Diff of the two buildlogs: -- --- b1/build.log 2021-11-22 03:00:03.060215126 +0000 +++ b2/build.log 2021-11-22 03:00:29.943294116 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Nov 21 14:59:24 -12 2021 -I: pbuilder-time-stamp: 1637549964 +I: Current time: Sun Dec 25 23:23:05 +14 2022 +I: pbuilder-time-stamp: 1671960185 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -16,8 +16,8 @@ I: copying [./wham-align_0.1.5-8.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.8tVm_4Yn/trustedkeys.kbx': General error -gpgv: Signature made Thu Feb 18 19:13:34 2021 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.3yhl8P5Q/trustedkeys.kbx': General error +gpgv: Signature made Fri Feb 19 21:13:34 2021 +14 gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "npatra974@gmail.com" gpgv: Can't check signature: No public key @@ -32,135 +32,169 @@ dpkg-source: info: applying cross-build.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3463614/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3844676/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-amd64. +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/3844676/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3844676/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='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=15' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='amd64' + 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]="x86_64-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=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=16' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='01e9ac6607174c7a8aaf071b333aabdd' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='3463614' - PS1='# ' - PS2='> ' + INVOCATION_ID=d8dac6dd7f364cffa2183d697b218f67 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-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=3844676 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.M5gqS2aIzb/pbuilderrc_7qOb --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.M5gqS2aIzb/b1 --logfile b1/build.log wham-align_0.1.5-8.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://78.137.99.97:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.M5gqS2aIzb/pbuilderrc_VlDD --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.M5gqS2aIzb/b2 --logfile b2/build.log wham-align_0.1.5-8.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://85.184.249.68:3128 I: uname -a - Linux ionos11-amd64 5.10.0-9-amd64 #1 SMP Debian 5.10.70-1 (2021-09-30) x86_64 GNU/Linux + Linux i-capture-the-hostname 5.14.0-0.bpo.2-amd64 #1 SMP Debian 5.14.9-2~bpo11+1 (2021-10-10) x86_64 GNU/Linux I: ls -l /bin total 5476 - -rwxr-xr-x 1 root root 1234376 Aug 4 08:25 bash - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 38984 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 38984 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 18424 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 43936 Sep 23 2020 cat - -rwxr-xr-x 1 root root 72672 Sep 23 2020 chgrp - -rwxr-xr-x 1 root root 64448 Sep 23 2020 chmod - -rwxr-xr-x 1 root root 72672 Sep 23 2020 chown - -rwxr-xr-x 1 root root 151168 Sep 23 2020 cp - -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash - -rwxr-xr-x 1 root root 113664 Sep 23 2020 date - -rwxr-xr-x 1 root root 80968 Sep 23 2020 dd - -rwxr-xr-x 1 root root 93936 Sep 23 2020 df - -rwxr-xr-x 1 root root 147176 Sep 23 2020 dir - -rwxr-xr-x 1 root root 84440 Jul 28 07:09 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 39712 Sep 23 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 39680 Sep 23 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 69032 Jul 28 07:09 findmnt - -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount - -rwxr-xr-x 1 root root 203072 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 98048 Mar 2 2021 gzip - -rwxr-xr-x 1 root root 22600 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 72840 Sep 23 2020 ln - -rwxr-xr-x 1 root root 56952 Feb 7 2020 login - -rwxr-xr-x 1 root root 147176 Sep 23 2020 ls - -rwxr-xr-x 1 root root 149736 Jul 28 07:09 lsblk - -rwxr-xr-x 1 root root 85184 Sep 23 2020 mkdir - -rwxr-xr-x 1 root root 76896 Sep 23 2020 mknod - -rwxr-xr-x 1 root root 48064 Sep 23 2020 mktemp - -rwxr-xr-x 1 root root 59632 Jul 28 07:09 more - -rwsr-xr-x 1 root root 55528 Jul 28 07:09 mount - -rwxr-xr-x 1 root root 18664 Jul 28 07:09 mountpoint - -rwxr-xr-x 1 root root 147080 Sep 23 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 43872 Sep 23 2020 pwd - lrwxrwxrwx 1 root root 4 Aug 4 08:25 rbash -> bash - -rwxr-xr-x 1 root root 52032 Sep 23 2020 readlink - -rwxr-xr-x 1 root root 72704 Sep 23 2020 rm - -rwxr-xr-x 1 root root 52032 Sep 23 2020 rmdir - -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Nov 20 21:34 sh -> dash - -rwxr-xr-x 1 root root 43808 Sep 23 2020 sleep - -rwxr-xr-x 1 root root 84928 Sep 23 2020 stty - -rwsr-xr-x 1 root root 71912 Jul 28 07:09 su - -rwxr-xr-x 1 root root 39744 Sep 23 2020 sync - -rwxr-xr-x 1 root root 531928 Feb 16 2021 tar - -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 101408 Sep 23 2020 touch - -rwxr-xr-x 1 root root 39680 Sep 23 2020 true - -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server - -rwsr-xr-x 1 root root 35040 Jul 28 07:09 umount - -rwxr-xr-x 1 root root 39744 Sep 23 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress - -rwxr-xr-x 1 root root 147176 Sep 23 2020 vdir - -rwxr-xr-x 1 root root 63744 Jul 28 07:09 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/3463614/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1234376 Aug 5 2021 bash + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 38984 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 38984 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 18424 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 43936 Sep 24 2020 cat + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chgrp + -rwxr-xr-x 1 root root 64448 Sep 24 2020 chmod + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chown + -rwxr-xr-x 1 root root 151168 Sep 24 2020 cp + -rwxr-xr-x 1 root root 125560 Dec 11 2020 dash + -rwxr-xr-x 1 root root 113664 Sep 24 2020 date + -rwxr-xr-x 1 root root 80968 Sep 24 2020 dd + -rwxr-xr-x 1 root root 93936 Sep 24 2020 df + -rwxr-xr-x 1 root root 147176 Sep 24 2020 dir + -rwxr-xr-x 1 root root 84440 Jul 29 2021 dmesg + lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname + -rwxr-xr-x 1 root root 39712 Sep 24 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 39680 Sep 24 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 69032 Jul 29 2021 findmnt + -rwsr-xr-x 1 root root 34896 Feb 27 2021 fusermount + -rwxr-xr-x 1 root root 203072 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 2021 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 2021 gzexe + -rwxr-xr-x 1 root root 98048 Mar 3 2021 gzip + -rwxr-xr-x 1 root root 22600 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 72840 Sep 24 2020 ln + -rwxr-xr-x 1 root root 56952 Feb 8 2020 login + -rwxr-xr-x 1 root root 147176 Sep 24 2020 ls + -rwxr-xr-x 1 root root 149736 Jul 29 2021 lsblk + -rwxr-xr-x 1 root root 85184 Sep 24 2020 mkdir + -rwxr-xr-x 1 root root 76896 Sep 24 2020 mknod + -rwxr-xr-x 1 root root 48064 Sep 24 2020 mktemp + -rwxr-xr-x 1 root root 59632 Jul 29 2021 more + -rwsr-xr-x 1 root root 55528 Jul 29 2021 mount + -rwxr-xr-x 1 root root 18664 Jul 29 2021 mountpoint + -rwxr-xr-x 1 root root 147080 Sep 24 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 19 2021 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43872 Sep 24 2020 pwd + lrwxrwxrwx 1 root root 4 Aug 5 2021 rbash -> bash + -rwxr-xr-x 1 root root 52032 Sep 24 2020 readlink + -rwxr-xr-x 1 root root 72704 Sep 24 2020 rm + -rwxr-xr-x 1 root root 52032 Sep 24 2020 rmdir + -rwxr-xr-x 1 root root 27472 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Dec 25 23:23 sh -> bash + lrwxrwxrwx 1 root root 4 Dec 25 05:47 sh.distrib -> dash + -rwxr-xr-x 1 root root 43808 Sep 24 2020 sleep + -rwxr-xr-x 1 root root 84928 Sep 24 2020 stty + -rwsr-xr-x 1 root root 71912 Jul 29 2021 su + -rwxr-xr-x 1 root root 39744 Sep 24 2020 sync + -rwxr-xr-x 1 root root 531928 Feb 17 2021 tar + -rwxr-xr-x 1 root root 14456 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 101408 Sep 24 2020 touch + -rwxr-xr-x 1 root root 39680 Sep 24 2020 true + -rwxr-xr-x 1 root root 14328 Feb 27 2021 ulockmgr_server + -rwsr-xr-x 1 root root 35040 Jul 29 2021 umount + -rwxr-xr-x 1 root root 39744 Sep 24 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 2021 uncompress + -rwxr-xr-x 1 root root 147176 Sep 24 2020 vdir + -rwxr-xr-x 1 root root 63744 Jul 29 2021 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Mar 3 2021 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 2021 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 2021 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 2021 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 2021 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 2021 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 2021 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 2021 zless + -rwxr-xr-x 1 root root 1842 Mar 3 2021 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 2021 znew +I: user script /srv/workspace/pbuilder/3844676/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -227,7 +261,7 @@ Get: 29 http://deb.debian.org/debian bullseye/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 30 http://deb.debian.org/debian bullseye/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian bullseye/main amd64 debhelper all 13.3.4 [1049 kB] -Fetched 18.3 MB in 0s (69.5 MB/s) +Fetched 18.3 MB in 0s (88.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19655 files and directories currently installed.) @@ -367,7 +401,8 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/wham-align-0.1.5/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../wham-align_0.1.5-8_source.changes +hostname: Name or service not known +I: Running cd /build/wham-align-0.1.5/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../wham-align_0.1.5-8_source.changes dpkg-buildpackage: info: source package wham-align dpkg-buildpackage: info: source version 0.1.5-8 dpkg-buildpackage: info: source distribution unstable @@ -378,7 +413,7 @@ dh clean dh_auto_clean install -d /build/wham-align-0.1.5/debian/.debhelper/generated/_source/home - make -j15 clean + make -j16 clean make[1]: Entering directory '/build/wham-align-0.1.5' rm -f wham wham-build *.o make[1]: Leaving directory '/build/wham-align-0.1.5' @@ -402,7 +437,7 @@ dh_auto_configure install -d /build/wham-align-0.1.5/debian/.debhelper/generated/_source/home dh_auto_build - make -j15 "INSTALL=install --strip-program=true" + make -j16 "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 @@ -415,6 +450,9 @@ 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__; @@ -422,9 +460,39 @@ error.cpp:32:7: warning: unused variable 'lineno' [-Wunused-variable] 32 | int lineno = __LINE__; | ^~~~~~ -g++ -c -g -O2 -fdebug-prefix-map=/build/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings 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 +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; + | ^~ 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++) { @@ -443,6 +511,13 @@ 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.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) { + | ~~~~^~~~~~~~ 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)) { @@ -451,12 +526,6 @@ 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 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) { - | ~~~~^~~~~~~~ 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; @@ -485,58 +554,66 @@ 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 hitset.cpp:1: +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; | ^~~~ -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; - | ^~ -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; +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 'long 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 'long 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 hash.h:29, - from hash.cpp:27: -pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': -pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] - 265 | if (num > nError) { - | ~~~~^~~~~~~~ -In file included from hitset.h:31, - from hash.h:29, - from embedhash.cpp:27: + 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) { @@ -569,12 +646,23 @@ 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 hash.cpp:27: +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; + | ^~~~~~~~~ +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::pairAlignDP(int64*, int64*, int, int, int, bool)': pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable] 602 | int i, j, offset, min, tmp; @@ -599,40 +687,41 @@ pair.h:756:9: warning: unused variable 'a' [-Wunused-variable] 756 | int a; | ^ -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 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.cpp:27: -hash.h: In function 'uint32 murmurHash(int64*, uint32)': -hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] - 86 | uint32 sum = 0; - | ^~~ In file included from hash.h:29, - from embedhash.cpp:27: + 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::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 aligner.h:25, + from aligner.cpp:25: +hash.h: In function 'uint32 murmurHash(int64*, uint32)': +hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] + 86 | uint32 sum = 0; + | ^~~ In file included from hitset.h:31, - from writer.h:26, - from writer.cpp:21: + from hash.h:29, + from embedhash.cpp:27: +pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': +pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] + 265 | if (num > nError) { + | ~~~~^~~~~~~~ +In file included from hitset.h:31, + from hash.h:29, + from hash.cpp:27: 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; @@ -643,11 +732,6 @@ pair.h:685:9: warning: unused variable 'a' [-Wunused-variable] 685 | int a; | ^ -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::pairAlignBitVector(int64*, int64*, int, int, int)': pair.h:755:15: warning: unused variable 'num' [-Wunused-variable] 755 | int i, p, num, base, Cscore; @@ -658,27 +742,10 @@ 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 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::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 aligner.h:25, - from aligner.cpp:25: -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; @@ -689,6 +756,16 @@ pair.h:685:9: warning: unused variable 'a' [-Wunused-variable] 685 | int a; | ^ +pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)': +pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] + 974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); + | ~~~~~~~^~~~~~~~~~ +In file included from hash.h:29, + from embedhash.cpp:27: +hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)': +hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] + 86 | int size; + | ^~~~ 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; @@ -703,68 +780,51 @@ 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: +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; | ^~~~ -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; +In file included from embedhash.cpp:27: +hash.h: In function 'uint32 murmurHash(int64*, uint32)': +hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] + 86 | uint32 sum = 0; + | ^~~ +In file included from hash.cpp:27: +hash.h: In function 'uint32 murmurHash(int64*, uint32)': +hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] + 86 | uint32 sum = 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 'long 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 'long 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) { - | ~~~~~^~~~~~~ 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); | ~~~~~~~~~~~~^ +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; + | ^~ +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) { + | ~~~~^~~~~~~~ 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); @@ -784,14 +844,6 @@ short.cpp:510:14: note: 'sprintf' output between 4 and 268 bytes into a destination of size 256 510 | sprintf(partitions[i]->unFileName, "%s.t%d", unFileName, i); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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; @@ -827,20 +879,192 @@ 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; + | ^~~ +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++) { + | ~~^~~~~~~~~~~~ +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; + | ^~~~~~ +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; + | ^~~ In file included from hitset.h:31, from hash.h:29, from aligner.h:25, - from main.cpp:34: + 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) { | ~~~~^~~~~~~~ -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; +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; | ^~~ +In file included from hitset.h:31, + from hash.h:29, + from aligner.h:25, + from main.cpp:34: +pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': +pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] + 265 | if (num > nError) { + | ~~~~^~~~~~~~ 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; @@ -855,41 +1079,6 @@ pair.h:685:9: warning: unused variable 'a' [-Wunused-variable] 685 | int a; | ^ -pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)': -pair.h:755:15: warning: unused variable 'num' [-Wunused-variable] - 755 | int i, p, num, base, Cscore; - | ^~~ -pair.h:755:20: warning: unused variable 'base' [-Wunused-variable] - 755 | int i, p, num, base, Cscore; - | ^~~~ -pair.h:756:9: warning: unused variable 'a' [-Wunused-variable] - 756 | int a; - | ^ -pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)': -pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] - 974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); - | ~~~~~~~^~~~~~~~~~ -In file included from hash.h:29, - from aligner.h:25, - from main.cpp:34: -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 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 hitset.h:31, - from hash.h:29, - from aligner.h:25, - from sequence.cpp:30: -pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': -pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] - 265 | if (num > nError) { - | ~~~~^~~~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)': pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable] 602 | int i, j, offset, min, tmp; @@ -904,23 +1093,6 @@ pair.h:685:9: warning: unused variable 'a' [-Wunused-variable] 685 | int a; | ^ -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; - | ^~ 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; @@ -931,6 +1103,20 @@ pair.h:756:9: warning: unused variable 'a' [-Wunused-variable] 756 | int a; | ^ +pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)': +pair.h:755:15: warning: unused variable 'num' [-Wunused-variable] + 755 | int i, p, num, base, Cscore; + | ^~~ +pair.h:755:20: warning: unused variable 'base' [-Wunused-variable] + 755 | int i, p, num, base, Cscore; + | ^~~~ +pair.h:756:9: warning: unused variable 'a' [-Wunused-variable] + 756 | int a; + | ^ +pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)': +pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] + 974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); + | ~~~~~~~^~~~~~~~~~ pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)': pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] 974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); @@ -942,63 +1128,25 @@ hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] 86 | int size; | ^~~~ -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)(((long unsigned int)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; - | ^~~~~~~~~~~~~~ -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 hash.h:29, + from aligner.h:25, + from main.cpp:34: +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; | ^~~ +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; + | ^~~ sequence.cpp: In member function 'void CompactSequence::extractFileName(char*, char*)': sequence.cpp:97:10: warning: unused variable 'str' [-Wunused-variable] 97 | char * str; @@ -1064,6 +1212,68 @@ sequence.cpp:804:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] 804 | if (ret != size) { | ~~~~^~~~~~~ +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(); + | ^~~~~ +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)(((long unsigned int)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; + | ^~~~~~~~~~~~~~ +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; + | ^~~~~~~ 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) @@ -1201,13 +1411,10 @@ hash.cpp:1321:34: warning: variable 'offset' set but not used [-Wunused-but-set-variable] 1321 | uint32 entryOffset, seqOffset, offset; | ^~~~~~ -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) { - | ~~~~^~~~ +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::checkRepeat(uint32)': hash.cpp:1673:34: warning: variable 'offset' set but not used [-Wunused-but-set-variable] 1673 | uint32 entryOffset, seqOffset, offset; @@ -1215,172 +1422,6 @@ hash.cpp:1690:5: warning: label 'restart' defined but not used [-Wunused-label] 1690 | restart: if (buckets[bucketId] == HASH_EMPTY | ^~~~~~~ -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 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 '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; - | ^~~~~~ -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; - | ^~~ -main.cpp: In function 'int getArguVal(char*)': -main.cpp:159:15: warning: suggest parentheses around assignment used as truth value [-Wparentheses] - 159 | else if (*c = 'g' || *c == 'G') - | ~~~^~~~~~~~~~~~~~~~~~ main.cpp: In function 'int align(char*, AlignInfo*, char*, int)': main.cpp:350:7: warning: unused variable 'i' [-Wunused-variable] 350 | int i, j, ret; @@ -1404,6 +1445,16 @@ main.cpp:536:9: warning: unused variable 'threadid' [-Wunused-variable] 536 | int * threadid; | ^~~~~~~~ +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 }; + | ^~~~~~~~~~~~~ +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 }; + | ^~~~~~~~~~~~~ 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 | } @@ -1418,26 +1469,19 @@ 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 }; | ^~~~~~~~~~~~~ -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 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 aligner.cpp:25: +hash.h: In member function 'int Aligner::initLookupArray()': +hash.h:353:18: warning: 'keySpan' may be used uninitialized in this function [-Wmaybe-uninitialized] + 353 | widthKeySpan = keySpan; + | ~~~~~~~~~~~~~^~~~~~~~~ +aligner.cpp:360:7: note: 'keySpan' was declared here + 360 | int keySpan; + | ^~~~~~~ main.cpp: In function 'void mergeFiles(std::string)': main.cpp:269:21: warning: '%d' directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] 269 | sprintf(buf, ".t%d ", i); @@ -1457,15 +1501,6 @@ main.cpp:276:12: note: 'sprintf' output between 4 and 13 bytes into a destination of size 10 276 | sprintf(buf, ".t%d", i); | ~~~~~~~^~~~~~~~~~~~~~~~ -In file included from aligner.h:25, - from aligner.cpp:25: -hash.h: In member function 'int Aligner::initLookupArray()': -hash.h:353:18: warning: 'keySpan' may be used uninitialized in this function [-Wmaybe-uninitialized] - 353 | widthKeySpan = keySpan; - | ~~~~~~~~~~~~~^~~~~~~~~ -aligner.cpp:360:7: note: 'keySpan' was declared here - 360 | int keySpan; - | ^~~~~~~ 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)); @@ -1478,7 +1513,7 @@ 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-1a_ErWsc + rm -fr -- /tmp/dh-xdg-rundir-aQ1cT5_t create-stamp debian/debhelper-build-stamp dh_prep rm -f -- debian/wham-align.substvars @@ -1513,10 +1548,10 @@ 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.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 + 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 dh_perl dh_link dh_strip_nondeterminism @@ -1585,12 +1620,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/3844676/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3844676/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/3463614 and its subdirectories -I: Current time: Sun Nov 21 15:00:02 -12 2021 -I: pbuilder-time-stamp: 1637550002 +I: removing directory /srv/workspace/pbuilder/3844676 and its subdirectories +I: Current time: Sun Dec 25 23:23:31 +14 2022 +I: pbuilder-time-stamp: 1671960211