Diff of the two buildlogs: -- --- b1/build.log 2024-08-06 17:54:25.194894652 +0000 +++ b2/build.log 2024-08-06 17:55:23.764406457 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Aug 6 05:53:49 -12 2024 -I: pbuilder-time-stamp: 1722966829 +I: Current time: Tue Sep 9 14:17:27 +14 2025 +I: pbuilder-time-stamp: 1757377047 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.uGy4fB1L/trustedkeys.kbx': General error -gpgv: Signature made Thu Feb 18 19:13:34 2021 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.8M_faiNa/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 @@ -33,134 +33,165 @@ 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/3004909/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1754347/tmp/hooks/D01_modify_environment starting +debug: Running on infom02-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 +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Sep 9 14:17 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/1754347/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1754347/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' + 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/reproducible-path + 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=12 ' - DISTRIBUTION='bullseye' - HOME='/root' - HOST_ARCH='amd64' + DIRSTACK=() + DISTRIBUTION=bullseye + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='c13b9e4eee0e4b1bbbd5f702abe1e310' - 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='3004909' - PS1='# ' - PS2='> ' + INVOCATION_ID=d7e193430fe540dbbd1efc7269d5e10c + 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=1754347 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.Agl7Cyoo/pbuilderrc_FeZo --distribution bullseye --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Agl7Cyoo/b1 --logfile b1/build.log wham-align_0.1.5-8.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.Agl7Cyoo/pbuilderrc_FNZv --distribution bullseye --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Agl7Cyoo/b2 --logfile b2/build.log wham-align_0.1.5-8.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' I: uname -a - Linux infom01-amd64 6.1.0-23-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.99-1 (2024-07-15) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.9.7+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.9.7-1~bpo12+1 (2024-07-03) x86_64 GNU/Linux I: ls -l /bin total 5476 - -rwxr-xr-x 1 root root 1234376 Mar 27 2022 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 Mar 27 22:09 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 Jan 24 2023 egrep - -rwxr-xr-x 1 root root 39680 Sep 23 2020 false - -rwxr-xr-x 1 root root 28 Jan 24 2023 fgrep - -rwxr-xr-x 1 root root 69032 Mar 27 22:09 findmnt - -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount - -rwxr-xr-x 1 root root 203072 Jan 24 2023 grep - -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip - -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe - -rwxr-xr-x 1 root root 98048 Apr 9 2022 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 Mar 27 22:09 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 Mar 27 22:09 more - -rwsr-xr-x 1 root root 55528 Mar 27 22:09 mount - -rwxr-xr-x 1 root root 18664 Mar 27 22:09 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 Dec 16 2021 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 43872 Sep 23 2020 pwd - lrwxrwxrwx 1 root root 4 Mar 27 2022 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 Jul 6 21:25 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 Mar 27 22:09 su - -rwxr-xr-x 1 root root 39744 Sep 23 2020 sync - -rwxr-xr-x 1 root root 531928 Jan 19 2024 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 Mar 27 22:09 umount - -rwxr-xr-x 1 root root 39744 Sep 23 2020 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 147176 Sep 23 2020 vdir - -rwxr-xr-x 1 root root 63744 Mar 27 22:09 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 5898 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8049 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/3004909/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1234376 Mar 28 2022 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 Mar 29 2024 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 Jan 25 2023 egrep + -rwxr-xr-x 1 root root 39680 Sep 24 2020 false + -rwxr-xr-x 1 root root 28 Jan 25 2023 fgrep + -rwxr-xr-x 1 root root 69032 Mar 29 2024 findmnt + -rwsr-xr-x 1 root root 34896 Feb 27 2021 fusermount + -rwxr-xr-x 1 root root 203072 Jan 25 2023 grep + -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip + -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe + -rwxr-xr-x 1 root root 98048 Apr 10 2022 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 Mar 29 2024 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 Mar 29 2024 more + -rwsr-xr-x 1 root root 55528 Mar 29 2024 mount + -rwxr-xr-x 1 root root 18664 Mar 29 2024 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 Dec 17 2021 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43872 Sep 24 2020 pwd + lrwxrwxrwx 1 root root 4 Mar 28 2022 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 9 Sep 9 14:17 sh -> /bin/bash + -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 Mar 29 2024 su + -rwxr-xr-x 1 root root 39744 Sep 24 2020 sync + -rwxr-xr-x 1 root root 531928 Jan 20 2024 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 Mar 29 2024 umount + -rwxr-xr-x 1 root root 39744 Sep 24 2020 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 147176 Sep 24 2020 vdir + -rwxr-xr-x 1 root root 63744 Mar 29 2024 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat + -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp + -rwxr-xr-x 1 root root 5898 Apr 10 2022 zdiff + -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep + -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep + -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce + -rwxr-xr-x 1 root root 8049 Apr 10 2022 zgrep + -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless + -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore + -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew +I: user script /srv/workspace/pbuilder/1754347/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -227,7 +258,7 @@ 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 1s (14.3 MB/s) +Fetched 18.3 MB in 2s (11.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19711 files and directories currently installed.) @@ -367,7 +398,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/wham-align-0.1.5/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../wham-align_0.1.5-8_source.changes +I: user script /srv/workspace/pbuilder/1754347/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bullseye +I: user script /srv/workspace/pbuilder/1754347/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/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 @@ -423,6 +458,8 @@ error.cpp:32:7: warning: unused variable 'lineno' [-Wunused-variable] 32 | int lineno = __LINE__; | ^~~~~~ +g++ -c -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings builder.cpp interval.cpp: In constructor 'IntervalTree::IntervalTree(uint32, uint32)': interval.cpp:67:21: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] 67 | for (int i = 0; i < numLevel - 1; i++) { @@ -488,7 +525,6 @@ 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) { | ~~~~^~~~~~~~ -g++ -c -g -O2 -fdebug-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings writer.cpp 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; @@ -527,15 +563,8 @@ 90 | bool pairMatch = false; | ^~~~~~~~~ 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) { - | ~~~~^~~~~~~~ -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) { @@ -568,12 +597,46 @@ 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 embedhash.cpp:27: hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)': hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] 86 | int size; | ^~~~ +In file included from hitset.h:31, + from 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) { + | ~~~~^~~~~~~~ +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) { + | ~~~~^~~~~~~~ +In file included from embedhash.cpp:27: +hash.h: In function 'uint32 murmurHash(int64*, uint32)': +hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] + 86 | uint32 sum = 0; + | ^~~ +pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)': +pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable] + 602 | int i, j, offset, min, tmp; + | ^~~~~~ +pair.h: In static member function 'static bool PairAligner::pairAlignBitVector64(int64*, int64*, int, int, int)': +pair.h:684:15: warning: unused variable 'num' [-Wunused-variable] + 684 | int i, p, num, base, Cscore; + | ^~~ +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::pairAlignDP(int64*, int64*, int, int, int, bool)': pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable] 602 | int i, j, offset, min, tmp; @@ -598,51 +661,52 @@ 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 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) { - | ~~~~^~~~~~~~ +pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)': +pair.h:755:15: warning: unused variable 'num' [-Wunused-variable] + 755 | int i, p, num, base, Cscore; + | ^~~ +pair.h:755:20: warning: unused variable 'base' [-Wunused-variable] + 755 | int i, p, num, base, Cscore; + | ^~~~ +pair.h:756:9: warning: unused variable 'a' [-Wunused-variable] + 756 | int a; + | ^ +pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)': +pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] + 974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); + | ~~~~~~~^~~~~~~~~~ pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)': pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] 974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); | ~~~~~~~^~~~~~~~~~ +In file included from 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; + | ^~~~ In file included from hash.h:29, - from hash.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; | ^~~~ -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; -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.cpp:27: +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; | ^~~ +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; | ^~~~~~~ -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; - | ^ 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; @@ -662,13 +726,6 @@ writer.cpp:272:16: warning: unused variable 'code2' [-Wunused-variable] 272 | int64 code1, code2; | ^~~~~ -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; - | ^~~~ writer.cpp:278:10: warning: unused variable 'p' [-Wunused-variable] 278 | double p, sump; | ^ @@ -681,45 +738,21 @@ writer.cpp:281:8: warning: unused variable 'shortread' [-Wunused-variable] 281 | char shortread[256]; | ^~~~~~~~~ -pair.h:756:9: warning: unused variable 'a' [-Wunused-variable] - 756 | int a; - | ^ 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++) { | ~~^~~~~~~~~~~~~~~ -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); - | ~~~~~~~~~~~~^ -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)); - | ~~~~~~~^~~~~~~~~~ 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++) { | ~~^~~~~~~~~~~~~~~ -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; - | ^~~~ 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 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; - | ^~~ -g++ -c -g -O2 -fdebug-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings builder.cpp In file included from hitset.h:31, from hash.h:29, - from aligner.h:25, - 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) { @@ -753,18 +786,37 @@ 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: + 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 aligner.h:25, - from aligner.cpp:25: +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; | ^~~ +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; + | ^ +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: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); @@ -784,27 +836,10 @@ 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); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 main.cpp:34: + 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) { @@ -839,13 +874,13 @@ | ~~~~~~~^~~~~~~~~~ In file included from hash.h:29, from aligner.h:25, - from main.cpp:34: + 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; | ^~~~ In file included from aligner.h:25, - from main.cpp:34: + 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; @@ -853,7 +888,7 @@ In file included from hitset.h:31, from hash.h:29, from aligner.h:25, - from builder.cpp:31: + 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) { @@ -888,13 +923,13 @@ | ~~~~~~~^~~~~~~~~~ In file included from hash.h:29, from aligner.h:25, - from builder.cpp:31: + 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 builder.cpp:31: + 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; @@ -921,10 +956,6 @@ pair.h:685:9: warning: unused variable 'a' [-Wunused-variable] 685 | int a; | ^ -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) - | ~~^~~~~~~~~~~~~ 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; @@ -935,41 +966,10 @@ pair.h:756:9: warning: unused variable 'a' [-Wunused-variable] 756 | int a; | ^ -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) { - | ~~~~^~~~~~~~~~~~~~~~ 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++) { - | ~~^~~~~~~~~~~~~~~~ -hash.cpp: In member function 'void HashTable::insert(int64*, unsigned int)': -hash.cpp:460:38: warning: operation on '*(((HashTable*)this)->HashTable::overflowPool + ((sizetype)(((long unsigned int)curOverflowEntry) * 4)))' may be undefined [-Wsequence-point] - 460 | overflowPool[curOverflowEntry] = -hash.cpp:411:10: warning: unused variable 'seqOffset' [-Wunused-variable] - 411 | uint32 seqOffset; - | ^~~~~~~~~ -hash.cpp:413:10: warning: unused variable 'counter' [-Wunused-variable] - 413 | uint32 counter = 0; - | ^~~~~~~ -hash.cpp:414:11: warning: variable 'seqVector' set but not used [-Wunused-but-set-variable] - 414 | int64 * seqVector; - | ^~~~~~~~~ -hash.cpp:416:11: warning: unused variable 'target' [-Wunused-variable] - 416 | int64 * target = &tspace[8]; - | ^~~~~~ -hash.cpp:417:8: warning: unused variable 'isBloomFilter' [-Wunused-variable] - 417 | bool isBloomFilter; - | ^~~~~~~~~~~~~ -hash.cpp:418:12: warning: unused variable 'bloomFilter' [-Wunused-variable] - 418 | uint32 * bloomFilter; - | ^~~~~~~~~~~ -hash.cpp:419:10: warning: unused variable 'bloomFilterNum' [-Wunused-variable] - 419 | uint32 bloomFilterNum; - | ^~~~~~~~~~~~~~ In file included from hash.h:29, from aligner.h:25, from sequence.cpp:30: @@ -977,140 +977,20 @@ hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] 86 | int size; | ^~~~ -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], - | ^~~~ -hash.cpp:469:55: warning: unused variable 'rest1' [-Wunused-variable] - 469 | int64 * query = &ttspace[8], *rest = &ttspace[24], *rest1 = &ttspace[40], - | ^~~~~ -hash.cpp:470:8: warning: unused variable 'rest2' [-Wunused-variable] - 470 | *rest2 = &ttspace[56], *noheadkey = &ttspace[72]; - | ^~~~~ -hash.cpp:470:31: warning: unused variable 'noheadkey' [-Wunused-variable] - 470 | *rest2 = &ttspace[56], *noheadkey = &ttspace[72]; - | ^~~~~~~~~ -hash.cpp:472:34: warning: variable 'startOffset' set but not used [-Wunused-but-set-variable] - 472 | uint32 seqOffset, entryOffset, startOffset; - | ^~~~~~~~~~~ -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]; - | ^~~~~~~~~ -hash.cpp:590:8: warning: unused variable 'subkey4' [-Wunused-variable] - 590 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; - | ^~~~~~~ -hash.cpp:590:32: warning: unused variable 'subkey5' [-Wunused-variable] - 590 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; - | ^~~~~~~ -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]; - | ^~~~~~~~~ -hash.cpp:665:8: warning: unused variable 'subkey4' [-Wunused-variable] - 665 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; - | ^~~~~~~ -hash.cpp:665:32: warning: unused variable 'subkey5' [-Wunused-variable] - 665 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; - | ^~~~~~~ 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; | ^~~ -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; - | ^~~ -hash.cpp:750:11: warning: unused variable 'diff' [-Wunused-variable] - 750 | int64 * diff = &tspace1[8], *target = &tspace2[8]; - | ^~~~ -hash.cpp:753:10: warning: unused variable 'sid' [-Wunused-variable] - 753 | uint32 sid, soffset; - | ^~~ -hash.cpp:753:15: warning: unused variable 'soffset' [-Wunused-variable] - 753 | uint32 sid, soffset; - | ^~~~~~~ -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]; - | ^~~~~~~~~ -hash.cpp:965:8: warning: unused variable 'subkey4' [-Wunused-variable] - 965 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; - | ^~~~~~~ -hash.cpp:965:32: warning: unused variable 'subkey5' [-Wunused-variable] - 965 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; - | ^~~~~~~ -hash.cpp:973:11: warning: unused variable 'seqVector' [-Wunused-variable] - 973 | int64 * seqVector = sequence->getSequence(); - | ^~~~~~~~~ -hash.cpp: In member function 'bool HashTable::lookup(int64*, uint32)': -hash.cpp:1052:7: warning: unused variable 'num' [-Wunused-variable] - 1052 | int num; - | ^~~ -hash.cpp:1056:11: warning: unused variable 'diff' [-Wunused-variable] - 1056 | int64 * diff = &tspace1[8], *target = &tspace2[8]; - | ^~~~ -hash.cpp:1056:32: warning: unused variable 'target' [-Wunused-variable] - 1056 | int64 * diff = &tspace1[8], *target = &tspace2[8]; - | ^~~~~~ -hash.cpp:1057:11: warning: variable 'seqVector' set but not used [-Wunused-but-set-variable] - 1057 | int64 * seqVector; - | ^~~~~~~~~ -hash.cpp:1059:10: warning: unused variable 'sid' [-Wunused-variable] - 1059 | uint32 sid, soffset; - | ^~~ -hash.cpp:1059:15: warning: unused variable 'soffset' [-Wunused-variable] - 1059 | uint32 sid, soffset; - | ^~~~~~~ -sequence.cpp: In member function 'void CompactSequence::extractFileName(char*, char*)': -sequence.cpp:97:10: warning: unused variable 'str' [-Wunused-variable] - 97 | char * str; - | ^~~ -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++) -hash.cpp:1188:23: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] - 1188 | for (int i = 0; i < (lenSeq - keyOffset - lenKey) / BITS_PER_BASE; i++) -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++) { - | ~~^~~~~~~~~ -hash.cpp:1247:27: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] - 1247 | for (int j = 0; j < strlen(set[i].str); j++) - | ~~^~~~~~~~~~~~~~~~~~~~ -hash.cpp:1254:25: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] - 1254 | for (int j = 0; j < strlen(set[i].str); j++) - | ~~^~~~~~~~~~~~~~~~~~~~ -sequence.cpp:309:13: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 309 | ( i = 0; i < nSeq; i++) - | ~~^~~~~~ -hash.cpp:1137:11: warning: unused variable 'diff' [-Wunused-variable] - 1137 | int64 * diff = &tspace1[8], *target = &tspace2[8]; - | ^~~~ -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; - | ^~~~ embedhash.cpp: In member function 'int EmbedHashTable::preProcessEnd()': embedhash.cpp:137:16: warning: unused variable 'ln2' [-Wunused-variable] 137 | const double ln2 = log(2); | ^~~ -sequence.cpp:223:22: warning: unused variable 'nextstep' [-Wunused-variable] - 223 | unsigned int step, nextstep; - | ^~~~~~~~ +sequence.cpp: In member function 'void CompactSequence::extractFileName(char*, char*)': +sequence.cpp:97:10: warning: unused variable 'str' [-Wunused-variable] + 97 | char * str; + | ^~~ embedhash.cpp: In member function 'void EmbedHashTable::setScanThreshold(double)': embedhash.cpp:253:9: warning: unused variable 'sum' [-Wunused-variable] 253 | int64 sum = 0; @@ -1118,16 +998,9 @@ embedhash.cpp:255:9: warning: unused variable 'top' [-Wunused-variable] 255 | int64 top = total - total * r; | ^~~ -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; - | ^~~~~~ -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: 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++) { | ~~^~~~~~~~~ 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] @@ -1141,18 +1014,59 @@ embedhash.cpp:331:11: warning: variable 'seqVector' set but not used [-Wunused-but-set-variable] 331 | int64 * seqVector; | ^~~~~~~~~ +sequence.cpp:309:13: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 309 | ( i = 0; i < nSeq; i++) + | ~~^~~~~~ 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; | ^~~~~~~~~~~~~ +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++) { + | ~~^~~~~~~~~ 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; | ^~~~~~~~~~~~~~ +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) { + | ~~~~~~~~~~~~^~~~~~~~~~~~~~ +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; + | ^~~ +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; + | ^~~~~~~~ +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; + | ^~~~~~~ +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) | ~~~~~~~~~~~~^~~~~~~~~~~~ @@ -1177,41 +1091,14 @@ sequence.cpp:521:54: warning: unused variable 'nNSegment' [-Wunused-variable] 521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment; | ^~~~~~~~~ -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; - | ^~~~~~~ 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) { | ~~~~^~~~~~~ -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; - | ^~~~~~ -hash.cpp:1690:5: warning: label 'restart' defined but not used [-Wunused-label] - 1690 | restart: if (buckets[bucketId] == HASH_EMPTY - | ^~~~~~~ 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) { | ~~~~^~~~~~~ -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') - | ~~~^~~~~~~~~~~~~~~~~~ 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) { @@ -1223,13 +1110,6 @@ 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++) { | ~~^~~~~~~~~~~~ -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; - | ^ 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++) { | ~~^~~~~~~~~~~~ @@ -1295,22 +1175,6 @@ 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++) { | ~~^~~~~~~~~~~~ -main.cpp: In function 'int main(int, char**)': -main.cpp:523:7: warning: unused variable 'numKeys' [-Wunused-variable] - 523 | int numKeys; - | ^~~~~~~ -main.cpp:526:7: warning: unused variable 'nSeq' [-Wunused-variable] - 526 | int nSeq = 1; - | ^~~~ -main.cpp:532:21: warning: unused variable 'sequence' [-Wunused-variable] - 532 | CompactSequence * sequence; - | ^~~~~~~~ -main.cpp:534:15: warning: unused variable 'threadpool' [-Wunused-variable] - 534 | pthread_t * threadpool; - | ^~~~~~~~~~ -main.cpp:536:9: warning: unused variable 'threadid' [-Wunused-variable] - 536 | int * threadid; - | ^~~~~~~~ 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; @@ -1399,25 +1263,182 @@ aligner.cpp:1874:10: warning: unused variable 'ret' [-Wunused-variable] 1874 | int i, ret; | ^~~ +hash.cpp: In member function 'int HashTable::preProcessEnd()': +hash.cpp:236:11: warning: comparison of integer expressions of different signedness: 'int' and 'const uint32' {aka 'const unsigned int'} [-Wsign-compare] + 236 | if (h >= nHistogram) + | ~~^~~~~~~~~~~~~ +hash.cpp:285:33: warning: comparison of integer expressions of different signedness: 'uint32' {aka 'unsigned int'} and 'int' [-Wsign-compare] + 285 | if (useEmbedTables() && tmp > embedShreshold) { + | ~~~~^~~~~~~~~~~~~~~~ +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::setScanThreshold(double)': +hash.cpp:343:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] + 343 | for (int i = 0; i < nHistogram - 1; i++) { + | ~~^~~~~~~~~~~~~~~~ +hash.cpp: In member function 'void HashTable::insert(int64*, unsigned int)': +hash.cpp:460:38: warning: operation on '*(((HashTable*)this)->HashTable::overflowPool + ((sizetype)(((long unsigned int)curOverflowEntry) * 4)))' may be undefined [-Wsequence-point] + 460 | overflowPool[curOverflowEntry] = +hash.cpp:411:10: warning: unused variable 'seqOffset' [-Wunused-variable] + 411 | uint32 seqOffset; + | ^~~~~~~~~ +hash.cpp:413:10: warning: unused variable 'counter' [-Wunused-variable] + 413 | uint32 counter = 0; + | ^~~~~~~ +hash.cpp:414:11: warning: variable 'seqVector' set but not used [-Wunused-but-set-variable] + 414 | int64 * seqVector; + | ^~~~~~~~~ +hash.cpp:416:11: warning: unused variable 'target' [-Wunused-variable] + 416 | int64 * target = &tspace[8]; + | ^~~~~~ +hash.cpp:417:8: warning: unused variable 'isBloomFilter' [-Wunused-variable] + 417 | bool isBloomFilter; + | ^~~~~~~~~~~~~ +hash.cpp:418:12: warning: unused variable 'bloomFilter' [-Wunused-variable] + 418 | uint32 * bloomFilter; + | ^~~~~~~~~~~ +hash.cpp:419:10: warning: unused variable 'bloomFilterNum' [-Wunused-variable] + 419 | uint32 bloomFilterNum; + | ^~~~~~~~~~~~~~ +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], + | ^~~~ +hash.cpp:469:55: warning: unused variable 'rest1' [-Wunused-variable] + 469 | int64 * query = &ttspace[8], *rest = &ttspace[24], *rest1 = &ttspace[40], + | ^~~~~ +hash.cpp:470:8: warning: unused variable 'rest2' [-Wunused-variable] + 470 | *rest2 = &ttspace[56], *noheadkey = &ttspace[72]; + | ^~~~~ +hash.cpp:470:31: warning: unused variable 'noheadkey' [-Wunused-variable] + 470 | *rest2 = &ttspace[56], *noheadkey = &ttspace[72]; + | ^~~~~~~~~ +hash.cpp:472:34: warning: variable 'startOffset' set but not used [-Wunused-but-set-variable] + 472 | uint32 seqOffset, entryOffset, startOffset; + | ^~~~~~~~~~~ +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]; + | ^~~~~~~~~ +hash.cpp:590:8: warning: unused variable 'subkey4' [-Wunused-variable] + 590 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; + | ^~~~~~~ +hash.cpp:590:32: warning: unused variable 'subkey5' [-Wunused-variable] + 590 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; + | ^~~~~~~ +main.cpp: In function 'int align(char*, AlignInfo*, char*, int)': +main.cpp:350:7: warning: unused variable 'i' [-Wunused-variable] + 350 | int i, j, ret; + | ^ +main.cpp:350:10: warning: unused variable 'j' [-Wunused-variable] + 350 | int i, j, ret; + | ^ In file included from 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 '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]; + | ^~~~~~~~~ +hash.cpp:665:8: warning: unused variable 'subkey4' [-Wunused-variable] + 665 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; + | ^~~~~~~ +hash.cpp:665:32: warning: unused variable 'subkey5' [-Wunused-variable] + 665 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; + | ^~~~~~~ +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; + | ^~~ +hash.cpp:750:11: warning: unused variable 'diff' [-Wunused-variable] + 750 | int64 * diff = &tspace1[8], *target = &tspace2[8]; + | ^~~~ +hash.cpp:753:10: warning: unused variable 'sid' [-Wunused-variable] + 753 | uint32 sid, soffset; + | ^~~ +hash.cpp:753:15: warning: unused variable 'soffset' [-Wunused-variable] + 753 | uint32 sid, soffset; + | ^~~~~~~ +main.cpp: In function 'int main(int, char**)': +main.cpp:523:7: warning: unused variable 'numKeys' [-Wunused-variable] + 523 | int numKeys; + | ^~~~~~~ +main.cpp:526:7: warning: unused variable 'nSeq' [-Wunused-variable] + 526 | int nSeq = 1; + | ^~~~ +main.cpp:532:21: warning: unused variable 'sequence' [-Wunused-variable] + 532 | CompactSequence * sequence; + | ^~~~~~~~ +main.cpp:534:15: warning: unused variable 'threadpool' [-Wunused-variable] + 534 | pthread_t * threadpool; + | ^~~~~~~~~~ +main.cpp:536:9: warning: unused variable 'threadid' [-Wunused-variable] + 536 | int * threadid; + | ^~~~~~~~ hash.cpp: In member function 'unsigned int HashTable::lookupEmbedTable(int64*, uint32, int, char*, strand, int, HitSet*, bool)': -hash.cpp:1049:1: warning: control reaches end of non-void function [-Wreturn-type] - 1049 | } - | ^ -In file included from hash.cpp:31: -edit_distance.h: At global scope: -edit_distance.h:25:18: warning: 'obj_score_mat' defined but not used [-Wunused-variable] - 25 | static score_mat obj_score_mat = { 1, 1, 1, 1 }; - | ^~~~~~~~~~~~~ -In file included from main.cpp:38: -edit_distance.h: At global scope: -edit_distance.h:25:18: warning: 'obj_score_mat' defined but not used [-Wunused-variable] - 25 | static score_mat obj_score_mat = { 1, 1, 1, 1 }; - | ^~~~~~~~~~~~~ +hash.cpp:962:11: warning: unused variable 'noheadkey' [-Wunused-variable] + 962 | int64 * noheadkey = &tspace[8], *rest = &tspace[24]; + | ^~~~~~~~~ +hash.cpp:965:8: warning: unused variable 'subkey4' [-Wunused-variable] + 965 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; + | ^~~~~~~ +hash.cpp:965:32: warning: unused variable 'subkey5' [-Wunused-variable] + 965 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; + | ^~~~~~~ +hash.cpp:973:11: warning: unused variable 'seqVector' [-Wunused-variable] + 973 | int64 * seqVector = sequence->getSequence(); + | ^~~~~~~~~ +hash.cpp: In member function 'bool HashTable::lookup(int64*, uint32)': +hash.cpp:1052:7: warning: unused variable 'num' [-Wunused-variable] + 1052 | int num; + | ^~~ +hash.cpp:1056:11: warning: unused variable 'diff' [-Wunused-variable] + 1056 | int64 * diff = &tspace1[8], *target = &tspace2[8]; + | ^~~~ +hash.cpp:1056:32: warning: unused variable 'target' [-Wunused-variable] + 1056 | int64 * diff = &tspace1[8], *target = &tspace2[8]; + | ^~~~~~ +hash.cpp:1057:11: warning: variable 'seqVector' set but not used [-Wunused-but-set-variable] + 1057 | int64 * seqVector; + | ^~~~~~~~~ +hash.cpp:1059:10: warning: unused variable 'sid' [-Wunused-variable] + 1059 | uint32 sid, soffset; + | ^~~ +hash.cpp:1059:15: warning: unused variable 'soffset' [-Wunused-variable] + 1059 | uint32 sid, soffset; + | ^~~~~~~ +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++) +hash.cpp:1188:23: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] + 1188 | for (int i = 0; i < (lenSeq - keyOffset - lenKey) / BITS_PER_BASE; i++) +hash.cpp:1247:27: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] + 1247 | for (int j = 0; j < strlen(set[i].str); j++) + | ~~^~~~~~~~~~~~~~~~~~~~ +hash.cpp:1254:25: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] + 1254 | for (int j = 0; j < strlen(set[i].str); j++) + | ~~^~~~~~~~~~~~~~~~~~~~ +hash.cpp:1137:11: warning: unused variable 'diff' [-Wunused-variable] + 1137 | int64 * diff = &tspace1[8], *target = &tspace2[8]; + | ^~~~ +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; + | ^~~~~~ +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; + | ^~~~~~ +hash.cpp:1690:5: warning: label 'restart' defined but not used [-Wunused-label] + 1690 | restart: if (buckets[bucketId] == HASH_EMPTY + | ^~~~~~~ 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') @@ -1429,11 +1450,25 @@ builder.cpp:277:7: warning: unused variable 'nChar' [-Wunused-variable] 277 | int nChar = sequence->getNum(); | ^~~~~ +In file included from main.cpp:38: +edit_distance.h: At global scope: +edit_distance.h:25:18: warning: 'obj_score_mat' defined but not used [-Wunused-variable] + 25 | static score_mat obj_score_mat = { 1, 1, 1, 1 }; + | ^~~~~~~~~~~~~ +hash.cpp: In member function '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 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 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 }; + | ^~~~~~~~~~~~~ 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); @@ -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/reproducible-path/wham-align-0.1.5' dh_auto_test - rm -fr -- /tmp/dh-xdg-rundir-kD9ySOm0 + rm -fr -- /tmp/dh-xdg-rundir-udYHo1Nx create-stamp debian/debhelper-build-stamp dh_prep rm -f -- debian/wham-align.substvars @@ -1576,8 +1611,8 @@ 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-dbgsym' in '../wham-align-dbgsym_0.1.5-8_amd64.deb'. dpkg-deb: building package 'wham-align' in '../wham-align_0.1.5-8_amd64.deb'. +dpkg-deb: building package 'wham-align-dbgsym' in '../wham-align-dbgsym_0.1.5-8_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../wham-align_0.1.5-8_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -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/1754347/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1754347/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/3004909 and its subdirectories -I: Current time: Tue Aug 6 05:54:24 -12 2024 -I: pbuilder-time-stamp: 1722966864 +I: removing directory /srv/workspace/pbuilder/1754347 and its subdirectories +I: Current time: Tue Sep 9 14:18:22 +14 2025 +I: pbuilder-time-stamp: 1757377102