Diff of the two buildlogs: -- --- b1/build.log 2023-05-02 05:37:15.896243840 +0000 +++ b2/build.log 2023-05-02 05:40:10.716566102 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon May 1 17:29:12 -12 2023 -I: pbuilder-time-stamp: 1683005352 +I: Current time: Tue May 2 19:37:37 +14 2023 +I: pbuilder-time-stamp: 1683005857 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./wham-align_0.1.5.orig.tar.gz] I: copying [./wham-align_0.1.5-8.debian.tar.xz] I: Extracting source -gpgv: Signature made Thu Feb 18 19:13:34 2021 -12 +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 @@ -31,135 +31,167 @@ 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/22592/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/27802/tmp/hooks/D01_modify_environment starting +debug: Running on virt64b. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 May 2 19:37 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/27802/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/27802/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 parallel=3' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='armhf' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.2.15(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 parallel=4' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='e926a4e3f69e4ba389c3bdbc493249d3' - 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='22592' - PS1='# ' - PS2='> ' + INVOCATION_ID=a00ebd13390c46d0a8506e3638d09d51 + 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=27802 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.hTrIPxfT/pbuilderrc_orIA --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.hTrIPxfT/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://10.0.0.15:3142/' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.hTrIPxfT/pbuilderrc_K6aN --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.hTrIPxfT/b2 --logfile b2/build.log --extrapackages usrmerge wham-align_0.1.5-8.dsc' + SUDO_GID=113 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux ff4a 5.10.0-22-armmp-lpae #1 SMP Debian 5.10.178-3 (2023-04-22) armv7l GNU/Linux + Linux i-capture-the-hostname 5.10.0-22-arm64 #1 SMP Debian 5.10.178-3 (2023-04-22) aarch64 GNU/Linux I: ls -l /bin total 5072 - -rwxr-xr-x 1 root root 838488 Apr 23 09:24 bash - -rwxr-xr-x 3 root root 67144 Sep 18 2022 bunzip2 - -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzcat - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep - -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzip2 - -rwxr-xr-x 1 root root 67112 Sep 18 2022 bzip2recover - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore - -rwxr-xr-x 1 root root 67632 Sep 20 2022 cat - -rwxr-xr-x 1 root root 67676 Sep 20 2022 chgrp - -rwxr-xr-x 1 root root 67644 Sep 20 2022 chmod - -rwxr-xr-x 1 root root 67684 Sep 20 2022 chown - -rwxr-xr-x 1 root root 133532 Sep 20 2022 cp - -rwxr-xr-x 1 root root 132868 Jan 5 01:20 dash - -rwxr-xr-x 1 root root 133220 Sep 20 2022 date - -rwxr-xr-x 1 root root 67732 Sep 20 2022 dd - -rwxr-xr-x 1 root root 68104 Sep 20 2022 df - -rwxr-xr-x 1 root root 133632 Sep 20 2022 dir - -rwxr-xr-x 1 root root 59128 Mar 22 21:02 dmesg - lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname - -rwxr-xr-x 1 root root 67560 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep - -rwxr-xr-x 1 root root 67548 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep - -rwxr-xr-x 1 root root 55748 Mar 22 21:02 findmnt - -rwsr-xr-x 1 root root 26208 Mar 22 20:15 fusermount - -rwxr-xr-x 1 root root 128608 Jan 24 02:43 grep - -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip - -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe - -rwxr-xr-x 1 root root 64220 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 67032 Dec 19 01:33 hostname - -rwxr-xr-x 1 root root 67720 Sep 20 2022 ln - -rwxr-xr-x 1 root root 35132 Mar 22 21:51 login - -rwxr-xr-x 1 root root 133632 Sep 20 2022 ls - -rwxr-xr-x 1 root root 136808 Mar 22 21:02 lsblk - -rwxr-xr-x 1 root root 67800 Sep 20 2022 mkdir - -rwxr-xr-x 1 root root 67764 Sep 20 2022 mknod - -rwxr-xr-x 1 root root 67596 Sep 20 2022 mktemp - -rwxr-xr-x 1 root root 38504 Mar 22 21:02 more - -rwsr-xr-x 1 root root 38496 Mar 22 21:02 mount - -rwxr-xr-x 1 root root 9824 Mar 22 21:02 mountpoint - -rwxr-xr-x 1 root root 133532 Sep 20 2022 mv - lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 67608 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Apr 23 09:24 rbash -> bash - -rwxr-xr-x 1 root root 67600 Sep 20 2022 readlink - -rwxr-xr-x 1 root root 67672 Sep 20 2022 rm - -rwxr-xr-x 1 root root 67600 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 67400 Nov 2 04:31 run-parts - -rwxr-xr-x 1 root root 133372 Jan 5 07:55 sed - lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash - -rwxr-xr-x 1 root root 67584 Sep 20 2022 sleep - -rwxr-xr-x 1 root root 67644 Sep 20 2022 stty - -rwsr-xr-x 1 root root 50800 Mar 22 21:02 su - -rwxr-xr-x 1 root root 67584 Sep 20 2022 sync - -rwxr-xr-x 1 root root 336764 Apr 6 02:25 tar - -rwxr-xr-x 1 root root 67144 Nov 2 04:31 tempfile - -rwxr-xr-x 1 root root 133224 Sep 20 2022 touch - -rwxr-xr-x 1 root root 67548 Sep 20 2022 true - -rwxr-xr-x 1 root root 9768 Mar 22 20:15 ulockmgr_server - -rwsr-xr-x 1 root root 22108 Mar 22 21:02 umount - -rwxr-xr-x 1 root root 67572 Sep 20 2022 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 133632 Sep 20 2022 vdir - -rwxr-xr-x 1 root root 42608 Mar 22 21:02 wdctl - lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/22592/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 838488 Apr 24 11:24 bash + -rwxr-xr-x 3 root root 67144 Sep 19 2022 bunzip2 + -rwxr-xr-x 3 root root 67144 Sep 19 2022 bzcat + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep + -rwxr-xr-x 3 root root 67144 Sep 19 2022 bzip2 + -rwxr-xr-x 1 root root 67112 Sep 19 2022 bzip2recover + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore + -rwxr-xr-x 1 root root 67632 Sep 21 2022 cat + -rwxr-xr-x 1 root root 67676 Sep 21 2022 chgrp + -rwxr-xr-x 1 root root 67644 Sep 21 2022 chmod + -rwxr-xr-x 1 root root 67684 Sep 21 2022 chown + -rwxr-xr-x 1 root root 133532 Sep 21 2022 cp + -rwxr-xr-x 1 root root 132868 Jan 6 03:20 dash + -rwxr-xr-x 1 root root 133220 Sep 21 2022 date + -rwxr-xr-x 1 root root 67732 Sep 21 2022 dd + -rwxr-xr-x 1 root root 68104 Sep 21 2022 df + -rwxr-xr-x 1 root root 133632 Sep 21 2022 dir + -rwxr-xr-x 1 root root 59128 Mar 23 23:02 dmesg + lrwxrwxrwx 1 root root 8 Dec 20 03:33 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Dec 20 03:33 domainname -> hostname + -rwxr-xr-x 1 root root 67560 Sep 21 2022 echo + -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep + -rwxr-xr-x 1 root root 67548 Sep 21 2022 false + -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep + -rwxr-xr-x 1 root root 55748 Mar 23 23:02 findmnt + -rwsr-xr-x 1 root root 26208 Mar 23 22:15 fusermount + -rwxr-xr-x 1 root root 128608 Jan 25 04:43 grep + -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip + -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe + -rwxr-xr-x 1 root root 64220 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 67032 Dec 20 03:33 hostname + -rwxr-xr-x 1 root root 67720 Sep 21 2022 ln + -rwxr-xr-x 1 root root 35132 Mar 23 23:51 login + -rwxr-xr-x 1 root root 133632 Sep 21 2022 ls + -rwxr-xr-x 1 root root 136808 Mar 23 23:02 lsblk + -rwxr-xr-x 1 root root 67800 Sep 21 2022 mkdir + -rwxr-xr-x 1 root root 67764 Sep 21 2022 mknod + -rwxr-xr-x 1 root root 67596 Sep 21 2022 mktemp + -rwxr-xr-x 1 root root 38504 Mar 23 23:02 more + -rwsr-xr-x 1 root root 38496 Mar 23 23:02 mount + -rwxr-xr-x 1 root root 9824 Mar 23 23:02 mountpoint + -rwxr-xr-x 1 root root 133532 Sep 21 2022 mv + lrwxrwxrwx 1 root root 8 Dec 20 03:33 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 67608 Sep 21 2022 pwd + lrwxrwxrwx 1 root root 4 Apr 24 11:24 rbash -> bash + -rwxr-xr-x 1 root root 67600 Sep 21 2022 readlink + -rwxr-xr-x 1 root root 67672 Sep 21 2022 rm + -rwxr-xr-x 1 root root 67600 Sep 21 2022 rmdir + -rwxr-xr-x 1 root root 67400 Nov 3 06:31 run-parts + -rwxr-xr-x 1 root root 133372 Jan 6 09:55 sed + lrwxrwxrwx 1 root root 9 May 2 19:37 sh -> /bin/bash + -rwxr-xr-x 1 root root 67584 Sep 21 2022 sleep + -rwxr-xr-x 1 root root 67644 Sep 21 2022 stty + -rwsr-xr-x 1 root root 50800 Mar 23 23:02 su + -rwxr-xr-x 1 root root 67584 Sep 21 2022 sync + -rwxr-xr-x 1 root root 336764 Apr 7 04:25 tar + -rwxr-xr-x 1 root root 67144 Nov 3 06:31 tempfile + -rwxr-xr-x 1 root root 133224 Sep 21 2022 touch + -rwxr-xr-x 1 root root 67548 Sep 21 2022 true + -rwxr-xr-x 1 root root 9768 Mar 23 22:15 ulockmgr_server + -rwsr-xr-x 1 root root 22108 Mar 23 23:02 umount + -rwxr-xr-x 1 root root 67572 Sep 21 2022 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 133632 Sep 21 2022 vdir + -rwxr-xr-x 1 root root 42608 Mar 23 23:02 wdctl + lrwxrwxrwx 1 root root 8 Dec 20 03:33 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat + -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp + -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff + -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep + -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep + -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce + -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep + -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless + -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore + -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew +I: user script /srv/workspace/pbuilder/27802/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -225,7 +257,7 @@ Get: 28 http://deb.debian.org/debian bookworm/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian bookworm/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian bookworm/main armhf debhelper all 13.11.4 [942 kB] -Fetched 18.0 MB in 2s (9516 kB/s) +Fetched 18.0 MB in 2s (11.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (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 ... 19329 files and directories currently installed.) @@ -359,8 +391,19 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 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 +I: user script /srv/workspace/pbuilder/27802/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +removed '/etc/unsupported-skip-usrmerge-conversion' +The system has been successfully converted. +I: user script /srv/workspace/pbuilder/27802/tmp/hooks/A99_set_merged_usr finished +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 @@ -370,7 +413,7 @@ debian/rules clean dh clean dh_auto_clean - 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' @@ -393,11 +436,19 @@ dh_autoreconf dh_auto_configure 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 -ffile-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 -ffile-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 -ffile-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 -ffile-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: +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 hitset.h:31, from hash.h:29, from hash.cpp:27: @@ -444,6 +495,53 @@ pair.h:756:9: warning: unused variable 'a' [-Wunused-variable] 756 | int a; | ^ +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:682:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 682 | register unsigned long long P, M, X, U, Y; + | ^ +pair.h:682:36: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 682 | register unsigned long long P, M, X, U, Y; + | ^ +pair.h:682:39: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 682 | register unsigned long long P, M, X, U, Y; + | ^ +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:682:42: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 682 | register unsigned long long P, M, X, U, Y; + | ^ +pair.h:682:45: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 682 | register unsigned long long P, M, X, U, Y; + | ^ +pair.h:684:15: warning: unused variable 'num' [-Wunused-variable] + 684 | int i, p, num, base, Cscore; + | ^~~ +pair.h:684:20: warning: unused variable 'base' [-Wunused-variable] + 684 | int i, p, num, base, Cscore; + | ^~~~ +pair.h:685:9: warning: unused variable 'a' [-Wunused-variable] + 685 | int a; + | ^ +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; + | ^~~~ +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)); @@ -456,9 +554,14 @@ hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] 86 | uint32 sum = 0; | ^~~ +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 hitset.h:31, from hash.h:29, - from embedhash.cpp:27: + from aligner.h:25, + from main.cpp:34: 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) { @@ -651,14 +754,6 @@ hash.cpp:1321:34: warning: variable 'offset' set but not used [-Wunused-but-set-variable] 1321 | uint32 entryOffset, seqOffset, offset; | ^~~~~~ -In file included from hitset.h:31, - from hash.h:29, - from aligner.h:25, - from main.cpp:34: -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: 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; @@ -666,57 +761,10 @@ hash.cpp:1690:5: warning: label 'restart' defined but not used [-Wunused-label] 1690 | restart: if (buckets[bucketId] == HASH_EMPTY | ^~~~~~~ -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:682:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 682 | register unsigned long long P, M, X, U, Y; - | ^ -pair.h:682:36: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 682 | register unsigned long long P, M, X, U, Y; - | ^ -pair.h:682:39: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 682 | register unsigned long long P, M, X, U, Y; - | ^ -pair.h:682:42: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 682 | register unsigned long long P, M, X, U, Y; - | ^ -pair.h:682:45: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 682 | register unsigned long long P, M, X, U, Y; - | ^ -pair.h:684:15: warning: unused variable 'num' [-Wunused-variable] - 684 | int i, p, num, base, Cscore; - | ^~~ -pair.h:684:20: warning: unused variable 'base' [-Wunused-variable] - 684 | int i, p, num, base, Cscore; - | ^~~~ -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)); - | ~~~~~~~^~~~~~~~~~ -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; - | ^~~~ -hash.h: In function 'uint32 murmurHash(int64*, uint32)': -hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] - 86 | uint32 sum = 0; - | ^~~ +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') + | ~~~^~~~~~~~~~~~~~~~~~ embedhash.cpp: In member function 'int EmbedHashTable::preProcessEnd()': embedhash.cpp:137:16: warning: unused variable 'ln2' [-Wunused-variable] 137 | const double ln2 = log(2); @@ -768,17 +816,64 @@ 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; | ^ +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) { + | ~~~~^~~~~~~~ main.cpp:350:10: warning: unused variable 'j' [-Wunused-variable] 350 | int i, j, ret; | ^ +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:682:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 682 | register unsigned long long P, M, X, U, Y; + | ^ +pair.h:682:36: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 682 | register unsigned long long P, M, X, U, Y; + | ^ +pair.h:682:39: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 682 | register unsigned long long P, M, X, U, Y; + | ^ +pair.h:682:42: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 682 | register unsigned long long P, M, X, U, Y; + | ^ +pair.h:682:45: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 682 | register unsigned long long P, M, X, U, Y; + | ^ +pair.h:684:15: warning: unused variable 'num' [-Wunused-variable] + 684 | int i, p, num, base, Cscore; + | ^~~ +pair.h:684:20: warning: unused variable 'base' [-Wunused-variable] + 684 | int i, p, num, base, Cscore; + | ^~~~ +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)); + | ~~~~~~~^~~~~~~~~~ main.cpp: In function 'int main(int, char**)': main.cpp:523:7: warning: unused variable 'numKeys' [-Wunused-variable] 523 | int numKeys; @@ -795,6 +890,79 @@ main.cpp:536:9: warning: unused variable 'threadid' [-Wunused-variable] 536 | int * threadid; | ^~~~~~~~ +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; + | ^~~~ +hash.h: In function 'uint32 murmurHash(int64*, uint32)': +hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] + 86 | uint32 sum = 0; + | ^~~ +sequence.cpp: In member function 'void CompactSequence::extractFileName(char*, char*)': +sequence.cpp:97:10: warning: unused variable 'str' [-Wunused-variable] + 97 | char * str; + | ^~~ +sequence.cpp: In member function 'int CompactSequence::build(char**, int, int, int)': +sequence.cpp:238:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 238 | for (i = 0; i < numFile; i++) { + | ~~^~~~~~~~~ +sequence.cpp:309:13: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 309 | ( i = 0; i < nSeq; i++) + | ~~^~~~~~ +sequence.cpp:324:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 324 | for (i = 0; i < numFile; i++) { + | ~~^~~~~~~~~ +sequence.cpp:344:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 344 | for (j = 0; j < numError + 1; j++) { + | ~~^~~~~~~~~~~~~~ +sequence.cpp:410:27: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 410 | if (lenSegmentN > numError + 1) { + | ~~~~~~~~~~~~^~~~~~~~~~~~~~ +sequence.cpp:429:27: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 429 | if (lenSegmentN > numError + 1) { + | ~~~~~~~~~~~~^~~~~~~~~~~~~~ +sequence.cpp:223:16: warning: unused variable 'step' [-Wunused-variable] + 223 | unsigned int step, nextstep; + | ^~~~ +sequence.cpp:223:22: warning: unused variable 'nextstep' [-Wunused-variable] + 223 | unsigned int step, nextstep; + | ^~~~~~~~ +sequence.cpp: In member function 'int CompactSequence::filter(Aligner*, char**, int, char*)': +sequence.cpp:534:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 534 | for (i = 0; i < numFile; i++) { + | ~~^~~~~~~~~ +sequence.cpp:599:27: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 599 | if (lenSegmentN > nError + 1) + | ~~~~~~~~~~~~^~~~~~~~~~~~ +sequence.cpp:520:16: warning: unused variable 'step' [-Wunused-variable] + 520 | unsigned int step, nextstep; + | ^~~~ +sequence.cpp:520:22: warning: unused variable 'nextstep' [-Wunused-variable] + 520 | unsigned int step, nextstep; + | ^~~~~~~~ +sequence.cpp:521:9: warning: unused variable 'numFileChar' [-Wunused-variable] + 521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment; + | ^~~~~~~~~~~ +sequence.cpp:521:22: warning: unused variable 'numFileNSeg' [-Wunused-variable] + 521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment; + | ^~~~~~~~~~~ +sequence.cpp:521:35: warning: unused variable 'numFileSeq' [-Wunused-variable] + 521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment; + | ^~~~~~~~~~ +sequence.cpp:521:47: warning: unused variable 'nChar' [-Wunused-variable] + 521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment; + | ^~~~~ +sequence.cpp:521:54: warning: unused variable 'nNSegment' [-Wunused-variable] + 521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment; + | ^~~~~~~~~ +sequence.cpp: In member function 'int CompactSequence::save(char*)': +sequence.cpp:738:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] + 738 | if (ret != size) { + | ~~~~^~~~~~~ +sequence.cpp: In member function 'int CompactSequence::load(char*)': +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] @@ -849,8 +1017,41 @@ 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 -ffile-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 +sequence.cpp: In member function 'int CompactSequence::build(char**, int, int, int)': +sequence.cpp:506:15: warning: 'offsetInOrgSeq' may be used uninitialized [-Wmaybe-uninitialized] + 506 | itree->flush(offsetInCmptSeq, 0, curSeq, offsetInOrgSeq); + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +sequence.cpp:221:33: note: 'offsetInOrgSeq' was declared here + 221 | unsigned int offsetInCmptSeq, offsetInOrgSeq; + | ^~~~~~~~~~~~~~ +sequence.cpp: In static member function 'static void CompactSequence::compose(char*, int, int64*)': +sequence.cpp:674:20: warning: 'code' may be used uninitialized [-Wmaybe-uninitialized] + 674 | forward_word = ~((~code) | (-1LL << forward_offset)); + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +sequence.cpp:630:23: note: 'code' was declared here + 630 | int64 forward_word, code; + | ^~~~ g++ -c -g -O2 -ffile-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 -ffile-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 -ffile-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, @@ -910,130 +1111,15 @@ hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] 86 | uint32 sum = 0; | ^~~ -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:682:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 682 | register unsigned long long P, M, X, U, Y; - | ^ -pair.h:682:36: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 682 | register unsigned long long P, M, X, U, Y; - | ^ -pair.h:682:39: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 682 | register unsigned long long P, M, X, U, Y; - | ^ -pair.h:682:42: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 682 | register unsigned long long P, M, X, U, Y; - | ^ -pair.h:682:45: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 682 | register unsigned long long P, M, X, U, Y; - | ^ -pair.h:684:15: warning: unused variable 'num' [-Wunused-variable] - 684 | int i, p, num, base, Cscore; - | ^~~ -pair.h:684:20: warning: unused variable 'base' [-Wunused-variable] - 684 | int i, p, num, base, Cscore; - | ^~~~ -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)); - | ~~~~~~~^~~~~~~~~~ -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; - | ^~~~ -hash.h: In function 'uint32 murmurHash(int64*, uint32)': -hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] - 86 | uint32 sum = 0; - | ^~~ -sequence.cpp: In member function 'void CompactSequence::extractFileName(char*, char*)': -sequence.cpp:97:10: warning: unused variable 'str' [-Wunused-variable] - 97 | char * str; - | ^~~ -sequence.cpp: In member function 'int CompactSequence::build(char**, int, int, int)': -sequence.cpp:238:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 238 | for (i = 0; i < numFile; i++) { - | ~~^~~~~~~~~ -sequence.cpp:309:13: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 309 | ( i = 0; i < nSeq; i++) - | ~~^~~~~~ -sequence.cpp:324:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 324 | for (i = 0; i < numFile; i++) { - | ~~^~~~~~~~~ -sequence.cpp:344:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 344 | for (j = 0; j < numError + 1; j++) { - | ~~^~~~~~~~~~~~~~ -sequence.cpp:410:27: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 410 | if (lenSegmentN > numError + 1) { - | ~~~~~~~~~~~~^~~~~~~~~~~~~~ -sequence.cpp:429:27: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 429 | if (lenSegmentN > numError + 1) { - | ~~~~~~~~~~~~^~~~~~~~~~~~~~ -sequence.cpp:223:16: warning: unused variable 'step' [-Wunused-variable] - 223 | unsigned int step, nextstep; - | ^~~~ -sequence.cpp:223:22: warning: unused variable 'nextstep' [-Wunused-variable] - 223 | unsigned int step, nextstep; - | ^~~~~~~~ -sequence.cpp: In member function 'int CompactSequence::filter(Aligner*, char**, int, char*)': -sequence.cpp:534:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 534 | for (i = 0; i < numFile; i++) { - | ~~^~~~~~~~~ -sequence.cpp:599:27: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 599 | if (lenSegmentN > nError + 1) - | ~~~~~~~~~~~~^~~~~~~~~~~~ -sequence.cpp:520:16: warning: unused variable 'step' [-Wunused-variable] - 520 | unsigned int step, nextstep; - | ^~~~ -sequence.cpp:520:22: warning: unused variable 'nextstep' [-Wunused-variable] - 520 | unsigned int step, nextstep; - | ^~~~~~~~ -sequence.cpp:521:9: warning: unused variable 'numFileChar' [-Wunused-variable] - 521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment; - | ^~~~~~~~~~~ -sequence.cpp:521:22: warning: unused variable 'numFileNSeg' [-Wunused-variable] - 521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment; - | ^~~~~~~~~~~ -sequence.cpp:521:35: warning: unused variable 'numFileSeq' [-Wunused-variable] - 521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment; - | ^~~~~~~~~~ -sequence.cpp:521:47: warning: unused variable 'nChar' [-Wunused-variable] - 521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment; - | ^~~~~ -sequence.cpp:521:54: warning: unused variable 'nNSegment' [-Wunused-variable] - 521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment; - | ^~~~~~~~~ -sequence.cpp: In member function 'int CompactSequence::save(char*)': -sequence.cpp:738:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] - 738 | if (ret != size) { - | ~~~~^~~~~~~ -sequence.cpp: In member function 'int CompactSequence::load(char*)': -sequence.cpp:804:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] - 804 | if (ret != size) { - | ~~~~^~~~~~~ +g++ -c -g -O2 -ffile-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 -ffile-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 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) { @@ -1198,49 +1284,6 @@ aligner.cpp:1874:10: warning: unused variable 'ret' [-Wunused-variable] 1874 | int i, ret; | ^~~ -sequence.cpp: In member function 'int CompactSequence::build(char**, int, int, int)': -sequence.cpp:506:15: warning: 'offsetInOrgSeq' may be used uninitialized [-Wmaybe-uninitialized] - 506 | itree->flush(offsetInCmptSeq, 0, curSeq, offsetInOrgSeq); - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -sequence.cpp:221:33: note: 'offsetInOrgSeq' was declared here - 221 | unsigned int offsetInCmptSeq, offsetInOrgSeq; - | ^~~~~~~~~~~~~~ -sequence.cpp: In static member function 'static void CompactSequence::compose(char*, int, int64*)': -sequence.cpp:674:20: warning: 'code' may be used uninitialized [-Wmaybe-uninitialized] - 674 | forward_word = ~((~code) | (-1LL << forward_offset)); - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -sequence.cpp:630:23: note: 'code' was declared here - 630 | int64 forward_word, code; - | ^~~~ -In member function 'void HashTable::setLookupInfo(int, int*)', - inlined from 'int Aligner::initLookupArray()' at aligner.cpp:375:32: -hash.h:353:18: warning: 'keySpan' may be used uninitialized [-Wmaybe-uninitialized] - 353 | widthKeySpan = keySpan; - | ~~~~~~~~~~~~~^~~~~~~~~ -aligner.cpp: In member function 'int Aligner::initLookupArray()': -aligner.cpp:360:7: note: 'keySpan' was declared here - 360 | int keySpan; - | ^~~~~~~ -g++ -c -g -O2 -ffile-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 -ffile-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; @@ -1258,15 +1301,6 @@ edit_distance.cpp:178:7: warning: unused variable 'kk' [-Wunused-variable] 178 | int kk = 0; | ^~ -g++ -c -g -O2 -ffile-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 -ffile-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)) { @@ -1282,6 +1316,7 @@ short.cpp:310:38: note: 'code' was declared here 310 | int64 forward_word, backward_word, code; | ^~~~ +g++ -c -g -O2 -ffile-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 short.cpp: In member function 'ShortRead** ShortRead::split(int)': short.cpp:503:45: warning: '.t' directive writing 2 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 503 | sprintf(partitions[i]->alFileName, "%s.t%d", alFileName, i); @@ -1301,7 +1336,17 @@ short.cpp:510:14: note: 'sprintf' output between 4 and 267 bytes into a destination of size 256 510 | sprintf(partitions[i]->unFileName, "%s.t%d", unFileName, i); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -c -g -O2 -ffile-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 -ffile-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 -ffile-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 member function 'void HashTable::setLookupInfo(int, int*)', + inlined from 'int Aligner::initLookupArray()' at aligner.cpp:375:32: +hash.h:353:18: warning: 'keySpan' may be used uninitialized [-Wmaybe-uninitialized] + 353 | widthKeySpan = keySpan; + | ~~~~~~~~~~~~~^~~~~~~~~ +aligner.cpp: In member function 'int Aligner::initLookupArray()': +aligner.cpp:360:7: note: 'keySpan' was declared here + 360 | int keySpan; + | ^~~~~~~ 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)': @@ -1359,9 +1404,6 @@ hitset.cpp:90:8: warning: unused variable 'pairMatch' [-Wunused-variable] 90 | bool pairMatch = false; | ^~~~~~~~~ -g++ -c -g -O2 -ffile-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 -ffile-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 -g++ -c -g -O2 -ffile-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 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; @@ -1395,6 +1437,8 @@ model.cpp:198:26: warning: variable 'p2' set but not used [-Wunused-but-set-variable] 198 | double nSpace, p0, p1, p2; | ^~ +g++ -c -g -O2 -ffile-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 -ffile-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: @@ -1501,7 +1545,6 @@ writer.cpp:619:47: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses] 619 | if (!mate1Unmatch && !mate2Unmatch & sid1 == sid2) { | ~~~~~^~~~~~~ -g++ -c -g -O2 -ffile-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, @@ -1588,7 +1631,7 @@ 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-KcaHRiZy + rm -fr -- /tmp/dh-xdg-rundir-XxbTagFE create-stamp debian/debhelper-build-stamp dh_prep rm -f -- debian/wham-align.substvars @@ -1695,8 +1738,8 @@ chmod 0644 -- debian/.debhelper/wham-align/dbgsym-root/DEBIAN/md5sums dh_builddeb dpkg-deb --root-owner-group --build debian/wham-align .. -dpkg-deb: building package 'wham-align' in '../wham-align_0.1.5-8_armhf.deb'. dpkg-deb --root-owner-group --build debian/.debhelper/wham-align/dbgsym-root .. +dpkg-deb: building package 'wham-align' in '../wham-align_0.1.5-8_armhf.deb'. dpkg-deb: building package 'wham-align-dbgsym' in '../wham-align-dbgsym_0.1.5-8_armhf.deb'. dpkg-genbuildinfo --build=binary -O../wham-align_0.1.5-8_armhf.buildinfo dpkg-genchanges --build=binary -O../wham-align_0.1.5-8_armhf.changes @@ -1705,12 +1748,14 @@ 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/27802/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/27802/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/22592 and its subdirectories -I: Current time: Mon May 1 17:33:59 -12 2023 -I: pbuilder-time-stamp: 1683005639 +I: removing directory /srv/workspace/pbuilder/27802 and its subdirectories +I: Current time: Tue May 2 19:39:32 +14 2023 +I: pbuilder-time-stamp: 1683005972