Diff of the two buildlogs: -- --- b1/build.log 2021-06-15 15:00:12.854616494 +0000 +++ b2/build.log 2021-06-15 15:01:17.512198999 +0000 @@ -1,8 +1,6 @@ -unshare: unshare failed: Cannot allocate memory -W: pbuilder: unshare CLONE_NEWNET not available -I: pbuilder: network access is available during build! -I: Current time: Tue Jun 15 02:54:39 -12 2021 -I: pbuilder-time-stamp: 1623768879 +I: pbuilder: network access will be disabled during build +I: Current time: Tue Jul 19 11:23:14 +14 2022 +I: pbuilder-time-stamp: 1658179394 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -19,8 +17,8 @@ I: copying [./sortmerna_2.1-5.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.M5b_R2su/trustedkeys.kbx': General error -gpgv: Signature made Fri Mar 20 10:03:57 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.wDaG8N_u/trustedkeys.kbx': General error +gpgv: Signature made Sat Mar 21 12:03:57 2020 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -32,137 +30,171 @@ dpkg-source: info: applying 2to3.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/20577/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/17767/tmp/hooks/D01_modify_environment starting +debug: Running on ionos16-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/17767/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/17767/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='77e297a26bdf49e7b754b7cc8fa11595' - 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='20577' - PS1='# ' - PS2='> ' + INVOCATION_ID=479d6d0217a048c98e289928aa543f98 + 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=17767 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.yDxb6sgLKn/pbuilderrc_ytsM --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.yDxb6sgLKn/b1 --logfile b1/build.log sortmerna_2.1-5.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.yDxb6sgLKn/pbuilderrc_GAMU --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.yDxb6sgLKn/b2 --logfile b2/build.log --extrapackages usrmerge sortmerna_2.1-5.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 ionos2-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 5788 - -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 13 21:26 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/20577/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 19 11:23 sh -> bash + lrwxrwxrwx 1 root root 4 Jul 18 05:46 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/17767/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -229,7 +261,7 @@ Get: 29 http://deb.debian.org/debian bullseye/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] 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] -Fetched 18.6 MB in 2s (9227 kB/s) +Fetched 18.6 MB in 0s (84.9 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.) @@ -368,8 +400,44 @@ 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 (5162 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 ... 21550 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/sortmerna-2.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b +I: Running cd /build/sortmerna-2.1/ && 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 sortmerna dpkg-buildpackage: info: source version 2.1-5 dpkg-buildpackage: info: source distribution unstable @@ -395,7 +463,7 @@ ./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 --includedir=/usr/include/sortmerna 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 @@ -420,8 +488,8 @@ checking dependency style of gcc... none checking for gcc option to support OpenMP... -fopenmp 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 @@ -452,7 +520,7 @@ make[1]: Entering directory '/build/sortmerna-2.1' touch index/.tobuild dh_auto_build - make -j10 + make -j18 make[2]: Entering directory '/build/sortmerna-2.1' gcc -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -msse2 -Wall -fopenmp -c -o cmph/bdz.o cmph/bdz.c gcc -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -msse2 -Wall -fopenmp -c -o cmph/bdz_ph.o cmph/bdz_ph.c @@ -489,6 +557,13 @@ g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o alp/njn_random.o alp/njn_random.cpp g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o alp/sls_alp.o alp/sls_alp.cpp g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o alp/sls_alp_data.o alp/sls_alp_data.cpp +g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o alp/sls_alp_regression.o alp/sls_alp_regression.cpp +g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o alp/sls_alp_sim.o alp/sls_alp_sim.cpp +g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o alp/sls_pvalues.o alp/sls_pvalues.cpp +g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o src/bitvector.o src/bitvector.cpp +gcc -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -msse2 -Wall -fopenmp -c -o src/ssw.o src/ssw.c +g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o src/outputformats.o src/outputformats.cpp +g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o src/paralleltraversal.o src/paralleltraversal.cpp In file included from alp/njn_matrix.hpp:43, from alp/njn_localmaxstatutil.hpp:39, from alp/njn_localmaxstatmatrix.cpp:37: @@ -508,6 +583,43 @@ alp/njn_matrix.hpp:598:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 598 | if (this->getM () > 0) delete [] d_matrix_p; d_matrix_p = 0; | ^~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o src/main.o src/main.cpp +src/indexdb.cpp: In function 'int main(int, char**)': +src/indexdb.cpp:1545:48: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] + 1545 | fprintf(stderr,"\n check sequence # %ld\n\n",strs); + | ~~^ ~~~~ + | | | + | | size_t {aka unsigned int} + | long int + | %d +src/indexdb.cpp:1583:16: warning: comparison of integer expressions of different signedness: 'int32_t' {aka 'int'} and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] + 1583 | if ( len < pread_gv ) + | ~~~~^~~~~~~~~~ +src/indexdb.cpp:1593:11: warning: comparison of integer expressions of different signedness: 'int32_t' {aka 'int'} and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] + 1593 | len > maxlen ? maxlen = len : maxlen; + | ~~~~^~~~~~~~ +src/indexdb.cpp:1761:24: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int32_t' {aka 'int'} [-Wsign-compare] + 1761 | for ( _j = 0; _j < len; _j++ ) myseqr[_j] = *ptr--; + | ~~~^~~~~ +src/indexdb.cpp:1877:39: warning: comparison of integer expressions of different signedness: 'int' and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] + 1877 | for ( int shift = 0; shift < interval; shift++ ) + | ~~~~~~^~~~~~~~~~ +src/indexdb.cpp:2030:25: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int32_t' {aka 'int'} [-Wsign-compare] + 2030 | for ( _j = 0; _j < len; _j++ ) myseqr[_j] = *ptr--; + | ~~~^~~~~ +src/indexdb.cpp:2074:39: warning: comparison of integer expressions of different signedness: 'int' and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] + 2074 | for ( int shift = 0; shift < interval; shift++ ) + | ~~~~~~^~~~~~~~~~ +In file included from alp/njn_matrix.hpp:43, + from alp/njn_localmaxstatutil.hpp:39, + from alp/njn_localmaxstat.cpp:42: +alp/njn_vector.hpp: In member function 'virtual void Njn::Vector::free2()': +alp/njn_vector.hpp:334:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation] + 334 | if (getM () > 0) delete [] d_vector_p; d_vector_p = 0; + | ^~ +alp/njn_vector.hpp:334:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' + 334 | if (getM () > 0) delete [] d_vector_p; d_vector_p = 0; + | ^~~~~~~~~~ In file included from alp/njn_matrix.hpp:43, from alp/njn_localmaxstatutil.hpp:39, from alp/njn_localmaxstatutil.cpp:37: @@ -527,16 +639,6 @@ alp/njn_matrix.hpp:598:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 598 | if (this->getM () > 0) delete [] d_matrix_p; d_matrix_p = 0; | ^~~~~~~~~~ -In file included from alp/njn_matrix.hpp:43, - from alp/njn_localmaxstatutil.hpp:39, - from alp/njn_localmaxstat.cpp:42: -alp/njn_vector.hpp: In member function 'virtual void Njn::Vector::free2()': -alp/njn_vector.hpp:334:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation] - 334 | if (getM () > 0) delete [] d_vector_p; d_vector_p = 0; - | ^~ -alp/njn_vector.hpp:334:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' - 334 | if (getM () > 0) delete [] d_vector_p; d_vector_p = 0; - | ^~~~~~~~~~ In file included from alp/njn_localmaxstatutil.hpp:39, from alp/njn_localmaxstat.cpp:42: alp/njn_matrix.hpp: In member function 'virtual void Njn::Matrix::free2()': @@ -580,21 +682,7 @@ alp/njn_matrix.hpp:598:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 598 | if (this->getM () > 0) delete [] d_matrix_p; d_matrix_p = 0; | ^~~~~~~~~~ -In file included from alp/sls_alp.hpp:47, - from alp/sls_alp.cpp:37: -alp/sls_alp_data.hpp:83:16: warning: 'Sls::dbl_max_log' defined but not used [-Wunused-variable] - 83 | static double dbl_max_log=log(DBL_MAX); - | ^~~~~~~~~~~ -In file included from alp/sls_pvalues.hpp:43, - from alp/gumbel_params.hpp:42, - from alp/sls_alp_data.hpp:69, - from alp/sls_alp.hpp:47, - from alp/sls_alp.cpp:37: -alp/sls_normal_distr_array.hpp:43:15: warning: 'Sls::normal_distr_array_for_P_values_calculation' defined but not used [-Wunused-variable] - 43 | static double normal_distr_array_for_P_values_calculation[NORMAL_DISTR_ARRAY_DIM+1]={ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from alp/njn_localmaxstatutil.cpp:44: -alp/sls_alp_data.hpp: At global scope: +In file included from alp/sls_alp_data.cpp:37: alp/sls_alp_data.hpp:83:16: warning: 'Sls::dbl_max_log' defined but not used [-Wunused-variable] 83 | static double dbl_max_log=log(DBL_MAX); | ^~~~~~~~~~~ @@ -604,95 +692,45 @@ In file included from alp/sls_pvalues.hpp:43, from alp/gumbel_params.hpp:42, from alp/sls_alp_data.hpp:69, - from alp/njn_localmaxstatutil.cpp:44: + from alp/sls_alp_data.cpp:37: alp/sls_normal_distr_array.hpp:43:15: warning: 'Sls::normal_distr_array_for_P_values_calculation' defined but not used [-Wunused-variable] 43 | static double normal_distr_array_for_P_values_calculation[NORMAL_DISTR_ARRAY_DIM+1]={ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -src/indexdb.cpp: In function 'int main(int, char**)': -src/indexdb.cpp:1545:48: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] - 1545 | fprintf(stderr,"\n check sequence # %ld\n\n",strs); - | ~~^ ~~~~ - | | | - | | size_t {aka unsigned int} - | long int - | %d -src/indexdb.cpp:1583:16: warning: comparison of integer expressions of different signedness: 'int32_t' {aka 'int'} and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] - 1583 | if ( len < pread_gv ) - | ~~~~^~~~~~~~~~ -src/indexdb.cpp:1593:11: warning: comparison of integer expressions of different signedness: 'int32_t' {aka 'int'} and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] - 1593 | len > maxlen ? maxlen = len : maxlen; - | ~~~~^~~~~~~~ -src/indexdb.cpp:1761:24: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int32_t' {aka 'int'} [-Wsign-compare] - 1761 | for ( _j = 0; _j < len; _j++ ) myseqr[_j] = *ptr--; - | ~~~^~~~~ -src/indexdb.cpp:1877:39: warning: comparison of integer expressions of different signedness: 'int' and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] - 1877 | for ( int shift = 0; shift < interval; shift++ ) - | ~~~~~~^~~~~~~~~~ -src/indexdb.cpp:2030:25: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int32_t' {aka 'int'} [-Wsign-compare] - 2030 | for ( _j = 0; _j < len; _j++ ) myseqr[_j] = *ptr--; - | ~~~^~~~~ -src/indexdb.cpp:2074:39: warning: comparison of integer expressions of different signedness: 'int' and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] - 2074 | for ( int shift = 0; shift < interval; shift++ ) - | ~~~~~~^~~~~~~~~~ In file included from alp/sls_alp.hpp:47, - from alp/gumbel_params.cpp:40: -alp/sls_alp_data.hpp: At global scope: + from alp/sls_alp.cpp:37: alp/sls_alp_data.hpp:83:16: warning: 'Sls::dbl_max_log' defined but not used [-Wunused-variable] 83 | static double dbl_max_log=log(DBL_MAX); | ^~~~~~~~~~~ -alp/sls_alp_data.hpp:82:18: warning: 'Sls::small_long' defined but not used [-Wunused-variable] - 82 | static long int small_long=(long int)((double)LONG_MIN/2.0); - | ^~~~~~~~~~ In file included from alp/sls_pvalues.hpp:43, from alp/gumbel_params.hpp:42, from alp/sls_alp_data.hpp:69, from alp/sls_alp.hpp:47, - from alp/gumbel_params.cpp:40: -alp/sls_normal_distr_array.hpp:43:15: warning: 'Sls::normal_distr_array_for_P_values_calculation' defined but not used [-Wunused-variable] - 43 | static double normal_distr_array_for_P_values_calculation[NORMAL_DISTR_ARRAY_DIM+1]={ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o alp/sls_alp_regression.o alp/sls_alp_regression.cpp -g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o alp/sls_alp_sim.o alp/sls_alp_sim.cpp -g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o alp/sls_pvalues.o alp/sls_pvalues.cpp -g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o src/bitvector.o src/bitvector.cpp -In file included from alp/sls_alp_data.cpp:37: -alp/sls_alp_data.hpp:83:16: warning: 'Sls::dbl_max_log' defined but not used [-Wunused-variable] - 83 | static double dbl_max_log=log(DBL_MAX); - | ^~~~~~~~~~~ -alp/sls_alp_data.hpp:82:18: warning: 'Sls::small_long' defined but not used [-Wunused-variable] - 82 | static long int small_long=(long int)((double)LONG_MIN/2.0); - | ^~~~~~~~~~ -In file included from alp/sls_pvalues.hpp:43, - from alp/gumbel_params.hpp:42, - from alp/sls_alp_data.hpp:69, - from alp/sls_alp_data.cpp:37: + from alp/sls_alp.cpp:37: alp/sls_normal_distr_array.hpp:43:15: warning: 'Sls::normal_distr_array_for_P_values_calculation' defined but not used [-Wunused-variable] 43 | static double normal_distr_array_for_P_values_calculation[NORMAL_DISTR_ARRAY_DIM+1]={ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -msse2 -Wall -fopenmp -c -o src/ssw.o src/ssw.c -In file included from alp/sls_pvalues.cpp:37: +In file included from alp/njn_localmaxstatutil.cpp:44: +alp/sls_alp_data.hpp: At global scope: alp/sls_alp_data.hpp:83:16: warning: 'Sls::dbl_max_log' defined but not used [-Wunused-variable] 83 | static double dbl_max_log=log(DBL_MAX); | ^~~~~~~~~~~ alp/sls_alp_data.hpp:82:18: warning: 'Sls::small_long' defined but not used [-Wunused-variable] 82 | static long int small_long=(long int)((double)LONG_MIN/2.0); | ^~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o src/outputformats.o src/outputformats.cpp -In file included from alp/sls_alp_sim.hpp:48, - from alp/sls_alp_sim.cpp:37: -alp/sls_alp_data.hpp:82:18: warning: 'Sls::small_long' defined but not used [-Wunused-variable] - 82 | static long int small_long=(long int)((double)LONG_MIN/2.0); - | ^~~~~~~~~~ In file included from alp/sls_pvalues.hpp:43, from alp/gumbel_params.hpp:42, from alp/sls_alp_data.hpp:69, - from alp/sls_alp_sim.hpp:48, - from alp/sls_alp_sim.cpp:37: + from alp/njn_localmaxstatutil.cpp:44: alp/sls_normal_distr_array.hpp:43:15: warning: 'Sls::normal_distr_array_for_P_values_calculation' defined but not used [-Wunused-variable] 43 | static double normal_distr_array_for_P_values_calculation[NORMAL_DISTR_ARRAY_DIM+1]={ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from alp/sls_alp_regression.hpp:47, - from alp/sls_alp_regression.cpp:37: +src/outputformats.cpp: In function 'void report_blast(std::ofstream&, s_align*, char*, char*, char*, char*, char*, double, uint32_t, uint32_t, bool, double, double, uint32_t, uint32_t)': +src/outputformats.cpp:176:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 176 | for ( int l = 0; l < user_opts.size(); l++ ) + | ~~^~~~~~~~~~~~~~~~~~ +In file included from alp/sls_alp.hpp:47, + from alp/gumbel_params.cpp:40: +alp/sls_alp_data.hpp: At global scope: alp/sls_alp_data.hpp:83:16: warning: 'Sls::dbl_max_log' defined but not used [-Wunused-variable] 83 | static double dbl_max_log=log(DBL_MAX); | ^~~~~~~~~~~ @@ -702,17 +740,11 @@ In file included from alp/sls_pvalues.hpp:43, from alp/gumbel_params.hpp:42, from alp/sls_alp_data.hpp:69, - from alp/sls_alp_regression.hpp:47, - from alp/sls_alp_regression.cpp:37: + from alp/sls_alp.hpp:47, + from alp/gumbel_params.cpp:40: alp/sls_normal_distr_array.hpp:43:15: warning: 'Sls::normal_distr_array_for_P_values_calculation' defined but not used [-Wunused-variable] 43 | static double normal_distr_array_for_P_values_calculation[NORMAL_DISTR_ARRAY_DIM+1]={ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o src/paralleltraversal.o src/paralleltraversal.cpp -g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o src/main.o src/main.cpp -src/outputformats.cpp: In function 'void report_blast(std::ofstream&, s_align*, char*, char*, char*, char*, char*, double, uint32_t, uint32_t, bool, double, double, uint32_t, uint32_t)': -src/outputformats.cpp:176:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 176 | for ( int l = 0; l < user_opts.size(); l++ ) - | ~~^~~~~~~~~~~~~~~~~~ src/outputformats.cpp: In function 'void report_fasta(char*, char*, char*, char**, int32_t, std::vector&, uint32_t, char*)': src/outputformats.cpp:493:33: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int32_t' {aka 'int'} [-Wsign-compare] 493 | for ( uint32_t i = 1; i < strs; i+=4 ) @@ -751,6 +783,42 @@ src/outputformats.cpp:692:30: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int32_t' {aka 'int'} [-Wsign-compare] 692 | if ( (i+2) < strs) end_read = reads[i+1]; | ~~~~~~^~~~~~ +In file included from alp/sls_alp_regression.hpp:47, + from alp/sls_alp_regression.cpp:37: +alp/sls_alp_data.hpp:83:16: warning: 'Sls::dbl_max_log' defined but not used [-Wunused-variable] + 83 | static double dbl_max_log=log(DBL_MAX); + | ^~~~~~~~~~~ +alp/sls_alp_data.hpp:82:18: warning: 'Sls::small_long' defined but not used [-Wunused-variable] + 82 | static long int small_long=(long int)((double)LONG_MIN/2.0); + | ^~~~~~~~~~ +In file included from alp/sls_pvalues.hpp:43, + from alp/gumbel_params.hpp:42, + from alp/sls_alp_data.hpp:69, + from alp/sls_alp_regression.hpp:47, + from alp/sls_alp_regression.cpp:37: +alp/sls_normal_distr_array.hpp:43:15: warning: 'Sls::normal_distr_array_for_P_values_calculation' defined but not used [-Wunused-variable] + 43 | static double normal_distr_array_for_P_values_calculation[NORMAL_DISTR_ARRAY_DIM+1]={ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from alp/sls_pvalues.cpp:37: +alp/sls_alp_data.hpp:83:16: warning: 'Sls::dbl_max_log' defined but not used [-Wunused-variable] + 83 | static double dbl_max_log=log(DBL_MAX); + | ^~~~~~~~~~~ +alp/sls_alp_data.hpp:82:18: warning: 'Sls::small_long' defined but not used [-Wunused-variable] + 82 | static long int small_long=(long int)((double)LONG_MIN/2.0); + | ^~~~~~~~~~ +In file included from alp/sls_alp_sim.hpp:48, + from alp/sls_alp_sim.cpp:37: +alp/sls_alp_data.hpp:82:18: warning: 'Sls::small_long' defined but not used [-Wunused-variable] + 82 | static long int small_long=(long int)((double)LONG_MIN/2.0); + | ^~~~~~~~~~ +In file included from alp/sls_pvalues.hpp:43, + from alp/gumbel_params.hpp:42, + from alp/sls_alp_data.hpp:69, + from alp/sls_alp_sim.hpp:48, + from alp/sls_alp_sim.cpp:37: +alp/sls_normal_distr_array.hpp:43:15: warning: 'Sls::normal_distr_array_for_P_values_calculation' defined but not used [-Wunused-variable] + 43 | static double normal_distr_array_for_P_values_calculation[NORMAL_DISTR_ARRAY_DIM+1]={ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/paralleltraversal.cpp: In function 'void traversetrie_align(NodeElement*, uint32_t, unsigned char, unsigned char*, unsigned char*, bool&, std::vector&, uint32_t, uint32_t, uint32_t)': src/paralleltraversal.cpp:387:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 387 | for ( int f = 0; f < id_hits.size(); f++ ) @@ -794,8 +862,7 @@ | long unsigned int std::map, std::vector > >::size_type {aka unsigned int} | %u In file included from src/../include/paralleltraversal.hpp:36, - from src/paralleltraversal.cpp:26: -src/../include/../alp/sls_alp_data.hpp: At global scope: + from src/main.cpp:26: src/../include/../alp/sls_alp_data.hpp:83:16: warning: 'Sls::dbl_max_log' defined but not used [-Wunused-variable] 83 | static double dbl_max_log=log(DBL_MAX); | ^~~~~~~~~~~ @@ -806,12 +873,13 @@ from src/../include/../alp/gumbel_params.hpp:42, from src/../include/../alp/sls_alp_data.hpp:69, from src/../include/paralleltraversal.hpp:36, - from src/paralleltraversal.cpp:26: + from src/main.cpp:26: src/../include/../alp/sls_normal_distr_array.hpp:43:15: warning: 'Sls::normal_distr_array_for_P_values_calculation' defined but not used [-Wunused-variable] 43 | static double normal_distr_array_for_P_values_calculation[NORMAL_DISTR_ARRAY_DIM+1]={ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from src/../include/paralleltraversal.hpp:36, - from src/main.cpp:26: + from src/paralleltraversal.cpp:26: +src/../include/../alp/sls_alp_data.hpp: At global scope: src/../include/../alp/sls_alp_data.hpp:83:16: warning: 'Sls::dbl_max_log' defined but not used [-Wunused-variable] 83 | static double dbl_max_log=log(DBL_MAX); | ^~~~~~~~~~~ @@ -822,7 +890,7 @@ from src/../include/../alp/gumbel_params.hpp:42, from src/../include/../alp/sls_alp_data.hpp:69, from src/../include/paralleltraversal.hpp:36, - from src/main.cpp:26: + from src/paralleltraversal.cpp:26: src/../include/../alp/sls_normal_distr_array.hpp:43:15: warning: 'Sls::normal_distr_array_for_P_values_calculation' defined but not used [-Wunused-variable] 43 | static double normal_distr_array_for_P_values_calculation[NORMAL_DISTR_ARRAY_DIM+1]={ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -879,12 +947,15 @@ 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/17767/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/17767/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/20577 and its subdirectories -I: Current time: Tue Jun 15 03:00:12 -12 2021 -I: pbuilder-time-stamp: 1623769212 +I: removing directory /srv/workspace/pbuilder/17767 and its subdirectories +I: Current time: Tue Jul 19 11:24:16 +14 2022 +I: pbuilder-time-stamp: 1658179456