Diff of the two buildlogs: -- --- b1/build.log 2021-07-28 18:41:01.127019348 +0000 +++ b2/build.log 2021-07-28 18:42:28.119751414 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Jul 28 06:39:37 -12 2021 -I: pbuilder-time-stamp: 1627497577 +I: Current time: Thu Jul 29 08:41:10 +14 2021 +I: pbuilder-time-stamp: 1627497670 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -16,8 +16,8 @@ I: copying [./wham-align_0.1.5-8.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.x_A4Z9dd/trustedkeys.kbx': General error -gpgv: Signature made Thu Feb 18 19:13:34 2021 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.HXsdAENt/trustedkeys.kbx': General error +gpgv: Signature made Fri Feb 19 21:13:34 2021 +14 gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "npatra974@gmail.com" gpgv: Can't check signature: No public key @@ -32,135 +32,169 @@ dpkg-source: info: applying cross-build.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/23323/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2821/tmp/hooks/D01_modify_environment starting +debug: Running on virt64a. +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/2821/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2821/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='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=3' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='armhf' + 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]="arm-unknown-linux-gnueabihf") + 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=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=4' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='4baa6888c48a4f7b895e4762d67e76b7' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='23323' - PS1='# ' - PS2='> ' + INVOCATION_ID=e72a009c01c84771a14b08013f3c67b2 + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + 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=2821 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.Lt6k83gz9i/pbuilderrc_Lx2p --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.Lt6k83gz9i/b1 --logfile b1/build.log wham-align_0.1.5-8.dsc' - SUDO_GID='113' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:8000/' + 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.Lt6k83gz9i/pbuilderrc_ktTb --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.Lt6k83gz9i/b2 --logfile b2/build.log --extrapackages usrmerge wham-align_0.1.5-8.dsc' + SUDO_GID=114 + SUDO_UID=108 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:8000/ I: uname -a - Linux virt32c 5.10.0-8-armmp-lpae #1 SMP Debian 5.10.46-2 (2021-07-20) armv7l GNU/Linux + Linux i-capture-the-hostname 5.10.0-8-arm64 #1 SMP Debian 5.10.46-2 (2021-07-20) aarch64 GNU/Linux I: ls -l /bin total 3580 - -rwxr-xr-x 1 root root 816764 Jun 21 14:26 bash - -rwxr-xr-x 3 root root 26052 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 26052 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 26052 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 9636 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 26668 Sep 22 2020 cat - -rwxr-xr-x 1 root root 43104 Sep 22 2020 chgrp - -rwxr-xr-x 1 root root 38984 Sep 22 2020 chmod - -rwxr-xr-x 1 root root 43112 Sep 22 2020 chown - -rwxr-xr-x 1 root root 92616 Sep 22 2020 cp - -rwxr-xr-x 1 root root 75524 Dec 10 2020 dash - -rwxr-xr-x 1 root root 75880 Sep 22 2020 date - -rwxr-xr-x 1 root root 55436 Sep 22 2020 dd - -rwxr-xr-x 1 root root 59912 Sep 22 2020 df - -rwxr-xr-x 1 root root 96764 Sep 22 2020 dir - -rwxr-xr-x 1 root root 55012 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 22508 Sep 22 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 22496 Sep 22 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 47492 Feb 7 02:38 findmnt - -rwsr-xr-x 1 root root 26076 Feb 26 04:12 fusermount - -rwxr-xr-x 1 root root 124508 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 64212 Mar 2 11:30 gzip - -rwxr-xr-x 1 root root 13784 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 43180 Sep 22 2020 ln - -rwxr-xr-x 1 root root 35068 Feb 7 2020 login - -rwxr-xr-x 1 root root 96764 Sep 22 2020 ls - -rwxr-xr-x 1 root root 99940 Feb 7 02:38 lsblk - -rwxr-xr-x 1 root root 51408 Sep 22 2020 mkdir - -rwxr-xr-x 1 root root 43184 Sep 22 2020 mknod - -rwxr-xr-x 1 root root 30780 Sep 22 2020 mktemp - -rwxr-xr-x 1 root root 34408 Feb 7 02:38 more - -rwsr-xr-x 1 root root 34400 Feb 7 02:38 mount - -rwxr-xr-x 1 root root 9824 Feb 7 02:38 mountpoint - -rwxr-xr-x 1 root root 88524 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 26652 Sep 22 2020 pwd - lrwxrwxrwx 1 root root 4 Jun 21 14:26 rbash -> bash - -rwxr-xr-x 1 root root 30740 Sep 22 2020 readlink - -rwxr-xr-x 1 root root 43104 Sep 22 2020 rm - -rwxr-xr-x 1 root root 30732 Sep 22 2020 rmdir - -rwxr-xr-x 1 root root 14144 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Jul 25 21:25 sh -> dash - -rwxr-xr-x 1 root root 22532 Sep 22 2020 sleep - -rwxr-xr-x 1 root root 55360 Sep 22 2020 stty - -rwsr-xr-x 1 root root 46704 Feb 7 02:38 su - -rwxr-xr-x 1 root root 22532 Sep 22 2020 sync - -rwxr-xr-x 1 root root 340872 Feb 16 21:55 tar - -rwxr-xr-x 1 root root 9808 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 67696 Sep 22 2020 touch - -rwxr-xr-x 1 root root 22496 Sep 22 2020 true - -rwxr-xr-x 1 root root 9636 Feb 26 04:12 ulockmgr_server - -rwsr-xr-x 1 root root 22108 Feb 7 02:38 umount - -rwxr-xr-x 1 root root 22520 Sep 22 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress - -rwxr-xr-x 1 root root 96764 Sep 22 2020 vdir - -rwxr-xr-x 1 root root 38512 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/23323/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 816764 Jun 22 16:26 bash + -rwxr-xr-x 3 root root 26052 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 26052 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 26052 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 9636 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 26668 Sep 23 2020 cat + -rwxr-xr-x 1 root root 43104 Sep 23 2020 chgrp + -rwxr-xr-x 1 root root 38984 Sep 23 2020 chmod + -rwxr-xr-x 1 root root 43112 Sep 23 2020 chown + -rwxr-xr-x 1 root root 92616 Sep 23 2020 cp + -rwxr-xr-x 1 root root 75524 Dec 11 2020 dash + -rwxr-xr-x 1 root root 75880 Sep 23 2020 date + -rwxr-xr-x 1 root root 55436 Sep 23 2020 dd + -rwxr-xr-x 1 root root 59912 Sep 23 2020 df + -rwxr-xr-x 1 root root 96764 Sep 23 2020 dir + -rwxr-xr-x 1 root root 55012 Feb 8 04:38 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 22508 Sep 23 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 22496 Sep 23 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 47492 Feb 8 04:38 findmnt + -rwsr-xr-x 1 root root 26076 Feb 27 06:12 fusermount + -rwxr-xr-x 1 root root 124508 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 13:30 gzexe + -rwxr-xr-x 1 root root 64212 Mar 3 13:30 gzip + -rwxr-xr-x 1 root root 13784 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 43180 Sep 23 2020 ln + -rwxr-xr-x 1 root root 35068 Feb 8 2020 login + -rwxr-xr-x 1 root root 96764 Sep 23 2020 ls + -rwxr-xr-x 1 root root 99940 Feb 8 04:38 lsblk + -rwxr-xr-x 1 root root 51408 Sep 23 2020 mkdir + -rwxr-xr-x 1 root root 43184 Sep 23 2020 mknod + -rwxr-xr-x 1 root root 30780 Sep 23 2020 mktemp + -rwxr-xr-x 1 root root 34408 Feb 8 04:38 more + -rwsr-xr-x 1 root root 34400 Feb 8 04:38 mount + -rwxr-xr-x 1 root root 9824 Feb 8 04:38 mountpoint + -rwxr-xr-x 1 root root 88524 Sep 23 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 19 05:38 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 26652 Sep 23 2020 pwd + lrwxrwxrwx 1 root root 4 Jun 22 16:26 rbash -> bash + -rwxr-xr-x 1 root root 30740 Sep 23 2020 readlink + -rwxr-xr-x 1 root root 43104 Sep 23 2020 rm + -rwxr-xr-x 1 root root 30732 Sep 23 2020 rmdir + -rwxr-xr-x 1 root root 14144 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 76012 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Jul 29 08:41 sh -> bash + lrwxrwxrwx 1 root root 4 Jul 27 23:27 sh.distrib -> dash + -rwxr-xr-x 1 root root 22532 Sep 23 2020 sleep + -rwxr-xr-x 1 root root 55360 Sep 23 2020 stty + -rwsr-xr-x 1 root root 46704 Feb 8 04:38 su + -rwxr-xr-x 1 root root 22532 Sep 23 2020 sync + -rwxr-xr-x 1 root root 340872 Feb 17 23:55 tar + -rwxr-xr-x 1 root root 9808 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 67696 Sep 23 2020 touch + -rwxr-xr-x 1 root root 22496 Sep 23 2020 true + -rwxr-xr-x 1 root root 9636 Feb 27 06:12 ulockmgr_server + -rwsr-xr-x 1 root root 22108 Feb 8 04:38 umount + -rwxr-xr-x 1 root root 22520 Sep 23 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 uncompress + -rwxr-xr-x 1 root root 96764 Sep 23 2020 vdir + -rwxr-xr-x 1 root root 38512 Feb 8 04:38 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Mar 3 13:30 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 13:30 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 13:30 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 13:30 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 13:30 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 13:30 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 13:30 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 13:30 zless + -rwxr-xr-x 1 root root 1842 Mar 3 13:30 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 13:30 znew +I: user script /srv/workspace/pbuilder/2821/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -227,7 +261,7 @@ Get: 29 http://deb.debian.org/debian bullseye/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 30 http://deb.debian.org/debian bullseye/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian bullseye/main armhf debhelper all 13.3.4 [1049 kB] -Fetched 17.7 MB in 2s (11.7 MB/s) +Fetched 17.7 MB in 1s (13.6 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 ... 19398 files and directories currently installed.) @@ -366,8 +400,45 @@ 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 armhf libnumber-compare-perl all 0.03-1.1 [6956 B] +Get:2 http://deb.debian.org/debian bullseye/main armhf libtext-glob-perl all 0.11-1 [8888 B] +Get:3 http://deb.debian.org/debian bullseye/main armhf libfile-find-rule-perl all 0.34-1 [30.6 kB] +Get:4 http://deb.debian.org/debian bullseye/main armhf usrmerge all 25 [13.0 kB] +debconf: delaying package configuration, since apt-utils is not installed +Fetched 59.5 kB in 0s (937 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 ... 21274 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/wham-align-0.1.5/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../wham-align_0.1.5-8_source.changes +hostname: Name or service not known +I: Running cd /build/wham-align-0.1.5/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../wham-align_0.1.5-8_source.changes dpkg-buildpackage: info: source package wham-align dpkg-buildpackage: info: source version 0.1.5-8 dpkg-buildpackage: info: source distribution unstable @@ -378,7 +449,7 @@ dh clean dh_auto_clean install -d /build/wham-align-0.1.5/debian/.debhelper/generated/_source/home - make -j3 clean + make -j4 clean make[1]: Entering directory '/build/wham-align-0.1.5' rm -f wham wham-build *.o make[1]: Leaving directory '/build/wham-align-0.1.5' @@ -402,11 +473,12 @@ dh_auto_configure install -d /build/wham-align-0.1.5/debian/.debhelper/generated/_source/home dh_auto_build - make -j3 "INSTALL=install --strip-program=true" + make -j4 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/wham-align-0.1.5' g++ -c -g -O2 -fdebug-prefix-map=/build/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings hash.cpp g++ -c -g -O2 -fdebug-prefix-map=/build/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings embedhash.cpp g++ -c -g -O2 -fdebug-prefix-map=/build/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings main.cpp +g++ -c -g -O2 -fdebug-prefix-map=/build/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings sequence.cpp In file included from hitset.h:31, from hash.h:29, from embedhash.cpp:27: @@ -414,6 +486,17 @@ pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 265 | if (num > nError) { | ~~~~^~~~~~~~ +In file included from hitset.h:31, + from hash.h:29, + from hash.cpp:27: +pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': +pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] + 265 | if (num > nError) { + | ~~~~^~~~~~~~ +pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)': +pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable] + 602 | int i, j, offset, min, tmp; + | ^~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)': pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable] 602 | int i, j, offset, min, tmp; @@ -428,42 +511,6 @@ pair.h:685:9: warning: unused variable 'a' [-Wunused-variable] 685 | int a; | ^ -pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)': -pair.h:755:15: warning: unused variable 'num' [-Wunused-variable] - 755 | int i, p, num, base, Cscore; - | ^~~ -pair.h:755:20: warning: unused variable 'base' [-Wunused-variable] - 755 | int i, p, num, base, Cscore; - | ^~~~ -pair.h:756:9: warning: unused variable 'a' [-Wunused-variable] - 756 | int a; - | ^ -pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)': -pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] - 974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); - | ~~~~~~~^~~~~~~~~~ -In file included from hash.h:29, - from embedhash.cpp:27: -hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)': -hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] - 86 | int size; - | ^~~~ -In file included from hitset.h:31, - from hash.h:29, - from hash.cpp:27: -pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': -pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] - 265 | if (num > nError) { - | ~~~~^~~~~~~~ -In file included from embedhash.cpp:27: -hash.h: In function 'uint32 murmurHash(int64*, uint32)': -hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] - 86 | uint32 sum = 0; - | ^~~ -pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)': -pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable] - 602 | int i, j, offset, min, tmp; - | ^~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector64(int64*, int64*, int, int, int)': pair.h:684:15: warning: unused variable 'num' [-Wunused-variable] 684 | int i, p, num, base, Cscore; @@ -484,16 +531,41 @@ pair.h:756:9: warning: unused variable 'a' [-Wunused-variable] 756 | int a; | ^ +pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)': +pair.h:755:15: warning: unused variable 'num' [-Wunused-variable] + 755 | int i, p, num, base, Cscore; + | ^~~ +pair.h:755:20: warning: unused variable 'base' [-Wunused-variable] + 755 | int i, p, num, base, Cscore; + | ^~~~ +pair.h:756:9: warning: unused variable 'a' [-Wunused-variable] + 756 | int a; + | ^ +pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)': +pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] + 974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); + | ~~~~~~~^~~~~~~~~~ pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)': pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] 974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); | ~~~~~~~^~~~~~~~~~ In file included from hash.h:29, + from embedhash.cpp:27: +hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)': +hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] + 86 | int size; + | ^~~~ +In file included from hash.h:29, from hash.cpp:27: hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)': hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] 86 | int size; | ^~~~ +In file included from embedhash.cpp:27: +hash.h: In function 'uint32 murmurHash(int64*, uint32)': +hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] + 86 | uint32 sum = 0; + | ^~~ In file included from hash.cpp:27: hash.h: In function 'uint32 murmurHash(int64*, uint32)': hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] @@ -559,6 +631,13 @@ embedhash.cpp:255:9: warning: unused variable 'top' [-Wunused-variable] 255 | int64 top = total - total * r; | ^~~ +hash.cpp: In member function 'int HashTable::preProcessEnd()': +hash.cpp:236:11: warning: comparison of integer expressions of different signedness: 'int' and 'const uint32' {aka 'const unsigned int'} [-Wsign-compare] + 236 | if (h >= nHistogram) + | ~~^~~~~~~~~~~~~ +hash.cpp:285:33: warning: comparison of integer expressions of different signedness: 'uint32' {aka 'unsigned int'} and 'int' [-Wsign-compare] + 285 | if (useEmbedTables() && tmp > embedShreshold) { + | ~~~~^~~~~~~~~~~~~~~~ embedhash.cpp: In member function 'void EmbedHashTable::insert(int64*, unsigned int)': embedhash.cpp:369:38: warning: operation on '*(((EmbedHashTable*)this)->EmbedHashTable::overflowPool + ((sizetype)(curOverflowEntry * 4)))' may be undefined [-Wsequence-point] 369 | overflowPool[curOverflowEntry] = @@ -583,6 +662,10 @@ embedhash.cpp:336:10: warning: unused variable 'bloomFilterNum' [-Wunused-variable] 336 | uint32 bloomFilterNum; | ^~~~~~~~~~~~~~ +hash.cpp: In member function 'void HashTable::setScanThreshold(double)': +hash.cpp:343:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] + 343 | for (int i = 0; i < nHistogram - 1; i++) { + | ~~^~~~~~~~~~~~~~~~ embedhash.cpp: In member function 'unsigned int EmbedHashTable::lookup(int64*, int64*, int, char*, strand, int, HitSet*, bool)': embedhash.cpp:385:7: warning: unused variable 'num' [-Wunused-variable] 385 | int num; @@ -599,62 +682,6 @@ embedhash.cpp:392:15: warning: unused variable 'soffset' [-Wunused-variable] 392 | uint32 sid, soffset; | ^~~~~~~ -main.cpp: In function 'int getArguVal(char*)': -main.cpp:159:15: warning: suggest parentheses around assignment used as truth value [-Wparentheses] - 159 | else if (*c = 'g' || *c == 'G') - | ~~~^~~~~~~~~~~~~~~~~~ -main.cpp: In function 'int align(char*, AlignInfo*, char*, int)': -main.cpp:350:7: warning: unused variable 'i' [-Wunused-variable] - 350 | int i, j, ret; - | ^ -main.cpp:350:10: warning: unused variable 'j' [-Wunused-variable] - 350 | int i, j, ret; - | ^ -main.cpp: In function 'int main(int, char**)': -main.cpp:523:7: warning: unused variable 'numKeys' [-Wunused-variable] - 523 | int numKeys; - | ^~~~~~~ -main.cpp:526:7: warning: unused variable 'nSeq' [-Wunused-variable] - 526 | int nSeq = 1; - | ^~~~ -main.cpp:532:21: warning: unused variable 'sequence' [-Wunused-variable] - 532 | CompactSequence * sequence; - | ^~~~~~~~ -main.cpp:534:15: warning: unused variable 'threadpool' [-Wunused-variable] - 534 | pthread_t * threadpool; - | ^~~~~~~~~~ -main.cpp:536:9: warning: unused variable 'threadid' [-Wunused-variable] - 536 | int * threadid; - | ^~~~~~~~ -In file included from embedhash.cpp:32: -edit_distance.h: At global scope: -edit_distance.h:25:18: warning: 'obj_score_mat' defined but not used [-Wunused-variable] - 25 | static score_mat obj_score_mat = { 1, 1, 1, 1 }; - | ^~~~~~~~~~~~~ -In file included from pair.h:26, - from hitset.h:31, - from hash.h:29, - from embedhash.cpp:27: -rdtsc.h: In function 'long long unsigned int curtick()': -rdtsc.h:32:10: warning: 'tick' is used uninitialized in this function [-Wuninitialized] - 32 | return tick; - | ^~~~ -In file included from main.cpp:38: -edit_distance.h: At global scope: -edit_distance.h:25:18: warning: 'obj_score_mat' defined but not used [-Wunused-variable] - 25 | static score_mat obj_score_mat = { 1, 1, 1, 1 }; - | ^~~~~~~~~~~~~ -hash.cpp: In member function 'int HashTable::preProcessEnd()': -hash.cpp:236:11: warning: comparison of integer expressions of different signedness: 'int' and 'const uint32' {aka 'const unsigned int'} [-Wsign-compare] - 236 | if (h >= nHistogram) - | ~~^~~~~~~~~~~~~ -hash.cpp:285:33: warning: comparison of integer expressions of different signedness: 'uint32' {aka 'unsigned int'} and 'int' [-Wsign-compare] - 285 | if (useEmbedTables() && tmp > embedShreshold) { - | ~~~~^~~~~~~~~~~~~~~~ -hash.cpp: In member function 'void HashTable::setScanThreshold(double)': -hash.cpp:343:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] - 343 | for (int i = 0; i < nHistogram - 1; i++) { - | ~~^~~~~~~~~~~~~~~~ hash.cpp: In member function 'void HashTable::insert(int64*, unsigned int)': hash.cpp:460:38: warning: operation on '*(((HashTable*)this)->HashTable::overflowPool + ((sizetype)(curOverflowEntry * 4)))' may be undefined [-Wsequence-point] 460 | overflowPool[curOverflowEntry] = @@ -765,6 +792,14 @@ 1184 | for (int i = 0; i < keyOffset / BITS_PER_BASE; i++) hash.cpp:1188:23: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] 1188 | for (int i = 0; i < (lenSeq - keyOffset - lenKey) / BITS_PER_BASE; i++) +In file included from hitset.h:31, + from hash.h:29, + from aligner.h:25, + from sequence.cpp:30: +pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': +pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] + 265 | if (num > nError) { + | ~~~~^~~~~~~~ hash.cpp:1247:27: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] 1247 | for (int j = 0; j < strlen(set[i].str); j++) | ~~^~~~~~~~~~~~~~~~~~~~ @@ -781,6 +816,10 @@ hash.cpp:1321:34: warning: variable 'offset' set but not used [-Wunused-but-set-variable] 1321 | uint32 entryOffset, seqOffset, offset; | ^~~~~~ +pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)': +pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable] + 602 | int i, j, offset, min, tmp; + | ^~~~~~ hash.cpp: In member function 'void HashTable::checkRepeat(uint32)': hash.cpp:1673:34: warning: variable 'offset' set but not used [-Wunused-but-set-variable] 1673 | uint32 entryOffset, seqOffset, offset; @@ -788,56 +827,6 @@ hash.cpp:1690:5: warning: label 'restart' defined but not used [-Wunused-label] 1690 | restart: if (buckets[bucketId] == HASH_EMPTY | ^~~~~~~ -hash.cpp: In member function 'unsigned int HashTable::lookupEmbedTable(int64*, uint32, int, char*, strand, int, HitSet*, bool)': -hash.cpp:1049:1: warning: control reaches end of non-void function [-Wreturn-type] - 1049 | } - | ^ -In file included from hash.cpp:31: -edit_distance.h: At global scope: -edit_distance.h:25:18: warning: 'obj_score_mat' defined but not used [-Wunused-variable] - 25 | static score_mat obj_score_mat = { 1, 1, 1, 1 }; - | ^~~~~~~~~~~~~ -In file included from pair.h:26, - from hitset.h:31, - from hash.h:29, - from hash.cpp:27: -rdtsc.h: In function 'long long unsigned int curtick()': -rdtsc.h:32:10: warning: 'tick' is used uninitialized in this function [-Wuninitialized] - 32 | return tick; - | ^~~~ -main.cpp: In function 'void mergeFiles(std::string)': -main.cpp:269:21: warning: '%d' directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] - 269 | sprintf(buf, ".t%d ", i); - | ^~ -main.cpp:269:18: note: directive argument in the range [0, 2147483647] - 269 | sprintf(buf, ".t%d ", i); - | ^~~~~~~ -main.cpp:269:12: note: 'sprintf' output between 5 and 14 bytes into a destination of size 10 - 269 | sprintf(buf, ".t%d ", i); - | ~~~~~~~^~~~~~~~~~~~~~~~~ -main.cpp:276:21: warning: '%d' directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] - 276 | sprintf(buf, ".t%d", i); - | ^~ -main.cpp:276:18: note: directive argument in the range [0, 2147483647] - 276 | sprintf(buf, ".t%d", i); - | ^~~~~~ -main.cpp:276:12: note: 'sprintf' output between 4 and 13 bytes into a destination of size 10 - 276 | sprintf(buf, ".t%d", i); - | ~~~~~~~^~~~~~~~~~~~~~~~ -g++ -c -g -O2 -fdebug-prefix-map=/build/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings sequence.cpp -g++ -c -g -O2 -fdebug-prefix-map=/build/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings aligner.cpp -In file included from hitset.h:31, - from hash.h:29, - from aligner.h:25, - from sequence.cpp:30: -pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': -pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] - 265 | if (num > nError) { - | ~~~~^~~~~~~~ -pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)': -pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable] - 602 | int i, j, offset, min, tmp; - | ^~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector64(int64*, int64*, int, int, int)': pair.h:684:15: warning: unused variable 'num' [-Wunused-variable] 684 | int i, p, num, base, Cscore; @@ -940,10 +929,116 @@ sequence.cpp:804:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] 804 | if (ret != size) { | ~~~~^~~~~~~ +In file included from embedhash.cpp:32: +edit_distance.h: At global scope: +edit_distance.h:25:18: warning: 'obj_score_mat' defined but not used [-Wunused-variable] + 25 | static score_mat obj_score_mat = { 1, 1, 1, 1 }; + | ^~~~~~~~~~~~~ +In file included from pair.h:26, + from hitset.h:31, + from hash.h:29, + from embedhash.cpp:27: +rdtsc.h: In function 'long long unsigned int curtick()': +rdtsc.h:32:10: warning: 'tick' is used uninitialized in this function [-Wuninitialized] + 32 | return tick; + | ^~~~ +main.cpp: In function 'int getArguVal(char*)': +main.cpp:159:15: warning: suggest parentheses around assignment used as truth value [-Wparentheses] + 159 | else if (*c = 'g' || *c == 'G') + | ~~~^~~~~~~~~~~~~~~~~~ +hash.cpp: In member function 'unsigned int HashTable::lookupEmbedTable(int64*, uint32, int, char*, strand, int, HitSet*, bool)': +hash.cpp:1049:1: warning: control reaches end of non-void function [-Wreturn-type] + 1049 | } + | ^ +main.cpp: In function 'int align(char*, AlignInfo*, char*, int)': +main.cpp:350:7: warning: unused variable 'i' [-Wunused-variable] + 350 | int i, j, ret; + | ^ +main.cpp:350:10: warning: unused variable 'j' [-Wunused-variable] + 350 | int i, j, ret; + | ^ +In file included from hash.cpp:31: +edit_distance.h: At global scope: +edit_distance.h:25:18: warning: 'obj_score_mat' defined but not used [-Wunused-variable] + 25 | static score_mat obj_score_mat = { 1, 1, 1, 1 }; + | ^~~~~~~~~~~~~ +main.cpp: In function 'int main(int, char**)': +main.cpp:523:7: warning: unused variable 'numKeys' [-Wunused-variable] + 523 | int numKeys; + | ^~~~~~~ +main.cpp:526:7: warning: unused variable 'nSeq' [-Wunused-variable] + 526 | int nSeq = 1; + | ^~~~ +main.cpp:532:21: warning: unused variable 'sequence' [-Wunused-variable] + 532 | CompactSequence * sequence; + | ^~~~~~~~ +main.cpp:534:15: warning: unused variable 'threadpool' [-Wunused-variable] + 534 | pthread_t * threadpool; + | ^~~~~~~~~~ +main.cpp:536:9: warning: unused variable 'threadid' [-Wunused-variable] + 536 | int * threadid; + | ^~~~~~~~ +In file included from pair.h:26, + from hitset.h:31, + from hash.h:29, + from hash.cpp:27: +rdtsc.h: In function 'long long unsigned int curtick()': +rdtsc.h:32:10: warning: 'tick' is used uninitialized in this function [-Wuninitialized] + 32 | return tick; + | ^~~~ +In file included from main.cpp:38: +edit_distance.h: At global scope: +edit_distance.h:25:18: warning: 'obj_score_mat' defined but not used [-Wunused-variable] + 25 | static score_mat obj_score_mat = { 1, 1, 1, 1 }; + | ^~~~~~~~~~~~~ sequence.cpp: In member function 'int CompactSequence::build(char**, int, int, int)': sequence.cpp:506:15: warning: 'offsetInOrgSeq' may be used uninitialized in this function [-Wmaybe-uninitialized] 506 | itree->flush(offsetInCmptSeq, 0, curSeq, offsetInOrgSeq); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +main.cpp: In function 'void mergeFiles(std::string)': +main.cpp:269:21: warning: '%d' directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] + 269 | sprintf(buf, ".t%d ", i); + | ^~ +main.cpp:269:18: note: directive argument in the range [0, 2147483647] + 269 | sprintf(buf, ".t%d ", i); + | ^~~~~~~ +main.cpp:269:12: note: 'sprintf' output between 5 and 14 bytes into a destination of size 10 + 269 | sprintf(buf, ".t%d ", i); + | ~~~~~~~^~~~~~~~~~~~~~~~~ +main.cpp:276:21: warning: '%d' directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] + 276 | sprintf(buf, ".t%d", i); + | ^~ +main.cpp:276:18: note: directive argument in the range [0, 2147483647] + 276 | sprintf(buf, ".t%d", i); + | ^~~~~~ +main.cpp:276:12: note: 'sprintf' output between 4 and 13 bytes into a destination of size 10 + 276 | sprintf(buf, ".t%d", i); + | ~~~~~~~^~~~~~~~~~~~~~~~ +sequence.cpp: In static member function 'static void CompactSequence::compose(char*, int, int64*)': +sequence.cpp:672:19: warning: 'code' may be used uninitialized in this function [-Wmaybe-uninitialized] + 672 | | (code >> (forward_offset + BITS_PER_BASE - BITS_PER_LONGWORD)); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -c -g -O2 -fdebug-prefix-map=/build/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings aligner.cpp +g++ -c -g -O2 -fdebug-prefix-map=/build/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings interval.cpp +interval.cpp: In constructor 'IntervalTree::IntervalTree(uint32, uint32)': +interval.cpp:67:21: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] + 67 | for (int i = 0; i < numLevel - 1; i++) { + | ~~^~~~~~~~~~~~~~ +interval.cpp: In member function 'int IntervalTree::save(char*)': +interval.cpp:304:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] + 304 | if (ret != numLEntry) { + | ~~~~^~~~~~~~~~~~ +interval.cpp:310:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] + 310 | if (ret != numIEntry) { + | ~~~~^~~~~~~~~~~~ +interval.cpp: In member function 'int IntervalTree::load(char*)': +interval.cpp:359:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] + 359 | if (ret != numLEntry) { + | ~~~~^~~~~~~~~~~~ +interval.cpp:370:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] + 370 | if (ret != numIEntry) { + | ~~~~^~~~~~~~~~~~ +g++ -c -g -O2 -fdebug-prefix-map=/build/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings edit_distance.cpp In file included from hitset.h:31, from hash.h:29, from aligner.h:25, @@ -993,6 +1088,36 @@ hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] 86 | uint32 sum = 0; | ^~~ +g++ -c -g -O2 -fdebug-prefix-map=/build/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings error.cpp +error.cpp: In function 'void elog(int, char*, ...)': +error.cpp:31:9: warning: unused variable 'filename' [-Wunused-variable] + 31 | char *filename = __FILE__; + | ^~~~~~~~ +error.cpp:32:7: warning: unused variable 'lineno' [-Wunused-variable] + 32 | int lineno = __LINE__; + | ^~~~~~ +g++ -c -g -O2 -fdebug-prefix-map=/build/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings short.cpp +edit_distance.cpp: In function 'scoreinfo edit_distance(char*, char*, int, int, char*, char*, int)': +edit_distance.cpp:61:7: warning: unused variable 'i' [-Wunused-variable] + 61 | int i; + | ^ +edit_distance.cpp: In function 'scoreinfo edit_distance_align(int**, char**, char*, char*, int, int, char*, char*, int)': +edit_distance.cpp:181:10: warning: unused variable 'tmp_trace' [-Wunused-variable] + 181 | char tmp_trace = traceback[i][j]; + | ^~~~~~~~~ +edit_distance.cpp:132:14: warning: unused variable 'x' [-Wunused-variable] + 132 | int k = 0, x = 0, y = 0; + | ^ +edit_distance.cpp:132:21: warning: unused variable 'y' [-Wunused-variable] + 132 | int k = 0, x = 0, y = 0; + | ^ +edit_distance.cpp:178:7: warning: unused variable 'kk' [-Wunused-variable] + 178 | int kk = 0; + | ^~ +short.cpp: In member function 'int ShortRead::preProcess(int)': +short.cpp:212:16: warning: suggest parentheses around assignment used as truth value [-Wparentheses] + 212 | while (len = readLine(file, str, 256)) { + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp: In member function 'int Aligner::initLookupArray()': aligner.cpp:365:37: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses] 365 | if ((indexBits[i] >> j) & 0x1 == 1) { @@ -1000,6 +1125,10 @@ aligner.cpp:371:37: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses] 371 | if ((indexBits[i] >> j) & 0x1 == 1) { | ~~~~^~~~ +short.cpp: In member function 'ShortRead** ShortRead::split(int)': +short.cpp:483:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] + 483 | if (szPartition <= nRead - curRead) + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ aligner.cpp: In member function 'int Aligner::preProcessHashTables()': aligner.cpp:534:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 534 | for (i = 0; i < nHashTable; i++) { @@ -1157,73 +1286,6 @@ aligner.cpp:1874:10: warning: unused variable 'ret' [-Wunused-variable] 1874 | int i, ret; | ^~~ -sequence.cpp: In static member function 'static void CompactSequence::compose(char*, int, int64*)': -sequence.cpp:672:19: warning: 'code' may be used uninitialized in this function [-Wmaybe-uninitialized] - 672 | | (code >> (forward_offset + BITS_PER_BASE - BITS_PER_LONGWORD)); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -c -g -O2 -fdebug-prefix-map=/build/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings interval.cpp -interval.cpp: In constructor 'IntervalTree::IntervalTree(uint32, uint32)': -interval.cpp:67:21: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] - 67 | for (int i = 0; i < numLevel - 1; i++) { - | ~~^~~~~~~~~~~~~~ -interval.cpp: In member function 'int IntervalTree::save(char*)': -interval.cpp:304:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] - 304 | if (ret != numLEntry) { - | ~~~~^~~~~~~~~~~~ -interval.cpp:310:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] - 310 | if (ret != numIEntry) { - | ~~~~^~~~~~~~~~~~ -interval.cpp: In member function 'int IntervalTree::load(char*)': -interval.cpp:359:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] - 359 | if (ret != numLEntry) { - | ~~~~^~~~~~~~~~~~ -interval.cpp:370:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] - 370 | if (ret != numIEntry) { - | ~~~~^~~~~~~~~~~~ -In file included from aligner.h:25, - from aligner.cpp:25: -hash.h: In member function 'int Aligner::initLookupArray()': -hash.h:353:18: warning: 'keySpan' may be used uninitialized in this function [-Wmaybe-uninitialized] - 353 | widthKeySpan = keySpan; - | ~~~~~~~~~~~~~^~~~~~~~~ -aligner.cpp:360:7: note: 'keySpan' was declared here - 360 | int keySpan; - | ^~~~~~~ -g++ -c -g -O2 -fdebug-prefix-map=/build/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings edit_distance.cpp -edit_distance.cpp: In function 'scoreinfo edit_distance(char*, char*, int, int, char*, char*, int)': -edit_distance.cpp:61:7: warning: unused variable 'i' [-Wunused-variable] - 61 | int i; - | ^ -edit_distance.cpp: In function 'scoreinfo edit_distance_align(int**, char**, char*, char*, int, int, char*, char*, int)': -edit_distance.cpp:181:10: warning: unused variable 'tmp_trace' [-Wunused-variable] - 181 | char tmp_trace = traceback[i][j]; - | ^~~~~~~~~ -edit_distance.cpp:132:14: warning: unused variable 'x' [-Wunused-variable] - 132 | int k = 0, x = 0, y = 0; - | ^ -edit_distance.cpp:132:21: warning: unused variable 'y' [-Wunused-variable] - 132 | int k = 0, x = 0, y = 0; - | ^ -edit_distance.cpp:178:7: warning: unused variable 'kk' [-Wunused-variable] - 178 | int kk = 0; - | ^~ -g++ -c -g -O2 -fdebug-prefix-map=/build/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings error.cpp -error.cpp: In function 'void elog(int, char*, ...)': -error.cpp:31:9: warning: unused variable 'filename' [-Wunused-variable] - 31 | char *filename = __FILE__; - | ^~~~~~~~ -error.cpp:32:7: warning: unused variable 'lineno' [-Wunused-variable] - 32 | int lineno = __LINE__; - | ^~~~~~ -g++ -c -g -O2 -fdebug-prefix-map=/build/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings short.cpp -short.cpp: In member function 'int ShortRead::preProcess(int)': -short.cpp:212:16: warning: suggest parentheses around assignment used as truth value [-Wparentheses] - 212 | while (len = readLine(file, str, 256)) { - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -short.cpp: In member function 'ShortRead** ShortRead::split(int)': -short.cpp:483:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] - 483 | if (szPartition <= nRead - curRead) - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ short.cpp: In member function 'int ShortRead::load(int)': short.cpp:436:34: warning: 'code' may be used uninitialized in this function [-Wmaybe-uninitialized] 436 | | (reverse[code] << backward_offset); @@ -1248,6 +1310,8 @@ 510 | sprintf(partitions[i]->unFileName, "%s.t%d", unFileName, i); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -g -O2 -fdebug-prefix-map=/build/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings hitset.cpp +g++ -c -g -O2 -fdebug-prefix-map=/build/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings perfcounters.cpp +g++ -c -g -O2 -fdebug-prefix-map=/build/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings model.cpp In file included from hitset.h:31, from hitset.cpp:1: pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': @@ -1291,8 +1355,6 @@ hitset.cpp:90:8: warning: unused variable 'pairMatch' [-Wunused-variable] 90 | bool pairMatch = false; | ^~~~~~~~~ -g++ -c -g -O2 -fdebug-prefix-map=/build/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings perfcounters.cpp -g++ -c -g -O2 -fdebug-prefix-map=/build/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings model.cpp model.cpp: In static member function 'static int AlignerModel::estimateNumPartition(unsigned int, int, int, bool)': model.cpp:76:16: warning: variable 'nIndex' set but not used [-Wunused-but-set-variable] 76 | unsigned int nIndex, nLookup, nBucket; @@ -1326,7 +1388,17 @@ model.cpp:198:26: warning: variable 'p2' set but not used [-Wunused-but-set-variable] 198 | double nSpace, p0, p1, p2; | ^~ +In file included from aligner.h:25, + from aligner.cpp:25: +hash.h: In member function 'int Aligner::initLookupArray()': +hash.h:353:18: warning: 'keySpan' may be used uninitialized in this function [-Wmaybe-uninitialized] + 353 | widthKeySpan = keySpan; + | ~~~~~~~~~~~~~^~~~~~~~~ +aligner.cpp:360:7: note: 'keySpan' was declared here + 360 | int keySpan; + | ^~~~~~~ g++ -c -g -O2 -fdebug-prefix-map=/build/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings writer.cpp +g++ -c -g -O2 -fdebug-prefix-map=/build/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings builder.cpp In file included from hitset.h:31, from writer.h:26, from writer.cpp:21: @@ -1420,7 +1492,6 @@ writer.cpp:619:47: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses] 619 | if (!mate1Unmatch && !mate2Unmatch & sid1 == sid2) { | ~~~~~^~~~~~~ -g++ -c -g -O2 -fdebug-prefix-map=/build/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings builder.cpp In file included from hitset.h:31, from hash.h:29, from aligner.h:25, @@ -1494,7 +1565,7 @@ g++ -o wham-build sequence.o hash.o embedhash.o builder.o aligner.o interval.o edit_distance.o error.o short.o hitset.o model.o perfcounters.o writer.o -lpthread make[1]: Leaving directory '/build/wham-align-0.1.5' dh_auto_test - rm -fr -- /tmp/dh-xdg-rundir-7gvddlo0 + rm -fr -- /tmp/dh-xdg-rundir-mljIfOBU create-stamp debian/debhelper-build-stamp dh_prep rm -f -- debian/wham-align.substvars @@ -1527,8 +1598,8 @@ install -d debian/wham-align/usr/share/man/man1/ install -p -m0644 ./debian/wham-build.1 debian/wham-align/usr/share/man/man1/wham-build.1 install -p -m0644 ./debian/wham.1 debian/wham-align/usr/share/man/man1/wham.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/wham-align/usr/share/man/man1/wham.1 man-recode --to-code UTF-8 --suffix .dh-new debian/wham-align/usr/share/man/man1/wham-build.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/wham-align/usr/share/man/man1/wham.1 mv debian/wham-align/usr/share/man/man1/wham-build.1.dh-new debian/wham-align/usr/share/man/man1/wham-build.1 chmod 0644 -- debian/wham-align/usr/share/man/man1/wham-build.1 mv debian/wham-align/usr/share/man/man1/wham.1.dh-new debian/wham-align/usr/share/man/man1/wham.1 @@ -1575,8 +1646,8 @@ dh_shlibdeps -a install -d debian/wham-align/DEBIAN dpkg-shlibdeps -Tdebian/wham-align.substvars debian/wham-align/usr/bin/wham-build debian/wham-align/usr/bin/wham -dpkg-shlibdeps: warning: debian/wham-align/usr/bin/wham-build contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/wham-align/usr/bin/wham contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/wham-align/usr/bin/wham-build contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb dh_gencontrol echo misc:Depends= >> debian/wham-align.substvars @@ -1603,12 +1674,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/2821/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2821/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/23323 and its subdirectories -I: Current time: Wed Jul 28 06:40:57 -12 2021 -I: pbuilder-time-stamp: 1627497657 +I: removing directory /srv/workspace/pbuilder/2821 and its subdirectories +I: Current time: Thu Jul 29 08:42:24 +14 2021 +I: pbuilder-time-stamp: 1627497744