Diff of the two buildlogs: -- --- b1/build.log 2021-06-11 10:12:57.126658178 +0000 +++ b2/build.log 2021-06-11 10:13:22.441708553 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Jun 10 22:08:53 -12 2021 -I: pbuilder-time-stamp: 1623406133 +I: Current time: Fri Jul 15 06:35:57 +14 2022 +I: pbuilder-time-stamp: 1657816557 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 [./maq_0.7.1-9.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.ogyzogBg/trustedkeys.kbx': General error -gpgv: Signature made Sun Nov 15 22:45:18 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.vJX1RGZW/trustedkeys.kbx': General error +gpgv: Signature made Tue Nov 17 00:45:18 2020 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -32,137 +32,171 @@ dpkg-source: info: applying mayhem.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/14043/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/57364/tmp/hooks/D01_modify_environment starting +debug: Running on ionos6-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/57364/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/57364/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,-fixfilepath parallel=10' - 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]="1" [2]="4" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.1.4(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=18' + 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='85346621488849c4a1230c13d233ed22' - 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='14043' - PS1='# ' - PS2='> ' + INVOCATION_ID=e9a00dd4aa9c4b5482ac6c5dab42b5b3 + 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=57364 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.IZ8IxzQK0a/pbuilderrc_hJLE --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.IZ8IxzQK0a/b1 --logfile b1/build.log maq_0.7.1-9.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://78.137.99.97:3128' + 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.IZ8IxzQK0a/pbuilderrc_p8ig --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.IZ8IxzQK0a/b2 --logfile b2/build.log --extrapackages usrmerge maq_0.7.1-9.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://85.184.249.68:3128 I: uname -a - Linux ionos12-i386 4.19.0-16-686-pae #1 SMP Debian 4.19.181-1 (2021-03-19) i686 GNU/Linux + Linux i-capture-the-hostname 4.19.0-16-amd64 #1 SMP Debian 4.19.181-1 (2021-03-19) x86_64 GNU/Linux I: ls -l /bin - total 5780 - -rwxr-xr-x 1 root root 1367848 Feb 24 08:57 bash - -rwxr-xr-x 3 root root 38280 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 38280 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 38280 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 17768 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 38824 Sep 22 2020 cat - -rwxr-xr-x 1 root root 71624 Sep 22 2020 chgrp - -rwxr-xr-x 1 root root 67528 Sep 22 2020 chmod - -rwxr-xr-x 1 root root 75752 Sep 22 2020 chown - -rwxr-xr-x 1 root root 157960 Sep 22 2020 cp - -rwxr-xr-x 1 root root 128724 Dec 10 2020 dash - -rwxr-xr-x 1 root root 124904 Sep 22 2020 date - -rwxr-xr-x 1 root root 92172 Sep 22 2020 dd - -rwxr-xr-x 1 root root 100752 Sep 22 2020 df - -rwxr-xr-x 1 root root 153964 Sep 22 2020 dir - -rwxr-xr-x 1 root root 83644 Feb 7 02:38 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 34664 Sep 22 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 34664 Sep 22 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 71928 Feb 7 02:38 findmnt - -rwsr-xr-x 1 root root 30112 Feb 26 04:12 fusermount - -rwxr-xr-x 1 root root 210488 Nov 9 2020 grep - -rwxr-xr-x 2 root root 2346 Mar 2 11:30 gunzip - -rwxr-xr-x 1 root root 6376 Mar 2 11:30 gzexe - -rwxr-xr-x 1 root root 100952 Mar 2 11:30 gzip - -rwxr-xr-x 1 root root 21916 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 83980 Sep 22 2020 ln - -rwxr-xr-x 1 root root 55572 Feb 7 2020 login - -rwxr-xr-x 1 root root 153964 Sep 22 2020 ls - -rwxr-xr-x 1 root root 153124 Feb 7 02:38 lsblk - -rwxr-xr-x 1 root root 96328 Sep 22 2020 mkdir - -rwxr-xr-x 1 root root 79912 Sep 22 2020 mknod - -rwxr-xr-x 1 root root 47048 Sep 22 2020 mktemp - -rwxr-xr-x 1 root root 58920 Feb 7 02:38 more - -rwsr-xr-x 1 root root 50720 Feb 7 02:38 mount - -rwxr-xr-x 1 root root 13856 Feb 7 02:38 mountpoint - -rwxr-xr-x 1 root root 157996 Sep 22 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 18 03:38 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 38824 Sep 22 2020 pwd - lrwxrwxrwx 1 root root 4 Feb 24 08:57 rbash -> bash - -rwxr-xr-x 1 root root 46984 Sep 22 2020 readlink - -rwxr-xr-x 1 root root 75720 Sep 22 2020 rm - -rwxr-xr-x 1 root root 46984 Sep 22 2020 rmdir - -rwxr-xr-x 1 root root 22292 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Jun 9 21:27 sh -> dash - -rwxr-xr-x 1 root root 34696 Sep 22 2020 sleep - -rwxr-xr-x 1 root root 83880 Sep 22 2020 stty - -rwsr-xr-x 1 root root 79396 Feb 7 02:38 su - -rwxr-xr-x 1 root root 34696 Sep 22 2020 sync - -rwxr-xr-x 1 root root 602584 Feb 16 21:55 tar - -rwxr-xr-x 1 root root 13860 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 108520 Sep 22 2020 touch - -rwxr-xr-x 1 root root 34664 Sep 22 2020 true - -rwxr-xr-x 1 root root 17768 Feb 26 04:12 ulockmgr_server - -rwsr-xr-x 1 root root 30236 Feb 7 02:38 umount - -rwxr-xr-x 1 root root 34664 Sep 22 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress - -rwxr-xr-x 1 root root 153964 Sep 22 2020 vdir - -rwxr-xr-x 1 root root 63024 Feb 7 02:38 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Mar 2 11:30 zcat - -rwxr-xr-x 1 root root 1678 Mar 2 11:30 zcmp - -rwxr-xr-x 1 root root 5880 Mar 2 11:30 zdiff - -rwxr-xr-x 1 root root 29 Mar 2 11:30 zegrep - -rwxr-xr-x 1 root root 29 Mar 2 11:30 zfgrep - -rwxr-xr-x 1 root root 2081 Mar 2 11:30 zforce - -rwxr-xr-x 1 root root 7585 Mar 2 11:30 zgrep - -rwxr-xr-x 1 root root 2206 Mar 2 11:30 zless - -rwxr-xr-x 1 root root 1842 Mar 2 11:30 zmore - -rwxr-xr-x 1 root root 4553 Mar 2 11:30 znew -I: user script /srv/workspace/pbuilder/14043/tmp/hooks/D02_print_environment finished + total 5776 + -rwxr-xr-x 1 root root 1367848 Feb 25 2021 bash + -rwxr-xr-x 3 root root 38280 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 38280 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 38280 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 17768 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 38824 Sep 23 2020 cat + -rwxr-xr-x 1 root root 71624 Sep 23 2020 chgrp + -rwxr-xr-x 1 root root 67528 Sep 23 2020 chmod + -rwxr-xr-x 1 root root 75752 Sep 23 2020 chown + -rwxr-xr-x 1 root root 157960 Sep 23 2020 cp + -rwxr-xr-x 1 root root 128724 Dec 11 2020 dash + -rwxr-xr-x 1 root root 124904 Sep 23 2020 date + -rwxr-xr-x 1 root root 92172 Sep 23 2020 dd + -rwxr-xr-x 1 root root 100752 Sep 23 2020 df + -rwxr-xr-x 1 root root 153964 Sep 23 2020 dir + -rwxr-xr-x 1 root root 83644 Feb 8 2021 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 34664 Sep 23 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 34664 Sep 23 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 71928 Feb 8 2021 findmnt + -rwsr-xr-x 1 root root 30112 Feb 27 2021 fusermount + -rwxr-xr-x 1 root root 210488 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 2021 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 2021 gzexe + -rwxr-xr-x 1 root root 100952 Mar 3 2021 gzip + -rwxr-xr-x 1 root root 21916 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 83980 Sep 23 2020 ln + -rwxr-xr-x 1 root root 55572 Feb 8 2020 login + -rwxr-xr-x 1 root root 153964 Sep 23 2020 ls + -rwxr-xr-x 1 root root 153124 Feb 8 2021 lsblk + -rwxr-xr-x 1 root root 96328 Sep 23 2020 mkdir + -rwxr-xr-x 1 root root 79912 Sep 23 2020 mknod + -rwxr-xr-x 1 root root 47048 Sep 23 2020 mktemp + -rwxr-xr-x 1 root root 58920 Feb 8 2021 more + -rwsr-xr-x 1 root root 50720 Feb 8 2021 mount + -rwxr-xr-x 1 root root 13856 Feb 8 2021 mountpoint + -rwxr-xr-x 1 root root 157996 Sep 23 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 19 2021 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 38824 Sep 23 2020 pwd + lrwxrwxrwx 1 root root 4 Feb 25 2021 rbash -> bash + -rwxr-xr-x 1 root root 46984 Sep 23 2020 readlink + -rwxr-xr-x 1 root root 75720 Sep 23 2020 rm + -rwxr-xr-x 1 root root 46984 Sep 23 2020 rmdir + -rwxr-xr-x 1 root root 22292 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 125036 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Jul 15 06:36 sh -> bash + lrwxrwxrwx 1 root root 4 Jul 15 05:47 sh.distrib -> dash + -rwxr-xr-x 1 root root 34696 Sep 23 2020 sleep + -rwxr-xr-x 1 root root 83880 Sep 23 2020 stty + -rwsr-xr-x 1 root root 79396 Feb 8 2021 su + -rwxr-xr-x 1 root root 34696 Sep 23 2020 sync + -rwxr-xr-x 1 root root 602584 Feb 17 2021 tar + -rwxr-xr-x 1 root root 13860 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 108520 Sep 23 2020 touch + -rwxr-xr-x 1 root root 34664 Sep 23 2020 true + -rwxr-xr-x 1 root root 17768 Feb 27 2021 ulockmgr_server + -rwsr-xr-x 1 root root 30236 Feb 8 2021 umount + -rwxr-xr-x 1 root root 34664 Sep 23 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 2021 uncompress + -rwxr-xr-x 1 root root 153964 Sep 23 2020 vdir + -rwxr-xr-x 1 root root 63024 Feb 8 2021 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Mar 3 2021 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 2021 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 2021 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 2021 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 2021 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 2021 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 2021 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 2021 zless + -rwxr-xr-x 1 root root 1842 Mar 3 2021 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 2021 znew +I: user script /srv/workspace/pbuilder/57364/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -232,7 +266,7 @@ Get: 30 http://deb.debian.org/debian bullseye/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian bullseye/main i386 debhelper all 13.3.4 [1049 kB] Get: 32 http://deb.debian.org/debian bullseye/main i386 zlib1g-dev i386 1:1.2.11.dfsg-2 [194 kB] -Fetched 18.8 MB in 2s (9085 kB/s) +Fetched 18.8 MB in 0s (88.0 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 ... 19675 files and directories currently installed.) @@ -375,8 +409,44 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +The following additional packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl +The following NEW packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge +0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. +Need to get 59.5 kB of archives. +After this operation, 157 kB of additional disk space will be used. +Get:1 http://deb.debian.org/debian bullseye/main i386 libnumber-compare-perl all 0.03-1.1 [6956 B] +Get:2 http://deb.debian.org/debian bullseye/main i386 libtext-glob-perl all 0.11-1 [8888 B] +Get:3 http://deb.debian.org/debian bullseye/main i386 libfile-find-rule-perl all 0.34-1 [30.6 kB] +Get:4 http://deb.debian.org/debian bullseye/main i386 usrmerge all 25 [13.0 kB] +debconf: delaying package configuration, since apt-utils is not installed +Fetched 59.5 kB in 0s (5112 kB/s) +Selecting previously unselected package libnumber-compare-perl. +(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21579 files and directories currently installed.) +Preparing to unpack .../libnumber-compare-perl_0.03-1.1_all.deb ... +Unpacking libnumber-compare-perl (0.03-1.1) ... +Selecting previously unselected package libtext-glob-perl. +Preparing to unpack .../libtext-glob-perl_0.11-1_all.deb ... +Unpacking libtext-glob-perl (0.11-1) ... +Selecting previously unselected package libfile-find-rule-perl. +Preparing to unpack .../libfile-find-rule-perl_0.34-1_all.deb ... +Unpacking libfile-find-rule-perl (0.34-1) ... +Selecting previously unselected package usrmerge. +Preparing to unpack .../archives/usrmerge_25_all.deb ... +Unpacking usrmerge (25) ... +Setting up libtext-glob-perl (0.11-1) ... +Setting up libnumber-compare-perl (0.03-1.1) ... +Setting up libfile-find-rule-perl (0.34-1) ... +Setting up usrmerge (25) ... +The system has been successfully converted. +Processing triggers for man-db (2.9.4-2) ... +Not building database; man-db/auto-update is not 'true'. I: Building the package -I: Running cd /build/maq-0.7.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b +I: Running cd /build/maq-0.7.1/ && 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 maq dpkg-buildpackage: info: source version 0.7.1-9 dpkg-buildpackage: info: source distribution unstable @@ -395,7 +465,7 @@ ./configure --build=i686-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/i386-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes -checking for a thread-safe mkdir -p... /bin/mkdir -p +checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes @@ -416,8 +486,8 @@ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking how to run the C preprocessor... gcc -E -checking for grep that handles long lines and -e... /bin/grep -checking for egrep... /bin/grep -E +checking for grep that handles long lines and -e... /usr/bin/grep +checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes @@ -436,7 +506,7 @@ config.status: creating Makefile config.status: creating config.h dh_auto_build - make -j10 + make -j18 make[1]: Entering directory '/build/maq-0.7.1' make all-am make[2]: Entering directory '/build/maq-0.7.1' @@ -451,6 +521,37 @@ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o match_aux.o match_aux.cc g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o match.o match.cc g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sort_mapping.o sort_mapping.cc +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o assemble.o assemble.cc +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pileup.o pileup.cc +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mapcheck.o mapcheck.cc +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o get_pos.o get_pos.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o assopt.o assopt.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o aux_utils.o aux_utils.c +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o rbcc.o rbcc.cc +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o subsnp.o subsnp.cc +bfa.c: In function 'nst_load_bfa1': +bfa.c:31:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 31 | fread(bfa1->name, sizeof(char), len, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +bfa.c:32:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 32 | fread(&bfa1->ori_len, sizeof(int), 1, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +bfa.c:33:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 33 | fread(&bfa1->len, sizeof(int), 1, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +bfa.c:35:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 35 | fread(bfa1->seq, sizeof(bit64_t), bfa1->len, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +bfa.c:37:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 37 | fread(bfa1->mask, sizeof(bit64_t), bfa1->len, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +bfa.c: In function 'nst_bfa_len': +bfa.c:46:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 46 | fread(&len, sizeof(int), 1, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +bfa.c:48:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 48 | fread(&len, sizeof(int), 1, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastq2bfq.c: In function 'fastq2bfq': fastq2bfq.c:30:5: warning: assignment to 'struct gzFile_s **' from incompatible pointer type 'gzFile' {aka 'struct gzFile_s *'} [-Wincompatible-pointer-types] 30 | fp = gzopen(str, "w"); @@ -483,32 +584,16 @@ | ^~ | | | struct gzFile_s ** -bfa.c: In function 'nst_load_bfa1': In file included from /usr/include/zlib.h:34, from fastq2bfq.c:1: /usr/include/zlib.h:1446:29: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' 1446 | ZEXTERN int ZEXPORT gzwrite OF((gzFile file, | ^~ -bfa.c:31:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 31 | fread(bfa1->name, sizeof(char), len, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -bfa.c:32:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 32 | fread(&bfa1->ori_len, sizeof(int), 1, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -bfa.c:33:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 33 | fread(&bfa1->len, sizeof(int), 1, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastq2bfq.c:50:11: warning: passing argument 1 of 'gzwrite' from incompatible pointer type [-Wincompatible-pointer-types] 50 | gzwrite(fp, seq.s, sizeof(char) * l); | ^~ | | | struct gzFile_s ** -bfa.c:35:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 35 | fread(bfa1->seq, sizeof(bit64_t), bfa1->len, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -bfa.c:37:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 37 | fread(bfa1->mask, sizeof(bit64_t), bfa1->len, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/zlib.h:34, from fastq2bfq.c:1: /usr/include/zlib.h:1446:29: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' @@ -534,13 +619,11 @@ /usr/include/zlib.h:1630:32: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' 1630 | ZEXTERN int ZEXPORT gzclose OF((gzFile file)); | ^~ -bfa.c: In function 'nst_bfa_len': -bfa.c:46:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 46 | fread(&len, sizeof(int), 1, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -bfa.c:48:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 48 | fread(&len, sizeof(int), 1, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pair_stat.o pair_stat.cc +sort_mapping.cc: In function 'int ma_make_pair(const match_aux_t*, const match_info_t*, const match_info_t*, pair_info_t*)': +sort_mapping.cc:59:61: warning: suggest parentheses around arithmetic in operand of '^' [-Wparentheses] + 59 | p->i1 = (((m1->i1>>24)+(m2->i1>>24))<<24) | (m1->i1^m2->i1&0xffffff); + | ~~~~~~^~~~~~~~~ match.cc: In function 'int alt_cal_mm(bit64_t)': match.cc:58:8: warning: suggest parentheses around '+' in operand of '&' [-Wparentheses] 58 | x = x + (x >> 4) & 0x0F0F0F0F0F0F0F0FLLU; @@ -555,6 +638,10 @@ match.cc:70:8: warning: suggest parentheses around '+' in operand of '&' [-Wparentheses] 70 | x = x + (x >> 32) & 0x0000007F; | ~~^~~~~~~~~~~ +assemble.cc: In function 'base_call_aux_t* assemble_cns_collect(assemble_pos_t*, const assemble_aux_t*)': +assemble.cc:106:63: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] + 106 | if (info>>24 < 4 && (info>>8&0x3f) != 0) info = 4<<24 | info&0xffffff; + | ~~~~^~~~~~~~~ match.cc: In function 'void process_candidate(const required_option_t*, int, bit64_t, match_data_t*, ref_canlist_t*)': match.cc:284:39: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct ref_canlist_t'; use assignment or value-initialization instead [-Wclass-memaccess] 284 | memset(list, 0, sizeof(ref_canlist_t)); @@ -562,49 +649,22 @@ match.cc:49:16: note: 'struct ref_canlist_t' declared here 49 | typedef struct { | ^ -sort_mapping.cc: In function 'int ma_make_pair(const match_aux_t*, const match_info_t*, const match_info_t*, pair_info_t*)': -sort_mapping.cc:59:61: warning: suggest parentheses around arithmetic in operand of '^' [-Wparentheses] - 59 | p->i1 = (((m1->i1>>24)+(m2->i1>>24))<<24) | (m1->i1^m2->i1&0xffffff); - | ~~~~~~^~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indel_soa.o indel_soa.cc +mapcheck.cc: In function 'int ma_mapcheck(int, char**)': +mapcheck.cc:60:17: warning: variable 'fpout' set but not used [-Wunused-but-set-variable] + 60 | FILE *fp_bfa, *fpout; + | ^~~~~ match.cc: In function 'void match_search(const match_aux_t*, match_data_t*, const nst_bfa1_t*, int, ref_canlist_t*)': match.cc:292:10: warning: variable 'n_reads' set but not used [-Wunused-but-set-variable] 292 | bit32_t n_reads; | ^~~~~~~ +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o maqmap.o maqmap.c match.cc: In function 'int ma_match(int, char**)': match.cc:525:10: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fscanf(tmpfp, "%s", adaptor); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o assemble.o assemble.cc -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pileup.o pileup.cc -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mapcheck.o mapcheck.cc -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o get_pos.o get_pos.c -assemble.cc: In function 'base_call_aux_t* assemble_cns_collect(assemble_pos_t*, const assemble_aux_t*)': -assemble.cc:106:63: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] - 106 | if (info>>24 < 4 && (info>>8&0x3f) != 0) info = 4<<24 | info&0xffffff; - | ~~~~^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o assopt.o assopt.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o aux_utils.o aux_utils.c -mapcheck.cc: In function 'int ma_mapcheck(int, char**)': -mapcheck.cc:60:17: warning: variable 'fpout' set but not used [-Wunused-but-set-variable] - 60 | FILE *fp_bfa, *fpout; - | ^~~~~ -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o rbcc.o rbcc.cc -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o subsnp.o subsnp.cc -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pair_stat.o pair_stat.cc -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indel_soa.o indel_soa.cc -rbcc.cc: In function 'hash_map_char* cns_load_dbSNP(FILE*)': -rbcc.cc:21:21: warning: '%d' directive writing between 1 and 11 bytes into a region of size between 0 and 255 [-Wformat-overflow=] - 21 | sprintf(str1, "%s.%d", name, pos); - | ^~ -In file included from /usr/include/stdio.h:867, - from rbcc.cc:7: -/usr/include/i386-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 3 and 268 bytes into a destination of size 256 - 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 37 | __bos (__s), __fmt, __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o maqmap.o maqmap.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o maqmap_conv.o maqmap_conv.c +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o altchr.o altchr.cc indel_soa.cc: In function 'void fill_counter(bit32_t*, int, nst_bfa1_t*, gzFile)': indel_soa.cc:42:40: warning: suggest parentheses around '-' inside '<<' [-Wparentheses] 42 | if (int(m1->seq[k]>>6) == int(s>>(31-j<<1)&3)) ++score; @@ -612,32 +672,21 @@ indel_soa.cc:56:40: warning: suggest parentheses around '-' inside '<<' [-Wparentheses] 56 | if (int(m1->seq[k]>>6) == int(s>>(31-j<<1)&3)) ++score; | ~~^~ -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o altchr.o altchr.cc gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o submap.o submap.c -subsnp.cc: In function 'hash_map_char* ma_load_snp(FILE*)': -subsnp.cc:20:20: warning: '%d' directive writing between 1 and 11 bytes into a region of size between 0 and 255 [-Wformat-overflow=] - 20 | sprintf(key, "%s.%d", name, pos); - | ^~ -In file included from /usr/include/stdio.h:867, - from subsnp.cc:2: -/usr/include/i386-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 3 and 268 bytes into a destination of size 256 - 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 37 | __bos (__s), __fmt, __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o rmdup.o rmdup.cc -subsnp.cc: In function 'hash_set_char* ma_load_snp_set(FILE*)': -subsnp.cc:35:20: warning: '%d' directive writing between 1 and 11 bytes into a region of size between 0 and 255 [-Wformat-overflow=] - 35 | sprintf(key, "%s.%d", name, pos); - | ^~ +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o simulate.o simulate.c +rbcc.cc: In function 'hash_map_char* cns_load_dbSNP(FILE*)': +rbcc.cc:21:21: warning: '%d' directive writing between 1 and 11 bytes into a region of size between 0 and 255 [-Wformat-overflow=] + 21 | sprintf(str1, "%s.%d", name, pos); + | ^~ In file included from /usr/include/stdio.h:867, - from subsnp.cc:2: + from rbcc.cc:7: /usr/include/i386-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 3 and 268 bytes into a destination of size 256 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o simulate.o simulate.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o genran.o genran.c simulate.c: In function 'maq_simutrain': simulate.c:83:8: warning: assignment to 'struct gzFile_s **' from incompatible pointer type 'gzFile' {aka 'struct gzFile_s *'} [-Wincompatible-pointer-types] 83 | fpout = gzopen(argv[1], "w"); @@ -662,6 +711,74 @@ /usr/include/zlib.h:1630:32: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' 1630 | ZEXTERN int ZEXPORT gzclose OF((gzFile file)); | ^~ +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indel_pe.o indel_pe.cc +subsnp.cc: In function 'hash_map_char* ma_load_snp(FILE*)': +subsnp.cc:20:20: warning: '%d' directive writing between 1 and 11 bytes into a region of size between 0 and 255 [-Wformat-overflow=] + 20 | sprintf(key, "%s.%d", name, pos); + | ^~ +In file included from /usr/include/stdio.h:867, + from subsnp.cc:2: +/usr/include/i386-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 3 and 268 bytes into a destination of size 256 + 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 37 | __bos (__s), __fmt, __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o stdaln.o stdaln.c +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indel_call.o indel_call.cc +subsnp.cc: In function 'hash_set_char* ma_load_snp_set(FILE*)': +subsnp.cc:35:20: warning: '%d' directive writing between 1 and 11 bytes into a region of size between 0 and 255 [-Wformat-overflow=] + 35 | sprintf(key, "%s.%d", name, pos); + | ^~ +In file included from /usr/include/stdio.h:867, + from subsnp.cc:2: +/usr/include/i386-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 3 and 268 bytes into a destination of size 256 + 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 37 | __bos (__s), __fmt, __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o eland2maq.o eland2maq.cc +stdaln.c: In function 'aln_local_core': +stdaln.c:534:25: warning: variable 'b' set but not used [-Wunused-but-set-variable] + 534 | int gap_open, gap_ext, b; + | ^ +In file included from /usr/include/string.h:495, + from maqmap.h:23, + from simulate.c:11: +In function 'memset', + inlined from 'simustat_core' at simulate.c:386:2: +/usr/include/i386-linux-gnu/bits/string_fortified.h:71:10: warning: '__builtin___memset_chk' offset [16, 31] is out of the bounds [0, 16] of object 'tc' with type 'int[2][2]' [-Warray-bounds] + 71 | return __builtin___memset_chk (__dest, __ch, __len, __bos0 (__dest)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +simulate.c: In function 'simustat_core': +simulate.c:381:12: note: 'tc' declared here + 381 | int i, k, tc[2][2]; + | ^~ +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o csmap2ntmap.o csmap2ntmap.cc +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o break_pair.o break_pair.c +In file included from break_pair.c:2: +break_pair.c: In function 'breakpair': +break_pair.c:16:9: warning: suggest parentheses around assignment used as truth value [-Wparentheses] + 16 | assert(fp = gzopen(str, "r")); + | ^~ +eland2maq.cc: In function 'void eland2maq_core(FILE*, FILE*, gzFile)': +eland2maq.cc:88:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 88 | fscanf(fp_eland, "%s", str); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ +eland2maq.cc:96:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 96 | fscanf(fp_eland, "%s", str); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ +eland2maq.cc:99:10: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 99 | fscanf(fp_eland, "%u%u%u%s%u%s", tmp, tmp+1, tmp+2, str, tmp+3, str2); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +eland2maq.cc: In function 'hash_map_char* read_list(FILE*)': +eland2maq.cc:33:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 33 | fscanf(fp, "%s", str); + | ~~~~~~^~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o glfgen.o glfgen.cc +eland2maq.cc: In function 'void novo2maq_core(FILE*, FILE*, gzFile)': +eland2maq.cc:323:18: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 323 | fgets( str2, 4096, fp_novo ); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:495, from rmdup.cc:2: In function 'char* strncpy(char*, const char*, size_t)', @@ -701,28 +818,6 @@ rmdup.cc:42:26: note: length computed here 42 | int c1, c2, tl = strlen(name); | ~~~~~~^~~~~~ -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o genran.o genran.c -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indel_pe.o indel_pe.cc -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o stdaln.o stdaln.c -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indel_call.o indel_call.cc -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o eland2maq.o eland2maq.cc -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o csmap2ntmap.o csmap2ntmap.cc -stdaln.c: In function 'aln_local_core': -stdaln.c:534:25: warning: variable 'b' set but not used [-Wunused-but-set-variable] - 534 | int gap_open, gap_ext, b; - | ^ -In file included from /usr/include/string.h:495, - from maqmap.h:23, - from simulate.c:11: -In function 'memset', - inlined from 'simustat_core' at simulate.c:386:2: -/usr/include/i386-linux-gnu/bits/string_fortified.h:71:10: warning: '__builtin___memset_chk' offset [16, 31] is out of the bounds [0, 16] of object 'tc' with type 'int[2][2]' [-Warray-bounds] - 71 | return __builtin___memset_chk (__dest, __ch, __len, __bos0 (__dest)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -simulate.c: In function 'simustat_core': -simulate.c:381:12: note: 'tc' declared here - 381 | int i, k, tc[2][2]; - | ^~ subsnp.cc: In function 'void maq_simucns_core(FILE*, gzFile, FILE*)': subsnp.cc:190:21: warning: '%d' directive writing between 1 and 11 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 190 | sprintf(key, "%s.%d", name, pos); @@ -744,31 +839,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o break_pair.o break_pair.c -In file included from break_pair.c:2: -break_pair.c: In function 'breakpair': -break_pair.c:16:9: warning: suggest parentheses around assignment used as truth value [-Wparentheses] - 16 | assert(fp = gzopen(str, "r")); - | ^~ -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o glfgen.o glfgen.cc -eland2maq.cc: In function 'void eland2maq_core(FILE*, FILE*, gzFile)': -eland2maq.cc:88:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 88 | fscanf(fp_eland, "%s", str); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ -eland2maq.cc:96:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 96 | fscanf(fp_eland, "%s", str); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ -eland2maq.cc:99:10: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 99 | fscanf(fp_eland, "%u%u%u%s%u%s", tmp, tmp+1, tmp+2, str, tmp+3, str2); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -eland2maq.cc: In function 'hash_map_char* read_list(FILE*)': -eland2maq.cc:33:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 33 | fscanf(fp, "%s", str); - | ~~~~~~^~~~~~~~~~~~~~~ -eland2maq.cc: In function 'void novo2maq_core(FILE*, FILE*, gzFile)': -eland2maq.cc:323:18: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 323 | fgets( str2, 4096, fp_novo ); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ glfgen.cc: In function 'glf1_t* glfgen1_core(assemble_pos_t*, const assemble_aux_t*, bit8_t)': glfgen.cc:43:63: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] 43 | if (info>>24 < 4 && (info>>8&0x3f) != 0) info = 4<<24 | info&0xffffff; @@ -788,18 +858,18 @@ make[2]: Leaving directory '/build/maq-0.7.1' make[1]: Leaving directory '/build/maq-0.7.1' dh_auto_test - make -j10 check VERBOSE=1 + make -j18 check VERBOSE=1 make[1]: Entering directory '/build/maq-0.7.1' make[1]: Leaving directory '/build/maq-0.7.1' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install - make -j10 install DESTDIR=/build/maq-0.7.1/debian/maq AM_UPDATE_INFO_DIR=no + make -j18 install DESTDIR=/build/maq-0.7.1/debian/maq AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/maq-0.7.1' make[2]: Entering directory '/build/maq-0.7.1' - /bin/mkdir -p '/build/maq-0.7.1/debian/maq/usr/bin' make[2]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/maq-0.7.1/debian/maq/usr/bin' + /usr/bin/mkdir -p '/build/maq-0.7.1/debian/maq/usr/bin' + /usr/bin/mkdir -p '/build/maq-0.7.1/debian/maq/usr/bin' /usr/bin/install -c maq '/build/maq-0.7.1/debian/maq/usr/bin' /usr/bin/install -c scripts/maq.pl scripts/farm-run.pl scripts/maq_plot.pl scripts/maq_eval.pl '/build/maq-0.7.1/debian/maq/usr/bin' make[2]: Leaving directory '/build/maq-0.7.1' @@ -835,20 +905,22 @@ dpkg-gencontrol: warning: package maq: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb -dpkg-deb: building package 'maq-dbgsym' in '../maq-dbgsym_0.7.1-9_i386.deb'. dpkg-deb: building package 'maq' in '../maq_0.7.1-9_i386.deb'. +dpkg-deb: building package 'maq-dbgsym' in '../maq-dbgsym_0.7.1-9_i386.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../maq_0.7.1-9_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/57364/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/57364/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/14043 and its subdirectories -I: Current time: Thu Jun 10 22:12:56 -12 2021 -I: pbuilder-time-stamp: 1623406376 +I: removing directory /srv/workspace/pbuilder/57364 and its subdirectories +I: Current time: Fri Jul 15 06:36:20 +14 2022 +I: pbuilder-time-stamp: 1657816580