Diff of the two buildlogs: -- --- b1/build.log 2024-07-19 19:05:26.643167015 +0000 +++ b2/build.log 2024-07-19 19:06:21.460838460 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Aug 21 13:27:35 -12 2025 -I: pbuilder-time-stamp: 1755826055 +I: Current time: Sat Jul 20 09:05:29 +14 2024 +I: pbuilder-time-stamp: 1721415929 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -17,8 +17,8 @@ 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.OW7yMUgn/trustedkeys.kbx': General error -gpgv: Signature made Sun Feb 23 19:26:03 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.BrUlEY7n/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 @@ -33,134 +33,165 @@ dpkg-source: info: applying spelling.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/151210/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3195579/tmp/hooks/D01_modify_environment starting +debug: Running on infom01-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 Jul 20 09:05 /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/3195579/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3195579/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - 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]="x86_64-pc-linux-gnu") + BASH_VERSION='5.1.4(1)-release' + BUILDDIR=/build/reproducible-path + 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,-fixfilepath parallel=12 ' - DISTRIBUTION='bullseye' - HOME='/root' - HOST_ARCH='amd64' + DIRSTACK=() + DISTRIBUTION=bullseye + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='fd649898f402485dae77e9c022c1ad92' - 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='151210' - PS1='# ' - PS2='> ' + INVOCATION_ID=c733a269fe37499aaf4058e3c88f1cf8 + 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=3195579 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.bGQXTKpT/pbuilderrc_1cpD --distribution bullseye --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.bGQXTKpT/b1 --logfile b1/build.log loki_2.4.7.4-10.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' + 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.bGQXTKpT/pbuilderrc_jXH2 --distribution bullseye --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.bGQXTKpT/b2 --logfile b2/build.log loki_2.4.7.4-10.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' I: uname -a - Linux infom02-amd64 6.7.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.7.12-1~bpo12+1 (2024-05-06) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-23-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.99-1 (2024-07-15) x86_64 GNU/Linux I: ls -l /bin total 5476 - -rwxr-xr-x 1 root root 1234376 Mar 27 2022 bash - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 38984 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 38984 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 18424 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 43936 Sep 23 2020 cat - -rwxr-xr-x 1 root root 72672 Sep 23 2020 chgrp - -rwxr-xr-x 1 root root 64448 Sep 23 2020 chmod - -rwxr-xr-x 1 root root 72672 Sep 23 2020 chown - -rwxr-xr-x 1 root root 151168 Sep 23 2020 cp - -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash - -rwxr-xr-x 1 root root 113664 Sep 23 2020 date - -rwxr-xr-x 1 root root 80968 Sep 23 2020 dd - -rwxr-xr-x 1 root root 93936 Sep 23 2020 df - -rwxr-xr-x 1 root root 147176 Sep 23 2020 dir - -rwxr-xr-x 1 root root 84440 Mar 27 2024 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 39712 Sep 23 2020 echo - -rwxr-xr-x 1 root root 28 Jan 24 2023 egrep - -rwxr-xr-x 1 root root 39680 Sep 23 2020 false - -rwxr-xr-x 1 root root 28 Jan 24 2023 fgrep - -rwxr-xr-x 1 root root 69032 Mar 27 2024 findmnt - -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount - -rwxr-xr-x 1 root root 203072 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 98048 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 22600 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 72840 Sep 23 2020 ln - -rwxr-xr-x 1 root root 56952 Feb 7 2020 login - -rwxr-xr-x 1 root root 147176 Sep 23 2020 ls - -rwxr-xr-x 1 root root 149736 Mar 27 2024 lsblk - -rwxr-xr-x 1 root root 85184 Sep 23 2020 mkdir - -rwxr-xr-x 1 root root 76896 Sep 23 2020 mknod - -rwxr-xr-x 1 root root 48064 Sep 23 2020 mktemp - -rwxr-xr-x 1 root root 59632 Mar 27 2024 more - -rwsr-xr-x 1 root root 55528 Mar 27 2024 mount - -rwxr-xr-x 1 root root 18664 Mar 27 2024 mountpoint - -rwxr-xr-x 1 root root 147080 Sep 23 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Dec 16 2021 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 43872 Sep 23 2020 pwd - lrwxrwxrwx 1 root root 4 Mar 27 2022 rbash -> bash - -rwxr-xr-x 1 root root 52032 Sep 23 2020 readlink - -rwxr-xr-x 1 root root 72704 Sep 23 2020 rm - -rwxr-xr-x 1 root root 52032 Sep 23 2020 rmdir - -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Aug 9 03:47 sh -> dash - -rwxr-xr-x 1 root root 43808 Sep 23 2020 sleep - -rwxr-xr-x 1 root root 84928 Sep 23 2020 stty - -rwsr-xr-x 1 root root 71912 Mar 27 2024 su - -rwxr-xr-x 1 root root 39744 Sep 23 2020 sync - -rwxr-xr-x 1 root root 531928 Jan 19 2024 tar - -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 101408 Sep 23 2020 touch - -rwxr-xr-x 1 root root 39680 Sep 23 2020 true - -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server - -rwsr-xr-x 1 root root 35040 Mar 27 2024 umount - -rwxr-xr-x 1 root root 39744 Sep 23 2020 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 147176 Sep 23 2020 vdir - -rwxr-xr-x 1 root root 63744 Mar 27 2024 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 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 5898 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 8049 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/151210/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1234376 Mar 28 2022 bash + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 38984 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 38984 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 18424 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 43936 Sep 24 2020 cat + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chgrp + -rwxr-xr-x 1 root root 64448 Sep 24 2020 chmod + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chown + -rwxr-xr-x 1 root root 151168 Sep 24 2020 cp + -rwxr-xr-x 1 root root 125560 Dec 11 2020 dash + -rwxr-xr-x 1 root root 113664 Sep 24 2020 date + -rwxr-xr-x 1 root root 80968 Sep 24 2020 dd + -rwxr-xr-x 1 root root 93936 Sep 24 2020 df + -rwxr-xr-x 1 root root 147176 Sep 24 2020 dir + -rwxr-xr-x 1 root root 84440 Mar 29 00:09 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 39712 Sep 24 2020 echo + -rwxr-xr-x 1 root root 28 Jan 25 2023 egrep + -rwxr-xr-x 1 root root 39680 Sep 24 2020 false + -rwxr-xr-x 1 root root 28 Jan 25 2023 fgrep + -rwxr-xr-x 1 root root 69032 Mar 29 00:09 findmnt + -rwsr-xr-x 1 root root 34896 Feb 27 2021 fusermount + -rwxr-xr-x 1 root root 203072 Jan 25 2023 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 98048 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 22600 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 72840 Sep 24 2020 ln + -rwxr-xr-x 1 root root 56952 Feb 8 2020 login + -rwxr-xr-x 1 root root 147176 Sep 24 2020 ls + -rwxr-xr-x 1 root root 149736 Mar 29 00:09 lsblk + -rwxr-xr-x 1 root root 85184 Sep 24 2020 mkdir + -rwxr-xr-x 1 root root 76896 Sep 24 2020 mknod + -rwxr-xr-x 1 root root 48064 Sep 24 2020 mktemp + -rwxr-xr-x 1 root root 59632 Mar 29 00:09 more + -rwsr-xr-x 1 root root 55528 Mar 29 00:09 mount + -rwxr-xr-x 1 root root 18664 Mar 29 00:09 mountpoint + -rwxr-xr-x 1 root root 147080 Sep 24 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Dec 17 2021 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43872 Sep 24 2020 pwd + lrwxrwxrwx 1 root root 4 Mar 28 2022 rbash -> bash + -rwxr-xr-x 1 root root 52032 Sep 24 2020 readlink + -rwxr-xr-x 1 root root 72704 Sep 24 2020 rm + -rwxr-xr-x 1 root root 52032 Sep 24 2020 rmdir + -rwxr-xr-x 1 root root 27472 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed + lrwxrwxrwx 1 root root 9 Jul 20 09:05 sh -> /bin/bash + -rwxr-xr-x 1 root root 43808 Sep 24 2020 sleep + -rwxr-xr-x 1 root root 84928 Sep 24 2020 stty + -rwsr-xr-x 1 root root 71912 Mar 29 00:09 su + -rwxr-xr-x 1 root root 39744 Sep 24 2020 sync + -rwxr-xr-x 1 root root 531928 Jan 20 23:59 tar + -rwxr-xr-x 1 root root 14456 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 101408 Sep 24 2020 touch + -rwxr-xr-x 1 root root 39680 Sep 24 2020 true + -rwxr-xr-x 1 root root 14328 Feb 27 2021 ulockmgr_server + -rwsr-xr-x 1 root root 35040 Mar 29 00:09 umount + -rwxr-xr-x 1 root root 39744 Sep 24 2020 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 147176 Sep 24 2020 vdir + -rwxr-xr-x 1 root root 63744 Mar 29 00:09 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 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 5898 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 8049 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/3195579/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -227,7 +258,7 @@ Get: 29 http://deb.debian.org/debian bullseye/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 30 http://deb.debian.org/debian bullseye/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian bullseye/main amd64 debhelper all 13.3.4 [1049 kB] -Fetched 18.3 MB in 0s (58.9 MB/s) +Fetched 18.3 MB in 0s (84.8 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 ... 19711 files and directories currently installed.) @@ -372,7 +403,11 @@ fakeroot is already the newest version (1.25.3-1.1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/reproducible-path/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 +I: user script /srv/workspace/pbuilder/3195579/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bullseye +I: user script /srv/workspace/pbuilder/3195579/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/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 +431,7 @@ Looking for dmalloc.h in ${prefix}/include and libdmalloc.a in ${prefix}/lib/x86_64-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 @@ -543,7 +578,6 @@ gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/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/reproducible-path/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 -lex.yy.c:2062:12: warning: 'input' defined but not used [-Wunused-function] setup_ped.c: In function 'setup_pedigree': setup_ped.c:426:13: warning: this statement may fall through [-Wimplicit-fallthrough=] 426 | if(i!=id) { @@ -551,10 +585,10 @@ setup_ped.c:430:11: note: here 430 | default: | ^~~~~~~ +lex.yy.c:2062:12: warning: 'input' defined but not used [-Wunused-function] gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/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_report.o write_report.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/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_utils.o prep_utils.c -gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 write_report.c: In function 'WriteReport': write_report.c:286:7: warning: suggest parentheses around operand of '!' or change '&' to '&&' or '!' to '~' [-Wparentheses] 286 | if(!elem->type&(ST_MODEL|ST_TRAIT)) continue; @@ -562,6 +596,7 @@ write_report.c:300:7: warning: suggest parentheses around operand of '!' or change '&' to '&&' or '!' to '~' [-Wparentheses] 300 | if(!elem->type&(ST_MODEL|ST_TRAIT)) continue; | ^~~~~~~~~~~ +gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/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 In file included from /usr/include/string.h:495, from control_lex.l:18: @@ -575,6 +610,10 @@ /usr/include/x86_64-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)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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; + | ^~~~ 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; @@ -586,11 +625,6 @@ gen_elim.c:1155:24: warning: variable 'order1' set but not used [-Wunused-but-set-variable] 1155 | int *g_perm,*order=0,*order1; | ^~~~~~ -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/reproducible-path/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 gen_elim.c: In function 'logical_peel': gen_elim.c:1268:17: warning: variable 'mark' set but not used [-Wunused-but-set-variable] 1268 | struct Marker *mark; @@ -598,6 +632,7 @@ 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/reproducible-path/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) @@ -764,11 +799,6 @@ param_lex.c:1260:17: warning: 'yyunput' defined but not used [-Wunused-function] 1260 | static void yyunput (int c, register char * yy_bp ) | ^~~~~~~ -gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 -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; - | ^~ 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)); @@ -782,21 +812,16 @@ | | | | int long unsigned int | %ld +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; + | ^~ +gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 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; | ^~~~~~ -gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/reproducible-path/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]; - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ -loki_init.c:126:4: note: here - 126 | case 1: - | ^~~~ 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); @@ -804,37 +829,54 @@ 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/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 +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]; + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +loki_init.c:126:4: note: here + 126 | case 1: + | ^~~~ +gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/reproducible-path/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: In function 'sample_mpos': loki_tlmoves.c:152:29: warning: variable 'idd' set but not used [-Wunused-but-set-variable] 152 | int i,j,locus,k2=-1,k3,ids,idd,sx,**seg,s,s1; | ^~~ -gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 meiosis_scan.c: In function 'meiosis_scan': 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/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 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))); | ~~^~~~ gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 loki_tlmoves.c: In function 'get_tl_position': +gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 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/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/reproducible-path/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); + | ^~~~~~~~~~~~~~~~~~~~~~~ +loki_output.c:346:3: note: here + 346 | case OUTPUT_VERSION_2_3: + | ^~~~ 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); @@ -842,19 +884,13 @@ | | | int | %ld -gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/reproducible-path/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: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/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/reproducible-path/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_output.c: In function 'OutputSample': -loki_output.c:345:3: warning: this statement may fall through [-Wimplicit-fallthrough=] - 345 | OutputSample_2(fptr,lp); - | ^~~~~~~~~~~~~~~~~~~~~~~ -loki_output.c:346:3: note: here - 346 | case OUTPUT_VERSION_2_3: - | ^~~~ gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 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] 25 | double *tp,p1,p2,z,z1,prob=0.0,pp[4],*tmp,*tpp1,*tpp2; @@ -862,14 +898,12 @@ loki_simple_sample.c:25:45: warning: variable 'tpp1' set but not used [-Wunused-but-set-variable] 25 | double *tp,p1,p2,z,z1,prob=0.0,pp[4],*tmp,*tpp1,*tpp2; | ^~~~ -gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 update_segs.o update_segs.c /usr/bin/ar cr libloki.a param_parse.o param_lex.o read_binfiles.o loki_utils.o kinship.o genedrop.o mat_utils.o output_recomb.o seg_pen.o gen_pen.o loki_ibd.o get_founders.o pass_founder_genes.o -/usr/bin/ranlib libloki.a 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; @@ -877,6 +911,7 @@ 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; | ~~~~~~~~~~^~~~ +/usr/bin/ranlib libloki.a loki_simple_peel.c: In function 'loki_simple_peelop_x': loki_simple_peel.c:1278:26: warning: 'cm[1]' may be used uninitialized in this function [-Wmaybe-uninitialized] 1278 | id_set1[i]=(cm[X_PAT]&a1)?l:i1; @@ -2625,8 +2660,8 @@ dh_md5sums dh_builddeb dpkg-deb: building package 'loki' in '../loki_2.4.7.4-10_amd64.deb'. -dpkg-deb: building package 'loki-dbgsym' in '../loki-dbgsym_2.4.7.4-10_amd64.deb'. dpkg-deb: building package 'loki-doc' in '../loki-doc_2.4.7.4-10_all.deb'. +dpkg-deb: building package 'loki-dbgsym' in '../loki-dbgsym_2.4.7.4-10_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../loki_2.4.7.4-10_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -2634,12 +2669,14 @@ 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/3195579/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3195579/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/151210 and its subdirectories -I: Current time: Thu Aug 21 13:28:25 -12 2025 -I: pbuilder-time-stamp: 1755826105 +I: removing directory /srv/workspace/pbuilder/3195579 and its subdirectories +I: Current time: Sat Jul 20 09:06:20 +14 2024 +I: pbuilder-time-stamp: 1721415980