Diff of the two buildlogs: -- --- b1/build.log 2020-08-06 01:43:42.410907306 +0000 +++ b2/build.log 2020-08-06 01:48:38.081727189 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Sep 7 20:06:11 -12 2021 -I: pbuilder-time-stamp: 1631088371 +I: Current time: Thu Aug 6 15:43:45 +14 2020 +I: pbuilder-time-stamp: 1596678225 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration @@ -18,7 +18,7 @@ I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error -gpgv: Signature made Thu Oct 11 17:06:53 2018 -12 +gpgv: Signature made Fri Oct 12 19:06:53 2018 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -33,138 +33,172 @@ dpkg-source: info: applying spelling.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/27381/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/30636/tmp/hooks/D01_modify_environment starting +debug: Running on profitbricks-build2-i386. +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/30636/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/30636/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='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=18' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='i386' + 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]="0" [2]="3" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.0.3(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=10' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='34c908f91ff3454284b3199e789fa968' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - 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='27381' - PS1='# ' - PS2='> ' + INVOCATION_ID=6bd9e270a0b84d1cbf189c33819c3a11 + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-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=30636 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.t3Cyhf61Rc/pbuilderrc_8FzU --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.t3Cyhf61Rc/b1 --logfile b1/build.log loki_2.4.7.4-8.dsc' - SUDO_GID='112' - SUDO_UID='107' - 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/tmp.t3Cyhf61Rc/pbuilderrc_bQ9N --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.t3Cyhf61Rc/b2 --logfile b2/build.log loki_2.4.7.4-8.dsc' + SUDO_GID=112 + SUDO_UID=107 + 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 profitbricks-build6-i386 4.19.0-10-amd64 #1 SMP Debian 4.19.132-1 (2020-07-24) x86_64 GNU/Linux + Linux i-capture-the-hostname 4.19.0-10-686-pae #1 SMP Debian 4.19.132-1 (2020-07-24) i686 GNU/Linux I: ls -l /bin - total 5476 - -rwxr-xr-x 1 root root 1302248 Apr 17 2019 bash - -rwxr-xr-x 3 root root 38280 Jul 10 2019 bunzip2 - -rwxr-xr-x 3 root root 38280 Jul 10 2019 bzcat - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep - -rwxr-xr-x 3 root root 38280 Jul 10 2019 bzip2 - -rwxr-xr-x 1 root root 17768 Jul 10 2019 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore - -rwxr-xr-x 1 root root 38692 Feb 28 2019 cat - -rwxr-xr-x 1 root root 75588 Feb 28 2019 chgrp - -rwxr-xr-x 1 root root 63268 Feb 28 2019 chmod - -rwxr-xr-x 1 root root 75588 Feb 28 2019 chown - -rwxr-xr-x 1 root root 153732 Feb 28 2019 cp - -rwxr-xr-x 1 root root 132820 Jan 17 2019 dash - -rwxr-xr-x 1 root root 120676 Feb 28 2019 date - -rwxr-xr-x 1 root root 92040 Feb 28 2019 dd - -rwxr-xr-x 1 root root 100620 Feb 28 2019 df - -rwxr-xr-x 1 root root 149736 Feb 28 2019 dir - -rwxr-xr-x 1 root root 79412 Jan 9 2019 dmesg - lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname - -rwxr-xr-x 1 root root 34532 Feb 28 2019 echo - -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep - -rwxr-xr-x 1 root root 34532 Feb 28 2019 false - -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep - -rwxr-xr-x 1 root root 67700 Jan 9 2019 findmnt - -rwsr-xr-x 1 root root 30112 Apr 22 2020 fusermount - -rwxr-xr-x 1 root root 206392 Jan 7 2019 grep - -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip - -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe - -rwxr-xr-x 1 root root 100952 Jan 5 2019 gzip - -rwxr-xr-x 1 root root 21916 Sep 26 2018 hostname - -rwxr-xr-x 1 root root 79752 Feb 28 2019 ln - -rwxr-xr-x 1 root root 55400 Jul 26 2018 login - -rwxr-xr-x 1 root root 149736 Feb 28 2019 ls - -rwxr-xr-x 1 root root 112032 Jan 9 2019 lsblk - -rwxr-xr-x 1 root root 87972 Feb 28 2019 mkdir - -rwxr-xr-x 1 root root 79748 Feb 28 2019 mknod - -rwxr-xr-x 1 root root 46916 Feb 28 2019 mktemp - -rwxr-xr-x 1 root root 42348 Jan 9 2019 more - -rwsr-xr-x 1 root root 50592 Jan 9 2019 mount - -rwxr-xr-x 1 root root 13724 Jan 9 2019 mountpoint - -rwxr-xr-x 1 root root 157832 Feb 28 2019 mv - lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 38660 Feb 28 2019 pwd - lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash - -rwxr-xr-x 1 root root 46852 Feb 28 2019 readlink - -rwxr-xr-x 1 root root 75588 Feb 28 2019 rm - -rwxr-xr-x 1 root root 42756 Feb 28 2019 rmdir - -rwxr-xr-x 1 root root 22276 Jan 21 2019 run-parts - -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Sep 7 02:47 sh -> dash - -rwxr-xr-x 1 root root 34532 Feb 28 2019 sleep - -rwxr-xr-x 1 root root 79652 Feb 28 2019 stty - -rwsr-xr-x 1 root root 71072 Jan 9 2019 su - -rwxr-xr-x 1 root root 34564 Feb 28 2019 sync - -rwxr-xr-x 1 root root 504024 Apr 23 2019 tar - -rwxr-xr-x 1 root root 13860 Jan 21 2019 tempfile - -rwxr-xr-x 1 root root 104292 Feb 28 2019 touch - -rwxr-xr-x 1 root root 34532 Feb 28 2019 true - -rwxr-xr-x 1 root root 17768 Apr 22 2020 ulockmgr_server - -rwsr-xr-x 1 root root 30108 Jan 9 2019 umount - -rwxr-xr-x 1 root root 34532 Feb 28 2019 uname - -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress - -rwxr-xr-x 1 root root 149736 Feb 28 2019 vdir - -rwxr-xr-x 1 root root 34208 Jan 9 2019 wdctl - -rwxr-xr-x 1 root root 946 Jan 21 2019 which - lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat - -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp - -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff - -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep - -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep - -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce - -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep - -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless - -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore - -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew -I: user script /srv/workspace/pbuilder/27381/tmp/hooks/D02_print_environment finished + total 5500 + -rwxr-xr-x 1 root root 1302248 Apr 18 2019 bash + -rwxr-xr-x 3 root root 38280 Jul 11 2019 bunzip2 + -rwxr-xr-x 3 root root 38280 Jul 11 2019 bzcat + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep + -rwxr-xr-x 3 root root 38280 Jul 11 2019 bzip2 + -rwxr-xr-x 1 root root 17768 Jul 11 2019 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore + -rwxr-xr-x 1 root root 38692 Mar 1 2019 cat + -rwxr-xr-x 1 root root 75588 Mar 1 2019 chgrp + -rwxr-xr-x 1 root root 63268 Mar 1 2019 chmod + -rwxr-xr-x 1 root root 75588 Mar 1 2019 chown + -rwxr-xr-x 1 root root 153732 Mar 1 2019 cp + -rwxr-xr-x 1 root root 132820 Jan 18 2019 dash + -rwxr-xr-x 1 root root 120676 Mar 1 2019 date + -rwxr-xr-x 1 root root 92040 Mar 1 2019 dd + -rwxr-xr-x 1 root root 100620 Mar 1 2019 df + -rwxr-xr-x 1 root root 149736 Mar 1 2019 dir + -rwxr-xr-x 1 root root 79412 Jan 10 2019 dmesg + lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname + -rwxr-xr-x 1 root root 34532 Mar 1 2019 echo + -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep + -rwxr-xr-x 1 root root 34532 Mar 1 2019 false + -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep + -rwxr-xr-x 1 root root 67700 Jan 10 2019 findmnt + -rwsr-xr-x 1 root root 30112 Apr 23 09:38 fusermount + -rwxr-xr-x 1 root root 206392 Jan 8 2019 grep + -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip + -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe + -rwxr-xr-x 1 root root 100952 Jan 6 2019 gzip + -rwxr-xr-x 1 root root 21916 Sep 27 2018 hostname + -rwxr-xr-x 1 root root 79752 Mar 1 2019 ln + -rwxr-xr-x 1 root root 55400 Jul 27 2018 login + -rwxr-xr-x 1 root root 149736 Mar 1 2019 ls + -rwxr-xr-x 1 root root 112032 Jan 10 2019 lsblk + -rwxr-xr-x 1 root root 87972 Mar 1 2019 mkdir + -rwxr-xr-x 1 root root 79748 Mar 1 2019 mknod + -rwxr-xr-x 1 root root 46916 Mar 1 2019 mktemp + -rwxr-xr-x 1 root root 42348 Jan 10 2019 more + -rwsr-xr-x 1 root root 50592 Jan 10 2019 mount + -rwxr-xr-x 1 root root 13724 Jan 10 2019 mountpoint + -rwxr-xr-x 1 root root 157832 Mar 1 2019 mv + lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 38660 Mar 1 2019 pwd + lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash + -rwxr-xr-x 1 root root 46852 Mar 1 2019 readlink + -rwxr-xr-x 1 root root 75588 Mar 1 2019 rm + -rwxr-xr-x 1 root root 42756 Mar 1 2019 rmdir + -rwxr-xr-x 1 root root 22276 Jan 22 2019 run-parts + -rwxr-xr-x 1 root root 125036 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Aug 6 15:46 sh -> bash + lrwxrwxrwx 1 root root 4 Aug 5 00:46 sh.distrib -> dash + -rwxr-xr-x 1 root root 34532 Mar 1 2019 sleep + -rwxr-xr-x 1 root root 79652 Mar 1 2019 stty + -rwsr-xr-x 1 root root 71072 Jan 10 2019 su + -rwxr-xr-x 1 root root 34564 Mar 1 2019 sync + -rwxr-xr-x 1 root root 504024 Apr 24 2019 tar + -rwxr-xr-x 1 root root 13860 Jan 22 2019 tempfile + -rwxr-xr-x 1 root root 104292 Mar 1 2019 touch + -rwxr-xr-x 1 root root 34532 Mar 1 2019 true + -rwxr-xr-x 1 root root 17768 Apr 23 09:38 ulockmgr_server + -rwsr-xr-x 1 root root 30108 Jan 10 2019 umount + -rwxr-xr-x 1 root root 34532 Mar 1 2019 uname + -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress + -rwxr-xr-x 1 root root 149736 Mar 1 2019 vdir + -rwxr-xr-x 1 root root 34208 Jan 10 2019 wdctl + -rwxr-xr-x 1 root root 946 Jan 22 2019 which + lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat + -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp + -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff + -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep + -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep + -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce + -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep + -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless + -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore + -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew +I: user script /srv/workspace/pbuilder/30636/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -233,7 +267,7 @@ Get: 31 http://deb.debian.org/debian buster/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 32 http://deb.debian.org/debian buster/main i386 po-debconf all 1.0.21 [248 kB] Get: 33 http://deb.debian.org/debian buster/main i386 debhelper all 12.1.1 [1016 kB] -Fetched 19.4 MB in 0s (77.8 MB/s) +Fetched 19.4 MB in 6s (3233 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:i386. (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 ... 19234 files and directories currently installed.) @@ -388,7 +422,7 @@ fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 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 +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 dpkg-buildpackage: info: source package loki dpkg-buildpackage: info: source version 2.4.7.4-8 dpkg-buildpackage: info: source distribution unstable @@ -413,7 +447,7 @@ Looking for dmalloc.h in ${prefix}/include and libdmalloc.a in ${prefix}/lib/i386-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 @@ -506,7 +540,7 @@ # nothing to do here make[1]: Leaving directory '/build/loki-2.4.7.4' dh_auto_build -Nloki-doc - make -j18 + make -j10 make[1]: Entering directory '/build/loki-2.4.7.4' for subdir in libsrc prepsrc lokisrc utils; do \ (cd $subdir; make depend) \ @@ -559,13 +593,6 @@ gcc -g -O2 -ffile-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 match_records.o match_records.c gcc -g -O2 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -gcc -g -O2 -ffile-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_report.o write_report.c -gcc -g -O2 -ffile-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_utils.o prep_utils.c -gcc -g -O2 -ffile-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 -ffile-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 setup_ped.c: In function 'setup_pedigree': setup_ped.c:426:13: warning: this statement may fall through [-Wimplicit-fallthrough=] if(i!=id) { @@ -574,7 +601,12 @@ default: ^~~~~~~ lex.yy.c:2062:12: warning: 'input' defined but not used [-Wunused-function] -gcc -g -O2 -ffile-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 +gcc -g -O2 -ffile-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 -ffile-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 -ffile-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 +gcc -g -O2 -ffile-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_report.o write_report.c +gcc -g -O2 -ffile-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_utils.o prep_utils.c +gcc -g -O2 -ffile-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 write_report.c: In function 'WriteReport': write_report.c:286:7: warning: suggest parentheses around operand of '!' or change '&' to '&&' or '!' to '~' [-Wparentheses] if(!elem->type&(ST_MODEL|ST_TRAIT)) continue; @@ -600,6 +632,8 @@ gen_elim.c:1266:27: warning: variable 'pp1' set but not used [-Wunused-but-set-variable] struct Peelseq_Head *pp,*pp1; ^~~ +gcc -g -O2 -ffile-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 -ffile-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] double max_terms,fill; @@ -636,12 +670,6 @@ gcc -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-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_recomb.o output_recomb.c gcc -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-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 -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-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 -gcc -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-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 param_lex.c: In function 'yy_get_next_buffer': param_lex.c:641:18: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] for ( n = 0; n < max_size && \ @@ -649,11 +677,10 @@ param_lex.c:1161:3: note: in expansion of macro 'YY_INPUT' YY_INPUT( (&YY_CURRENT_BUFFER_LVALUE->yy_ch_buf[number_to_move]), ^~~~~~~~ -gcc -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-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 -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] - int i,i1,j,s,**genes,**seg,comp,cs,nc,locus1; - ^~~~~~ +gen_pen.c: In function 'calc_degree': +gen_pen.c:321:24: warning: variable 'k2' set but not used [-Wunused-but-set-variable] + int i1,j,j1,j2,k=0,k1,k2; + ^~ At top level: param_lex.c:1301:16: warning: 'input' defined but not used [-Wunused-function] static int input (void) @@ -661,12 +688,23 @@ param_lex.c:1260:17: warning: 'yyunput' defined but not used [-Wunused-function] static void yyunput (int c, register char * yy_bp ) ^~~~~~~ -gcc -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-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 -gen_pen.c: In function 'calc_degree': -gen_pen.c:321:24: warning: variable 'k2' set but not used [-Wunused-but-set-variable] - int i1,j,j1,j2,k=0,k1,k2; - ^~ -gcc -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-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 -c -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-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 -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-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 +gcc -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-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 +param_lex.c: In function 'yylex': +gcc -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-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 +param_lex.l:91:11: warning: 'strncpy' specified bound 512 equals destination size [-Wstringop-truncation] + (void)strncpy(linebuf,yytext+1,512); + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +param_lex.l:64:11: warning: 'strncpy' specified bound 512 equals destination size [-Wstringop-truncation] + (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] + int i,i1,j,s,**genes,**seg,comp,cs,nc,locus1; + ^~~~~~ +gcc -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-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 loki_init.c: In function 'InitValues': loki_init.c:125:17: warning: this statement may fall through [-Wimplicit-fallthrough=] tau_beta[mod]*=residual_var[mod]; @@ -674,38 +712,38 @@ loki_init.c:126:4: note: here case 1: ^~~~ +gcc -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-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 +loki_peel.c: In function 'peel_locus': +loki_peel.c:434:11: warning: 'z' may be used uninitialized in this function [-Wmaybe-uninitialized] + like1+=z; + ~~~~~^~~ gcc -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-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 -gcc -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-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 loki_tlmoves.c: In function 'sample_mpos': loki_tlmoves.c:152:29: warning: variable 'idd' set but not used [-Wunused-but-set-variable] int i,j,locus,k2=-1,k3,ids,idd,sx,**seg,s,s1; ^~~ -param_lex.c: In function 'yylex': -param_lex.l:91:11: warning: 'strncpy' specified bound 512 equals destination size [-Wstringop-truncation] - (void)strncpy(linebuf,yytext+1,512); - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -param_lex.l:64:11: warning: 'strncpy' specified bound 512 equals destination size [-Wstringop-truncation] - (void)strncpy(linebuf,yytext,512); - ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-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 +loki_tlmoves.c:210:26: warning: 'x' may be used uninitialized in this function [-Wmaybe-uninitialized] + r=.5*(1.0-exp(.02*(x-x1))); + ~~^~~~ meiosis_scan.c: In function 'meiosis_scan': meiosis_scan.c:162:69: warning: variable 'n_comp1' set but not used [-Wunused-but-set-variable] int sex,kid,**seg,**seg1,kid1,nkids1,*kids1,lffg,symflag,n_qtl,qtl,n_comp1; ^~~~~~~ +gcc -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-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:210:26: warning: 'x' may be used uninitialized in this function [-Wmaybe-uninitialized] - r=.5*(1.0-exp(.02*(x-x1))); - ~~^~~~ gcc -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-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 +loki_tlmoves.c: In function 'get_tl_position': +loki_tlmoves.c:623:10: warning: 'z' may be used uninitialized in this function [-Wmaybe-uninitialized] + prior[i]+=z; + ^~ gcc -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-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 -loki_peel.c: In function 'peel_locus': -loki_peel.c:434:11: warning: 'z' may be used uninitialized in this function [-Wmaybe-uninitialized] - like1+=z; - ~~~~~^~~ gcc -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-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 @@ -716,17 +754,13 @@ loki_output.c:346:3: note: here case OUTPUT_VERSION_2_3: ^~~~ -loki_tlmoves.c: In function 'get_tl_position': -loki_tlmoves.c:623:10: warning: 'z' may be used uninitialized in this function [-Wmaybe-uninitialized] - prior[i]+=z; - ^~ gcc -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-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_complex_peel.c: In function 'loki_complex_peelop': loki_complex_peel.c:379:9: warning: variable 'max_terms' set but not used [-Wunused-but-set-variable] double max_terms,*tp,prob=0.0,z,p1,Konst=0.0; ^~~~~~~~~ -gcc -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-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 gcc -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-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 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] @@ -738,9 +772,6 @@ gcc -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-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 -gcc -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-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 update_segs.o update_segs.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] id_set2[i]=(cm[X_MAT]&a1)?lump[X_MAT]:i; @@ -748,6 +779,11 @@ loki_simple_peel.c:600:26: warning: 'cm[1]' may be used uninitialized in this function [-Wmaybe-uninitialized] id_set1[i]=(cm[X_PAT]&a1)?l:i1; ~~~~~~~~~~^~~~ +gcc -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-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 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-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 +gcc -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-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 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_x': loki_simple_peel.c:1278:26: warning: 'cm[1]' may be used uninitialized in this function [-Wmaybe-uninitialized] id_set1[i]=(cm[X_PAT]&a1)?l:i1; @@ -755,8 +791,6 @@ loki_simple_peel.c:1279:26: warning: 'cm[0]' may be used uninitialized in this function [-Wmaybe-uninitialized] id_set2[i]=(cm[X_MAT]&a1)?lump[X_MAT]:i; ~~~~~~~~~~^~~~ -/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 gcc -g -O2 -ffile-prefix-map=/build/loki-2.4.7.4=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-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 -o loki loki.o loki_peel.o loki_init.o alloc_loki.o loki_sample.o loki_pen.o loki_tlmoves.o meiosis_scan.o loki_identity.o sample_rand.o sample_effects.o loki_setup.o loki_dump.o sample_cens.o handle_res.o print_data.o calc_var_locus.o loki_output.o sample_nu.o loki_complex_peel.o loki_npl.o loki_simple_sample.o loki_simple_peel.o loki_trait_simple_peel.o loki_trait_simple_sample.o get_par_probs.o read_solar_idfile.o peel_to_par.o update_segs.o -Wl,-z,relro -Wl,-z,now -L. -L../libsrc -lloki -lgen -lm make[2]: Leaving directory '/build/loki-2.4.7.4/lokisrc' make[2]: Entering directory '/build/loki-2.4.7.4/utils' @@ -774,7 +808,7 @@ debian/rules override_dh_auto_install-arch make[1]: Entering directory '/build/loki-2.4.7.4' dh_auto_install -a - make -j18 install DESTDIR=/build/loki-2.4.7.4/debian/tmp AM_UPDATE_INFO_DIR=no + make -j10 install DESTDIR=/build/loki-2.4.7.4/debian/tmp AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/loki-2.4.7.4' for subdir in libsrc prepsrc lokisrc utils; do \ (cd $subdir; make) \ @@ -891,21 +925,23 @@ dpkg-gencontrol: warning: package loki: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb +dpkg-deb: building package 'loki-doc' in '../loki-doc_2.4.7.4-8_all.deb'. dpkg-deb: building package 'loki-dbgsym' in '../loki-dbgsym_2.4.7.4-8_i386.deb'. dpkg-deb: building package 'loki' in '../loki_2.4.7.4-8_i386.deb'. -dpkg-deb: building package 'loki-doc' in '../loki-doc_2.4.7.4-8_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../loki_2.4.7.4-8_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration +I: user script /srv/workspace/pbuilder/30636/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/30636/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/27381 and its subdirectories -I: Current time: Tue Sep 7 20:06:41 -12 2021 -I: pbuilder-time-stamp: 1631088401 +I: removing directory /srv/workspace/pbuilder/30636 and its subdirectories +I: Current time: Thu Aug 6 15:48:37 +14 2020 +I: pbuilder-time-stamp: 1596678517