Diff of the two buildlogs: -- --- b1/build.log 2023-06-04 08:05:14.278578474 +0000 +++ b2/build.log 2023-06-04 08:11:58.412896132 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Jun 3 19:55:11 -12 2023 -I: pbuilder-time-stamp: 1685865311 +I: Current time: Sun Jun 4 22:05:44 +14 2023 +I: pbuilder-time-stamp: 1685865944 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 [./libbpp-popgen_2.4.1.orig.tar.gz] I: copying [./libbpp-popgen_2.4.1-8.debian.tar.xz] I: Extracting source -gpgv: Signature made Sat Nov 26 09:16:55 2022 -12 +gpgv: Signature made Sun Nov 27 11:16:55 2022 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -28,135 +28,167 @@ dpkg-source: info: applying unforce-cxxflags.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/11475/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3318/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 Jun 4 22:06 /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/3318/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3318/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='ddbcb112596e412d810c7b75c40b0992' - 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='11475' - PS1='# ' - PS2='> ' + INVOCATION_ID=a0d89e540b524aaf97330d2f08d13e6c + 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=3318 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.iAoYLxxv/pbuilderrc_4P2U --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.iAoYLxxv/b1 --logfile b1/build.log libbpp-popgen_2.4.1-8.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.iAoYLxxv/pbuilderrc_Irub --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.iAoYLxxv/b2 --logfile b2/build.log --extrapackages usrmerge libbpp-popgen_2.4.1-8.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/11475/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 Jun 4 22:06 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/3318/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -253,7 +285,7 @@ Get: 51 http://deb.debian.org/debian bookworm/main armhf libbpp-core-dev armhf 2.4.1-9 [943 kB] Get: 52 http://deb.debian.org/debian bookworm/main armhf libbpp-seq12 armhf 2.4.1-9 [420 kB] Get: 53 http://deb.debian.org/debian bookworm/main armhf libbpp-seq-dev armhf 2.4.1-9 [733 kB] -Fetched 29.6 MB in 4s (8370 kB/s) +Fetched 29.6 MB in 13s (2314 kB/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 ... 19324 files and directories currently installed.) @@ -479,8 +511,19 @@ 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/libbpp-popgen-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 > ../libbpp-popgen_2.4.1-8_source.changes +I: user script /srv/workspace/pbuilder/3318/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/3318/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/libbpp-popgen-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 > ../libbpp-popgen_2.4.1-8_source.changes dpkg-buildpackage: info: source package libbpp-popgen dpkg-buildpackage: info: source version 2.4.1-8 dpkg-buildpackage: info: source distribution unstable @@ -531,72 +574,78 @@ -- Build files have been written to: /build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf 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/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/build/libbpp-popgen-2.4.1 -B/build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf/CMakeFiles /build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf' make -f src/CMakeFiles/bpp-popgen-static.dir/build.make src/CMakeFiles/bpp-popgen-static.dir/depend -make -f src/CMakeFiles/bpp-popgen-shared.dir/build.make src/CMakeFiles/bpp-popgen-shared.dir/depend make[3]: Entering directory '/build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf' +make -f src/CMakeFiles/bpp-popgen-shared.dir/build.make src/CMakeFiles/bpp-popgen-shared.dir/depend cd /build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libbpp-popgen-2.4.1 /build/libbpp-popgen-2.4.1/src /build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf /build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf/src /build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf/src/CMakeFiles/bpp-popgen-static.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf' cd /build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libbpp-popgen-2.4.1 /build/libbpp-popgen-2.4.1/src /build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf /build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf/src /build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf/src/CMakeFiles/bpp-popgen-shared.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf' -make[3]: Leaving directory '/build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf' make -f src/CMakeFiles/bpp-popgen-static.dir/build.make src/CMakeFiles/bpp-popgen-static.dir/build +make[3]: Leaving directory '/build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf' make -f src/CMakeFiles/bpp-popgen-shared.dir/build.make src/CMakeFiles/bpp-popgen-shared.dir/build make[3]: Entering directory '/build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf' -[ 4%] Building CXX object src/CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/BasicAlleleInfo.cpp.o -[ 4%] Building CXX object src/CMakeFiles/bpp-popgen-static.dir/Bpp/PopGen/BiAlleleMonolocusGenotype.cpp.o -[ 4%] Building CXX object src/CMakeFiles/bpp-popgen-static.dir/Bpp/PopGen/BasicAlleleInfo.cpp.o -cd /build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-popgen-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-popgen-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-popgen-static.dir/Bpp/PopGen/BiAlleleMonolocusGenotype.cpp.o -MF CMakeFiles/bpp-popgen-static.dir/Bpp/PopGen/BiAlleleMonolocusGenotype.cpp.o.d -o CMakeFiles/bpp-popgen-static.dir/Bpp/PopGen/BiAlleleMonolocusGenotype.cpp.o -c /build/libbpp-popgen-2.4.1/src/Bpp/PopGen/BiAlleleMonolocusGenotype.cpp +[ 1%] Building CXX object src/CMakeFiles/bpp-popgen-static.dir/Bpp/PopGen/BasicAlleleInfo.cpp.o cd /build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-popgen-2.4.1/src -g -O2 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src/CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/BiAlleleMonolocusGenotype.cpp.o +cd /build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-popgen-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-popgen-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-popgen-static.dir/Bpp/PopGen/BiAlleleMonolocusGenotype.cpp.o -MF CMakeFiles/bpp-popgen-static.dir/Bpp/PopGen/BiAlleleMonolocusGenotype.cpp.o.d -o CMakeFiles/bpp-popgen-static.dir/Bpp/PopGen/BiAlleleMonolocusGenotype.cpp.o -c /build/libbpp-popgen-2.4.1/src/Bpp/PopGen/BiAlleleMonolocusGenotype.cpp cd /build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_popgen_shared_EXPORTS -I/build/libbpp-popgen-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-popgen-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT 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src/CMakeFiles/bpp-popgen-static.dir/Bpp/PopGen/DataSet/MultiSeqIndividual.cpp.o +[ 50%] Building CXX object src/CMakeFiles/bpp-popgen-static.dir/Bpp/PopGen/DataSet/Io/PopgenlibIO.cpp.o +cd /build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-popgen-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-popgen-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-popgen-static.dir/Bpp/PopGen/DataSet/Io/PopgenlibIO.cpp.o -MF CMakeFiles/bpp-popgen-static.dir/Bpp/PopGen/DataSet/Io/PopgenlibIO.cpp.o.d -o CMakeFiles/bpp-popgen-static.dir/Bpp/PopGen/DataSet/Io/PopgenlibIO.cpp.o -c /build/libbpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/PopgenlibIO.cpp +[ 51%] Building CXX object src/CMakeFiles/bpp-popgen-static.dir/Bpp/PopGen/DataSet/MultiSeqIndividual.cpp.o cd /build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-popgen-2.4.1/src -g -O2 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CMakeFiles/bpp-popgen-static.dir/Bpp/PopGen/GeneralExceptions.cpp.o.d -o CMakeFiles/bpp-popgen-static.dir/Bpp/PopGen/GeneralExceptions.cpp.o -c /build/libbpp-popgen-2.4.1/src/Bpp/PopGen/GeneralExceptions.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Io/FileTools.h:46, @@ -645,14 +686,16 @@ /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); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 56%] Building CXX object src/CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/DataSet/Io/Genetix/Genetix.cpp.o -cd /build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_popgen_shared_EXPORTS -I/build/libbpp-popgen-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-popgen-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/DataSet/Io/Genetix/Genetix.cpp.o -MF CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/DataSet/Io/Genetix/Genetix.cpp.o.d -o CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/DataSet/Io/Genetix/Genetix.cpp.o -c /build/libbpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/Genetix/Genetix.cpp -[ 58%] Building CXX object src/CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/DataSet/Io/PopgenlibIO.cpp.o -cd /build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_popgen_shared_EXPORTS -I/build/libbpp-popgen-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-popgen-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/DataSet/Io/PopgenlibIO.cpp.o -MF CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/DataSet/Io/PopgenlibIO.cpp.o.d -o CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/DataSet/Io/PopgenlibIO.cpp.o -c 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src/CMakeFiles/bpp-popgen-static.dir/Bpp/PopGen/MonoAlleleMonolocusGenotype.cpp.o -MF CMakeFiles/bpp-popgen-static.dir/Bpp/PopGen/MonoAlleleMonolocusGenotype.cpp.o.d -o CMakeFiles/bpp-popgen-static.dir/Bpp/PopGen/MonoAlleleMonolocusGenotype.cpp.o -c /build/libbpp-popgen-2.4.1/src/Bpp/PopGen/MonoAlleleMonolocusGenotype.cpp +[ 59%] Building CXX object src/CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/DataSet/Io/Genetix/Genetix.cpp.o +cd /build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_popgen_shared_EXPORTS -I/build/libbpp-popgen-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-popgen-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/DataSet/Io/Genetix/Genetix.cpp.o -MF CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/DataSet/Io/Genetix/Genetix.cpp.o.d -o CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/DataSet/Io/Genetix/Genetix.cpp.o -c /build/libbpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/Genetix/Genetix.cpp +[ 61%] Building CXX object src/CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/DataSet/Io/PopgenlibIO.cpp.o +cd /build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_popgen_shared_EXPORTS -I/build/libbpp-popgen-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-popgen-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/DataSet/Io/PopgenlibIO.cpp.o -MF CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/DataSet/Io/PopgenlibIO.cpp.o.d -o CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/DataSet/Io/PopgenlibIO.cpp.o -c /build/libbpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/PopgenlibIO.cpp [ 62%] Building CXX object src/CMakeFiles/bpp-popgen-static.dir/Bpp/PopGen/MonolocusGenotypeTools.cpp.o cd /build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-popgen-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-popgen-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-popgen-static.dir/Bpp/PopGen/MonolocusGenotypeTools.cpp.o -MF CMakeFiles/bpp-popgen-static.dir/Bpp/PopGen/MonolocusGenotypeTools.cpp.o.d -o CMakeFiles/bpp-popgen-static.dir/Bpp/PopGen/MonolocusGenotypeTools.cpp.o -c /build/libbpp-popgen-2.4.1/src/Bpp/PopGen/MonolocusGenotypeTools.cpp [ 64%] Building CXX object src/CMakeFiles/bpp-popgen-static.dir/Bpp/PopGen/MultiAlleleMonolocusGenotype.cpp.o @@ -661,10 +704,10 @@ cd /build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_popgen_shared_EXPORTS -I/build/libbpp-popgen-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-popgen-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/DataSet/MultiSeqIndividual.cpp.o -MF CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/DataSet/MultiSeqIndividual.cpp.o.d -o CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/DataSet/MultiSeqIndividual.cpp.o -c /build/libbpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/MultiSeqIndividual.cpp [ 67%] Building CXX object src/CMakeFiles/bpp-popgen-static.dir/Bpp/PopGen/MultilocusGenotype.cpp.o cd /build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-popgen-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-popgen-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-popgen-static.dir/Bpp/PopGen/MultilocusGenotype.cpp.o -MF CMakeFiles/bpp-popgen-static.dir/Bpp/PopGen/MultilocusGenotype.cpp.o.d -o CMakeFiles/bpp-popgen-static.dir/Bpp/PopGen/MultilocusGenotype.cpp.o -c /build/libbpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotype.cpp -[ 69%] Building CXX object src/CMakeFiles/bpp-popgen-static.dir/Bpp/PopGen/MultilocusGenotypeStatistics.cpp.o -cd 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/build/libbpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp [ 72%] Building CXX object src/CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/LocusInfo.cpp.o cd /build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_popgen_shared_EXPORTS -I/build/libbpp-popgen-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-popgen-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/LocusInfo.cpp.o -MF CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/LocusInfo.cpp.o.d -o CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/LocusInfo.cpp.o -c /build/libbpp-popgen-2.4.1/src/Bpp/PopGen/LocusInfo.cpp [ 74%] Building CXX object src/CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/MonoAlleleMonolocusGenotype.cpp.o @@ -673,6 +716,12 @@ cd /build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_popgen_shared_EXPORTS -I/build/libbpp-popgen-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-popgen-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/MonolocusGenotypeTools.cpp.o -MF CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/MonolocusGenotypeTools.cpp.o.d -o CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/MonolocusGenotypeTools.cpp.o -c /build/libbpp-popgen-2.4.1/src/Bpp/PopGen/MonolocusGenotypeTools.cpp [ 77%] Building CXX object src/CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/MultiAlleleMonolocusGenotype.cpp.o cd /build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_popgen_shared_EXPORTS -I/build/libbpp-popgen-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-popgen-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/MultiAlleleMonolocusGenotype.cpp.o -MF CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/MultiAlleleMonolocusGenotype.cpp.o.d -o CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/MultiAlleleMonolocusGenotype.cpp.o -c /build/libbpp-popgen-2.4.1/src/Bpp/PopGen/MultiAlleleMonolocusGenotype.cpp +[ 79%] Building CXX object src/CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/MultilocusGenotype.cpp.o +cd /build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_popgen_shared_EXPORTS -I/build/libbpp-popgen-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-popgen-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/MultilocusGenotype.cpp.o -MF CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/MultilocusGenotype.cpp.o.d -o CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/MultilocusGenotype.cpp.o -c /build/libbpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotype.cpp +[ 80%] Building CXX object src/CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/MultilocusGenotypeStatistics.cpp.o +cd /build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_popgen_shared_EXPORTS -I/build/libbpp-popgen-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-popgen-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/MultilocusGenotypeStatistics.cpp.o -MF CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/MultilocusGenotypeStatistics.cpp.o.d -o CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/MultilocusGenotypeStatistics.cpp.o -c /build/libbpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp +[ 82%] Building CXX object src/CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/PolymorphismMultiGContainer.cpp.o +cd /build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_popgen_shared_EXPORTS -I/build/libbpp-popgen-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-popgen-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/PolymorphismMultiGContainer.cpp.o -MF CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/PolymorphismMultiGContainer.cpp.o.d -o CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/PolymorphismMultiGContainer.cpp.o -c /build/libbpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismMultiGContainer.cpp In file included from /usr/include/c++/12/map:60, from /usr/include/Bpp/Utils/MapTools.h:43, from /build/libbpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp:41: @@ -699,10 +748,8 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 79%] Building CXX object src/CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/MultilocusGenotype.cpp.o -cd /build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_popgen_shared_EXPORTS -I/build/libbpp-popgen-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-popgen-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/MultilocusGenotype.cpp.o -MF CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/MultilocusGenotype.cpp.o.d -o CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/MultilocusGenotype.cpp.o -c /build/libbpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotype.cpp -[ 80%] Building CXX object src/CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/MultilocusGenotypeStatistics.cpp.o -cd /build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_popgen_shared_EXPORTS -I/build/libbpp-popgen-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-popgen-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/MultilocusGenotypeStatistics.cpp.o -MF CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/MultilocusGenotypeStatistics.cpp.o.d -o CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/MultilocusGenotypeStatistics.cpp.o -c /build/libbpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp +[ 83%] Building CXX object src/CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/PolymorphismMultiGContainerTools.cpp.o +cd /build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_popgen_shared_EXPORTS -I/build/libbpp-popgen-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-popgen-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/PolymorphismMultiGContainerTools.cpp.o -MF CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/PolymorphismMultiGContainerTools.cpp.o.d -o CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/PolymorphismMultiGContainerTools.cpp.o -c /build/libbpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismMultiGContainerTools.cpp /usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = unsigned int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: @@ -1040,8 +1087,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 82%] Building CXX object src/CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/PolymorphismMultiGContainer.cpp.o -cd /build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_popgen_shared_EXPORTS -I/build/libbpp-popgen-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-popgen-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/PolymorphismMultiGContainer.cpp.o -MF CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/PolymorphismMultiGContainer.cpp.o.d -o CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/PolymorphismMultiGContainer.cpp.o -c /build/libbpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismMultiGContainer.cpp In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = unsigned int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'static double bpp::MultilocusGenotypeStatistics::getRHMultilocusFst(const bpp::PolymorphismMultiGContainer&, std::vector, const std::set&)' at /build/libbpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp:722:34: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 @@ -1051,7 +1096,9 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 83%] Building CXX object src/CMakeFiles/bpp-popgen-static.dir/Bpp/PopGen/PolymorphismMultiGContainer.cpp.o +[ 85%] Building CXX object src/CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/PolymorphismSequenceContainer.cpp.o +cd /build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_popgen_shared_EXPORTS -I/build/libbpp-popgen-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-popgen-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/PolymorphismSequenceContainer.cpp.o -MF CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/PolymorphismSequenceContainer.cpp.o.d -o CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/PolymorphismSequenceContainer.cpp.o -c /build/libbpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismSequenceContainer.cpp +[ 87%] Building CXX object src/CMakeFiles/bpp-popgen-static.dir/Bpp/PopGen/PolymorphismMultiGContainer.cpp.o cd /build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-popgen-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-popgen-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-popgen-static.dir/Bpp/PopGen/PolymorphismMultiGContainer.cpp.o -MF CMakeFiles/bpp-popgen-static.dir/Bpp/PopGen/PolymorphismMultiGContainer.cpp.o.d -o CMakeFiles/bpp-popgen-static.dir/Bpp/PopGen/PolymorphismMultiGContainer.cpp.o -c /build/libbpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismMultiGContainer.cpp In file included from /usr/include/c++/12/map:60, from /usr/include/Bpp/Utils/MapTools.h:43, @@ -1079,12 +1126,12 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 85%] Building CXX object src/CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/PolymorphismMultiGContainerTools.cpp.o -cd /build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_popgen_shared_EXPORTS -I/build/libbpp-popgen-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-popgen-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/PolymorphismMultiGContainerTools.cpp.o -MF CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/PolymorphismMultiGContainerTools.cpp.o.d -o CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/PolymorphismMultiGContainerTools.cpp.o -c /build/libbpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismMultiGContainerTools.cpp /usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = unsigned int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 88%] Building CXX object src/CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/PolymorphismSequenceContainerTools.cpp.o +cd /build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_popgen_shared_EXPORTS -I/build/libbpp-popgen-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-popgen-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/PolymorphismSequenceContainerTools.cpp.o -MF CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/PolymorphismSequenceContainerTools.cpp.o.d -o CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/PolymorphismSequenceContainerTools.cpp.o -c /build/libbpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismSequenceContainerTools.cpp In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = unsigned int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'static std::map bpp::MultilocusGenotypeStatistics::getVarianceComponents(const bpp::PolymorphismMultiGContainer&, size_t, const std::set&)' at /build/libbpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp:497:16: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 @@ -1418,8 +1465,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 87%] Building CXX object src/CMakeFiles/bpp-popgen-static.dir/Bpp/PopGen/PolymorphismMultiGContainerTools.cpp.o -cd /build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-popgen-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-popgen-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-popgen-static.dir/Bpp/PopGen/PolymorphismMultiGContainerTools.cpp.o -MF CMakeFiles/bpp-popgen-static.dir/Bpp/PopGen/PolymorphismMultiGContainerTools.cpp.o.d -o CMakeFiles/bpp-popgen-static.dir/Bpp/PopGen/PolymorphismMultiGContainerTools.cpp.o -c /build/libbpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismMultiGContainerTools.cpp In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = unsigned int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'static double bpp::MultilocusGenotypeStatistics::getRHMultilocusFst(const bpp::PolymorphismMultiGContainer&, std::vector, const std::set&)' at /build/libbpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp:722:34: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 @@ -1429,14 +1474,12 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 88%] Building CXX object src/CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/PolymorphismSequenceContainer.cpp.o -cd /build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_popgen_shared_EXPORTS -I/build/libbpp-popgen-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-popgen-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/PolymorphismSequenceContainer.cpp.o -MF CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/PolymorphismSequenceContainer.cpp.o.d -o CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/PolymorphismSequenceContainer.cpp.o -c /build/libbpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismSequenceContainer.cpp -[ 90%] Building CXX object src/CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/PolymorphismSequenceContainerTools.cpp.o -cd /build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_popgen_shared_EXPORTS -I/build/libbpp-popgen-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-popgen-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/PolymorphismSequenceContainerTools.cpp.o -MF CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/PolymorphismSequenceContainerTools.cpp.o.d -o CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/PolymorphismSequenceContainerTools.cpp.o -c /build/libbpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismSequenceContainerTools.cpp -[ 91%] Building CXX object src/CMakeFiles/bpp-popgen-static.dir/Bpp/PopGen/PolymorphismSequenceContainer.cpp.o -cd /build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-popgen-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-popgen-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-popgen-static.dir/Bpp/PopGen/PolymorphismSequenceContainer.cpp.o -MF CMakeFiles/bpp-popgen-static.dir/Bpp/PopGen/PolymorphismSequenceContainer.cpp.o.d -o CMakeFiles/bpp-popgen-static.dir/Bpp/PopGen/PolymorphismSequenceContainer.cpp.o -c /build/libbpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismSequenceContainer.cpp -[ 93%] Building CXX object src/CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/SequenceStatistics.cpp.o +[ 90%] Building CXX object src/CMakeFiles/bpp-popgen-static.dir/Bpp/PopGen/PolymorphismMultiGContainerTools.cpp.o +cd /build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-popgen-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-popgen-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-popgen-static.dir/Bpp/PopGen/PolymorphismMultiGContainerTools.cpp.o -MF CMakeFiles/bpp-popgen-static.dir/Bpp/PopGen/PolymorphismMultiGContainerTools.cpp.o.d -o CMakeFiles/bpp-popgen-static.dir/Bpp/PopGen/PolymorphismMultiGContainerTools.cpp.o -c /build/libbpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismMultiGContainerTools.cpp +[ 91%] Building CXX object src/CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/SequenceStatistics.cpp.o cd /build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_popgen_shared_EXPORTS -I/build/libbpp-popgen-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-popgen-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/SequenceStatistics.cpp.o -MF CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/SequenceStatistics.cpp.o.d -o CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/SequenceStatistics.cpp.o -c /build/libbpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp +[ 93%] Building CXX object src/CMakeFiles/bpp-popgen-static.dir/Bpp/PopGen/PolymorphismSequenceContainer.cpp.o +cd /build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-popgen-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-popgen-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-popgen-static.dir/Bpp/PopGen/PolymorphismSequenceContainer.cpp.o -MF CMakeFiles/bpp-popgen-static.dir/Bpp/PopGen/PolymorphismSequenceContainer.cpp.o.d -o CMakeFiles/bpp-popgen-static.dir/Bpp/PopGen/PolymorphismSequenceContainer.cpp.o -c /build/libbpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismSequenceContainer.cpp [ 95%] Building CXX object src/CMakeFiles/bpp-popgen-static.dir/Bpp/PopGen/PolymorphismSequenceContainerTools.cpp.o cd /build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-popgen-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-popgen-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-popgen-static.dir/Bpp/PopGen/PolymorphismSequenceContainerTools.cpp.o -MF CMakeFiles/bpp-popgen-static.dir/Bpp/PopGen/PolymorphismSequenceContainerTools.cpp.o.d -o CMakeFiles/bpp-popgen-static.dir/Bpp/PopGen/PolymorphismSequenceContainerTools.cpp.o -c /build/libbpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismSequenceContainerTools.cpp [ 96%] Building CXX object src/CMakeFiles/bpp-popgen-static.dir/Bpp/PopGen/SequenceStatistics.cpp.o @@ -1872,16 +1915,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, - from /usr/include/Bpp/Seq/SymbolList.h:43, - from /usr/include/Bpp/Seq/SymbolListTools.h:43, - from /build/libbpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.h:48, - from /build/libbpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:43: -/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>:: - | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::allocator >&&>, std::tuple<>}; _Key = std::__cxx11::basic_string; _Val = std::pair, double>; _KeyOfValue = std::_Select1st, double> >; _Compare = std::less >; _Alloc = std::allocator, double> >]': /usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator' changed in GCC 7.1 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: @@ -1894,14 +1927,16 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +In file included from /usr/include/c++/12/vector:70, + from /usr/include/Bpp/Seq/Alphabet/Alphabet.h:45, + from /usr/include/Bpp/Seq/SymbolList.h:43, + from /usr/include/Bpp/Seq/SymbolListTools.h:43, + from /build/libbpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.h:48, + from /build/libbpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:43: +/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 -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'double bpp::SequenceStatistics::fstHudson92(const bpp::PolymorphismSequenceContainer&, size_t, size_t)' at /build/libbpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:975:22: -/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)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = std::__cxx11::basic_string; _Tp = double; _Compare = std::less >; _Alloc = std::allocator, double> >]', inlined from 'static double bpp::SequenceStatistics::watterson75NonSynonymous(const bpp::PolymorphismSequenceContainer&, const bpp::GeneticCode&)' at /build/libbpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:664:48: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator' changed in GCC 7.1 @@ -1920,6 +1955,8 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {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 In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = std::__cxx11::basic_string; _Tp = double; _Compare = std::less >; _Alloc = std::allocator, double> >]', inlined from 'static double bpp::SequenceStatistics::watterson75(const bpp::PolymorphismSequenceContainer&, bool, bool, bool)' at /build/libbpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:308:27: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator' changed in GCC 7.1 @@ -1929,6 +1966,12 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'double bpp::SequenceStatistics::fstHudson92(const bpp::PolymorphismSequenceContainer&, size_t, size_t)' at /build/libbpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:975:22: +/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)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/map:60, from /usr/include/Bpp/Seq/SymbolListTools.h:48: /usr/include/c++/12/bits/stl_tree.h: In member function 'std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(const_iterator, const key_type&) [with _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': @@ -1992,6 +2035,9 @@ /usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 98%] Linking CXX shared library libbpp-popgen.so +cd /build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/bpp-popgen-shared.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/libbpp-popgen-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libbpp-popgen.so.8 -o libbpp-popgen.so.8.0.0 "CMakeFiles/bpp-popgen-shared.dir/Bpp/PopGen/BasicAlleleInfo.cpp.o" 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std::less, std::allocator > >::const_iterator' changed in GCC 7.1 @@ -2384,9 +2430,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -cd /build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/cmake -E cmake_symlink_library libbpp-popgen.so.8.0.0 libbpp-popgen.so.8 libbpp-popgen.so -make[3]: Leaving directory '/build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf' -[ 98%] Built target bpp-popgen-shared [100%] Linking CXX static library libbpp-popgen.a cd /build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/cmake -P CMakeFiles/bpp-popgen-static.dir/cmake_clean_target.cmake cd /build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/bpp-popgen-static.dir/link.txt --verbose=1 @@ -2401,7 +2444,7 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install - cd obj-arm-linux-gnueabihf && make -j3 install DESTDIR=/build/libbpp-popgen-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/libbpp-popgen-2.4.1/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/build/libbpp-popgen-2.4.1 -B/build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -2419,48 +2462,48 @@ -- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/lib/arm-linux-gnueabihf/libbpp-popgen.so -- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp -- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen --- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/MonoAlleleMonolocusGenotype.h --- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/PolymorphismMultiGContainer.h --- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/MonolocusGenotypeTools.h --- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/GeneralExceptions.h --- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/BiAlleleMonolocusGenotype.h --- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/MonolocusGenotype.h +-- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/SequenceStatistics.h +-- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/AlleleInfo.h -- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/PolymorphismSequenceContainer.h +-- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/MultilocusGenotype.h -- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/PolymorphismSequenceContainerTools.h --- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/AlleleInfo.h +-- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/LocusInfo.h -- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/MultilocusGenotypeStatistics.h --- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/MultiAlleleMonolocusGenotype.h --- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/SequenceStatistics.h +-- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/MonoAlleleMonolocusGenotype.h -- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/BasicAlleleInfo.h --- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/MultilocusGenotype.h +-- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/MultiAlleleMonolocusGenotype.h +-- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/PolymorphismMultiGContainer.h +-- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/MonolocusGenotypeTools.h +-- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/GeneralExceptions.h -- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/PolymorphismMultiGContainerTools.h --- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/LocusInfo.h +-- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/MonolocusGenotype.h -- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/DataSet --- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/DataSet/AnalyzedSequences.h -- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/DataSet/Locality.h --- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/DataSet/AnalyzedLoci.h +-- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/DataSet/AnalyzedSequences.h +-- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/DataSet/Individual.h -- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/DataSet/DataSet.h --- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/DataSet/Group.h -- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/DataSet/Io --- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/DataSet/Io/IDataSet.h +-- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/DataSet/Io/ODataSet.h -- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/DataSet/Io/AbstractIDataSet.h --- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/DataSet/Io/Genepop --- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/DataSet/Io/Genepop/Genepop.h +-- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/DataSet/Io/IDataSet.h +-- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/DataSet/Io/PopgenlibIO.h +-- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/DataSet/Io/IODataSet.h -- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/DataSet/Io/AbstractODataSet.h -- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/DataSet/Io/Genetix -- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/DataSet/Io/Genetix/Genetix.h --- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/DataSet/Io/IODataSet.h --- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/DataSet/Io/GeneMapper --- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/DataSet/Io/GeneMapper/GeneMapperCsvExport.h --- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/DataSet/Io/ODataSet.h -- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/DataSet/Io/Darwin --- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/DataSet/Io/Darwin/DarwinDon.h -- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/DataSet/Io/Darwin/DarwinVarSingle.h --- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/DataSet/Io/PopgenlibIO.h --- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/DataSet/Individual.h +-- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/DataSet/Io/Darwin/DarwinDon.h +-- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/DataSet/Io/GeneMapper +-- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/DataSet/Io/GeneMapper/GeneMapperCsvExport.h +-- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/DataSet/Io/Genepop +-- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/DataSet/Io/Genepop/Genepop.h -- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/DataSet/DataSetTools.h --- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/DataSet/Date.h +-- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/DataSet/Group.h -- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/DataSet/MultiSeqIndividual.h +-- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/DataSet/AnalyzedLoci.h +-- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/DataSet/Date.h +-- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/include/Bpp/PopGen/BiAlleleMonolocusGenotype.h -- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/lib/arm-linux-gnueabihf/cmake/bpp-popgen/bpp-popgen-targets.cmake -- Installing: /build/libbpp-popgen-2.4.1/debian/tmp/usr/lib/arm-linux-gnueabihf/cmake/bpp-popgen/bpp-popgen-targets-none.cmake make[1]: Leaving directory '/build/libbpp-popgen-2.4.1/obj-arm-linux-gnueabihf' @@ -2505,7 +2548,7 @@ dpkg-gensymbols: warning: some libraries disappeared in the symbols file: libbpp-popgen.so.8 dpkg-gensymbols: warning: the generated symbols file is empty --- debian/symbols (libbpp-popgen-dev_2.4.1-8_armhf) -+++ dpkg-gensymbolsdiXIhP 2023-06-03 20:04:42.820672181 -1200 ++++ dpkg-gensymbols9nFuAY 2023-06-04 22:11:36.519395632 +1400 @@ -1,1361 +0,0 @@ -libbpp-popgen.so.8 libbpp-popgen8 #MINVER# - _ZN3bpp10Individual11addSequenceEmRKNS_8SequenceE@Base 2.4.1 @@ -3874,8 +3917,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'libbpp-popgen-dev' in '../libbpp-popgen-dev_2.4.1-8_armhf.deb'. dpkg-deb: building package 'libbpp-popgen8' in '../libbpp-popgen8_2.4.1-8_armhf.deb'. +dpkg-deb: building package 'libbpp-popgen-dev' in '../libbpp-popgen-dev_2.4.1-8_armhf.deb'. dpkg-deb: building package 'libbpp-popgen8-dbgsym' in '../libbpp-popgen8-dbgsym_2.4.1-8_armhf.deb'. dpkg-genbuildinfo --build=binary -O../libbpp-popgen_2.4.1-8_armhf.buildinfo dpkg-genchanges --build=binary -O../libbpp-popgen_2.4.1-8_armhf.changes @@ -3884,12 +3927,14 @@ 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/3318/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3318/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/11475 and its subdirectories -I: Current time: Sat Jun 3 20:05:09 -12 2023 -I: pbuilder-time-stamp: 1685865909 +I: removing directory /srv/workspace/pbuilder/3318 and its subdirectories +I: Current time: Sun Jun 4 22:11:49 +14 2023 +I: pbuilder-time-stamp: 1685866309