Diff of the two buildlogs: -- --- b1/build.log 2023-04-16 13:38:49.280072977 +0000 +++ b2/build.log 2023-04-16 13:44:24.757202887 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat May 18 07:38:24 -12 2024 -I: pbuilder-time-stamp: 1716061104 +I: Current time: Mon Apr 17 03:38:50 +14 2023 +I: pbuilder-time-stamp: 1681652330 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 [./lambda-align_1.0.3.orig.tar.gz] I: copying [./lambda-align_1.0.3-6.debian.tar.xz] I: Extracting source -gpgv: Signature made Sat Feb 8 03:33:49 2020 -12 +gpgv: Signature made Sun Feb 9 05:33:49 2020 +14 gpgv: using RSA key 8451F9178172E7E2DC73F79551F84A8FECCA7E09 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./lambda-align_1.0.3-6.dsc: no acceptable signature found @@ -28,135 +28,167 @@ dpkg-source: info: applying force-link-rt-pthread.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1503918/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2848872/tmp/hooks/D01_modify_environment starting +debug: Running on ionos11-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Apr 17 03:38 /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/2848872/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2848872/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='5da0aad44d89442988f1a59a6c258c25' - 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='1503918' - PS1='# ' - PS2='> ' + INVOCATION_ID=fb1f3d8a12cd499ebb53c9155a7460aa + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=2848872 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.r8I4vTdq/pbuilderrc_vCrx --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.r8I4vTdq/b1 --logfile b1/build.log lambda-align_1.0.3-6.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://85.184.249.68:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.r8I4vTdq/pbuilderrc_5Yzn --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.r8I4vTdq/b2 --logfile b2/build.log --extrapackages usrmerge lambda-align_1.0.3-6.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://78.137.99.97:3128 I: uname -a - Linux ionos15-amd64 6.1.0-0.deb11.5-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.12-1~bpo11+1 (2023-03-05) x86_64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 GNU/Linux I: ls -l /bin total 5632 - -rwxr-xr-x 1 root root 1265648 Feb 12 2023 bash - -rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2 - -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzcat - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep - -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzip2 - -rwxr-xr-x 1 root root 14568 Sep 18 2022 bzip2recover - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore - -rwxr-xr-x 1 root root 44016 Sep 20 2022 cat - -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp - -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod - -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown - -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp - -rwxr-xr-x 1 root root 125640 Jan 5 2023 dash - -rwxr-xr-x 1 root root 121904 Sep 20 2022 date - -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd - -rwxr-xr-x 1 root root 102200 Sep 20 2022 df - -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir - -rwxr-xr-x 1 root root 88656 Mar 22 2023 dmesg - lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname - -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep - -rwxr-xr-x 1 root root 35664 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep - -rwxr-xr-x 1 root root 85600 Mar 22 2023 findmnt - -rwsr-xr-x 1 root root 35128 Mar 22 2023 fusermount - -rwxr-xr-x 1 root root 203152 Jan 24 2023 grep - -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip - -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe - -rwxr-xr-x 1 root root 98136 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 22680 Dec 19 2022 hostname - -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln - -rwxr-xr-x 1 root root 53024 Mar 23 2023 login - -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls - -rwxr-xr-x 1 root root 207168 Mar 22 2023 lsblk - -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir - -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod - -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp - -rwxr-xr-x 1 root root 59712 Mar 22 2023 more - -rwsr-xr-x 1 root root 59704 Mar 22 2023 mount - -rwxr-xr-x 1 root root 18744 Mar 22 2023 mountpoint - -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv - lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 2 2023 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Feb 12 2023 rbash -> bash - -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink - -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm - -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 27560 Nov 2 2022 run-parts - -rwxr-xr-x 1 root root 126424 Jan 5 2023 sed - lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash - -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep - -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty - -rwsr-xr-x 1 root root 72000 Mar 22 2023 su - -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync - -rwxr-xr-x 1 root root 531984 Apr 6 2023 tar - -rwxr-xr-x 1 root root 14520 Nov 2 2022 tempfile - -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch - -rwxr-xr-x 1 root root 35664 Sep 20 2022 true - -rwxr-xr-x 1 root root 14568 Mar 22 2023 ulockmgr_server - -rwsr-xr-x 1 root root 35128 Mar 22 2023 umount - -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir - -rwxr-xr-x 1 root root 72024 Mar 22 2023 wdctl - lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/1503918/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1265648 Feb 13 10:05 bash + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bunzip2 + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzcat + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzip2 + -rwxr-xr-x 1 root root 14568 Sep 19 2022 bzip2recover + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore + -rwxr-xr-x 1 root root 44016 Sep 21 2022 cat + -rwxr-xr-x 1 root root 68656 Sep 21 2022 chgrp + -rwxr-xr-x 1 root root 64496 Sep 21 2022 chmod + -rwxr-xr-x 1 root root 72752 Sep 21 2022 chown + -rwxr-xr-x 1 root root 151152 Sep 21 2022 cp + -rwxr-xr-x 1 root root 125640 Jan 6 03:20 dash + -rwxr-xr-x 1 root root 121904 Sep 21 2022 date + -rwxr-xr-x 1 root root 89240 Sep 21 2022 dd + -rwxr-xr-x 1 root root 102200 Sep 21 2022 df + -rwxr-xr-x 1 root root 151344 Sep 21 2022 dir + -rwxr-xr-x 1 root root 88656 Mar 24 00:02 dmesg + lrwxrwxrwx 1 root root 8 Dec 20 03:33 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Dec 20 03:33 domainname -> hostname + -rwxr-xr-x 1 root root 43856 Sep 21 2022 echo + -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep + -rwxr-xr-x 1 root root 35664 Sep 21 2022 false + -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep + -rwxr-xr-x 1 root root 85600 Mar 24 00:02 findmnt + -rwsr-xr-x 1 root root 35128 Mar 23 22:35 fusermount + -rwxr-xr-x 1 root root 203152 Jan 25 04:43 grep + -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip + -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe + -rwxr-xr-x 1 root root 98136 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 22680 Dec 20 03:33 hostname + -rwxr-xr-x 1 root root 72824 Sep 21 2022 ln + -rwxr-xr-x 1 root root 53024 Mar 24 02:40 login + -rwxr-xr-x 1 root root 151344 Sep 21 2022 ls + -rwxr-xr-x 1 root root 207168 Mar 24 00:02 lsblk + -rwxr-xr-x 1 root root 97552 Sep 21 2022 mkdir + -rwxr-xr-x 1 root root 72912 Sep 21 2022 mknod + -rwxr-xr-x 1 root root 43952 Sep 21 2022 mktemp + -rwxr-xr-x 1 root root 59712 Mar 24 00:02 more + -rwsr-xr-x 1 root root 59704 Mar 24 00:02 mount + -rwxr-xr-x 1 root root 18744 Mar 24 00:02 mountpoint + -rwxr-xr-x 1 root root 142968 Sep 21 2022 mv + lrwxrwxrwx 1 root root 8 Dec 20 03:33 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43952 Sep 21 2022 pwd + lrwxrwxrwx 1 root root 4 Feb 13 10:05 rbash -> bash + -rwxr-xr-x 1 root root 52112 Sep 21 2022 readlink + -rwxr-xr-x 1 root root 72752 Sep 21 2022 rm + -rwxr-xr-x 1 root root 56240 Sep 21 2022 rmdir + -rwxr-xr-x 1 root root 27560 Nov 3 06:31 run-parts + -rwxr-xr-x 1 root root 126424 Jan 6 09:55 sed + lrwxrwxrwx 1 root root 9 Apr 17 03:38 sh -> /bin/bash + -rwxr-xr-x 1 root root 43888 Sep 21 2022 sleep + -rwxr-xr-x 1 root root 85008 Sep 21 2022 stty + -rwsr-xr-x 1 root root 72000 Mar 24 00:02 su + -rwxr-xr-x 1 root root 39824 Sep 21 2022 sync + -rwxr-xr-x 1 root root 531984 Apr 7 04:25 tar + -rwxr-xr-x 1 root root 14520 Nov 3 06:31 tempfile + -rwxr-xr-x 1 root root 109616 Sep 21 2022 touch + -rwxr-xr-x 1 root root 35664 Sep 21 2022 true + -rwxr-xr-x 1 root root 14568 Mar 23 22:35 ulockmgr_server + -rwsr-xr-x 1 root root 35128 Mar 24 00:02 umount + -rwxr-xr-x 1 root root 43888 Sep 21 2022 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 151344 Sep 21 2022 vdir + -rwxr-xr-x 1 root root 72024 Mar 24 00:02 wdctl + lrwxrwxrwx 1 root root 8 Dec 20 03:33 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat + -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp + -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff + -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep + -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep + -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce + -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep + -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless + -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore + -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew +I: user script /srv/workspace/pbuilder/2848872/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -254,7 +286,7 @@ Get: 50 http://deb.debian.org/debian bookworm/main amd64 libseqan2-dev all 2.4.0+dfsg-15 [1215 kB] Get: 51 http://deb.debian.org/debian bookworm/main amd64 openssl amd64 3.0.8-1 [1407 kB] Get: 52 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB] -Fetched 35.9 MB in 1s (36.2 MB/s) +Fetched 35.9 MB in 1s (52.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libproc2-0:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19596 files and directories currently installed.) @@ -479,10 +511,17 @@ Reading package lists... Building dependency tree... Reading state information... +usrmerge is already the newest version (35). fakeroot is already the newest version (1.31-1.2). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/lambda-align-1.0.3/ && 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 > ../lambda-align_1.0.3-6_source.changes +I: user script /srv/workspace/pbuilder/2848872/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/2848872/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/lambda-align-1.0.3/ && 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 > ../lambda-align_1.0.3-6_source.changes dpkg-buildpackage: info: source package lambda-align dpkg-buildpackage: info: source version 1.0.3-6 dpkg-buildpackage: info: source distribution unstable @@ -551,28 +590,28 @@ -- Build files have been written to: /build/lambda-align-1.0.3/build make[1]: Leaving directory '/build/lambda-align-1.0.3' dh_auto_build -O--builddirectory=build - cd build && make -j16 "INSTALL=install --strip-program=true" VERBOSE=1 + cd build && make -j15 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/lambda-align-1.0.3/build' /usr/bin/cmake -S/build/lambda-align-1.0.3 -B/build/lambda-align-1.0.3/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/lambda-align-1.0.3/build/CMakeFiles /build/lambda-align-1.0.3/build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/lambda-align-1.0.3/build' make -f src/CMakeFiles/lambda.dir/build.make src/CMakeFiles/lambda.dir/depend +make -f src/CMakeFiles/lambda_indexer.dir/build.make src/CMakeFiles/lambda_indexer.dir/depend make[3]: Entering directory '/build/lambda-align-1.0.3/build' cd /build/lambda-align-1.0.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/lambda-align-1.0.3 /build/lambda-align-1.0.3/src /build/lambda-align-1.0.3/build /build/lambda-align-1.0.3/build/src /build/lambda-align-1.0.3/build/src/CMakeFiles/lambda.dir/DependInfo.cmake --color= -make -f src/CMakeFiles/lambda_indexer.dir/build.make src/CMakeFiles/lambda_indexer.dir/depend make[3]: Entering directory '/build/lambda-align-1.0.3/build' cd /build/lambda-align-1.0.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/lambda-align-1.0.3 /build/lambda-align-1.0.3/src /build/lambda-align-1.0.3/build /build/lambda-align-1.0.3/build/src /build/lambda-align-1.0.3/build/src/CMakeFiles/lambda_indexer.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/lambda-align-1.0.3/build' -make -f src/CMakeFiles/lambda.dir/build.make src/CMakeFiles/lambda.dir/build -make[3]: Entering directory '/build/lambda-align-1.0.3/build' make[3]: Leaving directory '/build/lambda-align-1.0.3/build' +make -f src/CMakeFiles/lambda.dir/build.make src/CMakeFiles/lambda.dir/build make -f src/CMakeFiles/lambda_indexer.dir/build.make src/CMakeFiles/lambda_indexer.dir/build make[3]: Entering directory '/build/lambda-align-1.0.3/build' -[ 25%] Building CXX object src/CMakeFiles/lambda.dir/lambda.cpp.o -cd /build/lambda-align-1.0.3/build/src && /usr/bin/c++ -DCMAKE_BUILD_TYPE=\"Release\" -DLAMBDA_MMAPPED_DB=1 -DSEQAN_APP_VERSION=\"1.0.2\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP="1 -DSEQAN_GLOBAL_EXCEPTION_HANDLER" -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"\" -DSEQAN_VERSION_STRING=\"2.4.0\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -g -O2 -ffile-prefix-map=/build/lambda-align-1.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-vla -flto=16 -O3 -DNDEBUG -s -MD -MT src/CMakeFiles/lambda.dir/lambda.cpp.o -MF CMakeFiles/lambda.dir/lambda.cpp.o.d -o CMakeFiles/lambda.dir/lambda.cpp.o -c /build/lambda-align-1.0.3/src/lambda.cpp -[ 50%] Building CXX object src/CMakeFiles/lambda_indexer.dir/lambda_indexer.cpp.o -cd /build/lambda-align-1.0.3/build/src && /usr/bin/c++ -DCMAKE_BUILD_TYPE=\"Release\" -DLAMBDA_MMAPPED_DB=1 -DSEQAN_APP_VERSION=\"1.0.2\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP="1 -DSEQAN_GLOBAL_EXCEPTION_HANDLER" -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"\" -DSEQAN_VERSION_STRING=\"2.4.0\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -g -O2 -ffile-prefix-map=/build/lambda-align-1.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-vla -flto=16 -O3 -DNDEBUG -s -MD -MT src/CMakeFiles/lambda_indexer.dir/lambda_indexer.cpp.o -MF CMakeFiles/lambda_indexer.dir/lambda_indexer.cpp.o.d -o CMakeFiles/lambda_indexer.dir/lambda_indexer.cpp.o -c /build/lambda-align-1.0.3/src/lambda_indexer.cpp +make[3]: Entering directory '/build/lambda-align-1.0.3/build' +[ 25%] Building CXX object src/CMakeFiles/lambda_indexer.dir/lambda_indexer.cpp.o +[ 50%] Building CXX object src/CMakeFiles/lambda.dir/lambda.cpp.o +cd /build/lambda-align-1.0.3/build/src && /usr/bin/c++ -DCMAKE_BUILD_TYPE=\"Release\" -DLAMBDA_MMAPPED_DB=1 -DSEQAN_APP_VERSION=\"1.0.2\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP="1 -DSEQAN_GLOBAL_EXCEPTION_HANDLER" -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"\" -DSEQAN_VERSION_STRING=\"2.4.0\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -g -O2 -ffile-prefix-map=/build/lambda-align-1.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-vla -flto=15 -O3 -DNDEBUG -s -MD -MT src/CMakeFiles/lambda_indexer.dir/lambda_indexer.cpp.o -MF CMakeFiles/lambda_indexer.dir/lambda_indexer.cpp.o.d -o CMakeFiles/lambda_indexer.dir/lambda_indexer.cpp.o -c /build/lambda-align-1.0.3/src/lambda_indexer.cpp +cd /build/lambda-align-1.0.3/build/src && /usr/bin/c++ -DCMAKE_BUILD_TYPE=\"Release\" -DLAMBDA_MMAPPED_DB=1 -DSEQAN_APP_VERSION=\"1.0.2\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP="1 -DSEQAN_GLOBAL_EXCEPTION_HANDLER" -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"\" -DSEQAN_VERSION_STRING=\"2.4.0\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -g -O2 -ffile-prefix-map=/build/lambda-align-1.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-vla -flto=15 -O3 -DNDEBUG -s -MD -MT src/CMakeFiles/lambda.dir/lambda.cpp.o -MF CMakeFiles/lambda.dir/lambda.cpp.o.d -o CMakeFiles/lambda.dir/lambda.cpp.o -c /build/lambda-align-1.0.3/src/lambda.cpp In file included from /build/lambda-align-1.0.3/src/lambda.cpp:32: /build/lambda-align-1.0.3/src/options.hpp:323:21: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 323 | setDate(parser, __DATE__); @@ -583,20 +622,6 @@ /build/lambda-align-1.0.3/src/options.hpp:323:21: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 323 | setDate(parser, __DATE__); | ^~~~~~~~ -In file included from /build/lambda-align-1.0.3/src/lambda.cpp:34: -/build/lambda-align-1.0.3/src/lambda.hpp:79:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 79 | public ::std::binary_function < TSav, TSav, bool > - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/string:48, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /usr/include/c++/12/iostream:39, - from /build/lambda-align-1.0.3/src/lambda.cpp:22: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ In file included from /build/lambda-align-1.0.3/src/lambda_indexer.hpp:37: /build/lambda-align-1.0.3/src/radix_inplace.h:121:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 121 | public std::unary_function @@ -620,6 +645,20 @@ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ +In file included from /build/lambda-align-1.0.3/src/lambda.cpp:34: +/build/lambda-align-1.0.3/src/lambda.hpp:79:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 79 | public ::std::binary_function < TSav, TSav, bool > + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/string:48, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from /usr/include/c++/12/iostream:39, + from /build/lambda-align-1.0.3/src/lambda.cpp:22: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ /build/lambda-align-1.0.3/src/lambda.hpp: In instantiation of 'int computeBlastMatch(TBlastMatch&, const typename TLocalHolder::TMatch&, TLocalHolder&) [with TBlastMatch = seqan::BlastMatch, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps, seqan::MMap<> >, seqan::InfixSegment>, seqan::Tag >, unsigned int, seqan::Segment >, seqan::InfixSegment>, seqan::Segment >, seqan::InfixSegment>, std::vector >, seqan::String > >; TLocalHolder = LocalDataHolder, seqan::IndexSa<>, seqan::Tag, seqan::BlastProgram::BLASTN, seqan::BlastTabularSpec::NO_COMMENTS>, seqan::Tag >; typename TLocalHolder::TMatch = Match >]': /build/lambda-align-1.0.3/src/lambda.hpp:1513:45: required from 'int iterateMatches(TLocalHolder&) [with TLocalHolder = LocalDataHolder, seqan::IndexSa<>, seqan::Tag, seqan::BlastProgram::BLASTN, seqan::BlastTabularSpec::NO_COMMENTS>, seqan::Tag >]' /build/lambda-align-1.0.3/src/lambda.cpp:462:33: required from 'int realMain(const LambdaOptions&, const TOutFormat&, const seqan::BlastTabularSpecSelector&, const seqan::BlastProgramSelector

&, const TRedAlph&, const TScoreExtension&) [with TIndexSpec = seqan::IndexSa<>; TRedAlph = seqan::SimpleType; TScoreExtension = seqan::Tag; TOutFormat = seqan::Tag; seqan::BlastProgram p = seqan::BlastProgram::BLASTN; seqan::BlastTabularSpec h = seqan::BlastTabularSpec::NO_COMMENTS]' @@ -1383,7 +1422,7 @@ | ~~~~~~^~~~~~~~~~~ [ 75%] Linking CXX executable ../bin/lambda_indexer cd /build/lambda-align-1.0.3/build/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/lambda_indexer.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/lambda-align-1.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-vla -flto=16 -O3 -DNDEBUG -s -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/lambda_indexer.dir/lambda_indexer.cpp.o -o ../bin/lambda_indexer -lrt -lz -lbz2 -lrt -lpthread -lz -lbz2 -lpthread +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/lambda-align-1.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-vla -flto=15 -O3 -DNDEBUG -s -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/lambda_indexer.dir/lambda_indexer.cpp.o -o ../bin/lambda_indexer -lrt -lz -lbz2 -lrt -lpthread -lz -lbz2 -lpthread In function 'allocate', inlined from '_allocateStorage' at /usr/include/seqan/sequence/string_alloc.h:372:13, inlined from '_reallocateStorage' at /usr/include/seqan/sequence/string_base.h:1532:28, @@ -1419,7 +1458,7 @@ inlined from 'pop' at /usr/include/seqan/pipe/pool_sorter.h:260:31, inlined from 'pop' at /usr/include/seqan/pipe/pool_base.h:613:42, inlined from 'operator++' at /usr/include/seqan/pipe/pool_base.h:870:24, - inlined from 'insertStream' at /usr/include/seqan/index/pipe_merger7.h:424:21: + inlined from 'insertStream' at /usr/include/seqan/index/pipe_merger7.h:280:21: /usr/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value '18446744073709551536' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ @@ -1440,7 +1479,7 @@ inlined from 'pop' at /usr/include/seqan/pipe/pool_sorter.h:260:31, inlined from 'pop' at /usr/include/seqan/pipe/pool_base.h:613:42, inlined from 'operator++' at /usr/include/seqan/pipe/pool_base.h:870:24, - inlined from 'insertStream' at /usr/include/seqan/index/pipe_merger7.h:433:21: + inlined from 'insertStream' at /usr/include/seqan/index/pipe_merger7.h:290:21: /usr/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value '18446744073709551536' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ @@ -1461,7 +1500,7 @@ inlined from 'pop' at /usr/include/seqan/pipe/pool_sorter.h:260:31, inlined from 'pop' at /usr/include/seqan/pipe/pool_base.h:613:42, inlined from 'operator++' at /usr/include/seqan/pipe/pool_base.h:870:24, - inlined from 'insertStream' at /usr/include/seqan/index/pipe_merger7.h:280:21: + inlined from 'insertStream' at /usr/include/seqan/index/pipe_merger7.h:424:21: /usr/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value '18446744073709551536' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ @@ -1482,7 +1521,7 @@ inlined from 'pop' at /usr/include/seqan/pipe/pool_sorter.h:260:31, inlined from 'pop' at /usr/include/seqan/pipe/pool_base.h:613:42, inlined from 'operator++' at /usr/include/seqan/pipe/pool_base.h:870:24, - inlined from 'insertStream' at /usr/include/seqan/index/pipe_merger7.h:290:21: + inlined from 'insertStream' at /usr/include/seqan/index/pipe_merger7.h:433:21: /usr/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value '18446744073709551536' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ @@ -1681,16 +1720,16 @@ inlined from 'pop' at /usr/include/seqan/pipe/pool_sorter.h:260:31, inlined from 'pop' at /usr/include/seqan/pipe/pool_base.h:613:42, inlined from 'operator++' at /usr/include/seqan/pipe/pool_base.h:870:24, - inlined from 'operator++' at /usr/include/seqan/pipe/pipe_namer.h:114:13, + inlined from 'operator++' at /usr/include/seqan/index/pipe_merger3.h:127:17, + inlined from 'operator++' at /usr/include/seqan/index/index_skew3.h:329:13, inlined from 'operator++' at /usr/include/seqan/pipe/pipe_filter.h:129:13, + inlined from 'operator++' at /usr/include/seqan/pipe/pipe_counter.h:90:13, inlined from 'append' at /usr/include/seqan/pipe/pool_base.h:1330:13, - inlined from 'assign' at /usr/include/seqan/pipe/pool_base.h:1369:42, - inlined from 'operator<<' at /usr/include/seqan/pipe/pool_base.h:1376:22, - inlined from 'process.isra' at /usr/include/seqan/index/index_skew7_multi.h:328:26: + inlined from 'assign.constprop.isra' at /usr/include/seqan/pipe/pool_base.h:1369:42: /usr/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value '18446744073709551536' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ -/usr/include/c++/12/new: In member function 'process.isra': +/usr/include/c++/12/new: In function 'assign.constprop.isra': /usr/include/c++/12/new:126:26: note: in a call to allocation function 'operator new' declared here 126 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ @@ -1707,16 +1746,16 @@ inlined from 'pop' at /usr/include/seqan/pipe/pool_sorter.h:260:31, inlined from 'pop' at /usr/include/seqan/pipe/pool_base.h:613:42, inlined from 'operator++' at /usr/include/seqan/pipe/pool_base.h:870:24, - inlined from 'operator++' at /usr/include/seqan/index/pipe_merger3.h:127:17, - inlined from 'operator++' at /usr/include/seqan/index/index_skew3.h:329:13, + inlined from 'operator++' at /usr/include/seqan/pipe/pipe_namer.h:114:13, inlined from 'operator++' at /usr/include/seqan/pipe/pipe_filter.h:129:13, - inlined from 'operator++' at /usr/include/seqan/pipe/pipe_counter.h:90:13, inlined from 'append' at /usr/include/seqan/pipe/pool_base.h:1330:13, - inlined from 'assign.constprop.isra' at /usr/include/seqan/pipe/pool_base.h:1369:42: + inlined from 'assign' at /usr/include/seqan/pipe/pool_base.h:1369:42, + inlined from 'operator<<' at /usr/include/seqan/pipe/pool_base.h:1376:22, + inlined from 'process.isra' at /usr/include/seqan/index/index_skew7_multi.h:328:26: /usr/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value '18446744073709551536' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ -/usr/include/c++/12/new: In function 'assign.constprop.isra': +/usr/include/c++/12/new: In member function 'process.isra': /usr/include/c++/12/new:126:26: note: in a call to allocation function 'operator new' declared here 126 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ @@ -1724,7 +1763,7 @@ [ 75%] Built target lambda_indexer [100%] Linking CXX executable ../bin/lambda cd /build/lambda-align-1.0.3/build/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/lambda.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/lambda-align-1.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-vla -flto=16 -O3 -DNDEBUG -s -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/lambda.dir/lambda.cpp.o -o ../bin/lambda -lrt -lz -lbz2 -lrt -lpthread -lz -lbz2 -lpthread +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/lambda-align-1.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-vla -flto=15 -O3 -DNDEBUG -s -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/lambda.dir/lambda.cpp.o -o ../bin/lambda -lrt -lz -lbz2 -lrt -lpthread -lz -lbz2 -lpthread In function 'allocate', inlined from '_allocateStorage' at /usr/include/seqan/sequence/string_alloc.h:372:13, inlined from '_reallocateStorage' at /usr/include/seqan/sequence/string_base.h:1532:28, @@ -2241,16 +2280,25 @@ inlined from '_reserveStorage' at /usr/include/seqan/sequence/string_base.h:1665:1, inlined from 'reserve' at /usr/include/seqan/sequence/string_base.h:1697:20, inlined from 'resize_' at /usr/include/seqan/sequence/string_base.h:1725:45, - inlined from 'resize' at /usr/include/seqan/sequence/string_base.h:1785:50, - inlined from 'pop' at /usr/include/seqan/misc/priority_type_heap.h:289:11, - inlined from 'pop' at /usr/include/seqan/pipe/pool_sorter.h:260:31, - inlined from 'pop' at /usr/include/seqan/pipe/pool_base.h:613:42, - inlined from 'operator++' at /usr/include/seqan/pipe/pool_base.h:870:24, - inlined from 'insertStream' at /usr/include/seqan/index/pipe_merger7.h:280:21: -/usr/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value '18446744073709551536' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] + inlined from 'resize' at /usr/include/seqan/sequence/string_base.h:1785:0, + inlined from 'resize' at /usr/include/seqan/sequence/sequence_interface.h:1149:0, + inlined from 'eraseBack' at /usr/include/seqan/sequence/sequence_interface.h:1259:0, + inlined from '_popIterators' at /usr/include/seqan/index/find2_backtracking.h:707:0, + inlined from '_pushState' at /usr/include/seqan/index/find2_backtracking.h:442:18, + inlined from '_find' at /usr/include/seqan/index/find2_backtracking.h:1311:31, + inlined from '_find' at /usr/include/seqan/index/find2_backtracking.h:1315:30, + inlined from '_find' at /usr/include/seqan/index/find2_backtracking.h:1281:1, + inlined from '_find' at /usr/include/seqan/index/find2_backtracking.h:1315:30, + inlined from '_find' at /usr/include/seqan/index/find2_backtracking.h:1281:1, + inlined from '_find' at /usr/include/seqan/index/find2_backtracking.h:1315:30, + inlined from '_find' at /usr/include/seqan/index/find2_backtracking.h:1281:1, + inlined from '_find' at /usr/include/seqan/index/find2_backtracking.h:1315:30, + inlined from '_find' at /usr/include/seqan/index/find2_backtracking.h:1281:1, + inlined from '_ZN5seqan5_findINS_9StringSetINS_6StringINS_10SimpleTypeIhNS_5Dna5_EEENS_4MMapINS_10MMapConfigINS_4FileINS_5AsyncIvEEEEmEEEEEENS_5OwnerINS_12ConcatDirectIvEEEEEENS_7FMIndexIv19LambdaFMIndexConfigEENS1_INS_7SegmentINS2_IS5_NS_5AllocIvEEEENS_12InfixSegmentEEENSF_INS_3TagINS_8Default_EEEEEEENS_7IndexSaIvEENST_INS_16HammingDistance_EEENST_INS_23BacktrackingSemiGlobal_EEENS_11StageExact_EZ19__searchDoubleIndexINS_12BacktrackingIS11_S13_EE15LocalDataHolderI16GlobalDataHolderIS5_SM_NST_INS_13BlastTabular_EEELNS_12BlastProgramE0ELNS_16BlastTabularSpecE1EENST_INS_11AffineGaps_EEEEEvRT0_EUlRKNS_7Finder_INS_5IndexISJ_SM_EENS1L_ISX_SZ_EES17_EEE_EEvRNS1K_INS1L_IT_S1I_EENS1L_IT1_T2_EENS16_IT3_T4_EEEERT6_RKT5_.part.0' at /usr/include/seqan/index/find2_backtracking.h:1315:30: +/usr/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value '18446744073709551440' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ -/usr/include/c++/12/new: In member function 'insertStream': +/usr/include/c++/12/new: In function '_ZN5seqan5_findINS_9StringSetINS_6StringINS_10SimpleTypeIhNS_5Dna5_EEENS_4MMapINS_10MMapConfigINS_4FileINS_5AsyncIvEEEEmEEEEEENS_5OwnerINS_12ConcatDirectIvEEEEEENS_7FMIndexIv19LambdaFMIndexConfigEENS1_INS_7SegmentINS2_IS5_NS_5AllocIvEEEENS_12InfixSegmentEEENSF_INS_3TagINS_8Default_EEEEEEENS_7IndexSaIvEENST_INS_16HammingDistance_EEENST_INS_23BacktrackingSemiGlobal_EEENS_11StageExact_EZ19__searchDoubleIndexINS_12BacktrackingIS11_S13_EE15LocalDataHolderI16GlobalDataHolderIS5_SM_NST_INS_13BlastTabular_EEELNS_12BlastProgramE0ELNS_16BlastTabularSpecE1EENST_INS_11AffineGaps_EEEEEvRT0_EUlRKNS_7Finder_INS_5IndexISJ_SM_EENS1L_ISX_SZ_EES17_EEE_EEvRNS1K_INS1L_IT_S1I_EENS1L_IT1_T2_EENS16_IT3_T4_EEEERT6_RKT5_.part.0': /usr/include/c++/12/new:126:26: note: in a call to allocation function 'operator new' declared here 126 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ @@ -2267,7 +2315,7 @@ inlined from 'pop' at /usr/include/seqan/pipe/pool_sorter.h:260:31, inlined from 'pop' at /usr/include/seqan/pipe/pool_base.h:613:42, inlined from 'operator++' at /usr/include/seqan/pipe/pool_base.h:870:24, - inlined from 'insertStream' at /usr/include/seqan/index/pipe_merger7.h:290:21: + inlined from 'insertStream' at /usr/include/seqan/index/pipe_merger7.h:280:21: /usr/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value '18446744073709551536' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ @@ -2283,25 +2331,16 @@ inlined from '_reserveStorage' at /usr/include/seqan/sequence/string_base.h:1665:1, inlined from 'reserve' at /usr/include/seqan/sequence/string_base.h:1697:20, inlined from 'resize_' at /usr/include/seqan/sequence/string_base.h:1725:45, - inlined from 'resize' at /usr/include/seqan/sequence/string_base.h:1785:0, - inlined from 'resize' at /usr/include/seqan/sequence/sequence_interface.h:1149:0, - inlined from 'eraseBack' at /usr/include/seqan/sequence/sequence_interface.h:1259:0, - inlined from '_popIterators' at /usr/include/seqan/index/find2_backtracking.h:707:0, - inlined from '_pushState' at /usr/include/seqan/index/find2_backtracking.h:442:18, - inlined from '_find' at /usr/include/seqan/index/find2_backtracking.h:1311:31, - inlined from '_find' at /usr/include/seqan/index/find2_backtracking.h:1315:30, - inlined from '_find' at /usr/include/seqan/index/find2_backtracking.h:1281:1, - inlined from '_find' at /usr/include/seqan/index/find2_backtracking.h:1315:30, - inlined from '_find' at /usr/include/seqan/index/find2_backtracking.h:1281:1, - inlined from '_find' at /usr/include/seqan/index/find2_backtracking.h:1315:30, - inlined from '_find' at /usr/include/seqan/index/find2_backtracking.h:1281:1, - inlined from '_find' at /usr/include/seqan/index/find2_backtracking.h:1315:30, - inlined from '_find' at /usr/include/seqan/index/find2_backtracking.h:1281:1, - inlined from '_ZN5seqan5_findINS_9StringSetINS_6StringINS_10SimpleTypeIhNS_5Dna5_EEENS_4MMapINS_10MMapConfigINS_4FileINS_5AsyncIvEEEEmEEEEEENS_5OwnerINS_12ConcatDirectIvEEEEEENS_7FMIndexIv19LambdaFMIndexConfigEENS1_INS_7SegmentINS2_IS5_NS_5AllocIvEEEENS_12InfixSegmentEEENSF_INS_3TagINS_8Default_EEEEEEENS_7IndexSaIvEENST_INS_16HammingDistance_EEENST_INS_23BacktrackingSemiGlobal_EEENS_11StageExact_EZ19__searchDoubleIndexINS_12BacktrackingIS11_S13_EE15LocalDataHolderI16GlobalDataHolderIS5_SM_NST_INS_13BlastTabular_EEELNS_12BlastProgramE0ELNS_16BlastTabularSpecE1EENST_INS_11AffineGaps_EEEEEvRT0_EUlRKNS_7Finder_INS_5IndexISJ_SM_EENS1L_ISX_SZ_EES17_EEE_EEvRNS1K_INS1L_IT_S1I_EENS1L_IT1_T2_EENS16_IT3_T4_EEEERT6_RKT5_.part.0' at /usr/include/seqan/index/find2_backtracking.h:1315:30: -/usr/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value '18446744073709551440' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] + inlined from 'resize' at /usr/include/seqan/sequence/string_base.h:1785:50, + inlined from 'pop' at /usr/include/seqan/misc/priority_type_heap.h:289:11, + inlined from 'pop' at /usr/include/seqan/pipe/pool_sorter.h:260:31, + inlined from 'pop' at /usr/include/seqan/pipe/pool_base.h:613:42, + inlined from 'operator++' at /usr/include/seqan/pipe/pool_base.h:870:24, + inlined from 'insertStream' at /usr/include/seqan/index/pipe_merger7.h:290:21: +/usr/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value '18446744073709551536' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ -/usr/include/c++/12/new: In function '_ZN5seqan5_findINS_9StringSetINS_6StringINS_10SimpleTypeIhNS_5Dna5_EEENS_4MMapINS_10MMapConfigINS_4FileINS_5AsyncIvEEEEmEEEEEENS_5OwnerINS_12ConcatDirectIvEEEEEENS_7FMIndexIv19LambdaFMIndexConfigEENS1_INS_7SegmentINS2_IS5_NS_5AllocIvEEEENS_12InfixSegmentEEENSF_INS_3TagINS_8Default_EEEEEEENS_7IndexSaIvEENST_INS_16HammingDistance_EEENST_INS_23BacktrackingSemiGlobal_EEENS_11StageExact_EZ19__searchDoubleIndexINS_12BacktrackingIS11_S13_EE15LocalDataHolderI16GlobalDataHolderIS5_SM_NST_INS_13BlastTabular_EEELNS_12BlastProgramE0ELNS_16BlastTabularSpecE1EENST_INS_11AffineGaps_EEEEEvRT0_EUlRKNS_7Finder_INS_5IndexISJ_SM_EENS1L_ISX_SZ_EES17_EEE_EEvRNS1K_INS1L_IT_S1I_EENS1L_IT1_T2_EENS16_IT3_T4_EEEERT6_RKT5_.part.0': +/usr/include/c++/12/new: In member function 'insertStream': /usr/include/c++/12/new:126:26: note: in a call to allocation function 'operator new' declared here 126 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ @@ -2405,27 +2444,6 @@ inlined from 'pop' at /usr/include/seqan/pipe/pool_sorter.h:260:31, inlined from 'pop' at /usr/include/seqan/pipe/pool_base.h:613:42, inlined from 'operator++' at /usr/include/seqan/pipe/pool_base.h:870:24, - inlined from 'operator++.isra' at /usr/include/seqan/index/pipe_merger3.h:127:17: -/usr/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value '18446744073709551536' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] - 211 | data = (TValue *) operator new(count * sizeof(TValue)); - | ^ -/usr/include/c++/12/new: In member function 'operator++.isra': -/usr/include/c++/12/new:126:26: note: in a call to allocation function 'operator new' declared here - 126 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) - | ^ -In function 'allocate', - inlined from '_allocateStorage' at /usr/include/seqan/sequence/string_alloc.h:372:13, - inlined from '_reallocateStorage' at /usr/include/seqan/sequence/string_base.h:1532:28, - inlined from '_reallocateStorage' at /usr/include/seqan/sequence/string_base.h:1577:30, - inlined from '_reserveStorage' at /usr/include/seqan/sequence/string_base.h:1679:83, - inlined from '_reserveStorage' at /usr/include/seqan/sequence/string_base.h:1665:1, - inlined from 'reserve' at /usr/include/seqan/sequence/string_base.h:1697:20, - inlined from 'resize_' at /usr/include/seqan/sequence/string_base.h:1725:45, - inlined from 'resize' at /usr/include/seqan/sequence/string_base.h:1785:50, - inlined from 'pop' at /usr/include/seqan/misc/priority_type_heap.h:289:11, - inlined from 'pop' at /usr/include/seqan/pipe/pool_sorter.h:260:31, - inlined from 'pop' at /usr/include/seqan/pipe/pool_base.h:613:42, - inlined from 'operator++' at /usr/include/seqan/pipe/pool_base.h:870:24, inlined from 'operator++' at /usr/include/seqan/pipe/pipe_namer.h:114:13, inlined from 'operator++' at /usr/include/seqan/pipe/pipe_filter.h:129:13, inlined from 'append' at /usr/include/seqan/pipe/pool_base.h:1330:13, @@ -2452,16 +2470,11 @@ inlined from 'pop' at /usr/include/seqan/pipe/pool_sorter.h:260:31, inlined from 'pop' at /usr/include/seqan/pipe/pool_base.h:613:42, inlined from 'operator++' at /usr/include/seqan/pipe/pool_base.h:870:24, - inlined from 'operator++' at /usr/include/seqan/pipe/pipe_namer.h:114:13, - inlined from 'operator++' at /usr/include/seqan/pipe/pipe_filter.h:129:13, - inlined from 'append' at /usr/include/seqan/pipe/pool_base.h:1330:13, - inlined from 'assign' at /usr/include/seqan/pipe/pool_base.h:1369:42, - inlined from 'operator<<' at /usr/include/seqan/pipe/pool_base.h:1376:22, - inlined from 'process.isra' at /usr/include/seqan/index/index_skew7_multi.h:328:26: + inlined from 'operator++.isra' at /usr/include/seqan/index/pipe_merger3.h:127:17: /usr/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value '18446744073709551536' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ -/usr/include/c++/12/new: In member function 'process.isra': +/usr/include/c++/12/new: In member function 'operator++.isra': /usr/include/c++/12/new:126:26: note: in a call to allocation function 'operator new' declared here 126 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ @@ -2547,6 +2560,32 @@ /usr/include/c++/12/new:126:26: note: in a call to allocation function 'operator new' declared here 126 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ +In function 'allocate', + inlined from '_allocateStorage' at /usr/include/seqan/sequence/string_alloc.h:372:13, + inlined from '_reallocateStorage' at /usr/include/seqan/sequence/string_base.h:1532:28, + inlined from '_reallocateStorage' at /usr/include/seqan/sequence/string_base.h:1577:30, + inlined from '_reserveStorage' at /usr/include/seqan/sequence/string_base.h:1679:83, + inlined from '_reserveStorage' at /usr/include/seqan/sequence/string_base.h:1665:1, + inlined from 'reserve' at /usr/include/seqan/sequence/string_base.h:1697:20, + inlined from 'resize_' at /usr/include/seqan/sequence/string_base.h:1725:45, + inlined from 'resize' at /usr/include/seqan/sequence/string_base.h:1785:50, + inlined from 'pop' at /usr/include/seqan/misc/priority_type_heap.h:289:11, + inlined from 'pop' at /usr/include/seqan/pipe/pool_sorter.h:260:31, + inlined from 'pop' at /usr/include/seqan/pipe/pool_base.h:613:42, + inlined from 'operator++' at /usr/include/seqan/pipe/pool_base.h:870:24, + inlined from 'operator++' at /usr/include/seqan/pipe/pipe_namer.h:114:13, + inlined from 'operator++' at /usr/include/seqan/pipe/pipe_filter.h:129:13, + inlined from 'append' at /usr/include/seqan/pipe/pool_base.h:1330:13, + inlined from 'assign' at /usr/include/seqan/pipe/pool_base.h:1369:42, + inlined from 'operator<<' at /usr/include/seqan/pipe/pool_base.h:1376:22, + inlined from 'process.isra' at /usr/include/seqan/index/index_skew7_multi.h:328:26: +/usr/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value '18446744073709551536' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] + 211 | data = (TValue *) operator new(count * sizeof(TValue)); + | ^ +/usr/include/c++/12/new: In member function 'process.isra': +/usr/include/c++/12/new:126:26: note: in a call to allocation function 'operator new' declared here + 126 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) + | ^ make[3]: Leaving directory '/build/lambda-align-1.0.3/build' [100%] Built target lambda make[2]: Leaving directory '/build/lambda-align-1.0.3/build' @@ -2554,172 +2593,172 @@ make[1]: Leaving directory '/build/lambda-align-1.0.3/build' debian/rules override_dh_auto_test make[1]: Entering directory '/build/lambda-align-1.0.3' -cd build/tests && ctest 16 +cd build/tests && ctest 15 Test project /build/lambda-align-1.0.3/build/tests Start 1: test_mkindex_blastn_sa - 1/80 Test #1: test_mkindex_blastn_sa ........... Passed 1.14 sec + 1/80 Test #1: test_mkindex_blastn_sa ........... Passed 0.18 sec Start 2: test_mkindex_blastn_fm - 2/80 Test #2: test_mkindex_blastn_fm ........... Passed 0.81 sec + 2/80 Test #2: test_mkindex_blastn_fm ........... Passed 0.25 sec Start 3: test_mkindex_blastp_sa - 3/80 Test #3: test_mkindex_blastp_sa ........... Passed 0.44 sec + 3/80 Test #3: test_mkindex_blastp_sa ........... Passed 0.08 sec Start 4: test_mkindex_blastp_fm - 4/80 Test #4: test_mkindex_blastp_fm ........... Passed 0.51 sec + 4/80 Test #4: test_mkindex_blastp_fm ........... Passed 0.11 sec Start 5: test_mkindex_blastx_sa - 5/80 Test #5: test_mkindex_blastx_sa ........... Passed 0.40 sec + 5/80 Test #5: test_mkindex_blastx_sa ........... Passed 0.08 sec Start 6: test_mkindex_blastx_fm - 6/80 Test #6: test_mkindex_blastx_fm ........... Passed 0.52 sec + 6/80 Test #6: test_mkindex_blastx_fm ........... Passed 0.13 sec Start 7: test_mkindex_tblastn_sa - 7/80 Test #7: test_mkindex_tblastn_sa .......... Passed 0.82 sec + 7/80 Test #7: test_mkindex_tblastn_sa .......... Passed 0.20 sec Start 8: test_mkindex_tblastn_fm - 8/80 Test #8: test_mkindex_tblastn_fm .......... Passed 1.00 sec + 8/80 Test #8: test_mkindex_tblastn_fm .......... Passed 0.24 sec Start 9: test_mkindex_tblastx_sa - 9/80 Test #9: test_mkindex_tblastx_sa .......... Passed 0.89 sec + 9/80 Test #9: test_mkindex_tblastx_sa .......... Passed 0.20 sec Start 10: test_mkindex_tblastx_fm -10/80 Test #10: test_mkindex_tblastx_fm .......... Passed 1.05 sec +10/80 Test #10: test_mkindex_tblastx_fm .......... Passed 0.25 sec Start 11: test_search_blastn_sa_m0 -11/80 Test #11: test_search_blastn_sa_m0 ......... Passed 8.46 sec +11/80 Test #11: test_search_blastn_sa_m0 ......... Passed 2.32 sec Start 12: test_search_blastn_sa_m8 -12/80 Test #12: test_search_blastn_sa_m8 ......... Passed 5.69 sec +12/80 Test #12: test_search_blastn_sa_m8 ......... Passed 1.95 sec Start 13: test_search_blastn_sa_m9 -13/80 Test #13: test_search_blastn_sa_m9 ......... Passed 6.01 sec +13/80 Test #13: test_search_blastn_sa_m9 ......... Passed 1.95 sec Start 14: test_search_blastn_sa_sam -14/80 Test #14: test_search_blastn_sa_sam ........ Passed 7.48 sec +14/80 Test #14: test_search_blastn_sa_sam ........ Passed 2.05 sec Start 15: test_search_blastn_sa_bam -15/80 Test #15: test_search_blastn_sa_bam ........ Passed 6.83 sec +15/80 Test #15: test_search_blastn_sa_bam ........ Passed 1.94 sec Start 16: test_search_blastn_sa_m9.gz -16/80 Test #16: test_search_blastn_sa_m9.gz ...... Passed 8.46 sec +16/80 Test #16: test_search_blastn_sa_m9.gz ...... Passed 2.10 sec Start 17: test_search_blastn_sa_sam.bz2 -17/80 Test #17: test_search_blastn_sa_sam.bz2 .... Passed 10.67 sec +17/80 Test #17: test_search_blastn_sa_sam.bz2 .... Passed 2.72 sec Start 18: test_search_blastn_fm_m0 -18/80 Test #18: test_search_blastn_fm_m0 ......... Passed 10.14 sec +18/80 Test #18: test_search_blastn_fm_m0 ......... Passed 2.48 sec Start 19: test_search_blastn_fm_m8 -19/80 Test #19: test_search_blastn_fm_m8 ......... Passed 8.24 sec +19/80 Test #19: test_search_blastn_fm_m8 ......... Passed 2.12 sec Start 20: test_search_blastn_fm_m9 -20/80 Test #20: test_search_blastn_fm_m9 ......... Passed 7.30 sec +20/80 Test #20: test_search_blastn_fm_m9 ......... Passed 2.11 sec Start 21: test_search_blastn_fm_sam -21/80 Test #21: test_search_blastn_fm_sam ........ Passed 7.07 sec +21/80 Test #21: test_search_blastn_fm_sam ........ Passed 2.25 sec Start 22: test_search_blastn_fm_bam -22/80 Test #22: test_search_blastn_fm_bam ........ Passed 7.56 sec +22/80 Test #22: test_search_blastn_fm_bam ........ Passed 2.09 sec Start 23: test_search_blastn_fm_m9.gz -23/80 Test #23: test_search_blastn_fm_m9.gz ...... Passed 8.65 sec +23/80 Test #23: test_search_blastn_fm_m9.gz ...... Passed 2.24 sec Start 24: test_search_blastn_fm_sam.bz2 -24/80 Test #24: test_search_blastn_fm_sam.bz2 .... Passed 10.90 sec +24/80 Test #24: test_search_blastn_fm_sam.bz2 .... Passed 2.89 sec Start 25: test_search_blastp_sa_m0 -25/80 Test #25: test_search_blastp_sa_m0 ......... Passed 1.39 sec +25/80 Test #25: test_search_blastp_sa_m0 ......... Passed 0.28 sec Start 26: test_search_blastp_sa_m8 -26/80 Test #26: test_search_blastp_sa_m8 ......... Passed 1.35 sec +26/80 Test #26: test_search_blastp_sa_m8 ......... Passed 0.28 sec Start 27: test_search_blastp_sa_m9 -27/80 Test #27: test_search_blastp_sa_m9 ......... Passed 1.14 sec +27/80 Test #27: test_search_blastp_sa_m9 ......... Passed 0.25 sec Start 28: test_search_blastp_sa_sam -28/80 Test #28: test_search_blastp_sa_sam ........ Passed 0.93 sec +28/80 Test #28: test_search_blastp_sa_sam ........ Passed 0.25 sec Start 29: test_search_blastp_sa_bam -29/80 Test #29: test_search_blastp_sa_bam ........ Passed 1.20 sec +29/80 Test #29: test_search_blastp_sa_bam ........ Passed 0.24 sec Start 30: test_search_blastp_sa_m9.gz -30/80 Test #30: test_search_blastp_sa_m9.gz ...... Passed 1.16 sec +30/80 Test #30: test_search_blastp_sa_m9.gz ...... Passed 0.27 sec Start 31: test_search_blastp_sa_sam.bz2 -31/80 Test #31: test_search_blastp_sa_sam.bz2 .... Passed 1.15 sec +31/80 Test #31: test_search_blastp_sa_sam.bz2 .... Passed 0.34 sec Start 32: test_search_blastp_fm_m0 -32/80 Test #32: test_search_blastp_fm_m0 ......... Passed 1.53 sec +32/80 Test #32: test_search_blastp_fm_m0 ......... Passed 0.31 sec Start 33: test_search_blastp_fm_m8 -33/80 Test #33: test_search_blastp_fm_m8 ......... Passed 1.51 sec +33/80 Test #33: test_search_blastp_fm_m8 ......... Passed 0.29 sec Start 34: test_search_blastp_fm_m9 -34/80 Test #34: test_search_blastp_fm_m9 ......... Passed 1.30 sec +34/80 Test #34: test_search_blastp_fm_m9 ......... Passed 0.29 sec Start 35: test_search_blastp_fm_sam -35/80 Test #35: test_search_blastp_fm_sam ........ Passed 1.19 sec +35/80 Test #35: test_search_blastp_fm_sam ........ Passed 0.31 sec Start 36: test_search_blastp_fm_bam -36/80 Test #36: test_search_blastp_fm_bam ........ Passed 1.38 sec +36/80 Test #36: test_search_blastp_fm_bam ........ Passed 0.30 sec Start 37: test_search_blastp_fm_m9.gz -37/80 Test #37: test_search_blastp_fm_m9.gz ...... Passed 1.26 sec +37/80 Test #37: test_search_blastp_fm_m9.gz ...... Passed 0.34 sec Start 38: test_search_blastp_fm_sam.bz2 -38/80 Test #38: test_search_blastp_fm_sam.bz2 .... Passed 1.26 sec +38/80 Test #38: test_search_blastp_fm_sam.bz2 .... Passed 0.37 sec Start 39: test_search_blastx_sa_m0 -39/80 Test #39: test_search_blastx_sa_m0 ......... Passed 4.03 sec +39/80 Test #39: test_search_blastx_sa_m0 ......... Passed 0.94 sec Start 40: test_search_blastx_sa_m8 -40/80 Test #40: test_search_blastx_sa_m8 ......... Passed 3.05 sec +40/80 Test #40: test_search_blastx_sa_m8 ......... Passed 0.86 sec Start 41: test_search_blastx_sa_m9 -41/80 Test #41: test_search_blastx_sa_m9 ......... Passed 2.85 sec +41/80 Test #41: test_search_blastx_sa_m9 ......... Passed 0.85 sec Start 42: test_search_blastx_sa_sam -42/80 Test #42: test_search_blastx_sa_sam ........ Passed 3.54 sec +42/80 Test #42: test_search_blastx_sa_sam ........ Passed 0.88 sec Start 43: test_search_blastx_sa_bam -43/80 Test #43: test_search_blastx_sa_bam ........ Passed 3.90 sec +43/80 Test #43: test_search_blastx_sa_bam ........ Passed 0.85 sec Start 44: test_search_blastx_sa_m9.gz -44/80 Test #44: test_search_blastx_sa_m9.gz ...... Passed 3.86 sec +44/80 Test #44: test_search_blastx_sa_m9.gz ...... Passed 0.92 sec Start 45: test_search_blastx_sa_sam.bz2 -45/80 Test #45: test_search_blastx_sa_sam.bz2 .... Passed 5.92 sec +45/80 Test #45: test_search_blastx_sa_sam.bz2 .... Passed 1.62 sec Start 46: test_search_blastx_fm_m0 -46/80 Test #46: test_search_blastx_fm_m0 ......... Passed 4.04 sec +46/80 Test #46: test_search_blastx_fm_m0 ......... Passed 1.14 sec Start 47: test_search_blastx_fm_m8 -47/80 Test #47: test_search_blastx_fm_m8 ......... Passed 4.37 sec +47/80 Test #47: test_search_blastx_fm_m8 ......... Passed 1.03 sec Start 48: test_search_blastx_fm_m9 -48/80 Test #48: test_search_blastx_fm_m9 ......... Passed 4.14 sec +48/80 Test #48: test_search_blastx_fm_m9 ......... Passed 0.99 sec Start 49: test_search_blastx_fm_sam -49/80 Test #49: test_search_blastx_fm_sam ........ Passed 4.52 sec +49/80 Test #49: test_search_blastx_fm_sam ........ Passed 1.04 sec Start 50: test_search_blastx_fm_bam -50/80 Test #50: test_search_blastx_fm_bam ........ Passed 3.82 sec +50/80 Test #50: test_search_blastx_fm_bam ........ Passed 1.03 sec Start 51: test_search_blastx_fm_m9.gz -51/80 Test #51: test_search_blastx_fm_m9.gz ...... Passed 5.07 sec +51/80 Test #51: test_search_blastx_fm_m9.gz ...... Passed 1.12 sec Start 52: test_search_blastx_fm_sam.bz2 -52/80 Test #52: test_search_blastx_fm_sam.bz2 .... Passed 4.68 sec +52/80 Test #52: test_search_blastx_fm_sam.bz2 .... Passed 1.53 sec Start 53: test_search_tblastn_sa_m0 -53/80 Test #53: test_search_tblastn_sa_m0 ........ Passed 3.65 sec +53/80 Test #53: test_search_tblastn_sa_m0 ........ Passed 0.97 sec Start 54: test_search_tblastn_sa_m8 -54/80 Test #54: test_search_tblastn_sa_m8 ........ Passed 2.93 sec +54/80 Test #54: test_search_tblastn_sa_m8 ........ Passed 0.72 sec Start 55: test_search_tblastn_sa_m9 -55/80 Test #55: test_search_tblastn_sa_m9 ........ Passed 3.13 sec +55/80 Test #55: test_search_tblastn_sa_m9 ........ Passed 0.74 sec Start 56: test_search_tblastn_sa_sam -56/80 Test #56: test_search_tblastn_sa_sam ....... Passed 2.64 sec +56/80 Test #56: test_search_tblastn_sa_sam ....... Passed 0.76 sec Start 57: test_search_tblastn_sa_bam -57/80 Test #57: test_search_tblastn_sa_bam ....... Passed 3.25 sec +57/80 Test #57: test_search_tblastn_sa_bam ....... Passed 0.72 sec Start 58: test_search_tblastn_sa_m9.gz -58/80 Test #58: test_search_tblastn_sa_m9.gz ..... Passed 3.46 sec +58/80 Test #58: test_search_tblastn_sa_m9.gz ..... Passed 0.83 sec Start 59: test_search_tblastn_sa_sam.bz2 -59/80 Test #59: test_search_tblastn_sa_sam.bz2 ... Passed 5.71 sec +59/80 Test #59: test_search_tblastn_sa_sam.bz2 ... Passed 1.10 sec Start 60: test_search_tblastn_fm_m0 -60/80 Test #60: test_search_tblastn_fm_m0 ........ Passed 3.37 sec +60/80 Test #60: test_search_tblastn_fm_m0 ........ Passed 0.97 sec Start 61: test_search_tblastn_fm_m8 -61/80 Test #61: test_search_tblastn_fm_m8 ........ Passed 2.69 sec +61/80 Test #61: test_search_tblastn_fm_m8 ........ Passed 0.75 sec Start 62: test_search_tblastn_fm_m9 -62/80 Test #62: test_search_tblastn_fm_m9 ........ Passed 3.24 sec +62/80 Test #62: test_search_tblastn_fm_m9 ........ Passed 0.80 sec Start 63: test_search_tblastn_fm_sam -63/80 Test #63: test_search_tblastn_fm_sam ....... Passed 3.21 sec +63/80 Test #63: test_search_tblastn_fm_sam ....... Passed 0.80 sec Start 64: test_search_tblastn_fm_bam -64/80 Test #64: test_search_tblastn_fm_bam ....... Passed 3.24 sec +64/80 Test #64: test_search_tblastn_fm_bam ....... Passed 0.77 sec Start 65: test_search_tblastn_fm_m9.gz -65/80 Test #65: test_search_tblastn_fm_m9.gz ..... Passed 3.40 sec +65/80 Test #65: test_search_tblastn_fm_m9.gz ..... Passed 0.86 sec Start 66: test_search_tblastn_fm_sam.bz2 -66/80 Test #66: test_search_tblastn_fm_sam.bz2 ... Passed 4.70 sec +66/80 Test #66: test_search_tblastn_fm_sam.bz2 ... Passed 1.14 sec Start 67: test_search_tblastx_sa_m0 -67/80 Test #67: test_search_tblastx_sa_m0 ........ Passed 15.78 sec +67/80 Test #67: test_search_tblastx_sa_m0 ........ Passed 3.92 sec Start 68: test_search_tblastx_sa_m8 -68/80 Test #68: test_search_tblastx_sa_m8 ........ Passed 11.27 sec +68/80 Test #68: test_search_tblastx_sa_m8 ........ Passed 3.24 sec Start 69: test_search_tblastx_sa_m9 -69/80 Test #69: test_search_tblastx_sa_m9 ........ Passed 21.05 sec +69/80 Test #69: test_search_tblastx_sa_m9 ........ Passed 3.11 sec Start 70: test_search_tblastx_sa_sam -70/80 Test #70: test_search_tblastx_sa_sam ....... Passed 12.73 sec +70/80 Test #70: test_search_tblastx_sa_sam ....... Passed 3.44 sec Start 71: test_search_tblastx_sa_bam -71/80 Test #71: test_search_tblastx_sa_bam ....... Passed 16.16 sec +71/80 Test #71: test_search_tblastx_sa_bam ....... Passed 3.78 sec Start 72: test_search_tblastx_sa_m9.gz -72/80 Test #72: test_search_tblastx_sa_m9.gz ..... Passed 18.90 sec +72/80 Test #72: test_search_tblastx_sa_m9.gz ..... Passed 3.69 sec Start 73: test_search_tblastx_sa_sam.bz2 -73/80 Test #73: test_search_tblastx_sa_sam.bz2 ... Passed 21.57 sec +73/80 Test #73: test_search_tblastx_sa_sam.bz2 ... Passed 6.27 sec Start 74: test_search_tblastx_fm_m0 -74/80 Test #74: test_search_tblastx_fm_m0 ........ Passed 18.32 sec +74/80 Test #74: test_search_tblastx_fm_m0 ........ Passed 3.92 sec Start 75: test_search_tblastx_fm_m8 -75/80 Test #75: test_search_tblastx_fm_m8 ........ Passed 18.22 sec +75/80 Test #75: test_search_tblastx_fm_m8 ........ Passed 3.25 sec Start 76: test_search_tblastx_fm_m9 -76/80 Test #76: test_search_tblastx_fm_m9 ........ Passed 20.76 sec +76/80 Test #76: test_search_tblastx_fm_m9 ........ Passed 3.63 sec Start 77: test_search_tblastx_fm_sam -77/80 Test #77: test_search_tblastx_fm_sam ....... Passed 19.73 sec +77/80 Test #77: test_search_tblastx_fm_sam ....... Passed 3.71 sec Start 78: test_search_tblastx_fm_bam -78/80 Test #78: test_search_tblastx_fm_bam ....... Passed 15.21 sec +78/80 Test #78: test_search_tblastx_fm_bam ....... Passed 3.62 sec Start 79: test_search_tblastx_fm_m9.gz -79/80 Test #79: test_search_tblastx_fm_m9.gz ..... Passed 20.10 sec +79/80 Test #79: test_search_tblastx_fm_m9.gz ..... Passed 4.33 sec Start 80: test_search_tblastx_fm_sam.bz2 -80/80 Test #80: test_search_tblastx_fm_sam.bz2 ... Passed 37.75 sec +80/80 Test #80: test_search_tblastx_fm_sam.bz2 ... Passed 6.23 sec 100% tests passed, 0 tests failed out of 80 -Total Test time (real) = 512.83 sec +Total Test time (real) = 119.96 sec make[1]: Leaving directory '/build/lambda-align-1.0.3' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary @@ -2727,7 +2766,7 @@ dh_testroot -O--builddirectory=build dh_prep -O--builddirectory=build dh_auto_install --destdir=debian/lambda-align/ -O--builddirectory=build - cd build && make -j16 install DESTDIR=/build/lambda-align-1.0.3/debian/lambda-align AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd build && make -j15 install DESTDIR=/build/lambda-align-1.0.3/debian/lambda-align AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/lambda-align-1.0.3/build' /usr/bin/cmake -S/build/lambda-align-1.0.3 -B/build/lambda-align-1.0.3/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/lambda-align-1.0.3/build/CMakeFiles /build/lambda-align-1.0.3/build//CMakeFiles/progress.marks @@ -2740,9 +2779,9 @@ make[3]: Entering directory '/build/lambda-align-1.0.3/build' cd /build/lambda-align-1.0.3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/lambda-align-1.0.3 /build/lambda-align-1.0.3/src /build/lambda-align-1.0.3/build /build/lambda-align-1.0.3/build/src /build/lambda-align-1.0.3/build/src/CMakeFiles/lambda_indexer.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/lambda-align-1.0.3/build' -make -f src/CMakeFiles/lambda.dir/build.make src/CMakeFiles/lambda.dir/build -make[3]: Leaving directory '/build/lambda-align-1.0.3/build' make -f src/CMakeFiles/lambda_indexer.dir/build.make src/CMakeFiles/lambda_indexer.dir/build +make[3]: Leaving directory '/build/lambda-align-1.0.3/build' +make -f src/CMakeFiles/lambda.dir/build.make src/CMakeFiles/lambda.dir/build make[3]: Entering directory '/build/lambda-align-1.0.3/build' make[3]: Nothing to be done for 'src/CMakeFiles/lambda_indexer.dir/build'. make[3]: Leaving directory '/build/lambda-align-1.0.3/build' @@ -2817,12 +2856,14 @@ 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/2848872/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2848872/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/1503918 and its subdirectories -I: Current time: Sat May 18 08:01:50 -12 2024 -I: pbuilder-time-stamp: 1716062510 +I: removing directory /srv/workspace/pbuilder/2848872 and its subdirectories +I: Current time: Mon Apr 17 03:44:24 +14 2023 +I: pbuilder-time-stamp: 1681652664