Diff of the two buildlogs: -- --- b1/build.log 2021-08-05 06:44:07.351727782 +0000 +++ b2/build.log 2021-08-05 06:45:24.224844720 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Sep 7 01:05:48 -12 2022 -I: pbuilder-time-stamp: 1662555948 +I: Current time: Thu Aug 5 20:44:10 +14 2021 +I: pbuilder-time-stamp: 1628145850 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -16,8 +16,8 @@ I: copying [./loki_2.4.7.4-10.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig._WzYxxRf/trustedkeys.kbx': General error -gpgv: Signature made Sun Feb 23 19:26:03 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.sqpe3Hqc/trustedkeys.kbx': General error +gpgv: Signature made Mon Feb 24 21:26:03 2020 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -32,135 +32,169 @@ dpkg-source: info: applying spelling.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/21280/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/11952/tmp/hooks/D01_modify_environment starting +debug: Running on codethink12-arm64. +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 +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by 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/11952/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/11952/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='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.1.4(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=8' - DISTRIBUTION='' - HOME='/var/lib/jenkins' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/var/lib/jenkins + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - 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='21280' - PS1='# ' - PS2='> ' + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-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=11952 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/tmp.kn7skF7KOw/pbuilderrc_UAOw --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.kn7skF7KOw/b1 --logfile b1/build.log loki_2.4.7.4-10.dsc' - SUDO_GID='117' - SUDO_UID='110' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - USERNAME='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.16:3128' + 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/tmp.kn7skF7KOw/pbuilderrc_fYK9 --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.kn7skF7KOw/b2 --logfile b2/build.log --extrapackages usrmerge loki_2.4.7.4-10.dsc' + SUDO_GID=117 + SUDO_UID=110 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + USERNAME=root + _='I: set' + http_proxy=http://192.168.101.16:3128 I: uname -a - Linux codethink13-arm64 4.15.0-153-generic #160-Ubuntu SMP Thu Jul 29 07:06:07 UTC 2021 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-153-generic #160-Ubuntu SMP Thu Jul 29 07:06:07 UTC 2021 aarch64 GNU/Linux I: ls -l /bin total 5252 - -rwxr-xr-x 1 root root 1282512 Jun 21 2021 bash - -rwxr-xr-x 3 root root 34808 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 34808 Jul 20 2020 bzcat - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep - -rwxr-xr-x 3 root root 34808 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 14264 Jul 20 2020 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore - -rwxr-xr-x 1 root root 39832 Sep 22 2020 cat - -rwxr-xr-x 1 root root 64512 Sep 22 2020 chgrp - -rwxr-xr-x 1 root root 60368 Sep 22 2020 chmod - -rwxr-xr-x 1 root root 64528 Sep 22 2020 chown - -rwxr-xr-x 1 root root 138896 Sep 22 2020 cp - -rwxr-xr-x 1 root root 129544 Dec 10 2020 dash - -rwxr-xr-x 1 root root 101384 Sep 22 2020 date - -rwxr-xr-x 1 root root 80984 Sep 22 2020 dd - -rwxr-xr-x 1 root root 89824 Sep 22 2020 df - -rwxr-xr-x 1 root root 143088 Sep 22 2020 dir - -rwxr-xr-x 1 root root 76152 Jul 28 2021 dmesg - lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname - -rwxr-xr-x 1 root root 35632 Sep 22 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 31512 Sep 22 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 64856 Jul 28 2021 findmnt - -rwsr-xr-x 1 root root 34824 Feb 26 2021 fusermount - -rwxr-xr-x 1 root root 178400 Nov 9 2020 grep - -rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip - -rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe - -rwxr-xr-x 1 root root 93744 Mar 2 2021 gzip - -rwxr-xr-x 1 root root 18440 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 68720 Sep 22 2020 ln - -rwxr-xr-x 1 root root 52720 Feb 7 2020 login - -rwxr-xr-x 1 root root 143088 Sep 22 2020 ls - -rwxr-xr-x 1 root root 161960 Jul 28 2021 lsblk - -rwxr-xr-x 1 root root 85200 Sep 22 2020 mkdir - -rwxr-xr-x 1 root root 68744 Sep 22 2020 mknod - -rwxr-xr-x 1 root root 43976 Sep 22 2020 mktemp - -rwxr-xr-x 1 root root 51368 Jul 28 2021 more - -rwsr-xr-x 1 root root 51360 Jul 28 2021 mount - -rwxr-xr-x 1 root root 14496 Jul 28 2021 mountpoint - -rwxr-xr-x 1 root root 134808 Sep 22 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 18 2021 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 35720 Sep 22 2020 pwd - lrwxrwxrwx 1 root root 4 Jun 21 2021 rbash -> bash - -rwxr-xr-x 1 root root 43872 Sep 22 2020 readlink - -rwxr-xr-x 1 root root 68592 Sep 22 2020 rm - -rwxr-xr-x 1 root root 43880 Sep 22 2020 rmdir - -rwxr-xr-x 1 root root 19208 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Sep 5 03:47 sh -> dash - -rwxr-xr-x 1 root root 35656 Sep 22 2020 sleep - -rwxr-xr-x 1 root root 72640 Sep 22 2020 stty - -rwsr-xr-x 1 root root 67776 Jul 28 2021 su - -rwxr-xr-x 1 root root 35672 Sep 22 2020 sync - -rwxr-xr-x 1 root root 535768 Feb 16 2021 tar - -rwxr-xr-x 1 root root 10568 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 89120 Sep 22 2020 touch - -rwxr-xr-x 1 root root 31512 Sep 22 2020 true - -rwxr-xr-x 1 root root 14264 Feb 26 2021 ulockmgr_server - -rwsr-xr-x 1 root root 30880 Jul 28 2021 umount - -rwxr-xr-x 1 root root 35640 Sep 22 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress - -rwxr-xr-x 1 root root 143088 Sep 22 2020 vdir - -rwxr-xr-x 1 root root 59584 Jul 28 2021 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat - -rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp - -rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff - -rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep - -rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep - -rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce - -rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep - -rwxr-xr-x 1 root root 2206 Mar 2 2021 zless - -rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore - -rwxr-xr-x 1 root root 4553 Mar 2 2021 znew -I: user script /srv/workspace/pbuilder/21280/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1282512 Jun 22 16:26 bash + -rwxr-xr-x 3 root root 34808 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 34808 Jul 21 2020 bzcat + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep + -rwxr-xr-x 3 root root 34808 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 14264 Jul 21 2020 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore + -rwxr-xr-x 1 root root 39832 Sep 23 2020 cat + -rwxr-xr-x 1 root root 64512 Sep 23 2020 chgrp + -rwxr-xr-x 1 root root 60368 Sep 23 2020 chmod + -rwxr-xr-x 1 root root 64528 Sep 23 2020 chown + -rwxr-xr-x 1 root root 138896 Sep 23 2020 cp + -rwxr-xr-x 1 root root 129544 Dec 11 2020 dash + -rwxr-xr-x 1 root root 101384 Sep 23 2020 date + -rwxr-xr-x 1 root root 80984 Sep 23 2020 dd + -rwxr-xr-x 1 root root 89824 Sep 23 2020 df + -rwxr-xr-x 1 root root 143088 Sep 23 2020 dir + -rwxr-xr-x 1 root root 76152 Jul 29 09:09 dmesg + lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname + -rwxr-xr-x 1 root root 35632 Sep 23 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 31512 Sep 23 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 64856 Jul 29 09:09 findmnt + -rwsr-xr-x 1 root root 34824 Feb 27 06:12 fusermount + -rwxr-xr-x 1 root root 178400 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 13:30 gzexe + -rwxr-xr-x 1 root root 93744 Mar 3 13:30 gzip + -rwxr-xr-x 1 root root 18440 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 68720 Sep 23 2020 ln + -rwxr-xr-x 1 root root 52720 Feb 8 2020 login + -rwxr-xr-x 1 root root 143088 Sep 23 2020 ls + -rwxr-xr-x 1 root root 161960 Jul 29 09:09 lsblk + -rwxr-xr-x 1 root root 85200 Sep 23 2020 mkdir + -rwxr-xr-x 1 root root 68744 Sep 23 2020 mknod + -rwxr-xr-x 1 root root 43976 Sep 23 2020 mktemp + -rwxr-xr-x 1 root root 51368 Jul 29 09:09 more + -rwsr-xr-x 1 root root 51360 Jul 29 09:09 mount + -rwxr-xr-x 1 root root 14496 Jul 29 09:09 mountpoint + -rwxr-xr-x 1 root root 134808 Sep 23 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 19 05:38 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 35720 Sep 23 2020 pwd + lrwxrwxrwx 1 root root 4 Jun 22 16:26 rbash -> bash + -rwxr-xr-x 1 root root 43872 Sep 23 2020 readlink + -rwxr-xr-x 1 root root 68592 Sep 23 2020 rm + -rwxr-xr-x 1 root root 43880 Sep 23 2020 rmdir + -rwxr-xr-x 1 root root 19208 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 114016 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Aug 5 20:44 sh -> bash + lrwxrwxrwx 1 root root 4 Aug 3 23:24 sh.distrib -> dash + -rwxr-xr-x 1 root root 35656 Sep 23 2020 sleep + -rwxr-xr-x 1 root root 72640 Sep 23 2020 stty + -rwsr-xr-x 1 root root 67776 Jul 29 09:09 su + -rwxr-xr-x 1 root root 35672 Sep 23 2020 sync + -rwxr-xr-x 1 root root 535768 Feb 17 23:55 tar + -rwxr-xr-x 1 root root 10568 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 89120 Sep 23 2020 touch + -rwxr-xr-x 1 root root 31512 Sep 23 2020 true + -rwxr-xr-x 1 root root 14264 Feb 27 06:12 ulockmgr_server + -rwsr-xr-x 1 root root 30880 Jul 29 09:09 umount + -rwxr-xr-x 1 root root 35640 Sep 23 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 uncompress + -rwxr-xr-x 1 root root 143088 Sep 23 2020 vdir + -rwxr-xr-x 1 root root 59584 Jul 29 09:09 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Mar 3 13:30 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 13:30 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 13:30 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 13:30 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 13:30 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 13:30 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 13:30 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 13:30 zless + -rwxr-xr-x 1 root root 1842 Mar 3 13:30 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 13:30 znew +I: user script /srv/workspace/pbuilder/11952/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -227,7 +261,7 @@ Get: 29 http://deb.debian.org/debian bullseye/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 30 http://deb.debian.org/debian bullseye/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian bullseye/main arm64 debhelper all 13.3.4 [1049 kB] -Fetched 17.9 MB in 0s (55.3 MB/s) +Fetched 17.9 MB in 0s (55.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19646 files and directories currently installed.) @@ -370,9 +404,42 @@ Building dependency tree... Reading state information... fakeroot is already the newest version (1.25.3-1.1). -0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +The following additional packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl +The following NEW packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge +0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. +Need to get 59.5 kB of archives. +After this operation, 157 kB of additional disk space will be used. +Get:1 http://deb.debian.org/debian bullseye/main arm64 libnumber-compare-perl all 0.03-1.1 [6956 B] +Get:2 http://deb.debian.org/debian bullseye/main arm64 libtext-glob-perl all 0.11-1 [8888 B] +Get:3 http://deb.debian.org/debian bullseye/main arm64 libfile-find-rule-perl all 0.34-1 [30.6 kB] +Get:4 http://deb.debian.org/debian bullseye/main arm64 usrmerge all 25 [13.0 kB] +debconf: delaying package configuration, since apt-utils is not installed +Fetched 59.5 kB in 0s (3107 kB/s) +Selecting previously unselected package libnumber-compare-perl. +(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 ... 21522 files and directories currently installed.) +Preparing to unpack .../libnumber-compare-perl_0.03-1.1_all.deb ... +Unpacking libnumber-compare-perl (0.03-1.1) ... +Selecting previously unselected package libtext-glob-perl. +Preparing to unpack .../libtext-glob-perl_0.11-1_all.deb ... +Unpacking libtext-glob-perl (0.11-1) ... +Selecting previously unselected package libfile-find-rule-perl. +Preparing to unpack .../libfile-find-rule-perl_0.34-1_all.deb ... +Unpacking libfile-find-rule-perl (0.34-1) ... +Selecting previously unselected package usrmerge. +Preparing to unpack .../archives/usrmerge_25_all.deb ... +Unpacking usrmerge (25) ... +Setting up libtext-glob-perl (0.11-1) ... +Setting up libnumber-compare-perl (0.03-1.1) ... +Setting up libfile-find-rule-perl (0.34-1) ... +Setting up usrmerge (25) ... +The system has been successfully converted. +Processing triggers for man-db (2.9.4-2) ... +Not building database; man-db/auto-update is not 'true'. I: Building the package -I: Running cd /build/loki-2.4.7.4/ && 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 > ../loki_2.4.7.4-10_source.changes +hostname: Temporary failure in name resolution +I: Running cd /build/loki-2.4.7.4/ && 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 > ../loki_2.4.7.4-10_source.changes dpkg-buildpackage: info: source package loki dpkg-buildpackage: info: source version 2.4.7.4-10 dpkg-buildpackage: info: source distribution unstable @@ -396,7 +463,7 @@ Looking for dmalloc.h in ${prefix}/include and libdmalloc.a in ${prefix}/lib/aarch64-linux-gnu Looking for dmalloc.h in /usr/local/include and libdmalloc.a in /usr/local/lib Looking for dmalloc.h in /usr/include and libdmalloc.a in /usr/lib -Looking for dmalloc.h in /nonexistent/first-build/include and libdmalloc.a in /nonexistent/first-build/lib +Looking for dmalloc.h in /nonexistent/second-build/include and libdmalloc.a in /nonexistent/second-build/lib checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out @@ -412,19 +479,19 @@ checking for byacc... no checking for ranlib... /usr/bin/ranlib checking for ar... /usr/bin/ar -checking for sed... /bin/sed -checking for cp... /bin/cp -checking for grep... /bin/grep -checking for mv... /bin/mv -checking for gzip... /bin/gzip -checking for chmod... /bin/chmod +checking for sed... /usr/bin/sed +checking for cp... /usr/bin/cp +checking for grep... /usr/bin/grep +checking for mv... /usr/bin/mv +checking for gzip... /usr/bin/gzip +checking for chmod... /usr/bin/chmod checking for perl... /usr/bin/perl checking for makedepend... : checking for sin in -lm... yes checking for accept in -lsocket... no checking how to run the C preprocessor... gcc -E -checking for grep that handles long lines and -e... (cached) /bin/grep -checking for egrep... /bin/grep -E +checking for grep that handles long lines and -e... (cached) /usr/bin/grep +checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/wait.h that is POSIX.1 compatible... yes checking for sys/types.h... yes @@ -548,6 +615,7 @@ | ^~~~~~~ lex.yy.c:2062:12: warning: 'input' defined but not used [-Wunused-function] gcc -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o init_fam.o init_fam.c +gcc -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o output_data.o output_data.c In file included from /usr/include/string.h:495, from control_lex.l:18: In function 'strncpy', @@ -560,7 +628,6 @@ /usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound 4096 equals destination size [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o output_data.o output_data.c gcc -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o get_marker_name.o get_marker_name.c gcc -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o prep.o prep.c gcc -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o calc_nrm.o calc_nrm.c @@ -574,6 +641,7 @@ 300 | if(!elem->type&(ST_MODEL|ST_TRAIT)) continue; | ^~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gen_elim.o gen_elim.c +gcc -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o prep_do_peel_op.o prep_do_peel_op.c gen_elim.c: In function 'min_degree': gen_elim.c:1075:24: warning: variable 'best_fg' set but not used [-Wunused-but-set-variable] 1075 | int x,i1,k1,k2,*trans,best_fg=0; @@ -592,12 +660,11 @@ gen_elim.c:1266:27: warning: variable 'pp1' set but not used [-Wunused-but-set-variable] 1266 | struct Peelseq_Head *pp,*pp1; | ^~~ -gcc -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o prep_do_peel_op.o prep_do_peel_op.c +gcc -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o write_data.o write_data.c prep_do_peel_op.c: In function 'do_peel_op': prep_do_peel_op.c:238:19: warning: variable 'fill' set but not used [-Wunused-but-set-variable] 238 | double max_terms,fill; | ^~~~ -gcc -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o write_data.o write_data.c /usr/bin/ar cr libprep.a control_parse.o control_lex.o read_data.o setup_ped.o recode_fact.o cleanup.o restrict_data.o match_records.o init_fam.o output_data.o get_marker_name.o /usr/bin/ranlib libprep.a (cd compat; make) @@ -762,20 +829,12 @@ | ^~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o seg_pen.o seg_pen.c gcc -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gen_pen.o gen_pen.c -gcc -c -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -DIBD_COMPRESS_PROG=\"/bin/gzip\" loki_ibd.c +gcc -c -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -DIBD_COMPRESS_PROG=\"/usr/bin/gzip\" loki_ibd.c +gcc -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o get_founders.o get_founders.c gen_pen.c: In function 'calc_degree': gen_pen.c:321:24: warning: variable 'k2' set but not used [-Wunused-but-set-variable] 321 | int i1,j,j1,j2,k=0,k1,k2; | ^~ -param_lex.c: In function 'yylex': -param_lex.l:91:11: warning: 'strncpy' specified bound 512 equals destination size [-Wstringop-truncation] - 91 | (void)strncpy(linebuf,yytext+1,512); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -param_lex.l:64:11: warning: 'strncpy' specified bound 512 equals destination size [-Wstringop-truncation] - 64 | (void)strncpy(linebuf,yytext,512); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o get_founders.o get_founders.c -gcc -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o pass_founder_genes.o pass_founder_genes.c loki_ibd.c: In function 'SetupIBD': loki_ibd.c:215:74: warning: format '%d' expects argument of type 'int', but argument 5 has type 'long unsigned int' [-Wformat=] 215 | fprintf(stderr,"Asked for 2*n_locations*n_pairs*sizeof(int)=2*%d*%d*%d=%d bytes\n",j,np,sizeof(int),2*j*np*sizeof(int)); @@ -789,6 +848,14 @@ | | | | int long unsigned int | %ld +gcc -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o pass_founder_genes.o pass_founder_genes.c +param_lex.c: In function 'yylex': +param_lex.l:91:11: warning: 'strncpy' specified bound 512 equals destination size [-Wstringop-truncation] + 91 | (void)strncpy(linebuf,yytext+1,512); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +param_lex.l:64:11: warning: 'strncpy' specified bound 512 equals destination size [-Wstringop-truncation] + 64 | (void)strncpy(linebuf,yytext,512); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ pass_founder_genes.c: In function 'pass_founder_genes': pass_founder_genes.c:35:40: warning: variable 'locus1' set but not used [-Wunused-but-set-variable] 35 | int i,i1,j,s,**genes,**seg,comp,cs,nc,locus1; @@ -796,7 +863,6 @@ gcc -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki.o loki.c gcc -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_peel.o loki_peel.c gcc -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_init.o loki_init.c -gcc -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o alloc_loki.o alloc_loki.c loki_init.c: In function 'InitValues': loki_init.c:125:17: warning: this statement may fall through [-Wimplicit-fallthrough=] 125 | tau_beta[mod]*=residual_var[mod]; @@ -804,6 +870,7 @@ loki_init.c:126:4: note: here 126 | case 1: | ^~~~ +gcc -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o alloc_loki.o alloc_loki.c gcc -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_sample.o loki_sample.c gcc -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_pen.o loki_pen.c gcc -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_tlmoves.o loki_tlmoves.c @@ -812,7 +879,6 @@ 152 | int i,j,locus,k2=-1,k3,ids,idd,sx,**seg,s,s1; | ^~~ gcc -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o meiosis_scan.o meiosis_scan.c -gcc -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_identity.o loki_identity.c loki_tlmoves.c:210:26: warning: 'x' may be used uninitialized in this function [-Wmaybe-uninitialized] 210 | r=.5*(1.0-exp(.02*(x-x1))); | ~~^~~~ @@ -820,19 +886,22 @@ meiosis_scan.c:162:69: warning: variable 'n_comp1' set but not used [-Wunused-but-set-variable] 162 | int sex,kid,**seg,**seg1,kid1,nkids1,*kids1,lffg,symflag,n_qtl,qtl,n_comp1; | ^~~~~~~ +gcc -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_identity.o loki_identity.c gcc -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sample_rand.o sample_rand.c -gcc -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sample_effects.o sample_effects.c -gcc -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_setup.o loki_setup.c loki_tlmoves.c: In function 'get_tl_position': loki_tlmoves.c:623:10: warning: 'z' may be used uninitialized in this function [-Wmaybe-uninitialized] 623 | prior[i]+=z; | ^~ +gcc -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sample_effects.o sample_effects.c +gcc -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_setup.o loki_setup.c gcc -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_dump.o loki_dump.c gcc -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sample_cens.o sample_cens.c gcc -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o handle_res.o handle_res.c gcc -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o print_data.o print_data.c gcc -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o calc_var_locus.o calc_var_locus.c gcc -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_output.o loki_output.c +gcc -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sample_nu.o sample_nu.c +gcc -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_complex_peel.o loki_complex_peel.c loki_output.c: In function 'OutputSample': loki_output.c:345:3: warning: this statement may fall through [-Wimplicit-fallthrough=] 345 | OutputSample_2(fptr,lp); @@ -840,9 +909,6 @@ loki_output.c:346:3: note: here 346 | case OUTPUT_VERSION_2_3: | ^~~~ -gcc -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sample_nu.o sample_nu.c -gcc -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_complex_peel.o loki_complex_peel.c -gcc -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_npl.o loki_npl.c loki_complex_peel.c: In function 'loki_complex_peelop': loki_complex_peel.c:458:155: warning: format '%d' expects argument of type 'int', but argument 8 has type 'long unsigned int' [-Wformat=] 458 | (void)fprintf(stderr,"\nToo many individuals in output R-Function for marker %s\nn_peel = %d, n_all = %d, n_bits1 = %d, required size = %d, LONG_BIT = %d\n",marker[locus].name,n_peel,n_all,n_bits1,n_peel*n_bits1,LK_LONG_BIT); @@ -853,6 +919,7 @@ loki_complex_peel.c:379:9: warning: variable 'max_terms' set but not used [-Wunused-but-set-variable] 379 | double max_terms,*tp,prob=0.0,z,p1,Konst=0.0; | ^~~~~~~~~ +gcc -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_npl.o loki_npl.c gcc -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_simple_sample.o loki_simple_sample.c loki_simple_sample.c: In function 'loki_simple_sample': loki_simple_sample.c:25:51: warning: variable 'tpp2' set but not used [-Wunused-but-set-variable] @@ -863,7 +930,6 @@ | ^~~~ gcc -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_simple_peel.o loki_simple_peel.c gcc -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_trait_simple_peel.o loki_trait_simple_peel.c -gcc -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_trait_simple_sample.o loki_trait_simple_sample.c loki_simple_peel.c: In function 'loki_simple_peelop': loki_simple_peel.c:601:26: warning: 'cm[0]' may be used uninitialized in this function [-Wmaybe-uninitialized] 601 | id_set2[i]=(cm[X_MAT]&a1)?lump[X_MAT]:i; @@ -871,6 +937,7 @@ loki_simple_peel.c:600:26: warning: 'cm[1]' may be used uninitialized in this function [-Wmaybe-uninitialized] 600 | id_set1[i]=(cm[X_PAT]&a1)?l:i1; | ~~~~~~~~~~^~~~ +gcc -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loki_trait_simple_sample.o loki_trait_simple_sample.c gcc -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o get_par_probs.o get_par_probs.c gcc -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o read_solar_idfile.o read_solar_idfile.c gcc -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -W -Wall -pedantic -ffloat-store -Wno-long-long -I../include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o peel_to_par.o peel_to_par.c @@ -1117,10 +1184,10 @@ make[1]: Entering directory '/build/loki-2.4.7.4' cd test; if [ -f Makefile ] ; then make ; fi make[2]: Entering directory '/build/loki-2.4.7.4/test' -/bin/sed s+SED+/bin/sed+g loki_test.in|/bin/sed s+PREP+../prepsrc/prep+g|\ -/bin/sed s+LOKI+../lokisrc/loki+g|/bin/sed s+GREP+/bin/grep+g > tmp +/usr/bin/sed s+SED+/usr/bin/sed+g loki_test.in|/usr/bin/sed s+PREP+../prepsrc/prep+g|\ +/usr/bin/sed s+LOKI+../lokisrc/loki+g|/usr/bin/sed s+GREP+/usr/bin/grep+g > tmp cp tmp loki_test && chmod 755 loki_test -/bin/sed s+COMPRESS+/bin/gzip+g control_gaw9.in > tmp +/usr/bin/sed s+COMPRESS+/usr/bin/gzip+g control_gaw9.in > tmp cp tmp control_gaw9 JV test 1 ... Failed JV test 2 ... Failed @@ -1858,12 +1925,12 @@ make[3]: Leaving directory '/build/loki-2.4.7.4/lokisrc' make[3]: Entering directory '/build/loki-2.4.7.4/utils' for file in ext count dist freq sort_error; do \ -/bin/sed 's!+PERLPROG+!/usr/bin/perl!' $file.in > /build/loki-2.4.7.4/debian/loki/usr/bin/loki_$file; \ -/bin/chmod 755 /build/loki-2.4.7.4/debian/loki/usr/bin/loki_$file; \ +/usr/bin/sed 's!+PERLPROG+!/usr/bin/perl!' $file.in > /build/loki-2.4.7.4/debian/loki/usr/bin/loki_$file; \ +/usr/bin/chmod 755 /build/loki-2.4.7.4/debian/loki/usr/bin/loki_$file; \ done for file in qavg hist; do \ -/bin/cp $file /build/loki-2.4.7.4/debian/loki/usr/bin/; \ -/bin/chmod 755 /build/loki-2.4.7.4/debian/loki/usr/bin/$file ; \ +/usr/bin/cp $file /build/loki-2.4.7.4/debian/loki/usr/bin/; \ +/usr/bin/chmod 755 /build/loki-2.4.7.4/debian/loki/usr/bin/$file ; \ done make[3]: Leaving directory '/build/loki-2.4.7.4/utils' make[2]: Leaving directory '/build/loki-2.4.7.4' @@ -2583,12 +2650,12 @@ make[3]: Leaving directory '/build/loki-2.4.7.4/lokisrc' make[3]: Entering directory '/build/loki-2.4.7.4/utils' for file in ext count dist freq sort_error; do \ -/bin/sed 's!+PERLPROG+!/usr/bin/perl!' $file.in > /build/loki-2.4.7.4/debian/loki/usr/bin/loki_$file; \ -/bin/chmod 755 /build/loki-2.4.7.4/debian/loki/usr/bin/loki_$file; \ +/usr/bin/sed 's!+PERLPROG+!/usr/bin/perl!' $file.in > /build/loki-2.4.7.4/debian/loki/usr/bin/loki_$file; \ +/usr/bin/chmod 755 /build/loki-2.4.7.4/debian/loki/usr/bin/loki_$file; \ done for file in qavg hist; do \ -/bin/cp $file /build/loki-2.4.7.4/debian/loki/usr/bin/; \ -/bin/chmod 755 /build/loki-2.4.7.4/debian/loki/usr/bin/$file ; \ +/usr/bin/cp $file /build/loki-2.4.7.4/debian/loki/usr/bin/; \ +/usr/bin/chmod 755 /build/loki-2.4.7.4/debian/loki/usr/bin/$file ; \ done make[3]: Leaving directory '/build/loki-2.4.7.4/utils' make[2]: Leaving directory '/build/loki-2.4.7.4' @@ -2634,12 +2701,14 @@ 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/11952/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/11952/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/21280 and its subdirectories -I: Current time: Wed Sep 7 01:07:06 -12 2022 -I: pbuilder-time-stamp: 1662556026 +I: removing directory /srv/workspace/pbuilder/11952 and its subdirectories +I: Current time: Thu Aug 5 20:45:23 +14 2021 +I: pbuilder-time-stamp: 1628145923