Diff of the two buildlogs: -- --- b1/build.log 2023-06-01 20:55:40.249397082 +0000 +++ b2/build.log 2023-06-01 21:05:41.259079216 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Jun 1 08:35:38 -12 2023 -I: pbuilder-time-stamp: 1685651738 +I: Current time: Fri Jun 2 10:56:18 +14 2023 +I: pbuilder-time-stamp: 1685652978 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 [./sibelia_3.0.7+dfsg.orig.tar.xz] I: copying [./sibelia_3.0.7+dfsg-3.debian.tar.xz] I: Extracting source -gpgv: Signature made Mon Apr 13 20:37:29 2020 -12 +gpgv: Signature made Tue Apr 14 22:37:29 2020 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tillea@rki.de" gpgv: Can't check signature: No public key @@ -31,135 +31,167 @@ dpkg-source: info: applying 2to3.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/21764/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/28025/tmp/hooks/D01_modify_environment starting +debug: Running on virt64b. +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 2 10:56 /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/28025/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/28025/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='a25184bb74d54e2a8897648ebf3a8359' - 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='21764' - PS1='# ' - PS2='> ' + INVOCATION_ID=be1aa1b185f54314a75b49ee5a344194 + 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=28025 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.kB7WtIEI/pbuilderrc_yDyk --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.kB7WtIEI/b1 --logfile b1/build.log sibelia_3.0.7+dfsg-3.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.kB7WtIEI/pbuilderrc_mo67 --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.kB7WtIEI/b2 --logfile b2/build.log --extrapackages usrmerge sibelia_3.0.7+dfsg-3.dsc' + SUDO_GID=113 + SUDO_UID=107 + 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/21764/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 2 10:56 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/28025/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -270,7 +302,7 @@ Get: 61 http://deb.debian.org/debian bookworm/main armhf libhts-dev armhf 1.16+ds-3 [1517 kB] Get: 62 http://deb.debian.org/debian bookworm/main armhf libseqan2-dev all 2.4.0+dfsg-15 [1215 kB] Get: 63 http://deb.debian.org/debian bookworm/main armhf libtclap-dev armhf 1.2.5-1+b1 [3359 kB] -Fetched 45.1 MB in 5s (9643 kB/s) +Fetched 45.1 MB in 4s (10.9 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 ... 19324 files and directories currently installed.) @@ -536,8 +568,19 @@ 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/sibelia-3.0.7+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../sibelia_3.0.7+dfsg-3_source.changes +I: user script /srv/workspace/pbuilder/28025/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/28025/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/sibelia-3.0.7+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../sibelia_3.0.7+dfsg-3_source.changes dpkg-buildpackage: info: source package sibelia dpkg-buildpackage: info: source version 3.0.7+dfsg-3 dpkg-buildpackage: info: source distribution unstable @@ -586,24 +629,35 @@ -- Build files have been written to: /build/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf dh_auto_build -O--sourcedirectory=src - cd obj-arm-linux-gnueabihf && make -j3 "INSTALL=install --strip-program=true" VERBOSE=1 -make[1]: Entering directory '/build/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf' + cd obj-arm-linux-gnueabihf && make -j4 "INSTALL=install --strip-program=true" VERBOSE=1 +make[1]: ingresso nella directory «/build/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf» /usr/bin/cmake -S/build/sibelia-3.0.7+dfsg/src -B/build/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf/CMakeFiles /build/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all -make[2]: Entering directory '/build/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf' +make[2]: ingresso nella directory «/build/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf» make -f CMakeFiles/Sibelia.dir/build.make CMakeFiles/Sibelia.dir/depend -make[3]: Entering directory '/build/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf' +make[3]: ingresso nella directory «/build/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf» cd /build/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sibelia-3.0.7+dfsg/src /build/sibelia-3.0.7+dfsg/src /build/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf /build/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf /build/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/Sibelia.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf' +make[3]: uscita dalla directory «/build/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf» make -f CMakeFiles/Sibelia.dir/build.make CMakeFiles/Sibelia.dir/build -make[3]: Entering directory '/build/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf' -[ 5%] Building CXX object CMakeFiles/Sibelia.dir/sibelia.cpp.o +make[3]: ingresso nella directory «/build/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf» +[ 10%] Building CXX object CMakeFiles/Sibelia.dir/sibelia.cpp.o +[ 10%] Building CXX object CMakeFiles/Sibelia.dir/indexedsequence.cpp.o +[ 20%] Building CXX object CMakeFiles/Sibelia.dir/util.cpp.o +[ 20%] Building CXX object CMakeFiles/Sibelia.dir/postprocessor.cpp.o /usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/sibelia.cpp.o -MF CMakeFiles/Sibelia.dir/sibelia.cpp.o.d -o CMakeFiles/Sibelia.dir/sibelia.cpp.o -c /build/sibelia-3.0.7+dfsg/src/sibelia.cpp -[ 10%] Building CXX object CMakeFiles/Sibelia.dir/postprocessor.cpp.o /usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/postprocessor.cpp.o -MF CMakeFiles/Sibelia.dir/postprocessor.cpp.o.d -o CMakeFiles/Sibelia.dir/postprocessor.cpp.o -c /build/sibelia-3.0.7+dfsg/src/postprocessor.cpp -[ 15%] Building CXX object CMakeFiles/Sibelia.dir/indexedsequence.cpp.o /usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/indexedsequence.cpp.o -MF CMakeFiles/Sibelia.dir/indexedsequence.cpp.o.d -o CMakeFiles/Sibelia.dir/indexedsequence.cpp.o -c /build/sibelia-3.0.7+dfsg/src/indexedsequence.cpp +/usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/util.cpp.o -MF CMakeFiles/Sibelia.dir/util.cpp.o.d -o CMakeFiles/Sibelia.dir/util.cpp.o -c /build/sibelia-3.0.7+dfsg/src/util.cpp +In file included from /usr/include/boost/bind.hpp:30, + from /build/sibelia-3.0.7+dfsg/src/common.h:31, + from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:10, + from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:10, + from /build/sibelia-3.0.7+dfsg/src/util.h:10, + from /build/sibelia-3.0.7+dfsg/src/util.cpp:7: +/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/bind.hpp:30, from /build/sibelia-3.0.7+dfsg/src/common.h:31, from /build/sibelia-3.0.7+dfsg/src/fasta.h:10, @@ -622,7 +676,8 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/sibelia-3.0.7+dfsg/src/dnasequence.h:12: +In file included from /build/sibelia-3.0.7+dfsg/src/dnasequence.h:12, + from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:11: /build/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ @@ -635,6 +690,7 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:11: /build/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 37 | std::auto_ptr sequence_; | ^~~~~~~~ @@ -649,58 +705,32 @@ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ -In file included from /usr/include/boost/bind.hpp:30, - from /build/sibelia-3.0.7+dfsg/src/common.h:31, - from /build/sibelia-3.0.7+dfsg/src/fasta.h:10, - from /build/sibelia-3.0.7+dfsg/src/postprocessor.h:13, - from /build/sibelia-3.0.7+dfsg/src/sibelia.cpp:8: -/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ /build/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, - from /usr/include/tclap/SwitchArg.h:29, - from /usr/include/tclap/CmdLine.h:27, - from /build/sibelia-3.0.7+dfsg/src/sibelia.cpp:7: + from /build/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/sibelia-3.0.7+dfsg/src/dnasequence.h:12, - from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:11, - from /build/sibelia-3.0.7+dfsg/src/postprocessor.h:14: +In file included from /build/sibelia-3.0.7+dfsg/src/dnasequence.h:12: /build/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /usr/include/boost/bind.hpp:30, - from /build/sibelia-3.0.7+dfsg/src/common.h:31, - from /build/sibelia-3.0.7+dfsg/src/fasta.h:10, - from /build/sibelia-3.0.7+dfsg/src/postprocessor.h:13, - from /build/sibelia-3.0.7+dfsg/src/postprocessor.cpp:9: -/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ /build/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:11, - from /build/sibelia-3.0.7+dfsg/src/util.h:10, - from /build/sibelia-3.0.7+dfsg/src/sibelia.cpp:9: /build/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 37 | std::auto_ptr sequence_; | ^~~~~~~~ In file included from /usr/include/c++/12/memory:76, - from /usr/include/seqan/basic/test_system.h:53, - from /usr/include/seqan/basic.h:65, - from /usr/include/seqan/align.h:55, - from /build/sibelia-3.0.7+dfsg/src/postprocessor.h:10: + from /build/sibelia-3.0.7+dfsg/src/common.h:20: /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ @@ -710,15 +740,36 @@ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ -/build/sibelia-3.0.7+dfsg/src/sibelia.cpp: In function ‘int main(int, char**)’: -/build/sibelia-3.0.7+dfsg/src/sibelia.cpp:239:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 239 | std::auto_ptr finder(inRAM.isSet() ? new SyntenyFinder::BlockFinder(chrList) : new SyntenyFinder::BlockFinder(chrList, tempDir)); - | ^~~~~~~~ -/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here - 64 | template class auto_ptr; - | ^~~~~~~~ -[ 20%] Building CXX object CMakeFiles/Sibelia.dir/util.cpp.o -/usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/util.cpp.o -MF CMakeFiles/Sibelia.dir/util.cpp.o.d -o CMakeFiles/Sibelia.dir/util.cpp.o -c /build/sibelia-3.0.7+dfsg/src/util.cpp +[ 25%] Building CXX object CMakeFiles/Sibelia.dir/outputgenerator.cpp.o +/usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/outputgenerator.cpp.o -MF CMakeFiles/Sibelia.dir/outputgenerator.cpp.o.d -o CMakeFiles/Sibelia.dir/outputgenerator.cpp.o -c /build/sibelia-3.0.7+dfsg/src/outputgenerator.cpp +In file included from /usr/include/boost/bind.hpp:30, + from /build/sibelia-3.0.7+dfsg/src/common.h:31, + from /build/sibelia-3.0.7+dfsg/src/fasta.h:10, + from /build/sibelia-3.0.7+dfsg/src/postprocessor.h:13, + from /build/sibelia-3.0.7+dfsg/src/postprocessor.cpp:9: +/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/bind.hpp:30, + from /build/sibelia-3.0.7+dfsg/src/common.h:31, + from /build/sibelia-3.0.7+dfsg/src/fasta.h:10, + from /build/sibelia-3.0.7+dfsg/src/postprocessor.h:13, + from /build/sibelia-3.0.7+dfsg/src/sibelia.cpp:8: +/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +[ 30%] Building CXX object CMakeFiles/Sibelia.dir/blockfinder.cpp.o +/usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/blockfinder.cpp.o -MF CMakeFiles/Sibelia.dir/blockfinder.cpp.o.d -o CMakeFiles/Sibelia.dir/blockfinder.cpp.o -c /build/sibelia-3.0.7+dfsg/src/blockfinder.cpp +In file included from /usr/include/boost/bind.hpp:30, + from /build/sibelia-3.0.7+dfsg/src/common.h:31, + from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:10, + from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:10, + from /build/sibelia-3.0.7+dfsg/src/util.h:10, + from /build/sibelia-3.0.7+dfsg/src/outputgenerator.h:10, + from /build/sibelia-3.0.7+dfsg/src/outputgenerator.cpp:9: +/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ /build/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ @@ -744,25 +795,19 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /usr/include/boost/bind.hpp:30, - from /build/sibelia-3.0.7+dfsg/src/common.h:31, - from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:10, - from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:10, - from /build/sibelia-3.0.7+dfsg/src/util.h:10, - from /build/sibelia-3.0.7+dfsg/src/util.cpp:7: -/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ /build/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, - from /build/sibelia-3.0.7+dfsg/src/common.h:12: + from /usr/include/tclap/SwitchArg.h:29, + from /usr/include/tclap/CmdLine.h:27, + from /build/sibelia-3.0.7+dfsg/src/sibelia.cpp:7: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/sibelia-3.0.7+dfsg/src/dnasequence.h:12, - from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:11: + from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:11, + from /build/sibelia-3.0.7+dfsg/src/postprocessor.h:14: /build/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ @@ -775,12 +820,17 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:11: +In file included from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:11, + from /build/sibelia-3.0.7+dfsg/src/util.h:10, + from /build/sibelia-3.0.7+dfsg/src/sibelia.cpp:9: /build/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 37 | std::auto_ptr sequence_; | ^~~~~~~~ In file included from /usr/include/c++/12/memory:76, - from /build/sibelia-3.0.7+dfsg/src/common.h:20: + from /usr/include/seqan/basic/test_system.h:53, + from /usr/include/seqan/basic.h:65, + from /usr/include/seqan/align.h:55, + from /build/sibelia-3.0.7+dfsg/src/postprocessor.h:10: /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ @@ -790,18 +840,13 @@ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ -[ 25%] Building CXX object CMakeFiles/Sibelia.dir/outputgenerator.cpp.o -/usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/outputgenerator.cpp.o -MF CMakeFiles/Sibelia.dir/outputgenerator.cpp.o.d -o CMakeFiles/Sibelia.dir/outputgenerator.cpp.o -c /build/sibelia-3.0.7+dfsg/src/outputgenerator.cpp -In file included from /usr/include/boost/bind.hpp:30, - from /build/sibelia-3.0.7+dfsg/src/common.h:31, - from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:10, - from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:10, - from /build/sibelia-3.0.7+dfsg/src/util.h:10, - from /build/sibelia-3.0.7+dfsg/src/outputgenerator.h:10, - from /build/sibelia-3.0.7+dfsg/src/outputgenerator.cpp:9: -/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ +/build/sibelia-3.0.7+dfsg/src/sibelia.cpp: In function ‘int main(int, char**)’: +/build/sibelia-3.0.7+dfsg/src/sibelia.cpp:239:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 239 | std::auto_ptr finder(inRAM.isSet() ? new SyntenyFinder::BlockFinder(chrList) : new SyntenyFinder::BlockFinder(chrList, tempDir)); + | ^~~~~~~~ +/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here + 64 | template class auto_ptr; + | ^~~~~~~~ /build/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ @@ -839,14 +884,6 @@ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from /build/sibelia-3.0.7+dfsg/src/common.h:13: -/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 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -[ 30%] Building CXX object CMakeFiles/Sibelia.dir/blockfinder.cpp.o -/usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/blockfinder.cpp.o -MF CMakeFiles/Sibelia.dir/blockfinder.cpp.o.d -o CMakeFiles/Sibelia.dir/blockfinder.cpp.o -c /build/sibelia-3.0.7+dfsg/src/blockfinder.cpp In file included from /usr/include/boost/bind.hpp:30, from /build/sibelia-3.0.7+dfsg/src/common.h:31, from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:10, @@ -855,20 +892,6 @@ /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -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 ‘std::vector SyntenyFinder::{anonymous}::CalculateCoverage(const SyntenyFinder::ChrList&, std::vector > >::const_iterator, std::vector > >::const_iterator)’ at /build/sibelia-3.0.7+dfsg/src/outputgenerator.cpp:137:18, - inlined from ‘void SyntenyFinder::OutputGenerator::GenerateReport(const BlockList&, const std::string&) const’ at /build/sibelia-3.0.7+dfsg/src/outputgenerator.cpp:199:122: -/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 member function ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_insert_rval(const_iterator, value_type&&) [with _Tp = double; _Alloc = std::allocator]’, - inlined from ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1389:30, - inlined from ‘std::vector SyntenyFinder::{anonymous}::CalculateCoverage(const SyntenyFinder::ChrList&, std::vector > >::const_iterator, std::vector > >::const_iterator)’ at /build/sibelia-3.0.7+dfsg/src/outputgenerator.cpp:141:14, - inlined from ‘void SyntenyFinder::OutputGenerator::GenerateReport(const BlockList&, const std::string&) const’ at /build/sibelia-3.0.7+dfsg/src/outputgenerator.cpp:199:122: -/usr/include/c++/12/bits/vector.tcc:366:26: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 - 366 | _M_realloc_insert(begin() + __n, std::move(__v)); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ @@ -906,12 +929,14 @@ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ +In file included from /usr/include/c++/12/vector:70, + from /build/sibelia-3.0.7+dfsg/src/common.h:13: +/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 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ [ 35%] Building CXX object CMakeFiles/Sibelia.dir/blockinstance.cpp.o /usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/blockinstance.cpp.o -MF CMakeFiles/Sibelia.dir/blockinstance.cpp.o.d -o CMakeFiles/Sibelia.dir/blockinstance.cpp.o -c /build/sibelia-3.0.7+dfsg/src/blockinstance.cpp -[ 40%] Building CXX object CMakeFiles/Sibelia.dir/bifurcationstorage.cpp.o -/usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/bifurcationstorage.cpp.o -MF CMakeFiles/Sibelia.dir/bifurcationstorage.cpp.o.d -o CMakeFiles/Sibelia.dir/bifurcationstorage.cpp.o -c /build/sibelia-3.0.7+dfsg/src/bifurcationstorage.cpp -[ 45%] Building CXX object CMakeFiles/Sibelia.dir/bulgeremoval.cpp.o -/usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/bulgeremoval.cpp.o -MF CMakeFiles/Sibelia.dir/bulgeremoval.cpp.o.d -o CMakeFiles/Sibelia.dir/bulgeremoval.cpp.o -c /build/sibelia-3.0.7+dfsg/src/bulgeremoval.cpp In file included from /usr/include/boost/bind.hpp:30, from /build/sibelia-3.0.7+dfsg/src/common.h:31, from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:10, @@ -919,15 +944,6 @@ /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/bind.hpp:30, - from /build/sibelia-3.0.7+dfsg/src/common.h:31, - from /build/sibelia-3.0.7+dfsg/src/fasta.h:10, - from /build/sibelia-3.0.7+dfsg/src/dnasequence.h:10, - from /build/sibelia-3.0.7+dfsg/src/bifurcationstorage.h:11, - from /build/sibelia-3.0.7+dfsg/src/bifurcationstorage.cpp:7: -/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ /build/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ @@ -950,6 +966,43 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +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 ‘std::vector SyntenyFinder::{anonymous}::CalculateCoverage(const SyntenyFinder::ChrList&, std::vector > >::const_iterator, std::vector > >::const_iterator)’ at /build/sibelia-3.0.7+dfsg/src/outputgenerator.cpp:137:18, + inlined from ‘void SyntenyFinder::OutputGenerator::GenerateReport(const BlockList&, const std::string&) const’ at /build/sibelia-3.0.7+dfsg/src/outputgenerator.cpp:199:122: +/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 member function ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_insert_rval(const_iterator, value_type&&) [with _Tp = double; _Alloc = std::allocator]’, + inlined from ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1389:30, + inlined from ‘std::vector SyntenyFinder::{anonymous}::CalculateCoverage(const SyntenyFinder::ChrList&, std::vector > >::const_iterator, std::vector > >::const_iterator)’ at /build/sibelia-3.0.7+dfsg/src/outputgenerator.cpp:141:14, + inlined from ‘void SyntenyFinder::OutputGenerator::GenerateReport(const BlockList&, const std::string&) const’ at /build/sibelia-3.0.7+dfsg/src/outputgenerator.cpp:199:122: +/usr/include/c++/12/bits/vector.tcc:366:26: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 + 366 | _M_realloc_insert(begin() + __n, std::move(__v)); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 40%] Building CXX object CMakeFiles/Sibelia.dir/bifurcationstorage.cpp.o +/usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/bifurcationstorage.cpp.o -MF CMakeFiles/Sibelia.dir/bifurcationstorage.cpp.o.d -o CMakeFiles/Sibelia.dir/bifurcationstorage.cpp.o -c /build/sibelia-3.0.7+dfsg/src/bifurcationstorage.cpp +[ 45%] Building CXX object CMakeFiles/Sibelia.dir/bulgeremoval.cpp.o +/usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/bulgeremoval.cpp.o -MF CMakeFiles/Sibelia.dir/bulgeremoval.cpp.o.d -o CMakeFiles/Sibelia.dir/bulgeremoval.cpp.o -c /build/sibelia-3.0.7+dfsg/src/bulgeremoval.cpp +[ 50%] Building CXX object CMakeFiles/Sibelia.dir/dnasequence.cpp.o +/usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/dnasequence.cpp.o -MF CMakeFiles/Sibelia.dir/dnasequence.cpp.o.d -o CMakeFiles/Sibelia.dir/dnasequence.cpp.o -c /build/sibelia-3.0.7+dfsg/src/dnasequence.cpp +In file included from /usr/include/boost/bind.hpp:30, + from /build/sibelia-3.0.7+dfsg/src/common.h:31, + from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:10, + from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:10, + from /build/sibelia-3.0.7+dfsg/src/bulgeremoval.cpp:7: +/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/bind.hpp:30, + from /build/sibelia-3.0.7+dfsg/src/common.h:31, + from /build/sibelia-3.0.7+dfsg/src/fasta.h:10, + from /build/sibelia-3.0.7+dfsg/src/dnasequence.h:10, + from /build/sibelia-3.0.7+dfsg/src/bifurcationstorage.h:11, + from /build/sibelia-3.0.7+dfsg/src/bifurcationstorage.cpp:7: +/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ /build/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ @@ -958,29 +1011,14 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/sibelia-3.0.7+dfsg/src/dnasequence.h:12: +In file included from /build/sibelia-3.0.7+dfsg/src/dnasequence.h:12, + from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:11: /build/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -/build/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] - 51 | class StrandIterator: public std::iterator - | ^~~~~~~~ -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /usr/include/boost/bind.hpp:30, - from /build/sibelia-3.0.7+dfsg/src/common.h:31, - from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:10, - from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:10, - from /build/sibelia-3.0.7+dfsg/src/bulgeremoval.cpp:7: -/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -[ 50%] Building CXX object CMakeFiles/Sibelia.dir/dnasequence.cpp.o -/usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/dnasequence.cpp.o -MF CMakeFiles/Sibelia.dir/dnasequence.cpp.o.d -o CMakeFiles/Sibelia.dir/dnasequence.cpp.o -c /build/sibelia-3.0.7+dfsg/src/dnasequence.cpp /build/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ @@ -989,8 +1027,13 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/sibelia-3.0.7+dfsg/src/dnasequence.h:12, - from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:11: +/build/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] + 51 | class StrandIterator: public std::iterator + | ^~~~~~~~ +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/sibelia-3.0.7+dfsg/src/dnasequence.h:12: /build/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ @@ -1003,6 +1046,14 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /usr/include/boost/bind.hpp:30, + from /build/sibelia-3.0.7+dfsg/src/common.h:31, + from /build/sibelia-3.0.7+dfsg/src/fasta.h:10, + from /build/sibelia-3.0.7+dfsg/src/dnasequence.h:10, + from /build/sibelia-3.0.7+dfsg/src/dnasequence.cpp:7: +/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ In file included from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:11: /build/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 37 | std::auto_ptr sequence_; @@ -1018,16 +1069,6 @@ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ -In file included from /usr/include/boost/bind.hpp:30, - from /build/sibelia-3.0.7+dfsg/src/common.h:31, - from /build/sibelia-3.0.7+dfsg/src/fasta.h:10, - from /build/sibelia-3.0.7+dfsg/src/dnasequence.h:10, - from /build/sibelia-3.0.7+dfsg/src/dnasequence.cpp:7: -/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -[ 55%] Building CXX object CMakeFiles/Sibelia.dir/edge.cpp.o -/usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/edge.cpp.o -MF CMakeFiles/Sibelia.dir/edge.cpp.o.d -o CMakeFiles/Sibelia.dir/edge.cpp.o -c /build/sibelia-3.0.7+dfsg/src/edge.cpp /build/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ @@ -1049,8 +1090,12 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 55%] Building CXX object CMakeFiles/Sibelia.dir/edge.cpp.o +/usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/edge.cpp.o -MF CMakeFiles/Sibelia.dir/edge.cpp.o.d -o CMakeFiles/Sibelia.dir/edge.cpp.o -c /build/sibelia-3.0.7+dfsg/src/edge.cpp [ 60%] Building CXX object CMakeFiles/Sibelia.dir/fasta.cpp.o /usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/fasta.cpp.o -MF CMakeFiles/Sibelia.dir/fasta.cpp.o.d -o CMakeFiles/Sibelia.dir/fasta.cpp.o -c /build/sibelia-3.0.7+dfsg/src/fasta.cpp +[ 65%] Building CXX object CMakeFiles/Sibelia.dir/serialization.cpp.o +/usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/serialization.cpp.o -MF CMakeFiles/Sibelia.dir/serialization.cpp.o.d -o CMakeFiles/Sibelia.dir/serialization.cpp.o -c /build/sibelia-3.0.7+dfsg/src/serialization.cpp In file included from /usr/include/boost/bind.hpp:30, from /build/sibelia-3.0.7+dfsg/src/common.h:31, from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:10, @@ -1059,6 +1104,8 @@ /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +[ 70%] Building CXX object CMakeFiles/Sibelia.dir/synteny.cpp.o +/usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/synteny.cpp.o -MF CMakeFiles/Sibelia.dir/synteny.cpp.o.d -o CMakeFiles/Sibelia.dir/synteny.cpp.o -c /build/sibelia-3.0.7+dfsg/src/synteny.cpp /build/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ @@ -1096,25 +1143,6 @@ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ -[ 65%] Building CXX object CMakeFiles/Sibelia.dir/serialization.cpp.o -/usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/serialization.cpp.o -MF CMakeFiles/Sibelia.dir/serialization.cpp.o.d -o CMakeFiles/Sibelia.dir/serialization.cpp.o -c /build/sibelia-3.0.7+dfsg/src/serialization.cpp -In file included from /usr/include/boost/bind.hpp:30, - from /build/sibelia-3.0.7+dfsg/src/common.h:31, - from /build/sibelia-3.0.7+dfsg/src/fasta.h:10, - from /build/sibelia-3.0.7+dfsg/src/fasta.cpp:7: -/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -[ 70%] Building CXX object CMakeFiles/Sibelia.dir/synteny.cpp.o -/usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/synteny.cpp.o -MF CMakeFiles/Sibelia.dir/synteny.cpp.o.d -o CMakeFiles/Sibelia.dir/synteny.cpp.o -c /build/sibelia-3.0.7+dfsg/src/synteny.cpp -/build/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] - 104 | struct FancyIterator: public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/string:45, - from /build/sibelia-3.0.7+dfsg/src/common.h:12: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ In file included from /usr/include/boost/bind.hpp:30, from /build/sibelia-3.0.7+dfsg/src/common.h:31, from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:10, @@ -1125,9 +1153,8 @@ | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/bind.hpp:30, from /build/sibelia-3.0.7+dfsg/src/common.h:31, - from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:10, - from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:10, - from /build/sibelia-3.0.7+dfsg/src/synteny.cpp:9: + from /build/sibelia-3.0.7+dfsg/src/fasta.h:10, + from /build/sibelia-3.0.7+dfsg/src/fasta.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -1170,6 +1197,22 @@ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ +In file included from /usr/include/boost/bind.hpp:30, + from /build/sibelia-3.0.7+dfsg/src/common.h:31, + from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:10, + from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:10, + from /build/sibelia-3.0.7+dfsg/src/synteny.cpp:9: +/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/build/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] + 104 | struct FancyIterator: public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/string:45, + from /build/sibelia-3.0.7+dfsg/src/common.h:12: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ /build/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ @@ -1207,6 +1250,8 @@ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ +[ 80%] Building CXX object CMakeFiles/Sibelia.dir/platform.cpp.o +/usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/platform.cpp.o -MF CMakeFiles/Sibelia.dir/platform.cpp.o.d -o CMakeFiles/Sibelia.dir/platform.cpp.o -c /build/sibelia-3.0.7+dfsg/src/platform.cpp In file included from /usr/include/boost/bind.hpp:30, from /build/sibelia-3.0.7+dfsg/src/test/../common.h:31, from /build/sibelia-3.0.7+dfsg/src/test/unrolledlisttest.h:10, @@ -1229,8 +1274,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 80%] Building CXX object CMakeFiles/Sibelia.dir/platform.cpp.o -/usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/platform.cpp.o -MF CMakeFiles/Sibelia.dir/platform.cpp.o.d -o CMakeFiles/Sibelia.dir/platform.cpp.o -c /build/sibelia-3.0.7+dfsg/src/platform.cpp In file included from /usr/include/boost/bind.hpp:30, from /build/sibelia-3.0.7+dfsg/src/common.h:31, from /build/sibelia-3.0.7+dfsg/src/platform.h:10, @@ -1250,6 +1293,8 @@ | ^~~~~~~~ [ 90%] Building CXX object CMakeFiles/Sibelia.dir/vertexenumeration.cpp.o /usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/vertexenumeration.cpp.o -MF CMakeFiles/Sibelia.dir/vertexenumeration.cpp.o.d -o CMakeFiles/Sibelia.dir/vertexenumeration.cpp.o -c /build/sibelia-3.0.7+dfsg/src/vertexenumeration.cpp +[ 95%] Building CXX object CMakeFiles/Sibelia.dir/resource.cpp.o +/usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/resource.cpp.o -MF CMakeFiles/Sibelia.dir/resource.cpp.o.d -o CMakeFiles/Sibelia.dir/resource.cpp.o -c /build/sibelia-3.0.7+dfsg/src/resource.cpp In file included from /usr/include/boost/bind.hpp:30, from /build/sibelia-3.0.7+dfsg/src/common.h:31, from /build/sibelia-3.0.7+dfsg/src/fasta.h:10, @@ -1279,8 +1324,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 95%] Building CXX object CMakeFiles/Sibelia.dir/resource.cpp.o -/usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/resource.cpp.o -MF CMakeFiles/Sibelia.dir/resource.cpp.o.d -o CMakeFiles/Sibelia.dir/resource.cpp.o -c /build/sibelia-3.0.7+dfsg/src/resource.cpp In file included from /usr/include/boost/bind.hpp:30, from /build/sibelia-3.0.7+dfsg/src/common.h:31, from /build/sibelia-3.0.7+dfsg/src/fasta.h:10, @@ -1291,6 +1334,13 @@ /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/bind.hpp:30, + from /build/sibelia-3.0.7+dfsg/src/common.h:31, + from /build/sibelia-3.0.7+dfsg/src/resource.h:6, + from /build/sibelia-3.0.7+dfsg/src/resource.cpp:6: +/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ /build/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ @@ -1326,13 +1376,6 @@ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ -In file included from /usr/include/boost/bind.hpp:30, - from /build/sibelia-3.0.7+dfsg/src/common.h:31, - from /build/sibelia-3.0.7+dfsg/src/resource.h:6, - from /build/sibelia-3.0.7+dfsg/src/resource.cpp:6: -/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ /build/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ @@ -1344,40 +1387,40 @@ [100%] Linking CXX executable Sibelia /usr/bin/cmake -E cmake_link_script CMakeFiles/Sibelia.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/Sibelia.dir/sibelia.cpp.o CMakeFiles/Sibelia.dir/postprocessor.cpp.o CMakeFiles/Sibelia.dir/indexedsequence.cpp.o CMakeFiles/Sibelia.dir/util.cpp.o CMakeFiles/Sibelia.dir/outputgenerator.cpp.o CMakeFiles/Sibelia.dir/blockfinder.cpp.o CMakeFiles/Sibelia.dir/blockinstance.cpp.o CMakeFiles/Sibelia.dir/bifurcationstorage.cpp.o CMakeFiles/Sibelia.dir/bulgeremoval.cpp.o CMakeFiles/Sibelia.dir/dnasequence.cpp.o CMakeFiles/Sibelia.dir/edge.cpp.o CMakeFiles/Sibelia.dir/fasta.cpp.o CMakeFiles/Sibelia.dir/serialization.cpp.o CMakeFiles/Sibelia.dir/synteny.cpp.o CMakeFiles/Sibelia.dir/test/unrolledlisttest.cpp.o CMakeFiles/Sibelia.dir/platform.cpp.o CMakeFiles/Sibelia.dir/stranditerator.cpp.o CMakeFiles/Sibelia.dir/vertexenumeration.cpp.o CMakeFiles/Sibelia.dir/resource.cpp.o -o Sibelia -ldivsufsort -make[3]: Leaving directory '/build/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf' +make[3]: uscita dalla directory «/build/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf» [100%] Built target Sibelia -make[2]: Leaving directory '/build/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf' +make[2]: uscita dalla directory «/build/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf» /usr/bin/cmake -E cmake_progress_start /build/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf/CMakeFiles 0 -make[1]: Leaving directory '/build/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf' +make[1]: uscita dalla directory «/build/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf» debian/rules override_dh_auto_test -make[1]: Entering directory '/build/sibelia-3.0.7+dfsg' +make[1]: ingresso nella directory «/build/sibelia-3.0.7+dfsg» dh_auto_test --no-parallel -make[1]: Leaving directory '/build/sibelia-3.0.7+dfsg' +make[1]: uscita dalla directory «/build/sibelia-3.0.7+dfsg» create-stamp debian/debhelper-build-stamp dh_testroot -O--sourcedirectory=src dh_prep -O--sourcedirectory=src dh_auto_install -O--sourcedirectory=src - cd obj-arm-linux-gnueabihf && make -j3 install DESTDIR=/build/sibelia-3.0.7\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" -make[1]: Entering directory '/build/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf' + cd obj-arm-linux-gnueabihf && make -j4 install DESTDIR=/build/sibelia-3.0.7\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" +make[1]: ingresso nella directory «/build/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf» /usr/bin/cmake -S/build/sibelia-3.0.7+dfsg/src -B/build/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf/CMakeFiles /build/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all -make[2]: Entering directory '/build/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf' +make[2]: ingresso nella directory «/build/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf» make -f CMakeFiles/Sibelia.dir/build.make CMakeFiles/Sibelia.dir/depend -make[3]: Entering directory '/build/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf' +make[3]: ingresso nella directory «/build/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf» cd /build/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sibelia-3.0.7+dfsg/src /build/sibelia-3.0.7+dfsg/src /build/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf /build/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf /build/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/Sibelia.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf' +make[3]: uscita dalla directory «/build/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf» make -f CMakeFiles/Sibelia.dir/build.make CMakeFiles/Sibelia.dir/build -make[3]: Entering directory '/build/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf' -make[3]: Nothing to be done for 'CMakeFiles/Sibelia.dir/build'. -make[3]: Leaving directory '/build/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf' +make[3]: ingresso nella directory «/build/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf» +make[3]: Nessuna operazione da eseguire per «CMakeFiles/Sibelia.dir/build». +make[3]: uscita dalla directory «/build/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf» [100%] Built target Sibelia -make[2]: Leaving directory '/build/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf' +make[2]: uscita dalla directory «/build/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf» /usr/bin/cmake -E cmake_progress_start /build/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall -make[2]: Entering directory '/build/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf' -make[2]: Nothing to be done for 'preinstall'. -make[2]: Leaving directory '/build/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf' +make[2]: ingresso nella directory «/build/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf» +make[2]: Nessuna operazione da eseguire per «preinstall». +make[2]: uscita dalla directory «/build/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf» Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" @@ -1391,67 +1434,67 @@ -- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/C-SIBELIA.md -- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/LICENSE.txt -- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples --- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/C-Sibelia --- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/C-Sibelia/Staphylococcus_aureus --- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/C-Sibelia/Staphylococcus_aureus/variant.vcf --- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/C-Sibelia/Staphylococcus_aureus/NCTC8325.fasta --- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/C-Sibelia/Staphylococcus_aureus/RN4220.fasta --- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/C-Sibelia/Staphylococcus_aureus/README.txt -- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia -- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus --- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/d3_blocks_diagram.html +-- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/README.txt -- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos --- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos/circos.highlight.txt --- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos/circos.conf --- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos/circos.sequences.txt -- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos/circos.image.conf +-- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos/circos.conf -- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos/circos.segdup.txt --- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos/circos.png +-- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos/circos.sequences.txt +-- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos/circos.highlight.txt -- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos/circos.svg +-- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos/circos.png -- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/genomes_permutations.txt --- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/Staphylococcus.fasta -- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/blocks_coords.txt --- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/README.txt +-- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/d3_blocks_diagram.html +-- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/Staphylococcus.fasta -- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/coverage_report.txt -- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori --- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/d3_blocks_diagram.html +-- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/README.txt -- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos --- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.highlight.txt --- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.conf --- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.sequences.txt --- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.highlight1.txt +-- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.highlight2.txt -- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.image.conf -- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.highlight4.txt +-- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.conf -- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.segdup.txt --- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.png --- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.svg --- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.highlight2.txt -- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.highlight3.txt +-- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.sequences.txt +-- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.highlight.txt +-- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.svg +-- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.png +-- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.highlight1.txt -- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/genomes_permutations.txt --- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/Helicobacter_pylori.fasta -- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/blocks_coords.txt --- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/README.txt +-- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/d3_blocks_diagram.html -- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/coverage_report.txt +-- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/Helicobacter_pylori.fasta +-- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/C-Sibelia +-- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/C-Sibelia/Staphylococcus_aureus +-- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/C-Sibelia/Staphylococcus_aureus/README.txt +-- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/C-Sibelia/Staphylococcus_aureus/RN4220.fasta +-- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/C-Sibelia/Staphylococcus_aureus/NCTC8325.fasta +-- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/C-Sibelia/Staphylococcus_aureus/variant.vcf -- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/bin/C-Sibelia.py -- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/utils -- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/utils/hidemappedcontigs.py -- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/utils/sortsequences.py -- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/lib/Sibelia -make[1]: Leaving directory '/build/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf' +make[1]: uscita dalla directory «/build/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf» debian/rules override_dh_install -make[1]: Entering directory '/build/sibelia-3.0.7+dfsg' +make[1]: ingresso nella directory «/build/sibelia-3.0.7+dfsg» dh_install find debian -name LICENSE.txt -delete find debian -name INSTALL.md -delete -make[1]: Leaving directory '/build/sibelia-3.0.7+dfsg' +make[1]: uscita dalla directory «/build/sibelia-3.0.7+dfsg» dh_installdocs -O--sourcedirectory=src dh_installchangelogs -O--sourcedirectory=src debian/rules override_dh_installman-arch -make[1]: Entering directory '/build/sibelia-3.0.7+dfsg' +make[1]: ingresso nella directory «/build/sibelia-3.0.7+dfsg» dh_installman -a mv debian/sibelia/usr/share/man/py/man1/C-Sibelia.1 debian/sibelia/usr/share/man/man1/C-Sibelia.py.1 rm -rf debian/sibelia/usr/share/man/py -make[1]: Leaving directory '/build/sibelia-3.0.7+dfsg' +make[1]: uscita dalla directory «/build/sibelia-3.0.7+dfsg» dh_installman -O--sourcedirectory=src -Nsibelia dh_installinit -O--sourcedirectory=src dh_installsystemduser -O--sourcedirectory=src @@ -1471,9 +1514,9 @@ dh_gencontrol -O--sourcedirectory=src dh_md5sums -O--sourcedirectory=src dh_builddeb -O--sourcedirectory=src -dpkg-deb: building package 'sibelia' in '../sibelia_3.0.7+dfsg-3_armhf.deb'. -dpkg-deb: building package 'sibelia-dbgsym' in '../sibelia-dbgsym_3.0.7+dfsg-3_armhf.deb'. -dpkg-deb: building package 'sibelia-examples' in '../sibelia-examples_3.0.7+dfsg-3_all.deb'. +dpkg-deb: generazione del pacchetto "sibelia-examples" in "../sibelia-examples_3.0.7+dfsg-3_all.deb". +dpkg-deb: generazione del pacchetto "sibelia" in "../sibelia_3.0.7+dfsg-3_armhf.deb". +dpkg-deb: generazione del pacchetto "sibelia-dbgsym" in "../sibelia-dbgsym_3.0.7+dfsg-3_armhf.deb". dpkg-genbuildinfo --build=binary -O../sibelia_3.0.7+dfsg-3_armhf.buildinfo dpkg-genchanges --build=binary -O../sibelia_3.0.7+dfsg-3_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1481,12 +1524,14 @@ 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/28025/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/28025/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/21764 and its subdirectories -I: Current time: Thu Jun 1 08:55:34 -12 2023 -I: pbuilder-time-stamp: 1685652934 +I: removing directory /srv/workspace/pbuilder/28025 and its subdirectories +I: Current time: Fri Jun 2 11:05:33 +14 2023 +I: pbuilder-time-stamp: 1685653533