Diff of the two buildlogs: -- --- b1/build.log 2021-05-27 09:03:07.999277516 +0000 +++ b2/build.log 2021-05-27 09:06:48.518713122 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Jun 29 03:25:44 -12 2022 -I: pbuilder-time-stamp: 1656516344 +I: Current time: Thu May 27 23:03:10 +14 2021 +I: pbuilder-time-stamp: 1622106190 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -17,8 +17,8 @@ I: copying [./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.jzNLlpcY/trustedkeys.kbx': General error -gpgv: Signature made Thu Feb 18 19:13:34 2021 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.jjLD_6BU/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 @@ -33,137 +33,171 @@ 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/31134/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/21663/tmp/hooks/D01_modify_environment starting +debug: Running on ionos12-i386. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/21663/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/21663/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=18' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='i386' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.1.4(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=10' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='13efd72462174b409b6958be4ff5ea18' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='31134' - PS1='# ' - PS2='> ' + INVOCATION_ID=6e88d292cee548a384d61133a01186c7 + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=21663 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.m81bWOfxQ2/pbuilderrc_T8CF --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.m81bWOfxQ2/b1 --logfile b1/build.log wham-align_0.1.5-8.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://85.184.249.68:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.m81bWOfxQ2/pbuilderrc_8zfh --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.m81bWOfxQ2/b2 --logfile b2/build.log --extrapackages usrmerge wham-align_0.1.5-8.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://78.137.99.97:3128 I: uname -a - Linux ionos6-i386 4.19.0-16-amd64 #1 SMP Debian 4.19.181-1 (2021-03-19) x86_64 GNU/Linux + Linux i-capture-the-hostname 4.19.0-16-686-pae #1 SMP Debian 4.19.181-1 (2021-03-19) i686 GNU/Linux I: ls -l /bin - total 5776 - -rwxr-xr-x 1 root root 1367848 Feb 24 2021 bash - -rwxr-xr-x 3 root root 38280 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzcat - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep - -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 17768 Jul 20 2020 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore - -rwxr-xr-x 1 root root 38824 Sep 22 2020 cat - -rwxr-xr-x 1 root root 71624 Sep 22 2020 chgrp - -rwxr-xr-x 1 root root 67528 Sep 22 2020 chmod - -rwxr-xr-x 1 root root 75752 Sep 22 2020 chown - -rwxr-xr-x 1 root root 157960 Sep 22 2020 cp - -rwxr-xr-x 1 root root 128724 Dec 10 2020 dash - -rwxr-xr-x 1 root root 124904 Sep 22 2020 date - -rwxr-xr-x 1 root root 92172 Sep 22 2020 dd - -rwxr-xr-x 1 root root 100752 Sep 22 2020 df - -rwxr-xr-x 1 root root 153964 Sep 22 2020 dir - -rwxr-xr-x 1 root root 83644 Feb 7 2021 dmesg - lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname - -rwxr-xr-x 1 root root 34664 Sep 22 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 34664 Sep 22 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 71928 Feb 7 2021 findmnt - -rwsr-xr-x 1 root root 30112 Feb 26 2021 fusermount - -rwxr-xr-x 1 root root 210488 Nov 9 2020 grep - -rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip - -rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe - -rwxr-xr-x 1 root root 100952 Mar 2 2021 gzip - -rwxr-xr-x 1 root root 21916 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 83980 Sep 22 2020 ln - -rwxr-xr-x 1 root root 55572 Feb 7 2020 login - -rwxr-xr-x 1 root root 153964 Sep 22 2020 ls - -rwxr-xr-x 1 root root 153124 Feb 7 2021 lsblk - -rwxr-xr-x 1 root root 96328 Sep 22 2020 mkdir - -rwxr-xr-x 1 root root 79912 Sep 22 2020 mknod - -rwxr-xr-x 1 root root 47048 Sep 22 2020 mktemp - -rwxr-xr-x 1 root root 58920 Feb 7 2021 more - -rwsr-xr-x 1 root root 50720 Feb 7 2021 mount - -rwxr-xr-x 1 root root 13856 Feb 7 2021 mountpoint - -rwxr-xr-x 1 root root 157996 Sep 22 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 18 2021 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 38824 Sep 22 2020 pwd - lrwxrwxrwx 1 root root 4 Feb 24 2021 rbash -> bash - -rwxr-xr-x 1 root root 46984 Sep 22 2020 readlink - -rwxr-xr-x 1 root root 75720 Sep 22 2020 rm - -rwxr-xr-x 1 root root 46984 Sep 22 2020 rmdir - -rwxr-xr-x 1 root root 22292 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Jun 28 02:13 sh -> dash - -rwxr-xr-x 1 root root 34696 Sep 22 2020 sleep - -rwxr-xr-x 1 root root 83880 Sep 22 2020 stty - -rwsr-xr-x 1 root root 79396 Feb 7 2021 su - -rwxr-xr-x 1 root root 34696 Sep 22 2020 sync - -rwxr-xr-x 1 root root 602584 Feb 16 2021 tar - -rwxr-xr-x 1 root root 13860 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 108520 Sep 22 2020 touch - -rwxr-xr-x 1 root root 34664 Sep 22 2020 true - -rwxr-xr-x 1 root root 17768 Feb 26 2021 ulockmgr_server - -rwsr-xr-x 1 root root 30236 Feb 7 2021 umount - -rwxr-xr-x 1 root root 34664 Sep 22 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress - -rwxr-xr-x 1 root root 153964 Sep 22 2020 vdir - -rwxr-xr-x 1 root root 63024 Feb 7 2021 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat - -rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp - -rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff - -rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep - -rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep - -rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce - -rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep - -rwxr-xr-x 1 root root 2206 Mar 2 2021 zless - -rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore - -rwxr-xr-x 1 root root 4553 Mar 2 2021 znew -I: user script /srv/workspace/pbuilder/31134/tmp/hooks/D02_print_environment finished + total 5792 + -rwxr-xr-x 1 root root 1367848 Feb 25 10:57 bash + -rwxr-xr-x 3 root root 38280 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 38280 Jul 21 2020 bzcat + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep + -rwxr-xr-x 3 root root 38280 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 17768 Jul 21 2020 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore + -rwxr-xr-x 1 root root 38824 Sep 23 2020 cat + -rwxr-xr-x 1 root root 71624 Sep 23 2020 chgrp + -rwxr-xr-x 1 root root 67528 Sep 23 2020 chmod + -rwxr-xr-x 1 root root 75752 Sep 23 2020 chown + -rwxr-xr-x 1 root root 157960 Sep 23 2020 cp + -rwxr-xr-x 1 root root 128724 Dec 11 03:23 dash + -rwxr-xr-x 1 root root 124904 Sep 23 2020 date + -rwxr-xr-x 1 root root 92172 Sep 23 2020 dd + -rwxr-xr-x 1 root root 100752 Sep 23 2020 df + -rwxr-xr-x 1 root root 153964 Sep 23 2020 dir + -rwxr-xr-x 1 root root 83644 Feb 8 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 34664 Sep 23 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 34664 Sep 23 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 71928 Feb 8 04:38 findmnt + -rwsr-xr-x 1 root root 30112 Feb 27 06:12 fusermount + -rwxr-xr-x 1 root root 210488 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 100952 Mar 3 13:30 gzip + -rwxr-xr-x 1 root root 21916 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 83980 Sep 23 2020 ln + -rwxr-xr-x 1 root root 55572 Feb 8 2020 login + -rwxr-xr-x 1 root root 153964 Sep 23 2020 ls + -rwxr-xr-x 1 root root 153124 Feb 8 04:38 lsblk + -rwxr-xr-x 1 root root 96328 Sep 23 2020 mkdir + -rwxr-xr-x 1 root root 79912 Sep 23 2020 mknod + -rwxr-xr-x 1 root root 47048 Sep 23 2020 mktemp + -rwxr-xr-x 1 root root 58920 Feb 8 04:38 more + -rwsr-xr-x 1 root root 50720 Feb 8 04:38 mount + -rwxr-xr-x 1 root root 13856 Feb 8 04:38 mountpoint + -rwxr-xr-x 1 root root 157996 Sep 23 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 19 05:38 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 38824 Sep 23 2020 pwd + lrwxrwxrwx 1 root root 4 Feb 25 10:57 rbash -> bash + -rwxr-xr-x 1 root root 46984 Sep 23 2020 readlink + -rwxr-xr-x 1 root root 75720 Sep 23 2020 rm + -rwxr-xr-x 1 root root 46984 Sep 23 2020 rmdir + -rwxr-xr-x 1 root root 22292 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 125036 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 May 27 23:05 sh -> bash + lrwxrwxrwx 1 root root 4 May 26 23:27 sh.distrib -> dash + -rwxr-xr-x 1 root root 34696 Sep 23 2020 sleep + -rwxr-xr-x 1 root root 83880 Sep 23 2020 stty + -rwsr-xr-x 1 root root 79396 Feb 8 04:38 su + -rwxr-xr-x 1 root root 34696 Sep 23 2020 sync + -rwxr-xr-x 1 root root 602584 Feb 17 23:55 tar + -rwxr-xr-x 1 root root 13860 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 108520 Sep 23 2020 touch + -rwxr-xr-x 1 root root 34664 Sep 23 2020 true + -rwxr-xr-x 1 root root 17768 Feb 27 06:12 ulockmgr_server + -rwsr-xr-x 1 root root 30236 Feb 8 04:38 umount + -rwxr-xr-x 1 root root 34664 Sep 23 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 uncompress + -rwxr-xr-x 1 root root 153964 Sep 23 2020 vdir + -rwxr-xr-x 1 root root 63024 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/21663/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -230,7 +264,7 @@ Get: 29 http://deb.debian.org/debian bullseye/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 30 http://deb.debian.org/debian bullseye/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian bullseye/main i386 debhelper all 13.3.4 [1049 kB] -Fetched 18.6 MB in 0s (76.5 MB/s) +Fetched 18.6 MB in 2s (9223 kB/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 ... 19674 files and directories currently installed.) @@ -369,8 +403,44 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +The following additional packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl +The following NEW packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge +0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. +Need to get 59.5 kB of archives. +After this operation, 157 kB of additional disk space will be used. +Get:1 http://deb.debian.org/debian bullseye/main i386 libnumber-compare-perl all 0.03-1.1 [6956 B] +Get:2 http://deb.debian.org/debian bullseye/main i386 libtext-glob-perl all 0.11-1 [8888 B] +Get:3 http://deb.debian.org/debian bullseye/main i386 libfile-find-rule-perl all 0.34-1 [30.6 kB] +Get:4 http://deb.debian.org/debian bullseye/main i386 usrmerge all 25 [13.0 kB] +debconf: delaying package configuration, since apt-utils is not installed +Fetched 59.5 kB in 0s (849 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 ... 21549 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 +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 dpkg-buildpackage: info: source package wham-align dpkg-buildpackage: info: source version 0.1.5-8 dpkg-buildpackage: info: source distribution unstable @@ -381,7 +451,7 @@ dh clean dh_auto_clean install -d /build/wham-align-0.1.5/debian/.debhelper/generated/_source/home - make -j18 clean + make -j10 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' @@ -405,7 +475,7 @@ dh_auto_configure install -d /build/wham-align-0.1.5/debian/.debhelper/generated/_source/home dh_auto_build - make -j18 "INSTALL=install --strip-program=true" + make -j10 "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 @@ -417,10 +487,6 @@ 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 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 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 -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 error.cpp: In function 'void elog(int, char*, ...)': error.cpp:31:9: warning: unused variable 'filename' [-Wunused-variable] 31 | char *filename = __FILE__; @@ -428,166 +494,14 @@ error.cpp:32:7: warning: unused variable 'lineno' [-Wunused-variable] 32 | int lineno = __LINE__; | ^~~~~~ -In file included from hitset.h:31, - from writer.h:26, - from writer.cpp:21: -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; - | ^~~ -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)); - | ~~~~~~~^~~~~~~~~~ -In file included from writer.h:26, - from writer.cpp:21: -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; - | ^~~~ -writer.cpp: In member function 'void SimpleWriter::writeField(int64*, int64*, strand)': -writer.cpp:154:27: warning: suggest parentheses around '-' in operand of '&' [-Wparentheses] - 154 | j = BITS_PER_LONGWORD - (length * BITS_PER_BASE) & BITS_LONGWORD_MASK; -writer.cpp:148:10: warning: unused variable 'sid' [-Wunused-variable] - 148 | uint32 sid = 0, soffset = 0; - | ^~~ -writer.cpp:148:19: warning: unused variable 'soffset' [-Wunused-variable] - 148 | uint32 sid = 0, soffset = 0; - | ^~~~~~~ -writer.cpp: In member function 'void SamWriter::writeValidAlignment(int, HitSet*)': -writer.cpp:271:7: warning: unused variable 'i' [-Wunused-variable] - 271 | int i, j, k, h, lastDiff; - | ^ -writer.cpp:271:10: warning: unused variable 'j' [-Wunused-variable] - 271 | int i, j, k, h, lastDiff; - | ^ -writer.cpp:271:13: warning: unused variable 'k' [-Wunused-variable] - 271 | int i, j, k, h, lastDiff; - | ^ -writer.cpp:271:19: warning: unused variable 'lastDiff' [-Wunused-variable] - 271 | int i, j, k, h, lastDiff; - | ^~~~~~~~ -writer.cpp:272:9: warning: unused variable 'code1' [-Wunused-variable] - 272 | int64 code1, code2; - | ^~~~~ -writer.cpp:272:16: warning: unused variable 'code2' [-Wunused-variable] - 272 | int64 code1, code2; - | ^~~~~ -writer.cpp:278:10: warning: unused variable 'p' [-Wunused-variable] - 278 | double p, sump; - | ^ -writer.cpp:278:13: warning: unused variable 'sump' [-Wunused-variable] - 278 | double p, sump; - | ^~~~ -writer.cpp:279:30: warning: unused variable 'tag' [-Wunused-variable] - 279 | char qseq[128], rseq[128], tag[128]; - | ^~~ -writer.cpp:281:8: warning: unused variable 'shortread' [-Wunused-variable] - 281 | char shortread[256]; - | ^~~~~~~~~ -writer.cpp: In member function 'void SamWriter::getCIGAR(char*, char*, char*, ErrorVector)': -writer.cpp:382:24: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] - 382 | for (i = 0, j = 0; i < strlen(query); i++, j++) { - | ~~^~~~~~~~~~~~~~~ -writer.cpp: In member function 'void SamWriter::getMDfield(char*, char*, char*, ErrorVector)': -writer.cpp:431:24: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] - 431 | for (i = 0, j = 0; i < strlen(query); i++, j++) { - | ~~^~~~~~~~~~~~~~~ -writer.cpp: In member function 'void SamPairWriter::writeValidAlignment(int, HitSet*)': -writer.cpp:619:47: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses] - 619 | if (!mate1Unmatch && !mate2Unmatch & sid1 == sid2) { - | ~~~~~^~~~~~~ -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)': -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) { - | ~~~~^~~~~~~~ -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; - | ^~~~~~ -model.cpp: In static member function 'static unsigned int AlignerModel::getFreeMemory()': -model.cpp:166:28: warning: format '%d' expects argument of type 'int*', but argument 3 has type 'unsigned int*' [-Wformat=] - 166 | fscanf(file, "MemTotal: %d kB\n", &memTotal); - | ~^ ~~~~~~~~~ - | | | - | int* unsigned int* - | %d -model.cpp:167:27: warning: format '%d' expects argument of type 'int*', but argument 3 has type 'unsigned int*' [-Wformat=] - 167 | fscanf(file, "MemFree: %d kB\n", &memFree); - | ~^ ~~~~~~~~ - | | | - | int* unsigned int* - | %d -model.cpp:168:27: warning: format '%d' expects argument of type 'int*', but argument 3 has type 'unsigned int*' [-Wformat=] - 168 | fscanf(file, "Buffers: %d kB\n", &memBuffer); - | ~^ ~~~~~~~~~~ - | | | - | int* unsigned int* - | %d 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++) { | ~~^~~~~~~~~~~~~~ -model.cpp:169:26: warning: format '%d' expects argument of type 'int*', but argument 3 has type 'unsigned int*' [-Wformat=] - 169 | fscanf(file, "Cached: %d kB\n", &memCache); - | ~^ ~~~~~~~~~ - | | | - | int* unsigned int* - | %d -model.cpp: In static member function 'static unsigned int AlignerModel::estimateHashtableSpace(unsigned int, int, int, int)': -model.cpp:198:26: warning: variable 'p2' set but not used [-Wunused-but-set-variable] - 198 | double nSpace, p0, p1, p2; - | ^~ -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; - | ^~~ -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; - | ^ +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)) { + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ 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) { @@ -595,10 +509,6 @@ interval.cpp:310:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] 310 | if (ret != numIEntry) { | ~~~~^~~~~~~~~~~~ -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)); - | ~~~~~~~^~~~~~~~~~ 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) { @@ -606,27 +516,12 @@ 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 hitset.cpp:1: -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; - | ^~~~ -hitset.cpp: In member function 'int HitPairSet::build(HitSet*, HitSet*, uint32, uint32, bool (*)[2], bool)': -hitset.cpp:90:8: warning: unused variable 'pairMatch' [-Wunused-variable] - 90 | bool pairMatch = false; - | ^~~~~~~~~ -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) | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ In file included from hitset.h:31, - from hash.h:29, - from aligner.h:25, - from builder.cpp:31: + from hitset.cpp:1: 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) { @@ -659,22 +554,24 @@ 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 aligner.h:25, - from builder.cpp:31: +In file included from hitset.cpp:1: 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 aligner.h:25, - from builder.cpp:31: -hash.h: In function 'uint32 murmurHash(int64*, uint32)': -hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] - 86 | uint32 sum = 0; - | ^~~ +hitset.cpp: In member function 'int HitPairSet::build(HitSet*, HitSet*, uint32, uint32, bool (*)[2], bool)': +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 +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); + | ~~~~~~~~~~~~^ In file included from hitset.h:31, from hash.h:29, - from hash.cpp:27: + 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) { @@ -683,6 +580,14 @@ pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable] 602 | int i, j, offset, min, tmp; | ^~~~~~ +In file included from hitset.h:31, + from hash.h:29, + from aligner.h:25, + from aligner.cpp:25: +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::pairAlignBitVector64(int64*, int64*, int, int, int)': pair.h:684:15: warning: unused variable 'num' [-Wunused-variable] 684 | int i, p, num, base, Cscore; @@ -708,31 +613,14 @@ 974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); | ~~~~~~~^~~~~~~~~~ In file included from hash.h:29, - from hash.cpp:27: + 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.cpp:27: -hash.h: In function 'uint32 murmurHash(int64*, uint32)': -hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] - 86 | uint32 sum = 0; - | ^~~ -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); - | ~~~~~~~~~~~~^ 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 aligner.h:25, - from aligner.cpp:25: + 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) { @@ -741,6 +629,11 @@ pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable] 602 | int i, j, offset, min, tmp; | ^~~~~~ +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::pairAlignBitVector64(int64*, int64*, int, int, int)': pair.h:684:15: warning: unused variable 'num' [-Wunused-variable] 684 | int i, p, num, base, Cscore; @@ -761,14 +654,21 @@ 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 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 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; + | ^~~~~~ +In file included from hash.h:29, + from aligner.h:25, + from aligner.cpp:25: +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::pairAlignBitVector64(int64*, int64*, int, int, int)': pair.h:684:15: warning: unused variable 'num' [-Wunused-variable] 684 | int i, p, num, base, Cscore; @@ -779,12 +679,6 @@ pair.h:685:9: warning: unused variable 'a' [-Wunused-variable] 685 | int a; | ^ -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; - | ^~~~ 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; @@ -799,35 +693,73 @@ pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] 974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); | ~~~~~~~^~~~~~~~~~ -builder.cpp: In function 'int getArguVal(char*)': -builder.cpp:115:15: warning: suggest parentheses around assignment used as truth value [-Wparentheses] - 115 | else if (*c = 'g' || *c == 'G') - | ~~~^~~~~~~~~~~~~~~~~~ -In file included from hash.h:29, - from aligner.h:25, +In file included from aligner.h:25, from aligner.cpp:25: -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; | ^~~ -builder.cpp: In function 'int main(int, char**)': -builder.cpp:159:7: warning: unused variable 'build_mode' [-Wunused-variable] - 159 | int build_mode = BUILD_MODE_ALL; - | ^~~~~~~~~~ -builder.cpp:277:7: warning: unused variable 'nChar' [-Wunused-variable] - 277 | int nChar = sequence->getNum(); - | ^~~~~ -In file included from aligner.h:25, - from aligner.cpp:25: +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 hash.cpp:27: hash.h: In function 'uint32 murmurHash(int64*, uint32)': hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] 86 | uint32 sum = 0; | ^~~ +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; + | ^~~~~~ +model.cpp: In static member function 'static unsigned int AlignerModel::getFreeMemory()': +model.cpp:166:28: warning: format '%d' expects argument of type 'int*', but argument 3 has type 'unsigned int*' [-Wformat=] + 166 | fscanf(file, "MemTotal: %d kB\n", &memTotal); + | ~^ ~~~~~~~~~ + | | | + | int* unsigned int* + | %d +model.cpp:167:27: warning: format '%d' expects argument of type 'int*', but argument 3 has type 'unsigned int*' [-Wformat=] + 167 | fscanf(file, "MemFree: %d kB\n", &memFree); + | ~^ ~~~~~~~~ + | | | + | int* unsigned int* + | %d +model.cpp:168:27: warning: format '%d' expects argument of type 'int*', but argument 3 has type 'unsigned int*' [-Wformat=] + 168 | fscanf(file, "Buffers: %d kB\n", &memBuffer); + | ~^ ~~~~~~~~~~ + | | | + | int* unsigned int* + | %d +model.cpp:169:26: warning: format '%d' expects argument of type 'int*', but argument 3 has type 'unsigned int*' [-Wformat=] + 169 | fscanf(file, "Cached: %d kB\n", &memCache); + | ~^ ~~~~~~~~~ + | | | + | int* unsigned int* + | %d +model.cpp: In static member function 'static unsigned int AlignerModel::estimateHashtableSpace(unsigned int, int, int, int)': +model.cpp:198:26: warning: variable 'p2' set but not used [-Wunused-but-set-variable] + 198 | double nSpace, p0, p1, p2; + | ^~ +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 '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); @@ -847,11 +779,7 @@ 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); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from builder.cpp:34: -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 }; - | ^~~~~~~~~~~~~ +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 In file included from hitset.h:31, from hash.h:29, from aligner.h:25, @@ -888,10 +816,41 @@ pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] 974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); | ~~~~~~~^~~~~~~~~~ -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; - | ^ +embedhash.cpp: In member function 'int EmbedHashTable::preProcessEnd()': +embedhash.cpp:137:16: warning: unused variable 'ln2' [-Wunused-variable] + 137 | const double ln2 = log(2); + | ^~~ +embedhash.cpp: In member function 'void EmbedHashTable::setScanThreshold(double)': +embedhash.cpp:253:9: warning: unused variable 'sum' [-Wunused-variable] + 253 | int64 sum = 0; + | ^~~ +embedhash.cpp:255:9: warning: unused variable 'top' [-Wunused-variable] + 255 | int64 top = total - total * r; + | ^~~ +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] = +embedhash.cpp:328:10: warning: unused variable 'seqOffset' [-Wunused-variable] + 328 | uint32 seqOffset; + | ^~~~~~~~~ +embedhash.cpp:330:10: warning: unused variable 'counter' [-Wunused-variable] + 330 | uint32 counter = 0; + | ^~~~~~~ +embedhash.cpp:331:11: warning: variable 'seqVector' set but not used [-Wunused-but-set-variable] + 331 | int64 * seqVector; + | ^~~~~~~~~ +embedhash.cpp:333:11: warning: unused variable 'target' [-Wunused-variable] + 333 | int64 * target = &tspace[8]; + | ^~~~~~ +embedhash.cpp:334:8: warning: unused variable 'isBloomFilter' [-Wunused-variable] + 334 | bool isBloomFilter; + | ^~~~~~~~~~~~~ +embedhash.cpp:335:12: warning: unused variable 'bloomFilter' [-Wunused-variable] + 335 | uint32 * bloomFilter; + | ^~~~~~~~~~~ +embedhash.cpp:336:10: warning: unused variable 'bloomFilterNum' [-Wunused-variable] + 336 | uint32 bloomFilterNum; + | ^~~~~~~~~~~~~~ In file included from hash.h:29, from aligner.h:25, from main.cpp:34: @@ -899,33 +858,168 @@ hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] 86 | int size; | ^~~~ -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; - | ^~ +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; + | ^~~ +embedhash.cpp:387:34: warning: variable 'startOffset' set but not used [-Wunused-but-set-variable] + 387 | uint32 seqOffset, entryOffset, startOffset; + | ^~~~~~~~~~~ +embedhash.cpp:389:11: warning: unused variable 'diff' [-Wunused-variable] + 389 | int64 * diff = &tspace1[8], *target = &tspace2[8]; + | ^~~~ +embedhash.cpp:392:10: warning: unused variable 'sid' [-Wunused-variable] + 392 | uint32 sid, soffset; + | ^~~ +embedhash.cpp:392:15: warning: unused variable 'soffset' [-Wunused-variable] + 392 | uint32 sid, soffset; + | ^~~~~~~ In file included from aligner.h:25, from main.cpp:34: 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 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 }; + | ^~~~~~~~~~~~~ +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) { + | ~~~~^~~~ +aligner.cpp:371:37: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses] + 371 | if ((indexBits[i] >> j) & 0x1 == 1) { + | ~~~~^~~~ +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++) { + | ~~^~~~~~~~~~~~ +aligner.cpp:712:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 712 | for (i = 0; i < nHashTable; i++) { + | ~~^~~~~~~~~~~~ +aligner.cpp: In member function 'int Aligner::build(char*)': +aligner.cpp:724:16: warning: unused variable 'i' [-Wunused-variable] + 724 | unsigned int i, j; + | ^ +aligner.cpp:724:19: warning: unused variable 'j' [-Wunused-variable] + 724 | unsigned int i, j; + | ^ +aligner.cpp: In member function 'int Aligner::buildHashTables(char*)': +aligner.cpp:807:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 807 | for (i = 0; i < nHashTable; i++) { + | ~~^~~~~~~~~~~~ +aligner.cpp:844:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 844 | for (i1 = 0; i1 < lenPartition * (nPartition - 1); i1 += lenPartition) { + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aligner.cpp:864:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 864 | for (i1 = 0; i1 < lenPartition * (nPartition - 2); i1 += lenPartition) { + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aligner.cpp:871:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 871 | for (i2 = i1; i2 < lenPartition * (nPartition - 2); + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aligner.cpp:894:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 894 | for (i1 = 0; i1 < lenPartition * (nPartition - 3); i1 += lenPartition) { + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aligner.cpp:901:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 901 | for (i2 = i1; i2 < lenPartition * (nPartition - 3); + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aligner.cpp:909:28: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 909 | for (i3 = i2; i3 < lenPartition * (nPartition - 3); + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aligner.cpp:928:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 928 | for (i1 = 0; i1 < lenPartition * (nPartition - 4); i1 += lenPartition) { + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aligner.cpp:930:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 930 | for (i2 = i1; i2 < lenPartition * (nPartition - 4); + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aligner.cpp:933:28: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 933 | for (i3 = i2; i3 < lenPartition * (nPartition - 4); + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aligner.cpp:936:30: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 936 | for (i4 = i3; i4 < lenPartition * (nPartition - 4); i4 += + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aligner.cpp:951:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 951 | for (i1 = 0; i1 < lenPartition * (nPartition - 5); i1 += lenPartition) { + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aligner.cpp:953:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 953 | for (i2 = i1; i2 < lenPartition * (nPartition - 5); + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aligner.cpp:956:28: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 956 | for (i3 = i2; i3 < lenPartition * (nPartition - 5); + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aligner.cpp:959:30: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 959 | for (i4 = i3; i4 < lenPartition * (nPartition - 5); i4 += + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aligner.cpp:962:32: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 962 | for (i5 = i4; i5 < lenPartition * (nPartition - 5); i5 += + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aligner.cpp:983:19: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 983 | for (i = 0; i < nHashTable; i++) { + | ~~^~~~~~~~~~~~ +aligner.cpp:1006:19: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 1006 | for (i = 0; i < nHashTable; i++) { + | ~~^~~~~~~~~~~~ In file included from hitset.h:31, - from hash.h:29, - from aligner.h:25, - from sequence.cpp:30: + from writer.h:26, + from writer.cpp:21: 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) { | ~~~~^~~~~~~~ +aligner.cpp: In member function 'unsigned int Aligner::alignFirst(int64*, char*, strand, int, HitSet*, bool)': +aligner.cpp:1035:10: warning: unused variable 'offset' [-Wunused-variable] + 1035 | uint32 offset; + | ^~~~~~ +aligner.cpp:1039:7: warning: unused variable 'nHit' [-Wunused-variable] + 1039 | int nHit = 0; + | ^~~~ +aligner.cpp: In member function 'unsigned int Aligner::align(int64*, char*, strand, int, HitSet*, bool, bool)': +aligner.cpp:1119:10: warning: variable 'offset' set but not used [-Wunused-but-set-variable] + 1119 | uint32 offset; + | ^~~~~~ +aligner.cpp:1123:7: warning: variable 'nHit' set but not used [-Wunused-but-set-variable] + 1123 | int nHit = 0; + | ^~~~ +aligner.cpp: In member function 'int Aligner::check(int)': +aligner.cpp:1436:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 1436 | for (i = 0; i < num; i++) { + | ~~^~~~~ +aligner.cpp:1452:19: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 1452 | for (j = 0; j < nError; j++) { + | ~~^~~~~~~~ +aligner.cpp:1426:7: warning: unused variable 'ret' [-Wunused-variable] + 1426 | int ret; + | ^~~ +aligner.cpp: In member function 'AlignRes Aligner::alignSingleEnd(AlignInfo*, char*)': +aligner.cpp:1541:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 1541 | for (i = 0; i < nHashTable; i++) { + | ~~^~~~~~~~~~~~ +aligner.cpp:1547:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 1547 | for (i = 0; i < res.nRead; i++) { + | ~~^~~~~~~~~~~ +aligner.cpp:1629:3: warning: deleting object of abstract class type 'Writer' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor] + 1629 | delete writer; + | ^~~~~~~~~~~~~ +aligner.cpp:1502:10: warning: unused variable 'file' [-Wunused-variable] + 1502 | FILE * file = NULL, *alfile = NULL, *unfile = NULL; + | ^~~~ +aligner.cpp:1502:24: warning: unused variable 'alfile' [-Wunused-variable] + 1502 | FILE * file = NULL, *alfile = NULL, *unfile = NULL; + | ^~~~~~ +aligner.cpp:1502:40: warning: unused variable 'unfile' [-Wunused-variable] + 1502 | FILE * file = NULL, *alfile = NULL, *unfile = NULL; + | ^~~~~~ +aligner.cpp:1505:7: warning: unused variable 'strand' [-Wunused-variable] + 1505 | int strand; + | ^~~~~~ +aligner.cpp:1508:9: warning: unused variable 'ratio' [-Wunused-variable] + 1508 | float ratio; + | ^~~~~ +aligner.cpp:1514:31: warning: unused variable 'strata' [-Wunused-variable] + 1514 | bool sorted = info->sorted, strata = info->strata; + | ^~~~~~ 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; @@ -940,6 +1034,28 @@ pair.h:685:9: warning: unused variable 'a' [-Wunused-variable] 685 | int a; | ^ +aligner.cpp: In member function 'AlignRes Aligner::alignPairEnd(AlignInfo*, char*)': +aligner.cpp:1685:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 1685 | for (i = 0; i < res.nRead; i++) { + | ~~^~~~~~~~~~~ +aligner.cpp:1754:3: warning: deleting object of abstract class type 'Writer' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor] + 1754 | delete writer; + | ^~~~~~~~~~~~~ +aligner.cpp:1637:8: warning: unused variable 'success' [-Wunused-variable] + 1637 | bool success; + | ^~~~~~~ +aligner.cpp:1638:16: warning: unused variable 'nSuccessRead' [-Wunused-variable] + 1638 | unsigned int nSuccessRead = 0; + | ^~~~~~~~~~~~ +aligner.cpp:1639:10: warning: unused variable 'file' [-Wunused-variable] + 1639 | FILE * file = NULL; + | ^~~~ +aligner.cpp:1646:8: warning: unused variable 'mateFilename' [-Wunused-variable] + 1646 | char mateFilename[256]; + | ^~~~~~~~~~~~ +aligner.cpp:1652:31: warning: unused variable 'strata' [-Wunused-variable] + 1652 | bool sorted = info->sorted, strata = info->strata; + | ^~~~~~ 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; @@ -950,88 +1066,6 @@ 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 aligner.h:25, - from sequence.cpp:30: -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 aligner.h:25, - from sequence.cpp:30: -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) { - | ~~~~^~~~~~~ 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) @@ -1039,10 +1073,31 @@ 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) { | ~~~~^~~~~~~~~~~~~~~~ +aligner.cpp: In member function 'AlignRes Aligner::mergeSingleEnd(AlignInfo*, int, char*)': +aligner.cpp:1851:3: warning: deleting object of abstract class type 'Writer' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor] + 1851 | delete writer; + | ^~~~~~~~~~~~~ +aligner.cpp:1775:10: warning: unused variable 'ret' [-Wunused-variable] + 1775 | int i, ret; + | ^~~ +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)); + | ~~~~~~~^~~~~~~~~~ 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++) { | ~~^~~~~~~~~~~~~~~~ +In file included from writer.h:26, + from writer.cpp:21: +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; + | ^~~~ +aligner.cpp: In member function 'AlignRes Aligner::mergePairEnd(AlignInfo*, int, char*)': +aligner.cpp:1989:3: warning: deleting object of abstract class type 'Writer' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor] + 1989 | delete writer; + | ^~~~~~~~~~~~~ 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] = @@ -1067,6 +1122,9 @@ hash.cpp:419:10: warning: unused variable 'bloomFilterNum' [-Wunused-variable] 419 | uint32 bloomFilterNum; | ^~~~~~~~~~~~~~ +aligner.cpp:1874:10: warning: unused variable 'ret' [-Wunused-variable] + 1874 | int i, ret; + | ^~~ hash.cpp: In member function 'int HashTable::buildEmbedTable()': hash.cpp:469:33: warning: unused variable 'rest' [-Wunused-variable] 469 | int64 * query = &ttspace[8], *rest = &ttspace[24], *rest1 = &ttspace[40], @@ -1083,10 +1141,6 @@ hash.cpp:472:34: warning: variable 'startOffset' set but not used [-Wunused-but-set-variable] 472 | uint32 seqOffset, entryOffset, startOffset; | ^~~~~~~~~~~ -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 'void HashTable::preinsertEmbedTableEntry(int64*, int, int)': hash.cpp:587:11: warning: unused variable 'noheadkey' [-Wunused-variable] 587 | int64 * noheadkey = &tspace[8], *rest = &tspace[24]; @@ -1097,6 +1151,10 @@ hash.cpp:590:32: warning: unused variable 'subkey5' [-Wunused-variable] 590 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; | ^~~~~~~ +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 'void HashTable::insertEmbedTableEntry(int64*, uint32, int, int)': hash.cpp:662:11: warning: unused variable 'noheadkey' [-Wunused-variable] 662 | int64 * noheadkey = &tspace[8], *rest = &tspace[24]; @@ -1107,6 +1165,9 @@ hash.cpp:665:32: warning: unused variable 'subkey5' [-Wunused-variable] 665 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; | ^~~~~~~ +writer.cpp: In member function 'void SimpleWriter::writeField(int64*, int64*, strand)': +writer.cpp:154:27: warning: suggest parentheses around '-' in operand of '&' [-Wparentheses] + 154 | j = BITS_PER_LONGWORD - (length * BITS_PER_BASE) & BITS_LONGWORD_MASK; hash.cpp: In member function 'unsigned int HashTable::lookup(int64*, int64*, int, char*, strand, int, HitSet*, bool)': hash.cpp:746:7: warning: unused variable 'num' [-Wunused-variable] 746 | int num; @@ -1120,6 +1181,43 @@ hash.cpp:753:15: warning: unused variable 'soffset' [-Wunused-variable] 753 | uint32 sid, soffset; | ^~~~~~~ +writer.cpp:148:10: warning: unused variable 'sid' [-Wunused-variable] + 148 | uint32 sid = 0, soffset = 0; + | ^~~ +writer.cpp:148:19: warning: unused variable 'soffset' [-Wunused-variable] + 148 | uint32 sid = 0, soffset = 0; + | ^~~~~~~ +writer.cpp: In member function 'void SamWriter::writeValidAlignment(int, HitSet*)': +writer.cpp:271:7: warning: unused variable 'i' [-Wunused-variable] + 271 | int i, j, k, h, lastDiff; + | ^ +writer.cpp:271:10: warning: unused variable 'j' [-Wunused-variable] + 271 | int i, j, k, h, lastDiff; + | ^ +writer.cpp:271:13: warning: unused variable 'k' [-Wunused-variable] + 271 | int i, j, k, h, lastDiff; + | ^ +writer.cpp:271:19: warning: unused variable 'lastDiff' [-Wunused-variable] + 271 | int i, j, k, h, lastDiff; + | ^~~~~~~~ +writer.cpp:272:9: warning: unused variable 'code1' [-Wunused-variable] + 272 | int64 code1, code2; + | ^~~~~ +writer.cpp:272:16: warning: unused variable 'code2' [-Wunused-variable] + 272 | int64 code1, code2; + | ^~~~~ +writer.cpp:278:10: warning: unused variable 'p' [-Wunused-variable] + 278 | double p, sump; + | ^ +writer.cpp:278:13: warning: unused variable 'sump' [-Wunused-variable] + 278 | double p, sump; + | ^~~~ +writer.cpp:279:30: warning: unused variable 'tag' [-Wunused-variable] + 279 | char qseq[128], rseq[128], tag[128]; + | ^~~ +writer.cpp:281:8: warning: unused variable 'shortread' [-Wunused-variable] + 281 | char shortread[256]; + | ^~~~~~~~~ hash.cpp: In member function 'unsigned int HashTable::lookupEmbedTable(int64*, uint32, int, char*, strand, int, HitSet*, bool)': hash.cpp:962:11: warning: unused variable 'noheadkey' [-Wunused-variable] 962 | int64 * noheadkey = &tspace[8], *rest = &tspace[24]; @@ -1133,13 +1231,10 @@ hash.cpp:973:11: warning: unused variable 'seqVector' [-Wunused-variable] 973 | int64 * seqVector = sequence->getSequence(); | ^~~~~~~~~ -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; - | ^ +writer.cpp: In member function 'void SamWriter::getCIGAR(char*, char*, char*, ErrorVector)': +writer.cpp:382:24: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] + 382 | for (i = 0, j = 0; i < strlen(query); i++, j++) { + | ~~^~~~~~~~~~~~~~~ hash.cpp: In member function 'bool HashTable::lookup(int64*, uint32)': hash.cpp:1052:7: warning: unused variable 'num' [-Wunused-variable] 1052 | int num; @@ -1159,6 +1254,17 @@ hash.cpp:1059:15: warning: unused variable 'soffset' [-Wunused-variable] 1059 | uint32 sid, soffset; | ^~~~~~~ +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; + | ^ +writer.cpp: In member function 'void SamWriter::getMDfield(char*, char*, char*, ErrorVector)': +writer.cpp:431:24: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] + 431 | for (i = 0, j = 0; i < strlen(query); i++, j++) { + | ~~^~~~~~~~~~~~~~~ hash.cpp: In member function 'uint32 HashTable::printOverflowList(uint32, uint32, int64*)': hash.cpp:1184:23: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] 1184 | for (int i = 0; i < keyOffset / BITS_PER_BASE; i++) @@ -1173,6 +1279,18 @@ hash.cpp:1137:11: warning: unused variable 'diff' [-Wunused-variable] 1137 | int64 * diff = &tspace1[8], *target = &tspace2[8]; | ^~~~ +writer.cpp: In member function 'void SamPairWriter::writeValidAlignment(int, HitSet*)': +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 +hash.cpp: In member function 'int HashTable::sortList()': +hash.cpp:1430:14: warning: variable 'pool' set but not used [-Wunused-but-set-variable] + 1430 | uint32 * pool; + | ^~~~ +hash.cpp:1321:34: warning: variable 'offset' set but not used [-Wunused-but-set-variable] + 1321 | uint32 entryOffset, seqOffset, offset; + | ^~~~~~ main.cpp: In function 'int main(int, char**)': main.cpp:523:7: warning: unused variable 'numKeys' [-Wunused-variable] 523 | int numKeys; @@ -1189,13 +1307,14 @@ main.cpp:536:9: warning: unused variable 'threadid' [-Wunused-variable] 536 | int * threadid; | ^~~~~~~~ -hash.cpp: In member function 'int HashTable::sortList()': -hash.cpp:1430:14: warning: variable 'pool' set but not used [-Wunused-but-set-variable] - 1430 | uint32 * pool; - | ^~~~ -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 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: 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; @@ -1203,240 +1322,122 @@ hash.cpp:1690:5: warning: label 'restart' defined but not used [-Wunused-label] 1690 | restart: if (buckets[bucketId] == HASH_EMPTY | ^~~~~~~ -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 }; - | ^~~~~~~~~~~~~ +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; + | ^~~ +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)); + | ~~~~~~~^~~~~~~~~~ +In file included from hash.h:29, + from aligner.h:25, + from sequence.cpp:30: +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 aligner.h:25, + from sequence.cpp:30: +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) { + | ~~~~^~~~~~~ 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: +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 }; | ^~~~~~~~~~~~~ -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) { - | ~~~~^~~~ -aligner.cpp:371:37: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses] - 371 | if ((indexBits[i] >> j) & 0x1 == 1) { - | ~~~~^~~~ -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++) { - | ~~^~~~~~~~~~~~ -aligner.cpp:712:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 712 | for (i = 0; i < nHashTable; i++) { - | ~~^~~~~~~~~~~~ -aligner.cpp: In member function 'int Aligner::build(char*)': -aligner.cpp:724:16: warning: unused variable 'i' [-Wunused-variable] - 724 | unsigned int i, j; - | ^ -aligner.cpp:724:19: warning: unused variable 'j' [-Wunused-variable] - 724 | unsigned int i, j; - | ^ -aligner.cpp: In member function 'int Aligner::buildHashTables(char*)': -aligner.cpp:807:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 807 | for (i = 0; i < nHashTable; i++) { - | ~~^~~~~~~~~~~~ -aligner.cpp:844:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 844 | for (i1 = 0; i1 < lenPartition * (nPartition - 1); i1 += lenPartition) { - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aligner.cpp:864:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 864 | for (i1 = 0; i1 < lenPartition * (nPartition - 2); i1 += lenPartition) { - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aligner.cpp:871:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 871 | for (i2 = i1; i2 < lenPartition * (nPartition - 2); - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aligner.cpp:894:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 894 | for (i1 = 0; i1 < lenPartition * (nPartition - 3); i1 += lenPartition) { - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aligner.cpp:901:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 901 | for (i2 = i1; i2 < lenPartition * (nPartition - 3); - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aligner.cpp:909:28: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 909 | for (i3 = i2; i3 < lenPartition * (nPartition - 3); - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aligner.cpp:928:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 928 | for (i1 = 0; i1 < lenPartition * (nPartition - 4); i1 += lenPartition) { - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aligner.cpp:930:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 930 | for (i2 = i1; i2 < lenPartition * (nPartition - 4); - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aligner.cpp:933:28: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 933 | for (i3 = i2; i3 < lenPartition * (nPartition - 4); - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aligner.cpp:936:30: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 936 | for (i4 = i3; i4 < lenPartition * (nPartition - 4); i4 += - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aligner.cpp:951:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 951 | for (i1 = 0; i1 < lenPartition * (nPartition - 5); i1 += lenPartition) { - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aligner.cpp:953:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 953 | for (i2 = i1; i2 < lenPartition * (nPartition - 5); - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aligner.cpp:956:28: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 956 | for (i3 = i2; i3 < lenPartition * (nPartition - 5); - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aligner.cpp:959:30: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 959 | for (i4 = i3; i4 < lenPartition * (nPartition - 5); i4 += - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aligner.cpp:962:32: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 962 | for (i5 = i4; i5 < lenPartition * (nPartition - 5); i5 += - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aligner.cpp:983:19: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 983 | for (i = 0; i < nHashTable; i++) { - | ~~^~~~~~~~~~~~ -aligner.cpp:1006:19: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 1006 | for (i = 0; i < nHashTable; i++) { - | ~~^~~~~~~~~~~~ -embedhash.cpp: In member function 'int EmbedHashTable::preProcessEnd()': -embedhash.cpp:137:16: warning: unused variable 'ln2' [-Wunused-variable] - 137 | const double ln2 = log(2); - | ^~~ -embedhash.cpp: In member function 'void EmbedHashTable::setScanThreshold(double)': -embedhash.cpp:253:9: warning: unused variable 'sum' [-Wunused-variable] - 253 | int64 sum = 0; - | ^~~ -embedhash.cpp:255:9: warning: unused variable 'top' [-Wunused-variable] - 255 | int64 top = total - total * r; - | ^~~ -aligner.cpp: In member function 'unsigned int Aligner::alignFirst(int64*, char*, strand, int, HitSet*, bool)': -aligner.cpp:1035:10: warning: unused variable 'offset' [-Wunused-variable] - 1035 | uint32 offset; - | ^~~~~~ -aligner.cpp:1039:7: warning: unused variable 'nHit' [-Wunused-variable] - 1039 | int nHit = 0; - | ^~~~ -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] = -embedhash.cpp:328:10: warning: unused variable 'seqOffset' [-Wunused-variable] - 328 | uint32 seqOffset; - | ^~~~~~~~~ -embedhash.cpp:330:10: warning: unused variable 'counter' [-Wunused-variable] - 330 | uint32 counter = 0; - | ^~~~~~~ -embedhash.cpp:331:11: warning: variable 'seqVector' set but not used [-Wunused-but-set-variable] - 331 | int64 * seqVector; - | ^~~~~~~~~ -embedhash.cpp:333:11: warning: unused variable 'target' [-Wunused-variable] - 333 | int64 * target = &tspace[8]; - | ^~~~~~ -embedhash.cpp:334:8: warning: unused variable 'isBloomFilter' [-Wunused-variable] - 334 | bool isBloomFilter; - | ^~~~~~~~~~~~~ -embedhash.cpp:335:12: warning: unused variable 'bloomFilter' [-Wunused-variable] - 335 | uint32 * bloomFilter; - | ^~~~~~~~~~~ -embedhash.cpp:336:10: warning: unused variable 'bloomFilterNum' [-Wunused-variable] - 336 | uint32 bloomFilterNum; - | ^~~~~~~~~~~~~~ -aligner.cpp: In member function 'unsigned int Aligner::align(int64*, char*, strand, int, HitSet*, bool, bool)': -aligner.cpp:1119:10: warning: variable 'offset' set but not used [-Wunused-but-set-variable] - 1119 | uint32 offset; - | ^~~~~~ -aligner.cpp:1123:7: warning: variable 'nHit' set but not used [-Wunused-but-set-variable] - 1123 | int nHit = 0; - | ^~~~ -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; - | ^~~ -embedhash.cpp:387:34: warning: variable 'startOffset' set but not used [-Wunused-but-set-variable] - 387 | uint32 seqOffset, entryOffset, startOffset; - | ^~~~~~~~~~~ -embedhash.cpp:389:11: warning: unused variable 'diff' [-Wunused-variable] - 389 | int64 * diff = &tspace1[8], *target = &tspace2[8]; - | ^~~~ -embedhash.cpp:392:10: warning: unused variable 'sid' [-Wunused-variable] - 392 | uint32 sid, soffset; - | ^~~ -embedhash.cpp:392:15: warning: unused variable 'soffset' [-Wunused-variable] - 392 | uint32 sid, soffset; - | ^~~~~~~ -aligner.cpp: In member function 'int Aligner::check(int)': -aligner.cpp:1436:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 1436 | for (i = 0; i < num; i++) { - | ~~^~~~~ -aligner.cpp:1452:19: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 1452 | for (j = 0; j < nError; j++) { - | ~~^~~~~~~~ -aligner.cpp:1426:7: warning: unused variable 'ret' [-Wunused-variable] - 1426 | int ret; - | ^~~ -aligner.cpp: In member function 'AlignRes Aligner::alignSingleEnd(AlignInfo*, char*)': -aligner.cpp:1541:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 1541 | for (i = 0; i < nHashTable; i++) { - | ~~^~~~~~~~~~~~ -aligner.cpp:1547:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 1547 | for (i = 0; i < res.nRead; i++) { - | ~~^~~~~~~~~~~ -aligner.cpp:1629:3: warning: deleting object of abstract class type 'Writer' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor] - 1629 | delete writer; - | ^~~~~~~~~~~~~ -aligner.cpp:1502:10: warning: unused variable 'file' [-Wunused-variable] - 1502 | FILE * file = NULL, *alfile = NULL, *unfile = NULL; - | ^~~~ -aligner.cpp:1502:24: warning: unused variable 'alfile' [-Wunused-variable] - 1502 | FILE * file = NULL, *alfile = NULL, *unfile = NULL; - | ^~~~~~ -aligner.cpp:1502:40: warning: unused variable 'unfile' [-Wunused-variable] - 1502 | FILE * file = NULL, *alfile = NULL, *unfile = NULL; - | ^~~~~~ -aligner.cpp:1505:7: warning: unused variable 'strand' [-Wunused-variable] - 1505 | int strand; - | ^~~~~~ -aligner.cpp:1508:9: warning: unused variable 'ratio' [-Wunused-variable] - 1508 | float ratio; - | ^~~~~ -aligner.cpp:1514:31: warning: unused variable 'strata' [-Wunused-variable] - 1514 | bool sorted = info->sorted, strata = info->strata; - | ^~~~~~ -aligner.cpp: In member function 'AlignRes Aligner::alignPairEnd(AlignInfo*, char*)': -aligner.cpp:1685:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 1685 | for (i = 0; i < res.nRead; i++) { - | ~~^~~~~~~~~~~ -aligner.cpp:1754:3: warning: deleting object of abstract class type 'Writer' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor] - 1754 | delete writer; - | ^~~~~~~~~~~~~ -aligner.cpp:1637:8: warning: unused variable 'success' [-Wunused-variable] - 1637 | bool success; - | ^~~~~~~ -aligner.cpp:1638:16: warning: unused variable 'nSuccessRead' [-Wunused-variable] - 1638 | unsigned int nSuccessRead = 0; - | ^~~~~~~~~~~~ -aligner.cpp:1639:10: warning: unused variable 'file' [-Wunused-variable] - 1639 | FILE * file = NULL; - | ^~~~ -aligner.cpp:1646:8: warning: unused variable 'mateFilename' [-Wunused-variable] - 1646 | char mateFilename[256]; - | ^~~~~~~~~~~~ -aligner.cpp:1652:31: warning: unused variable 'strata' [-Wunused-variable] - 1652 | bool sorted = info->sorted, strata = info->strata; - | ^~~~~~ -aligner.cpp: In member function 'AlignRes Aligner::mergeSingleEnd(AlignInfo*, int, char*)': -aligner.cpp:1851:3: warning: deleting object of abstract class type 'Writer' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor] - 1851 | delete writer; - | ^~~~~~~~~~~~~ -aligner.cpp:1775:10: warning: unused variable 'ret' [-Wunused-variable] - 1775 | int i, ret; - | ^~~ -aligner.cpp: In member function 'AlignRes Aligner::mergePairEnd(AlignInfo*, int, char*)': -aligner.cpp:1989:3: warning: deleting object of abstract class type 'Writer' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor] - 1989 | delete writer; - | ^~~~~~~~~~~~~ -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 in this function [-Wmaybe-uninitialized] - 506 | itree->flush(offsetInCmptSeq, 0, curSeq, offsetInOrgSeq); - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from embedhash.cpp:32: +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 }; @@ -1460,10 +1461,59 @@ 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)); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from hitset.h:31, + from hash.h:29, + from aligner.h:25, + from builder.cpp:31: +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; + | ^~~ +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)); + | ~~~~~~~^~~~~~~~~~ +In file included from hash.h:29, + from aligner.h:25, + from builder.cpp:31: +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; + | ^~~~ +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); + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from aligner.h:25, + from builder.cpp:31: +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 aligner.h:25, from aligner.cpp:25: hash.h: In member function 'int Aligner::initLookupArray()': @@ -1473,6 +1523,26 @@ aligner.cpp:360:7: note: 'keySpan' was declared here 360 | int keySpan; | ^~~~~~~ +builder.cpp: In function 'int getArguVal(char*)': +builder.cpp:115:15: warning: suggest parentheses around assignment used as truth value [-Wparentheses] + 115 | else if (*c = 'g' || *c == 'G') + | ~~~^~~~~~~~~~~~~~~~~~ +builder.cpp: In function 'int main(int, char**)': +builder.cpp:159:7: warning: unused variable 'build_mode' [-Wunused-variable] + 159 | int build_mode = BUILD_MODE_ALL; + | ^~~~~~~~~~ +builder.cpp:277:7: warning: unused variable 'nChar' [-Wunused-variable] + 277 | int nChar = sequence->getNum(); + | ^~~~~ +In file included from builder.cpp:34: +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 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)); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp: In member function 'unsigned int Aligner::alignFirst(int64*, char*, strand, int, HitSet*, bool)': aligner.cpp:1097:3: warning: 'ret' may be used uninitialized in this function [-Wmaybe-uninitialized] 1097 | if (ret == MSG_HITSETFULL) @@ -1481,7 +1551,7 @@ 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-p9c7fkZ6 + rm -fr -- /tmp/dh-xdg-rundir-XuOPKeWH create-stamp debian/debhelper-build-stamp dh_prep rm -f -- debian/wham-align.substvars @@ -1516,10 +1586,10 @@ 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-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 chmod 0644 -- 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 dh_perl dh_link dh_strip_nondeterminism @@ -1541,16 +1611,16 @@ dwz -mdebian/wham-align/usr/lib/debug/.dwz/i386-linux-gnu/wham-align.debug -M/usr/lib/debug/.dwz/i386-linux-gnu/wham-align.debug -- debian/wham-align/usr/bin/wham debian/wham-align/usr/bin/wham-build objcopy --compress-debug-sections debian/wham-align/usr/lib/debug/.dwz/i386-linux-gnu/wham-align.debug dh_strip -a - install -d debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/36 - objcopy --only-keep-debug --compress-debug-sections debian/wham-align/usr/bin/wham debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/36/894a9a63897980ac85ae30bab8221e7e7e83e5.debug - chmod 0644 -- debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/36/894a9a63897980ac85ae30bab8221e7e7e83e5.debug - strip --remove-section=.comment --remove-section=.note debian/wham-align/usr/bin/wham - objcopy --add-gnu-debuglink debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/36/894a9a63897980ac85ae30bab8221e7e7e83e5.debug debian/wham-align/usr/bin/wham install -d debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/e6 objcopy --only-keep-debug --compress-debug-sections debian/wham-align/usr/bin/wham-build debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/e6/fb5272bf10bbbb2a7514434f4154e0602e6bd8.debug chmod 0644 -- debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/e6/fb5272bf10bbbb2a7514434f4154e0602e6bd8.debug strip --remove-section=.comment --remove-section=.note debian/wham-align/usr/bin/wham-build objcopy --add-gnu-debuglink debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/e6/fb5272bf10bbbb2a7514434f4154e0602e6bd8.debug debian/wham-align/usr/bin/wham-build + install -d debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/36 + objcopy --only-keep-debug --compress-debug-sections debian/wham-align/usr/bin/wham debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/36/894a9a63897980ac85ae30bab8221e7e7e83e5.debug + chmod 0644 -- debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/36/894a9a63897980ac85ae30bab8221e7e7e83e5.debug + strip --remove-section=.comment --remove-section=.note debian/wham-align/usr/bin/wham + objcopy --add-gnu-debuglink debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/36/894a9a63897980ac85ae30bab8221e7e7e83e5.debug debian/wham-align/usr/bin/wham install -d debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/wham-align/usr/lib/debug/.dwz/i386-linux-gnu debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/wham-align/usr/lib/debug/.dwz @@ -1561,7 +1631,7 @@ rm -f debian/wham-align/DEBIAN/shlibs dh_shlibdeps -a install -d debian/wham-align/DEBIAN - dpkg-shlibdeps -Tdebian/wham-align.substvars debian/wham-align/usr/bin/wham debian/wham-align/usr/bin/wham-build + dpkg-shlibdeps -Tdebian/wham-align.substvars debian/wham-align/usr/bin/wham-build debian/wham-align/usr/bin/wham dh_installdeb dh_gencontrol echo misc:Depends= >> debian/wham-align.substvars @@ -1579,20 +1649,22 @@ dh_builddeb dpkg-deb --root-owner-group --build debian/wham-align .. 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_i386.deb'. dpkg-deb: building package 'wham-align-dbgsym' in '../wham-align-dbgsym_0.1.5-8_i386.deb'. +dpkg-deb: building package 'wham-align' in '../wham-align_0.1.5-8_i386.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../wham-align_0.1.5-8_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration +I: user script /srv/workspace/pbuilder/21663/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/21663/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/31134 and its subdirectories -I: Current time: Wed Jun 29 03:26:07 -12 2022 -I: pbuilder-time-stamp: 1656516367 +I: removing directory /srv/workspace/pbuilder/21663 and its subdirectories +I: Current time: Thu May 27 23:06:47 +14 2021 +I: pbuilder-time-stamp: 1622106407