Diff of the two buildlogs: -- --- b1/build.log 2024-07-29 17:54:36.633052799 +0000 +++ b2/build.log 2024-07-29 17:56:47.023511733 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Jul 29 05:51:03 -12 2024 -I: pbuilder-time-stamp: 1722275463 +I: Current time: Mon Sep 1 14:17:38 +14 2025 +I: pbuilder-time-stamp: 1756685858 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 [./snap-aligner_1.0.0+dfsg-2.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.o2PNBEzm/trustedkeys.kbx': General error -gpgv: Signature made Sat Nov 28 21:24:51 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.8OJr2qc8/trustedkeys.kbx': General error +gpgv: Signature made Sun Nov 29 23:24:51 2020 +14 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./snap-aligner_1.0.0+dfsg-2.dsc @@ -33,135 +33,166 @@ dpkg-source: info: applying simde I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2796423/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3763679/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 +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Sep 1 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/3763679/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3763679/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' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=20 ' - DISTRIBUTION='bullseye' - 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/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=42 ' + 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='30308e50ff374babb67784f02cee78ae' - 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='2796423' - PS1='# ' - PS2='> ' + INVOCATION_ID=556ee345d5c34121a1335a8be8a64f2d + 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=3763679 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.Nslia5L5/pbuilderrc_Iimw --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.Nslia5L5/b1 --logfile b1/build.log snap-aligner_1.0.0+dfsg-2.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + 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/r-b-build.Nslia5L5/pbuilderrc_6mY5 --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.Nslia5L5/b2 --logfile b2/build.log snap-aligner_1.0.0+dfsg-2.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://213.165.73.152:3128 I: uname -a - Linux ionos1-amd64 6.1.0-23-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 21:26 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/2796423/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 1 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/3763679/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -238,7 +269,7 @@ Get: 33 http://deb.debian.org/debian bullseye/main amd64 help2man amd64 1.48.1 [190 kB] Get: 34 http://deb.debian.org/debian bullseye/main amd64 libsimde-dev all 0.7.2-4 [259 kB] Get: 35 http://deb.debian.org/debian bullseye/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2+deb11u2 [191 kB] -Fetched 19.0 MB in 0s (39.0 MB/s) +Fetched 19.0 MB in 0s (44.4 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.) @@ -394,7 +425,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/snap-aligner-1.0.0+dfsg/ && 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 > ../snap-aligner_1.0.0+dfsg-2_source.changes +I: user script /srv/workspace/pbuilder/3763679/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bullseye +I: user script /srv/workspace/pbuilder/3763679/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/snap-aligner-1.0.0+dfsg/ && 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 > ../snap-aligner_1.0.0+dfsg-2_source.changes dpkg-buildpackage: info: source package snap-aligner dpkg-buildpackage: info: source version 1.0.0+dfsg-2 dpkg-buildpackage: info: source distribution unstable @@ -406,7 +441,7 @@ debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/snap-aligner-1.0.0+dfsg' dh_auto_clean - make -j20 clean + make -j42 clean make[2]: Entering directory '/build/reproducible-path/snap-aligner-1.0.0+dfsg' rm -f SNAPLib/AffineGap.o SNAPLib/AffineGapVectorized.o SNAPLib/AlignerContext.o SNAPLib/AlignerOptions.o SNAPLib/AlignerStats.o SNAPLib/AlignmentAdjuster.o SNAPLib/AlignmentResult.o SNAPLib/ApproximateCounter.o SNAPLib/Bam.o SNAPLib/BaseAligner.o SNAPLib/BigAlloc.o SNAPLib/BufferedAsync.o SNAPLib/ChimericPairedEndAligner.o SNAPLib/CommandProcessor.o SNAPLib/Compat.o SNAPLib/DataReader.o SNAPLib/DataWriter.o SNAPLib/Error.o SNAPLib/FASTA.o SNAPLib/FASTQ.o SNAPLib/GenericFile.o SNAPLib/GenericFile_Blob.o SNAPLib/GenericFile_HDFS.o SNAPLib/GenericFile_map.o SNAPLib/GenericFile_stdio.o SNAPLib/Genome.o SNAPLib/GenomeIndex.o SNAPLib/GzipDataWriter.o SNAPLib/HashTable.o SNAPLib/Histogram.o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/LandauVishkin.o SNAPLib/MultiInputReadSupplier.o SNAPLib/PairedAligner.o SNAPLib/PairedReadMatcher.o SNAPLib/ParallelTask.o SNAPLib/ProbabilityDistance.o SNAPLib/RangeSplitter.o SNAPLib/Read.o SNAPLib/ReadReader.o SNAPLib/ReadSupplierQueue.o SNAPLib/ReadWriter.o SNAPLib/SAM.o SNAPLib/Seed.o SNAPLib/SeedSequencer.o SNAPLib/SingleAligner.o SNAPLib/SortedDataWriter.o SNAPLib/Tables.o SNAPLib/Util.o SNAPLib/exit.o SNAPLib/mapq.o SNAPLib/stdafx.o apps/snap/Main.o apps/snap/stdafx.o tests/AffineGapTest.o tests/AffineGapVectorizedTest.o tests/EventTest.o tests/LandauVishkinTest.o tests/ProbabilityDistanceTest.o tests/TestLib.o tests/main.o apps/SNAPCommand/SNAPCommand.o apps/SNAPCommand/stdafx.o snap-aligner unit_tests SNAPCommand snap SNAP make[2]: Leaving directory '/build/reproducible-path/snap-aligner-1.0.0+dfsg' @@ -422,7 +457,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/snap-aligner-1.0.0+dfsg' dh_auto_build - make -j20 "INSTALL=install --strip-program=true" + make -j42 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/snap-aligner-1.0.0+dfsg' g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AffineGap.o SNAPLib/AffineGap.cpp g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AffineGapVectorized.o SNAPLib/AffineGapVectorized.cpp @@ -445,43 +480,76 @@ g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/FASTA.o SNAPLib/FASTA.cpp g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/FASTQ.o SNAPLib/FASTQ.cpp g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenericFile.o SNAPLib/GenericFile.cpp -SNAPLib/Error.cpp: In function 'void WriteProgressCounter(const char*, _int64)': -SNAPLib/Error.cpp:89:49: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type '_int64' {aka 'long int'} [-Wformat=] - 89 | fprintf(stderr,"reporter:counter:SNAP,%s,%lld\n", counterName, increment); - | ~~~^ ~~~~~~~~~ - | | | - | long long int _int64 {aka long int} - | %ld g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenericFile_Blob.o SNAPLib/GenericFile_Blob.cpp g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenericFile_HDFS.o SNAPLib/GenericFile_HDFS.cpp g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenericFile_map.o SNAPLib/GenericFile_map.cpp g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenericFile_stdio.o SNAPLib/GenericFile_stdio.cpp g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Genome.o SNAPLib/Genome.cpp g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenomeIndex.o SNAPLib/GenomeIndex.cpp -SNAPLib/AlignerContext.cpp: In member function 'void AlignerContext::printStats()': -SNAPLib/AlignerContext.cpp:486:75: warning: format '%lld' expects argument of type 'long long int', but argument 9 has type '_int64' {aka 'long int'} [-Wformat=] - 486 | fprintf(perfFile, "%d\t%d\t%0.2f%%\t%0.2f%%\t%0.2f%%\t%0.2f%%\t%lld\t%0.2f%%\t%lld\tt%.0f\n", - | ~~~^ - | | - | long long int - | %ld -...... - 492 | stats->lvCalls, - | ~~~~~~~~~~~~~~ - | | - | _int64 {aka long int} -SNAPLib/AlignerContext.cpp:486:90: warning: format '%lld' expects argument of type 'long long int', but argument 11 has type '_int64' {aka 'long int'} [-Wformat=] - 486 | fprintf(perfFile, "%d\t%d\t%0.2f%%\t%0.2f%%\t%0.2f%%\t%0.2f%%\t%lld\t%0.2f%%\t%lld\tt%.0f\n", - | ~~~^ - | | - | long long int - | %ld -...... - 494 | stats->totalReads, - | ~~~~~~~~~~~~~~~~~ - | | - | _int64 {aka long int} g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GzipDataWriter.o SNAPLib/GzipDataWriter.cpp +g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/HashTable.o SNAPLib/HashTable.cpp +g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Histogram.o SNAPLib/Histogram.cpp +g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/IntersectingPairedEndAligner.cpp +g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/LandauVishkin.o SNAPLib/LandauVishkin.cpp +g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/MultiInputReadSupplier.o SNAPLib/MultiInputReadSupplier.cpp +g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/PairedAligner.o SNAPLib/PairedAligner.cpp +g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/PairedReadMatcher.o SNAPLib/PairedReadMatcher.cpp +g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ParallelTask.o SNAPLib/ParallelTask.cpp +g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ProbabilityDistance.o SNAPLib/ProbabilityDistance.cpp +g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/RangeSplitter.o SNAPLib/RangeSplitter.cpp +g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Read.o SNAPLib/Read.cpp +g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ReadReader.o SNAPLib/ReadReader.cpp +g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ReadSupplierQueue.o SNAPLib/ReadSupplierQueue.cpp +g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ReadWriter.o SNAPLib/ReadWriter.cpp +g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/SAM.o SNAPLib/SAM.cpp +SNAPLib/Genome.cpp: In member function 'bool Genome::saveToFile(const char*) const': +SNAPLib/Genome.cpp:164:26: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'long int' [-Wformat=] + 164 | fprintf(saveFile,"%lld %d %d\n",nBases, nContigs, (areALTContigsMarked ? GENOME_FLAG_ALT_CONTIGS_MARKED : 0)); + | ~~~^ ~~~~~~ + | | | + | | long int + | long long int + | %ld +In file included from SNAPLib/IntersectingPairedEndAligner.cpp:24: +SNAPLib/IntersectingPairedEndAligner.h:668:104: warning: non-static data member initializers only available with '-std=c++11' or '-std=gnu++11' + 668 | Direction setPairDirection[NUM_SET_PAIRS][NUM_READS_PER_PAIR] = { {FORWARD, RC}, {RC, FORWARD} }; + | ^ +SNAPLib/IntersectingPairedEndAligner.h:668:104: warning: extended initializer lists only available with '-std=c++11' or '-std=gnu++11' +SNAPLib/Genome.cpp:174:26: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_int64' {aka 'long int'} [-Wformat=] + 174 | fprintf(saveFile, "%lld %x %s\n", GenomeLocationAsInt64(contigs[i].beginningLocation), (contigs[i].isALT ? GENOME_FLAG_CONTIG_IS_ALT : 0), contigs[i].name); + | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + | | | + | long long int _int64 {aka long int} + | %ld +SNAPLib/Genome.cpp:176:26: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_int64' {aka 'long int'} [-Wformat=] + 176 | fprintf(saveFile, "%lld %s\n", GenomeLocationAsInt64(contigs[i].beginningLocation), contigs[i].name); + | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + | | | + | long long int _int64 {aka long int} + | %ld +SNAPLib/Genome.cpp: In static member function 'static const Genome* Genome::loadFromFile(const char*, unsigned int, GenomeLocation, GenomeDistance, bool)': +SNAPLib/Genome.cpp:267:47: warning: format '%lld' expects argument of type 'long long int*', but argument 3 has type '_int64*' {aka 'long int*'} [-Wformat=] + 267 | if (1 != sscanf(contigNameBuffer, "%lld", &contigStart)) { + | ~~~^ ~~~~~~~~~~~~ + | | | + | | _int64* {aka long int*} + | long long int* + | %ld +SNAPLib/Genome.cpp: In static member function 'static bool Genome::openFileAndGetSizes(const char*, GenericFile**, GenomeDistance*, unsigned int*, bool, bool*)': +SNAPLib/Genome.cpp:401:51: warning: format '%lld' expects argument of type 'long long int*', but argument 3 has type 'GenomeDistance*' {aka 'long int*'} [-Wformat=] + 401 | if (NULL == retval || 2 != sscanf(linebuf,"%lld %d\n", nBases, nContigs)) { + | ~~~^ ~~~~~~ + | | | + | | GenomeDistance* {aka long int*} + | long long int* + | %ld +SNAPLib/Genome.cpp:410:31: warning: format '%lld' expects argument of type 'long long int*', but argument 3 has type 'GenomeDistance*' {aka 'long int*'} [-Wformat=] + 410 | if (3 == sscanf(linebuf, "%lld %d %d\n", nBases, nContigs, &flags)) + | ~~~^ ~~~~~~ + | | | + | | GenomeDistance* {aka long int*} + | long long int* + | %ld SNAPLib/DataReader.cpp: In member function 'char* DecompressDataReader::findPointer(void*)': SNAPLib/DataReader.cpp:1751:50: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type 'long int' [-Wformat=] 1751 | sprintf(result, "compressed #%d @ %lld", i, (char*)p - e->compressed); @@ -520,12 +588,41 @@ | | | | long long int _int64 {aka long int} | %ld -g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/HashTable.o SNAPLib/HashTable.cpp -g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Histogram.o SNAPLib/Histogram.cpp -g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/IntersectingPairedEndAligner.cpp -g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/LandauVishkin.o SNAPLib/LandauVishkin.cpp -g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/MultiInputReadSupplier.o SNAPLib/MultiInputReadSupplier.cpp -g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/PairedAligner.o SNAPLib/PairedAligner.cpp +SNAPLib/Error.cpp: In function 'void WriteProgressCounter(const char*, _int64)': +SNAPLib/Error.cpp:89:49: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type '_int64' {aka 'long int'} [-Wformat=] + 89 | fprintf(stderr,"reporter:counter:SNAP,%s,%lld\n", counterName, increment); + | ~~~^ ~~~~~~~~~ + | | | + | long long int _int64 {aka long int} + | %ld +g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Seed.o SNAPLib/Seed.cpp +g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/SeedSequencer.o SNAPLib/SeedSequencer.cpp +g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/SingleAligner.o SNAPLib/SingleAligner.cpp +g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/SortedDataWriter.o SNAPLib/SortedDataWriter.cpp +SNAPLib/AlignerContext.cpp: In member function 'void AlignerContext::printStats()': +SNAPLib/AlignerContext.cpp:486:75: warning: format '%lld' expects argument of type 'long long int', but argument 9 has type '_int64' {aka 'long int'} [-Wformat=] + 486 | fprintf(perfFile, "%d\t%d\t%0.2f%%\t%0.2f%%\t%0.2f%%\t%0.2f%%\t%lld\t%0.2f%%\t%lld\tt%.0f\n", + | ~~~^ + | | + | long long int + | %ld +...... + 492 | stats->lvCalls, + | ~~~~~~~~~~~~~~ + | | + | _int64 {aka long int} +SNAPLib/AlignerContext.cpp:486:90: warning: format '%lld' expects argument of type 'long long int', but argument 11 has type '_int64' {aka 'long int'} [-Wformat=] + 486 | fprintf(perfFile, "%d\t%d\t%0.2f%%\t%0.2f%%\t%0.2f%%\t%0.2f%%\t%lld\t%0.2f%%\t%lld\tt%.0f\n", + | ~~~^ + | | + | long long int + | %ld +...... + 494 | stats->totalReads, + | ~~~~~~~~~~~~~~~~~ + | | + | _int64 {aka long int} +g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Tables.o SNAPLib/Tables.cpp SNAPLib/GenomeIndex.cpp: In static member function 'static bool GenomeIndex::BuildIndexToDirectory(const Genome*, int, double, const char*, unsigned int, unsigned int, bool, unsigned int, bool, const char*, unsigned int, bool)': SNAPLib/GenomeIndex.cpp:419:21: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_int64' {aka 'long int'} [-Wformat=] 419 | fprintf(stderr,"%llds\n", (timeInMillis() + 500 - start) / 1000); @@ -571,7 +668,9 @@ | ~~~~~~~~~~~~~~~~~ | | | size_t {aka long unsigned int} -g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/PairedReadMatcher.o SNAPLib/PairedReadMatcher.cpp +g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Util.o SNAPLib/Util.cpp +g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/exit.o SNAPLib/exit.cpp +g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/mapq.o SNAPLib/mapq.cpp SNAPLib/GenomeIndex.cpp: In static member function 'static GenomeIndex* GenomeIndex::loadFromDirectory(char*, bool, bool)': SNAPLib/GenomeIndex.cpp:1707:57: warning: format '%lld' expects argument of type 'long long int*', but argument 6 has type '_int64*' {aka 'long int*'} [-Wformat=] 1707 | if (10 != (nRead = sscanf(indexFileBuf,"%d %d %d %lld %d %d %d %lld %d %d", &majorVersion, &minorVersion, &nHashTables, &overflowTableSize, &seedLen, &chromosomePadding, @@ -589,64 +688,10 @@ | ~~~~~~~~~~~~~~~~~~~ | | | size_t* {aka long unsigned int*} -SNAPLib/Genome.cpp: In member function 'bool Genome::saveToFile(const char*) const': -SNAPLib/Genome.cpp:164:26: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'long int' [-Wformat=] - 164 | fprintf(saveFile,"%lld %d %d\n",nBases, nContigs, (areALTContigsMarked ? GENOME_FLAG_ALT_CONTIGS_MARKED : 0)); - | ~~~^ ~~~~~~ - | | | - | | long int - | long long int - | %ld -SNAPLib/Genome.cpp:174:26: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_int64' {aka 'long int'} [-Wformat=] - 174 | fprintf(saveFile, "%lld %x %s\n", GenomeLocationAsInt64(contigs[i].beginningLocation), (contigs[i].isALT ? GENOME_FLAG_CONTIG_IS_ALT : 0), contigs[i].name); - | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - | | | - | long long int _int64 {aka long int} - | %ld -SNAPLib/Genome.cpp:176:26: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_int64' {aka 'long int'} [-Wformat=] - 176 | fprintf(saveFile, "%lld %s\n", GenomeLocationAsInt64(contigs[i].beginningLocation), contigs[i].name); - | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - | | | - | long long int _int64 {aka long int} - | %ld -SNAPLib/Genome.cpp: In static member function 'static const Genome* Genome::loadFromFile(const char*, unsigned int, GenomeLocation, GenomeDistance, bool)': -SNAPLib/Genome.cpp:267:47: warning: format '%lld' expects argument of type 'long long int*', but argument 3 has type '_int64*' {aka 'long int*'} [-Wformat=] - 267 | if (1 != sscanf(contigNameBuffer, "%lld", &contigStart)) { - | ~~~^ ~~~~~~~~~~~~ - | | | - | | _int64* {aka long int*} - | long long int* - | %ld -g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ParallelTask.o SNAPLib/ParallelTask.cpp -SNAPLib/Genome.cpp: In static member function 'static bool Genome::openFileAndGetSizes(const char*, GenericFile**, GenomeDistance*, unsigned int*, bool, bool*)': -SNAPLib/Genome.cpp:401:51: warning: format '%lld' expects argument of type 'long long int*', but argument 3 has type 'GenomeDistance*' {aka 'long int*'} [-Wformat=] - 401 | if (NULL == retval || 2 != sscanf(linebuf,"%lld %d\n", nBases, nContigs)) { - | ~~~^ ~~~~~~ - | | | - | | GenomeDistance* {aka long int*} - | long long int* - | %ld -SNAPLib/Genome.cpp:410:31: warning: format '%lld' expects argument of type 'long long int*', but argument 3 has type 'GenomeDistance*' {aka 'long int*'} [-Wformat=] - 410 | if (3 == sscanf(linebuf, "%lld %d %d\n", nBases, nContigs, &flags)) - | ~~~^ ~~~~~~ - | | | - | | GenomeDistance* {aka long int*} - | long long int* - | %ld -g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ProbabilityDistance.o SNAPLib/ProbabilityDistance.cpp -g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/RangeSplitter.o SNAPLib/RangeSplitter.cpp -g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Read.o SNAPLib/Read.cpp -g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ReadReader.o SNAPLib/ReadReader.cpp -In file included from SNAPLib/IntersectingPairedEndAligner.cpp:24: -SNAPLib/IntersectingPairedEndAligner.h:668:104: warning: non-static data member initializers only available with '-std=c++11' or '-std=gnu++11' - 668 | Direction setPairDirection[NUM_SET_PAIRS][NUM_READS_PER_PAIR] = { {FORWARD, RC}, {RC, FORWARD} }; - | ^ -g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ReadSupplierQueue.o SNAPLib/ReadSupplierQueue.cpp -SNAPLib/IntersectingPairedEndAligner.h:668:104: warning: extended initializer lists only available with '-std=c++11' or '-std=gnu++11' -g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ReadWriter.o SNAPLib/ReadWriter.cpp -g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/SAM.o SNAPLib/SAM.cpp -g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Seed.o SNAPLib/Seed.cpp -g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/SeedSequencer.o SNAPLib/SeedSequencer.cpp +SNAPLib/ReadReader.cpp: In member function 'virtual bool SimpleReadReader::getNextRead(Read*, AlignmentResult*, unsigned int*, bool*, unsigned int*, unsigned int*, const char**)': +SNAPLib/ReadReader.cpp:44:5: warning: no return statement in function returning non-void [-Wreturn-type] + 44 | } + | ^ In file included from SNAPLib/PairedAligner.cpp:47: SNAPLib/IntersectingPairedEndAligner.h:668:104: warning: non-static data member initializers only available with '-std=c++11' or '-std=gnu++11' 668 | Direction setPairDirection[NUM_SET_PAIRS][NUM_READS_PER_PAIR] = { {FORWARD, RC}, {RC, FORWARD} }; @@ -659,17 +704,6 @@ | | | | long long unsigned int long unsigned int | %lu -g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/SingleAligner.o SNAPLib/SingleAligner.cpp -g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/SortedDataWriter.o SNAPLib/SortedDataWriter.cpp -g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Tables.o SNAPLib/Tables.cpp -SNAPLib/ReadReader.cpp: In member function 'virtual bool SimpleReadReader::getNextRead(Read*, AlignmentResult*, unsigned int*, bool*, unsigned int*, unsigned int*, const char**)': -SNAPLib/ReadReader.cpp:44:5: warning: no return statement in function returning non-void [-Wreturn-type] - 44 | } - | ^ -g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Util.o SNAPLib/Util.cpp -g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/exit.o SNAPLib/exit.cpp -g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/mapq.o SNAPLib/mapq.cpp -g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/stdafx.o SNAPLib/stdafx.cpp SNAPLib/SAM.cpp: In member function 'virtual bool SAMFormat::writeHeader(const ReaderContext&, char*, size_t, size_t*, bool, int, const char**, const char*, const char*, bool) const': SNAPLib/SAM.cpp:1247:116: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'GenomeLocation' {aka 'long int'} [-Wformat=] 1247 | bytesConsumed += snprintf(header + bytesConsumed, headerBufferSize - bytesConsumed, "@SQ\tSN:%s\tLN:%llu\n", contigs[i].name, end - start); @@ -794,8 +828,32 @@ | | | | long long unsigned int GenomeDistance {aka long int} | %lu +g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/stdafx.o SNAPLib/stdafx.cpp g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o apps/snap/Main.o apps/snap/Main.cpp g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o apps/snap/stdafx.o apps/snap/stdafx.cpp +g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/AffineGapTest.o tests/AffineGapTest.cpp +g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/AffineGapVectorizedTest.o tests/AffineGapVectorizedTest.cpp +g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/EventTest.o tests/EventTest.cpp +g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/LandauVishkinTest.o tests/LandauVishkinTest.cpp +g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/ProbabilityDistanceTest.o tests/ProbabilityDistanceTest.cpp +g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/TestLib.o tests/TestLib.cpp +SNAPLib/SingleAligner.cpp: In member function 'virtual void SingleAlignerContext::runIterationThread()': +SNAPLib/SingleAligner.cpp:181:67: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] + 181 | fprintf(stderr,"reporter:counter:SNAP,readsAligned,%llu\n",stats->totalReads - readsWhenLastReported); + | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + | | | + | long long unsigned int long unsigned int + | %lu +SNAPLib/SAM.cpp: In member function 'virtual bool SAMFormat::writeHeader(const ReaderContext&, char*, size_t, size_t*, bool, int, const char**, const char*, const char*, bool) const': +SNAPLib/SAM.cpp:1183:17: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] + 1183 | commandLine[0] = '\0'; + | ~~~~~~~~~~~~~~~^~~~~~ +SNAPLib/SAM.cpp:1182:40: note: at offset 0 to an object with size 0 allocated by 'operator new []' here + 1182 | commandLine = new char[commandLineSize]; + | ^ +g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/main.o tests/main.cpp +g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o apps/SNAPCommand/SNAPCommand.o apps/SNAPCommand/SNAPCommand.cpp +g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o apps/SNAPCommand/stdafx.o apps/SNAPCommand/stdafx.cpp SNAPLib/Util.cpp: In function 'char* FormatUIntWithCommas(_uint64, char*, size_t, size_t)': SNAPLib/Util.cpp:166:28: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_uint64' {aka 'long unsigned int'} [-Wformat=] 166 | sprintf(tempBuf, ",%03lld", x % 1000); @@ -811,29 +869,6 @@ | | _uint64 {aka long unsigned int} | long long int | %ld -SNAPLib/SingleAligner.cpp: In member function 'virtual void SingleAlignerContext::runIterationThread()': -SNAPLib/SingleAligner.cpp:181:67: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] - 181 | fprintf(stderr,"reporter:counter:SNAP,readsAligned,%llu\n",stats->totalReads - readsWhenLastReported); - | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - | | | - | long long unsigned int long unsigned int - | %lu -g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/AffineGapTest.o tests/AffineGapTest.cpp -g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/AffineGapVectorizedTest.o tests/AffineGapVectorizedTest.cpp -g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/EventTest.o tests/EventTest.cpp -g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/LandauVishkinTest.o tests/LandauVishkinTest.cpp -g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/ProbabilityDistanceTest.o tests/ProbabilityDistanceTest.cpp -g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/TestLib.o tests/TestLib.cpp -g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/main.o tests/main.cpp -g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o apps/SNAPCommand/SNAPCommand.o apps/SNAPCommand/SNAPCommand.cpp -g++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o apps/SNAPCommand/stdafx.o apps/SNAPCommand/stdafx.cpp -SNAPLib/SAM.cpp: In member function 'virtual bool SAMFormat::writeHeader(const ReaderContext&, char*, size_t, size_t*, bool, int, const char**, const char*, const char*, bool) const': -SNAPLib/SAM.cpp:1183:17: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] - 1183 | commandLine[0] = '\0'; - | ~~~~~~~~~~~~~~~^~~~~~ -SNAPLib/SAM.cpp:1182:40: note: at offset 0 to an object with size 0 allocated by 'operator new []' here - 1182 | commandLine = new char[commandLineSize]; - | ^ SNAPLib/SAM.cpp: In static member function 'static const char* SAMFormat::computeCigarString(const Genome*, LandauVishkinWithCigar*, char*, int, char*, int, const char*, GenomeDistance, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)': SNAPLib/SAM.cpp:2687:55: warning: '%llu' directive output may be truncated writing between 1 and 19 bytes into a region of size 16 [-Wformat-truncation=] 2687 | snprintf(clipBefore, sizeof(clipBefore), "%lluS", basesClippedBefore + extraBasesClippedBefore); @@ -901,12 +936,12 @@ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -o snap-aligner -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Itests -Wl,-z,relro -Wl,-z,now -pthread SNAPLib/AffineGap.o SNAPLib/AffineGapVectorized.o SNAPLib/AlignerContext.o SNAPLib/AlignerOptions.o SNAPLib/AlignerStats.o SNAPLib/AlignmentAdjuster.o SNAPLib/AlignmentResult.o SNAPLib/ApproximateCounter.o SNAPLib/Bam.o SNAPLib/BaseAligner.o SNAPLib/BigAlloc.o SNAPLib/BufferedAsync.o SNAPLib/ChimericPairedEndAligner.o SNAPLib/CommandProcessor.o SNAPLib/Compat.o SNAPLib/DataReader.o SNAPLib/DataWriter.o SNAPLib/Error.o SNAPLib/FASTA.o SNAPLib/FASTQ.o SNAPLib/GenericFile.o SNAPLib/GenericFile_Blob.o SNAPLib/GenericFile_HDFS.o SNAPLib/GenericFile_map.o SNAPLib/GenericFile_stdio.o SNAPLib/Genome.o SNAPLib/GenomeIndex.o SNAPLib/GzipDataWriter.o SNAPLib/HashTable.o SNAPLib/Histogram.o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/LandauVishkin.o SNAPLib/MultiInputReadSupplier.o SNAPLib/PairedAligner.o SNAPLib/PairedReadMatcher.o SNAPLib/ParallelTask.o SNAPLib/ProbabilityDistance.o SNAPLib/RangeSplitter.o SNAPLib/Read.o SNAPLib/ReadReader.o SNAPLib/ReadSupplierQueue.o SNAPLib/ReadWriter.o SNAPLib/SAM.o SNAPLib/Seed.o SNAPLib/SeedSequencer.o SNAPLib/SingleAligner.o SNAPLib/SortedDataWriter.o SNAPLib/Tables.o SNAPLib/Util.o SNAPLib/exit.o SNAPLib/mapq.o SNAPLib/stdafx.o apps/snap/Main.o apps/snap/stdafx.o -lrt -lz +g++ -o unit_tests -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Itests -Wl,-z,relro -Wl,-z,now -pthread SNAPLib/AffineGap.o SNAPLib/AffineGapVectorized.o SNAPLib/AlignerContext.o SNAPLib/AlignerOptions.o SNAPLib/AlignerStats.o SNAPLib/AlignmentAdjuster.o SNAPLib/AlignmentResult.o SNAPLib/ApproximateCounter.o SNAPLib/Bam.o SNAPLib/BaseAligner.o SNAPLib/BigAlloc.o SNAPLib/BufferedAsync.o SNAPLib/ChimericPairedEndAligner.o SNAPLib/CommandProcessor.o SNAPLib/Compat.o SNAPLib/DataReader.o SNAPLib/DataWriter.o SNAPLib/Error.o SNAPLib/FASTA.o SNAPLib/FASTQ.o SNAPLib/GenericFile.o SNAPLib/GenericFile_Blob.o SNAPLib/GenericFile_HDFS.o SNAPLib/GenericFile_map.o SNAPLib/GenericFile_stdio.o SNAPLib/Genome.o SNAPLib/GenomeIndex.o SNAPLib/GzipDataWriter.o SNAPLib/HashTable.o SNAPLib/Histogram.o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/LandauVishkin.o SNAPLib/MultiInputReadSupplier.o SNAPLib/PairedAligner.o SNAPLib/PairedReadMatcher.o SNAPLib/ParallelTask.o SNAPLib/ProbabilityDistance.o SNAPLib/RangeSplitter.o SNAPLib/Read.o SNAPLib/ReadReader.o SNAPLib/ReadSupplierQueue.o SNAPLib/ReadWriter.o SNAPLib/SAM.o SNAPLib/Seed.o SNAPLib/SeedSequencer.o SNAPLib/SingleAligner.o SNAPLib/SortedDataWriter.o SNAPLib/Tables.o SNAPLib/Util.o SNAPLib/exit.o SNAPLib/mapq.o SNAPLib/stdafx.o tests/AffineGapTest.o tests/AffineGapVectorizedTest.o tests/EventTest.o tests/LandauVishkinTest.o tests/ProbabilityDistanceTest.o tests/TestLib.o tests/main.o -lrt -lz echo SNAPCOMMAND_OBJ is apps/SNAPCommand/SNAPCommand.o apps/SNAPCommand/stdafx.o SNAPCOMMAND_OBJ is apps/SNAPCommand/SNAPCommand.o apps/SNAPCommand/stdafx.o echo SNAP_OBJ is apps/snap/Main.o apps/snap/stdafx.o SNAP_OBJ is apps/snap/Main.o apps/snap/stdafx.o g++ -o SNAPCommand -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wl,-z,relro -Wl,-z,now -pthread SNAPLib/AffineGap.o SNAPLib/AffineGapVectorized.o SNAPLib/AlignerContext.o SNAPLib/AlignerOptions.o SNAPLib/AlignerStats.o SNAPLib/AlignmentAdjuster.o SNAPLib/AlignmentResult.o SNAPLib/ApproximateCounter.o SNAPLib/Bam.o SNAPLib/BaseAligner.o SNAPLib/BigAlloc.o SNAPLib/BufferedAsync.o SNAPLib/ChimericPairedEndAligner.o SNAPLib/CommandProcessor.o SNAPLib/Compat.o SNAPLib/DataReader.o SNAPLib/DataWriter.o SNAPLib/Error.o SNAPLib/FASTA.o SNAPLib/FASTQ.o SNAPLib/GenericFile.o SNAPLib/GenericFile_Blob.o SNAPLib/GenericFile_HDFS.o SNAPLib/GenericFile_map.o SNAPLib/GenericFile_stdio.o SNAPLib/Genome.o SNAPLib/GenomeIndex.o SNAPLib/GzipDataWriter.o SNAPLib/HashTable.o SNAPLib/Histogram.o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/LandauVishkin.o SNAPLib/MultiInputReadSupplier.o SNAPLib/PairedAligner.o SNAPLib/PairedReadMatcher.o SNAPLib/ParallelTask.o SNAPLib/ProbabilityDistance.o SNAPLib/RangeSplitter.o SNAPLib/Read.o SNAPLib/ReadReader.o SNAPLib/ReadSupplierQueue.o SNAPLib/ReadWriter.o SNAPLib/SAM.o SNAPLib/Seed.o SNAPLib/SeedSequencer.o SNAPLib/SingleAligner.o SNAPLib/SortedDataWriter.o SNAPLib/Tables.o SNAPLib/Util.o SNAPLib/exit.o SNAPLib/mapq.o SNAPLib/stdafx.o apps/SNAPCommand/SNAPCommand.o apps/SNAPCommand/stdafx.o -lrt -lz -g++ -o unit_tests -g -O2 -fdebug-prefix-map=/build/reproducible-path/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Itests -Wl,-z,relro -Wl,-z,now -pthread SNAPLib/AffineGap.o SNAPLib/AffineGapVectorized.o SNAPLib/AlignerContext.o SNAPLib/AlignerOptions.o SNAPLib/AlignerStats.o SNAPLib/AlignmentAdjuster.o SNAPLib/AlignmentResult.o SNAPLib/ApproximateCounter.o SNAPLib/Bam.o SNAPLib/BaseAligner.o SNAPLib/BigAlloc.o SNAPLib/BufferedAsync.o SNAPLib/ChimericPairedEndAligner.o SNAPLib/CommandProcessor.o SNAPLib/Compat.o SNAPLib/DataReader.o SNAPLib/DataWriter.o SNAPLib/Error.o SNAPLib/FASTA.o SNAPLib/FASTQ.o SNAPLib/GenericFile.o SNAPLib/GenericFile_Blob.o SNAPLib/GenericFile_HDFS.o SNAPLib/GenericFile_map.o SNAPLib/GenericFile_stdio.o SNAPLib/Genome.o SNAPLib/GenomeIndex.o SNAPLib/GzipDataWriter.o SNAPLib/HashTable.o SNAPLib/Histogram.o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/LandauVishkin.o SNAPLib/MultiInputReadSupplier.o SNAPLib/PairedAligner.o SNAPLib/PairedReadMatcher.o SNAPLib/ParallelTask.o SNAPLib/ProbabilityDistance.o SNAPLib/RangeSplitter.o SNAPLib/Read.o SNAPLib/ReadReader.o SNAPLib/ReadSupplierQueue.o SNAPLib/ReadWriter.o SNAPLib/SAM.o SNAPLib/Seed.o SNAPLib/SeedSequencer.o SNAPLib/SingleAligner.o SNAPLib/SortedDataWriter.o SNAPLib/Tables.o SNAPLib/Util.o SNAPLib/exit.o SNAPLib/mapq.o SNAPLib/stdafx.o tests/AffineGapTest.o tests/AffineGapVectorizedTest.o tests/EventTest.o tests/LandauVishkinTest.o tests/ProbabilityDistanceTest.o tests/TestLib.o tests/main.o -lrt -lz make[2]: Leaving directory '/build/reproducible-path/snap-aligner-1.0.0+dfsg' help2man --no-discard-stderr --no-info --version-string="1.0.0" \ --name "scalable nucleotide alignment program" \ @@ -973,8 +1008,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'snap-aligner-dbgsym' in '../snap-aligner-dbgsym_1.0.0+dfsg-2_amd64.deb'. dpkg-deb: building package 'snap-aligner' in '../snap-aligner_1.0.0+dfsg-2_amd64.deb'. +dpkg-deb: building package 'snap-aligner-dbgsym' in '../snap-aligner-dbgsym_1.0.0+dfsg-2_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../snap-aligner_1.0.0+dfsg-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -982,12 +1017,14 @@ 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/3763679/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3763679/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/2796423 and its subdirectories -I: Current time: Mon Jul 29 05:54:34 -12 2024 -I: pbuilder-time-stamp: 1722275674 +I: removing directory /srv/workspace/pbuilder/3763679 and its subdirectories +I: Current time: Mon Sep 1 14:19:45 +14 2025 +I: pbuilder-time-stamp: 1756685985