeFiles/bpptreedraw.dir/link.txt --verbose=1 /usr/bin/c++ -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/bpptreedraw.dir/bppTreeDraw.cpp.o -o bpptreedraw /usr/lib/arm-linux-gnueabihf/libbpp-phyl.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-popgen.so.8.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-seq.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.4.1.0 make[3]: Leaving directory '/build/bppsuite-2.4.1/obj-arm-linux-gnueabihf' -[ 97%] Built target bpptreedraw +[ 94%] Built target bpptreedraw +[ 97%] Linking CXX executable bppalnscore +cd /build/bppsuite-2.4.1/obj-arm-linux-gnueabihf/bppSuite && /usr/bin/cmake -E cmake_link_script CMakeFiles/bppalnscore.dir/link.txt --verbose=1 +/usr/bin/c++ -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/bppalnscore.dir/bppAlnScore.cpp.o -o bppalnscore /usr/lib/arm-linux-gnueabihf/libbpp-phyl.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-popgen.so.8.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-seq.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.4.1.0 +make[3]: Leaving directory '/build/bppsuite-2.4.1/obj-arm-linux-gnueabihf' +[ 97%] Built target bppalnscore In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Io/FileTools.h:46, from /usr/include/Bpp/App/ApplicationTools.h:44, @@ -1010,7 +1053,7 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install - cd obj-arm-linux-gnueabihf && make -j3 install DESTDIR=/build/bppsuite-2.4.1/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-arm-linux-gnueabihf && make -j4 install DESTDIR=/build/bppsuite-2.4.1/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/bppsuite-2.4.1/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/build/bppsuite-2.4.1 -B/build/bppsuite-2.4.1/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -1064,25 +1107,25 @@ dh_strip -a dh_makeshlibs -a dh_shlibdeps -a -dpkg-shlibdeps: warning: debian/bppsuite/usr/bin/bppreroot contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/bppsuite/usr/bin/bppdist contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/bppsuite/usr/bin/bppmixedlikelihoods contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/bppsuite/usr/bin/bppalnscore contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/bppsuite/usr/bin/bppseqman contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/bppsuite/usr/bin/bpptreedraw contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/bppsuite/usr/bin/bppseqgen contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/bppsuite/usr/bin/bppdist contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/bppsuite/usr/bin/bppml contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/bppsuite/usr/bin/bpppars contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/bppsuite/usr/bin/bppancestor contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/bppsuite/usr/bin/bppconsense contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/bppsuite/usr/bin/bppseqgen contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/bppsuite/usr/bin/bpppopstats contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/bppsuite/usr/bin/bppconsense contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/bppsuite/usr/bin/bpppars contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/bppsuite/usr/bin/bppalnscore contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/bppsuite/usr/bin/bppmixedlikelihoods contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/bppsuite/usr/bin/bpptreedraw contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/bppsuite/usr/bin/bppreroot contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'bppsuite' in '../bppsuite_2.4.1-6_armhf.deb'. dpkg-deb: building package 'bppsuite-dbgsym' in '../bppsuite-dbgsym_2.4.1-6_armhf.deb'. dpkg-deb: building package 'bppsuite-examples' in '../bppsuite-examples_2.4.1-6_all.deb'. +dpkg-deb: building package 'bppsuite' in '../bppsuite_2.4.1-6_armhf.deb'. dpkg-genbuildinfo --build=binary -O../bppsuite_2.4.1-6_armhf.buildinfo dpkg-genchanges --build=binary -O../bppsuite_2.4.1-6_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1090,12 +1133,14 @@ 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/19176/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/19176/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/26617 and its subdirectories -I: Current time: Fri May 19 11:24:03 -12 2023 -I: pbuilder-time-stamp: 1684538643 +I: removing directory /srv/workspace/pbuilder/19176 and its subdirectories +I: Current time: Sat May 20 13:27:31 +14 2023 +I: pbuilder-time-stamp: 1684538851