Diff of the two buildlogs: -- --- b1/build.log 2021-06-16 20:00:47.160744184 +0000 +++ b2/build.log 2021-06-16 20:04:37.396020114 +0000 @@ -1,6 +1,8 @@ -I: pbuilder: network access will be disabled during build -I: Current time: Tue Jul 19 14:23:23 -12 2022 -I: pbuilder-time-stamp: 1658283803 +unshare: unshare failed: Cannot allocate memory +W: pbuilder: unshare CLONE_NEWNET not available +I: pbuilder: network access is available during build! +I: Current time: Thu Jun 17 10:00:49 +14 2021 +I: pbuilder-time-stamp: 1623873649 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -17,8 +19,8 @@ I: copying [./proda_1.0-13.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.woORfxZK/trustedkeys.kbx': General error -gpgv: Signature made Mon Nov 23 08:10:25 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.ICj3ngdn/trustedkeys.kbx': General error +gpgv: Signature made Tue Nov 24 10:10:25 2020 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -35,137 +37,171 @@ dpkg-source: info: applying hardening.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2582/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/17593/tmp/hooks/D01_modify_environment starting +debug: Running on ionos12-i386. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/17593/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/17593/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=18' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='i386' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.1.4(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=10' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='2c1004796a6044e49fee9c6715523443' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='2582' - PS1='# ' - PS2='> ' + INVOCATION_ID=1f357adda06e4b93b34ad3a869e1db9f + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=17593 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.X3QTWZO1Yd/pbuilderrc_Z6Bo --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.X3QTWZO1Yd/b1 --logfile b1/build.log proda_1.0-13.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://85.184.249.68:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.X3QTWZO1Yd/pbuilderrc_KQsd --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.X3QTWZO1Yd/b2 --logfile b2/build.log --extrapackages usrmerge proda_1.0-13.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://78.137.99.97:3128 I: uname -a - Linux ionos16-i386 4.19.0-16-amd64 #1 SMP Debian 4.19.181-1 (2021-03-19) x86_64 GNU/Linux + Linux i-capture-the-hostname 4.19.0-16-686-pae #1 SMP Debian 4.19.181-1 (2021-03-19) i686 GNU/Linux I: ls -l /bin - total 5776 - -rwxr-xr-x 1 root root 1367848 Feb 24 2021 bash - -rwxr-xr-x 3 root root 38280 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzcat - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep - -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 17768 Jul 20 2020 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore - -rwxr-xr-x 1 root root 38824 Sep 22 2020 cat - -rwxr-xr-x 1 root root 71624 Sep 22 2020 chgrp - -rwxr-xr-x 1 root root 67528 Sep 22 2020 chmod - -rwxr-xr-x 1 root root 75752 Sep 22 2020 chown - -rwxr-xr-x 1 root root 157960 Sep 22 2020 cp - -rwxr-xr-x 1 root root 128724 Dec 10 2020 dash - -rwxr-xr-x 1 root root 124904 Sep 22 2020 date - -rwxr-xr-x 1 root root 92172 Sep 22 2020 dd - -rwxr-xr-x 1 root root 100752 Sep 22 2020 df - -rwxr-xr-x 1 root root 153964 Sep 22 2020 dir - -rwxr-xr-x 1 root root 83644 Feb 7 2021 dmesg - lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname - -rwxr-xr-x 1 root root 34664 Sep 22 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 34664 Sep 22 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 71928 Feb 7 2021 findmnt - -rwsr-xr-x 1 root root 30112 Feb 26 2021 fusermount - -rwxr-xr-x 1 root root 210488 Nov 9 2020 grep - -rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip - -rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe - -rwxr-xr-x 1 root root 100952 Mar 2 2021 gzip - -rwxr-xr-x 1 root root 21916 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 83980 Sep 22 2020 ln - -rwxr-xr-x 1 root root 55572 Feb 7 2020 login - -rwxr-xr-x 1 root root 153964 Sep 22 2020 ls - -rwxr-xr-x 1 root root 153124 Feb 7 2021 lsblk - -rwxr-xr-x 1 root root 96328 Sep 22 2020 mkdir - -rwxr-xr-x 1 root root 79912 Sep 22 2020 mknod - -rwxr-xr-x 1 root root 47048 Sep 22 2020 mktemp - -rwxr-xr-x 1 root root 58920 Feb 7 2021 more - -rwsr-xr-x 1 root root 50720 Feb 7 2021 mount - -rwxr-xr-x 1 root root 13856 Feb 7 2021 mountpoint - -rwxr-xr-x 1 root root 157996 Sep 22 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 18 2021 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 38824 Sep 22 2020 pwd - lrwxrwxrwx 1 root root 4 Feb 24 2021 rbash -> bash - -rwxr-xr-x 1 root root 46984 Sep 22 2020 readlink - -rwxr-xr-x 1 root root 75720 Sep 22 2020 rm - -rwxr-xr-x 1 root root 46984 Sep 22 2020 rmdir - -rwxr-xr-x 1 root root 22292 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Jul 19 03:46 sh -> dash - -rwxr-xr-x 1 root root 34696 Sep 22 2020 sleep - -rwxr-xr-x 1 root root 83880 Sep 22 2020 stty - -rwsr-xr-x 1 root root 79396 Feb 7 2021 su - -rwxr-xr-x 1 root root 34696 Sep 22 2020 sync - -rwxr-xr-x 1 root root 602584 Feb 16 2021 tar - -rwxr-xr-x 1 root root 13860 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 108520 Sep 22 2020 touch - -rwxr-xr-x 1 root root 34664 Sep 22 2020 true - -rwxr-xr-x 1 root root 17768 Feb 26 2021 ulockmgr_server - -rwsr-xr-x 1 root root 30236 Feb 7 2021 umount - -rwxr-xr-x 1 root root 34664 Sep 22 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress - -rwxr-xr-x 1 root root 153964 Sep 22 2020 vdir - -rwxr-xr-x 1 root root 63024 Feb 7 2021 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat - -rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp - -rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff - -rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep - -rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep - -rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce - -rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep - -rwxr-xr-x 1 root root 2206 Mar 2 2021 zless - -rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore - -rwxr-xr-x 1 root root 4553 Mar 2 2021 znew -I: user script /srv/workspace/pbuilder/2582/tmp/hooks/D02_print_environment finished + total 5780 + -rwxr-xr-x 1 root root 1367848 Feb 25 10:57 bash + -rwxr-xr-x 3 root root 38280 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 38280 Jul 21 2020 bzcat + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep + -rwxr-xr-x 3 root root 38280 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 17768 Jul 21 2020 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore + -rwxr-xr-x 1 root root 38824 Sep 23 2020 cat + -rwxr-xr-x 1 root root 71624 Sep 23 2020 chgrp + -rwxr-xr-x 1 root root 67528 Sep 23 2020 chmod + -rwxr-xr-x 1 root root 75752 Sep 23 2020 chown + -rwxr-xr-x 1 root root 157960 Sep 23 2020 cp + -rwxr-xr-x 1 root root 128724 Dec 11 2020 dash + -rwxr-xr-x 1 root root 124904 Sep 23 2020 date + -rwxr-xr-x 1 root root 92172 Sep 23 2020 dd + -rwxr-xr-x 1 root root 100752 Sep 23 2020 df + -rwxr-xr-x 1 root root 153964 Sep 23 2020 dir + -rwxr-xr-x 1 root root 83644 Feb 8 04:38 dmesg + lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname + -rwxr-xr-x 1 root root 34664 Sep 23 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 34664 Sep 23 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 71928 Feb 8 04:38 findmnt + -rwsr-xr-x 1 root root 30112 Feb 27 06:12 fusermount + -rwxr-xr-x 1 root root 210488 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 13:30 gzexe + -rwxr-xr-x 1 root root 100952 Mar 3 13:30 gzip + -rwxr-xr-x 1 root root 21916 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 83980 Sep 23 2020 ln + -rwxr-xr-x 1 root root 55572 Feb 8 2020 login + -rwxr-xr-x 1 root root 153964 Sep 23 2020 ls + -rwxr-xr-x 1 root root 153124 Feb 8 04:38 lsblk + -rwxr-xr-x 1 root root 96328 Sep 23 2020 mkdir + -rwxr-xr-x 1 root root 79912 Sep 23 2020 mknod + -rwxr-xr-x 1 root root 47048 Sep 23 2020 mktemp + -rwxr-xr-x 1 root root 58920 Feb 8 04:38 more + -rwsr-xr-x 1 root root 50720 Feb 8 04:38 mount + -rwxr-xr-x 1 root root 13856 Feb 8 04:38 mountpoint + -rwxr-xr-x 1 root root 157996 Sep 23 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 19 05:38 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 38824 Sep 23 2020 pwd + lrwxrwxrwx 1 root root 4 Feb 25 10:57 rbash -> bash + -rwxr-xr-x 1 root root 46984 Sep 23 2020 readlink + -rwxr-xr-x 1 root root 75720 Sep 23 2020 rm + -rwxr-xr-x 1 root root 46984 Sep 23 2020 rmdir + -rwxr-xr-x 1 root root 22292 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 125036 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Jun 17 10:03 sh -> bash + lrwxrwxrwx 1 root root 4 Jun 16 23:27 sh.distrib -> dash + -rwxr-xr-x 1 root root 34696 Sep 23 2020 sleep + -rwxr-xr-x 1 root root 83880 Sep 23 2020 stty + -rwsr-xr-x 1 root root 79396 Feb 8 04:38 su + -rwxr-xr-x 1 root root 34696 Sep 23 2020 sync + -rwxr-xr-x 1 root root 602584 Feb 17 23:55 tar + -rwxr-xr-x 1 root root 13860 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 108520 Sep 23 2020 touch + -rwxr-xr-x 1 root root 34664 Sep 23 2020 true + -rwxr-xr-x 1 root root 17768 Feb 27 06:12 ulockmgr_server + -rwsr-xr-x 1 root root 30236 Feb 8 04:38 umount + -rwxr-xr-x 1 root root 34664 Sep 23 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 uncompress + -rwxr-xr-x 1 root root 153964 Sep 23 2020 vdir + -rwxr-xr-x 1 root root 63024 Feb 8 04:38 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Mar 3 13:30 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 13:30 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 13:30 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 13:30 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 13:30 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 13:30 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 13:30 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 13:30 zless + -rwxr-xr-x 1 root root 1842 Mar 3 13:30 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 13:30 znew +I: user script /srv/workspace/pbuilder/17593/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -232,7 +268,7 @@ Get: 29 http://deb.debian.org/debian bullseye/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 30 http://deb.debian.org/debian bullseye/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian bullseye/main i386 debhelper all 13.3.4 [1049 kB] -Fetched 18.6 MB in 2s (9890 kB/s) +Fetched 18.6 MB in 2s (7926 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19675 files and directories currently installed.) @@ -371,8 +407,44 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +The following additional packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl +The following NEW packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge +0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. +Need to get 59.5 kB of archives. +After this operation, 157 kB of additional disk space will be used. +Get:1 http://deb.debian.org/debian bullseye/main i386 libnumber-compare-perl all 0.03-1.1 [6956 B] +Get:2 http://deb.debian.org/debian bullseye/main i386 libtext-glob-perl all 0.11-1 [8888 B] +Get:3 http://deb.debian.org/debian bullseye/main i386 libfile-find-rule-perl all 0.34-1 [30.6 kB] +Get:4 http://deb.debian.org/debian bullseye/main i386 usrmerge all 25 [13.0 kB] +debconf: delaying package configuration, since apt-utils is not installed +Fetched 59.5 kB in 0s (428 kB/s) +Selecting previously unselected package libnumber-compare-perl. +(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21550 files and directories currently installed.) +Preparing to unpack .../libnumber-compare-perl_0.03-1.1_all.deb ... +Unpacking libnumber-compare-perl (0.03-1.1) ... +Selecting previously unselected package libtext-glob-perl. +Preparing to unpack .../libtext-glob-perl_0.11-1_all.deb ... +Unpacking libtext-glob-perl (0.11-1) ... +Selecting previously unselected package libfile-find-rule-perl. +Preparing to unpack .../libfile-find-rule-perl_0.34-1_all.deb ... +Unpacking libfile-find-rule-perl (0.34-1) ... +Selecting previously unselected package usrmerge. +Preparing to unpack .../archives/usrmerge_25_all.deb ... +Unpacking usrmerge (25) ... +Setting up libtext-glob-perl (0.11-1) ... +Setting up libnumber-compare-perl (0.03-1.1) ... +Setting up libfile-find-rule-perl (0.34-1) ... +Setting up usrmerge (25) ... +The system has been successfully converted. +Processing triggers for man-db (2.9.4-2) ... +Not building database; man-db/auto-update is not 'true'. I: Building the package -I: Running cd /build/proda-1.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b +I: Running cd /build/proda-1.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package proda dpkg-buildpackage: info: source version 1.0-13 dpkg-buildpackage: info: source distribution unstable @@ -382,7 +454,7 @@ debian/rules clean dh clean dh_auto_clean - make -j18 clean + make -j10 clean make[1]: Entering directory '/build/proda-1.0' rm -f *.o make[1]: Leaving directory '/build/proda-1.0' @@ -393,7 +465,7 @@ dh_autoreconf dh_auto_configure dh_auto_build - make -j18 "INSTALL=install --strip-program=true" + make -j10 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/proda-1.0' g++ -g -O2 -fdebug-prefix-map=/build/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o AlignedFragment.o AlignedFragment.cc g++ -g -O2 -fdebug-prefix-map=/build/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Assert.o Assert.cc @@ -405,31 +477,8 @@ g++ -g -O2 -fdebug-prefix-map=/build/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o PairAligner.o PairAligner.cc g++ -g -O2 -fdebug-prefix-map=/build/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Matrix.o Matrix.cc g++ -g -O2 -fdebug-prefix-map=/build/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o MultiSequence.o MultiSequence.cc -g++ -g -O2 -fdebug-prefix-map=/build/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o ProbModel.o ProbModel.cc -g++ -g -O2 -fdebug-prefix-map=/build/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Score.o Score.cc -g++ -g -O2 -fdebug-prefix-map=/build/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o ScoreMatrix.o ScoreMatrix.cc -g++ -g -O2 -fdebug-prefix-map=/build/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Sequence.o Sequence.cc -g++ -g -O2 -fdebug-prefix-map=/build/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o SparseMatrix.o SparseMatrix.cc -g++ -g -O2 -fdebug-prefix-map=/build/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Tree.o Tree.cc -g++ -g -O2 -fdebug-prefix-map=/build/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Utilities.o Utilities.cc In file included from Matrix.h:12, - from LocalAlign.h:12, - from LocalAlign.cc:5: -SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 57 | const int GetRowSize (int layer, int row) const; - | ^~~~~ -SparseMatrix.h:60:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 60 | const int GetNumLayers() const; - | ^~~~~ -SparseMatrix.h:61:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 61 | const int GetNumRows() const; - | ^~~~~ -SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 62 | const int GetNumCols() const; - | ^~~~~ -In file included from Matrix.h:12, - from GlobalAlign.h:11, - from GlobalAlign.cc:7: + from Matrix.cc:7: SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 57 | const int GetRowSize (int layer, int row) const; | ^~~~~ @@ -443,7 +492,8 @@ 62 | const int GetNumCols() const; | ^~~~~ In file included from Matrix.h:12, - from Matrix.cc:7: + from LocalAlign.h:12, + from LocalAlign.cc:5: SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 57 | const int GetRowSize (int layer, int row) const; | ^~~~~ @@ -457,8 +507,8 @@ 62 | const int GetNumCols() const; | ^~~~~ In file included from Matrix.h:12, - from Tree.h:9, - from Tree.cc:6: + from GlobalAlign.h:11, + from GlobalAlign.cc:7: SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 57 | const int GetRowSize (int layer, int row) const; | ^~~~~ @@ -471,6 +521,7 @@ SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 62 | const int GetNumCols() const; | ^~~~~ +g++ -g -O2 -fdebug-prefix-map=/build/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o ProbModel.o ProbModel.cc In file included from Matrix.h:12, from Types.h:12, from Block.h:10, @@ -487,21 +538,13 @@ SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 62 | const int GetNumCols() const; | ^~~~~ -In file included from Matrix.h:12, - from Types.h:12, - from ProbModel.h:11, - from ProbModel.cc:8: -SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 57 | const int GetRowSize (int layer, int row) const; - | ^~~~~ -SparseMatrix.h:60:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 60 | const int GetNumLayers() const; - | ^~~~~ -SparseMatrix.h:61:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 61 | const int GetNumRows() const; +In file included from PairAligner.h:10, + from PairAligner.cc:9: +Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 51 | const int GetLength () const; | ^~~~~ -SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 62 | const int GetNumCols() const; +Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 52 | const int GetID () const; | ^~~~~ In file included from ScoreMatrix.h:12, from Matrix.h:13, @@ -553,28 +596,10 @@ SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 62 | const int GetNumCols() const; | ^~~~~ -In file included from ScoreMatrix.h:12, - from ScoreMatrix.cc:7: -Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 51 | const int GetLength () const; - | ^~~~~ -Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 52 | const int GetID () const; - | ^~~~~ -In file included from ScoreMatrix.cc:7: -ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 88 | const int GetNumLayers() const { - | ^~~~~ -ScoreMatrix.h:96:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 96 | const int GetNumRows() const { - | ^~~~~ -ScoreMatrix.h:104:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 104 | const int GetNumCols() const { - | ^~~~~ In file included from Matrix.h:12, from Types.h:12, from ProbModel.h:11, - from ScoreMatrix.cc:8: + from ProbModel.cc:8: SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 57 | const int GetRowSize (int layer, int row) const; | ^~~~~ @@ -587,47 +612,6 @@ SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 62 | const int GetNumCols() const; | ^~~~~ -In file included from Types.h:12, - from ProbModel.h:11, - from ScoreMatrix.cc:8: -Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 100 | const int GetNumLayers() const { - | ^~~~~ -Matrix.h:108:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 108 | const int GetNumRows() const { - | ^~~~~ -Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 116 | const int GetNumCols() const { - | ^~~~~ -In file included from Sequence.cc:8: -Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 51 | const int GetLength () const; - | ^~~~~ -Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 52 | const int GetID () const; - | ^~~~~ -Sequence.cc:121:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 121 | const int Sequence::GetLength () const { - | ^~~~~ -Sequence.cc:129:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 129 | const int Sequence::GetID () const { - | ^~~~~ -In file included from MultiSequence.h:12, - from MultiSequence.cc:10: -Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 51 | const int GetLength () const; - | ^~~~~ -Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 52 | const int GetID () const; - | ^~~~~ -In file included from PairAligner.h:10, - from PairAligner.cc:9: -Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 51 | const int GetLength () const; - | ^~~~~ -Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 52 | const int GetID () const; - | ^~~~~ In file included from MultiSequence.h:12, from Main.cc:12: Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] @@ -638,8 +622,8 @@ | ^~~~~ In file included from ScoreMatrix.h:12, from Matrix.h:13, - from LocalAlign.h:12, - from LocalAlign.cc:5: + from GlobalAlign.h:11, + from GlobalAlign.cc:7: Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 51 | const int GetLength () const; | ^~~~~ @@ -647,8 +631,8 @@ 52 | const int GetID () const; | ^~~~~ In file included from Matrix.h:13, - from LocalAlign.h:12, - from LocalAlign.cc:5: + from GlobalAlign.h:11, + from GlobalAlign.cc:7: ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 88 | const int GetNumLayers() const { | ^~~~~ @@ -658,8 +642,8 @@ ScoreMatrix.h:104:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 104 | const int GetNumCols() const { | ^~~~~ -In file included from LocalAlign.h:12, - from LocalAlign.cc:5: +In file included from GlobalAlign.h:11, + from GlobalAlign.cc:7: Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 100 | const int GetNumLayers() const { | ^~~~~ @@ -671,8 +655,15 @@ | ^~~~~ In file included from ScoreMatrix.h:12, from Matrix.h:13, - from SparseMatrix.h:12, - from SparseMatrix.cc:6: + from Matrix.cc:7: +Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 51 | const int GetLength () const; + | ^~~~~ +Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 52 | const int GetID () const; + | ^~~~~ +In file included from MultiSequence.h:12, + from MultiSequence.cc:10: Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 51 | const int GetLength () const; | ^~~~~ @@ -680,8 +671,7 @@ 52 | const int GetID () const; | ^~~~~ In file included from Matrix.h:13, - from SparseMatrix.h:12, - from SparseMatrix.cc:6: + from Matrix.cc:7: ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 88 | const int GetNumLayers() const { | ^~~~~ @@ -691,8 +681,7 @@ ScoreMatrix.h:104:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 104 | const int GetNumCols() const { | ^~~~~ -In file included from SparseMatrix.h:12, - from SparseMatrix.cc:6: +In file included from Matrix.cc:7: Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 100 | const int GetNumLayers() const { | ^~~~~ @@ -702,57 +691,22 @@ Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 116 | const int GetNumCols() const { | ^~~~~ -In file included from SparseMatrix.cc:6: -SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 57 | const int GetRowSize (int layer, int row) const; - | ^~~~~ -SparseMatrix.h:60:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 60 | const int GetNumLayers() const; - | ^~~~~ -SparseMatrix.h:61:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 61 | const int GetNumRows() const; - | ^~~~~ -SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 62 | const int GetNumCols() const; - | ^~~~~ -SparseMatrix.cc:199:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 199 | const int SparseMatrix::GetRowSize (int layer, int row) const { - | ^~~~~ -SparseMatrix.cc:209:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 209 | const int SparseMatrix::GetNumLayers() const { - | ^~~~~ -SparseMatrix.cc:217:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 217 | const int SparseMatrix::GetNumRows() const { - | ^~~~~ -SparseMatrix.cc:225:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 225 | const int SparseMatrix::GetNumCols() const { - | ^~~~~ -In file included from ScoreMatrix.h:12, - from Matrix.h:13, - from Tree.h:9, - from Tree.cc:6: -Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 51 | const int GetLength () const; - | ^~~~~ -Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 52 | const int GetID () const; - | ^~~~~ -In file included from Matrix.h:13, - from Tree.h:9, - from Tree.cc:6: -ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 88 | const int GetNumLayers() const { - | ^~~~~ -ScoreMatrix.h:96:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 96 | const int GetNumRows() const { - | ^~~~~ -ScoreMatrix.h:104:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 104 | const int GetNumCols() const { - | ^~~~~ +Matrix.cc: In member function 'float Matrix::SumOfRow(int, int) const': +Matrix.cc:165:6: warning: variable 'pos' set but not used [-Wunused-but-set-variable] + 165 | int pos = 0; + | ^~~ +Matrix.cc:166:9: warning: variable 'ptr' set but not used [-Wunused-but-set-variable] + 166 | float *ptr; + | ^~~ +Matrix.cc: In member function 'float Matrix::SumOfColumn(int, int) const': +Matrix.cc:186:6: warning: variable 'pos' set but not used [-Wunused-but-set-variable] + 186 | int pos = 0; + | ^~~ In file included from ScoreMatrix.h:12, from Matrix.h:13, - from GlobalAlign.h:11, - from GlobalAlign.cc:7: + from Types.h:12, + from Block.h:10, + from Block.cc:6: Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 51 | const int GetLength () const; | ^~~~~ @@ -760,8 +714,9 @@ 52 | const int GetID () const; | ^~~~~ In file included from Matrix.h:13, - from GlobalAlign.h:11, - from GlobalAlign.cc:7: + from Types.h:12, + from Block.h:10, + from Block.cc:6: ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 88 | const int GetNumLayers() const { | ^~~~~ @@ -771,8 +726,9 @@ ScoreMatrix.h:104:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 104 | const int GetNumCols() const { | ^~~~~ -In file included from Tree.h:9, - from Tree.cc:6: +In file included from Types.h:12, + from Block.h:10, + from Block.cc:6: Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 100 | const int GetNumLayers() const { | ^~~~~ @@ -784,30 +740,17 @@ | ^~~~~ In file included from ScoreMatrix.h:12, from Matrix.h:13, - from Types.h:12, - from Block.h:10, - from Block.cc:6: + from LocalAlign.h:12, + from LocalAlign.cc:5: Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 51 | const int GetLength () const; | ^~~~~ Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 52 | const int GetID () const; | ^~~~~ -In file included from GlobalAlign.h:11, - from GlobalAlign.cc:7: -Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 100 | const int GetNumLayers() const { - | ^~~~~ -Matrix.h:108:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 108 | const int GetNumRows() const { - | ^~~~~ -Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 116 | const int GetNumCols() const { - | ^~~~~ In file included from Matrix.h:13, - from Types.h:12, - from Block.h:10, - from Block.cc:6: + from LocalAlign.h:12, + from LocalAlign.cc:5: ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 88 | const int GetNumLayers() const { | ^~~~~ @@ -817,9 +760,8 @@ ScoreMatrix.h:104:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 104 | const int GetNumCols() const { | ^~~~~ -In file included from Types.h:12, - from Block.h:10, - from Block.cc:6: +In file included from LocalAlign.h:12, + from LocalAlign.cc:5: Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 100 | const int GetNumLayers() const { | ^~~~~ @@ -829,20 +771,11 @@ Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 116 | const int GetNumCols() const { | ^~~~~ -In file included from ScoreMatrix.h:12, - from Matrix.h:13, - from Matrix.cc:7: -Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 51 | const int GetLength () const; - | ^~~~~ -Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 52 | const int GetID () const; - | ^~~~~ In file included from Matrix.h:12, from Types.h:12, - from Block.h:10, - from MultiSequence.h:13, - from MultiSequence.cc:10: + from ProbModel.h:11, + from PairAligner.h:11, + from PairAligner.cc:9: SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 57 | const int GetRowSize (int layer, int row) const; | ^~~~~ @@ -856,7 +789,10 @@ 62 | const int GetNumCols() const; | ^~~~~ In file included from Matrix.h:13, - from Matrix.cc:7: + from Types.h:12, + from ProbModel.h:11, + from PairAligner.h:11, + from PairAligner.cc:9: ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 88 | const int GetNumLayers() const { | ^~~~~ @@ -866,6 +802,33 @@ ScoreMatrix.h:104:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 104 | const int GetNumCols() const { | ^~~~~ +In file included from Types.h:12, + from ProbModel.h:11, + from PairAligner.h:11, + from PairAligner.cc:9: +Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 100 | const int GetNumLayers() const { + | ^~~~~ +Matrix.h:108:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 108 | const int GetNumRows() const { + | ^~~~~ +Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 116 | const int GetNumCols() const { + | ^~~~~ +In file included from GlobalAlign.h:12, + from GlobalAlign.cc:7: +MultiSequence.h:24:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 24 | const int AutoDetectFileFormat (const char *filename) const; + | ^~~~~ +MultiSequence.h:28:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 28 | const char ComputeAnnotation (const char *data, const int size) const; + | ^~~~~ +MultiSequence.h:48:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 48 | const int GetNumSequences() const; + | ^~~~~ +MultiSequence.h:49:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 49 | const int GetLength() const; + | ^~~~~ In file included from Block.cc:9: MultiSequence.h:24:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 24 | const int AutoDetectFileFormat (const char *filename) const; @@ -879,11 +842,32 @@ MultiSequence.h:49:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 49 | const int GetLength() const; | ^~~~~ +Block.cc: In constructor 'Block::Block(std::vector&, MultiSequence*, bool, Block*)': +Block.cc:58:36: warning: variable 'end' set but not used [-Wunused-but-set-variable] + 58 | int best,best_id, best_pos, multi,end,bfrag,bk,best_end; + | ^~~ +In file included from Matrix.h:12, + from Types.h:12, + from Block.h:10, + from MultiSequence.h:13, + from Main.cc:12: +SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 57 | const int GetRowSize (int layer, int row) const; + | ^~~~~ +SparseMatrix.h:60:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 60 | const int GetNumLayers() const; + | ^~~~~ +SparseMatrix.h:61:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 61 | const int GetNumRows() const; + | ^~~~~ +SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 62 | const int GetNumCols() const; + | ^~~~~ In file included from Matrix.h:13, from Types.h:12, from Block.h:10, from MultiSequence.h:13, - from MultiSequence.cc:10: + from Main.cc:12: ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 88 | const int GetNumLayers() const { | ^~~~~ @@ -893,20 +877,10 @@ ScoreMatrix.h:104:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 104 | const int GetNumCols() const { | ^~~~~ -In file included from Matrix.cc:7: -Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 100 | const int GetNumLayers() const { - | ^~~~~ -Matrix.h:108:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 108 | const int GetNumRows() const { - | ^~~~~ -Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 116 | const int GetNumCols() const { - | ^~~~~ In file included from Types.h:12, from Block.h:10, from MultiSequence.h:13, - from MultiSequence.cc:10: + from Main.cc:12: Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 100 | const int GetNumLayers() const { | ^~~~~ @@ -916,22 +890,11 @@ Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 116 | const int GetNumCols() const { | ^~~~~ -Matrix.cc: In member function 'float Matrix::SumOfRow(int, int) const': -Matrix.cc:165:6: warning: variable 'pos' set but not used [-Wunused-but-set-variable] - 165 | int pos = 0; - | ^~~ -Matrix.cc:166:9: warning: variable 'ptr' set but not used [-Wunused-but-set-variable] - 166 | float *ptr; - | ^~~ -Matrix.cc: In member function 'float Matrix::SumOfColumn(int, int) const': -Matrix.cc:186:6: warning: variable 'pos' set but not used [-Wunused-but-set-variable] - 186 | int pos = 0; - | ^~~ In file included from Matrix.h:12, from Types.h:12, - from ProbModel.h:11, - from PairAligner.h:11, - from PairAligner.cc:9: + from Block.h:10, + from MultiSequence.h:13, + from MultiSequence.cc:10: SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 57 | const int GetRowSize (int layer, int row) const; | ^~~~~ @@ -944,26 +907,59 @@ SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 62 | const int GetNumCols() const; | ^~~~~ -In file included from MultiSequence.cc:10: -MultiSequence.h:24:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 24 | const int AutoDetectFileFormat (const char *filename) const; - | ^~~~~ In file included from Matrix.h:13, from Types.h:12, - from ProbModel.h:11, - from PairAligner.h:11, - from PairAligner.cc:9: + from Block.h:10, + from MultiSequence.h:13, + from MultiSequence.cc:10: ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 88 | const int GetNumLayers() const { | ^~~~~ +In file included from Main.cc:12: +MultiSequence.h:24:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 24 | const int AutoDetectFileFormat (const char *filename) const; + | ^~~~~ ScoreMatrix.h:96:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 96 | const int GetNumRows() const { | ^~~~~ +ScoreMatrix.h:104:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 104 | const int GetNumCols() const { + | ^~~~~ MultiSequence.h:28:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 28 | const char ComputeAnnotation (const char *data, const int size) const; | ^~~~~ -ScoreMatrix.h:104:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 104 | const int GetNumCols() const { +MultiSequence.h:48:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 48 | const int GetNumSequences() const; + | ^~~~~ +MultiSequence.h:49:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 49 | const int GetLength() const; + | ^~~~~ +In file included from Types.h:12, + from Block.h:10, + from MultiSequence.h:13, + from MultiSequence.cc:10: +Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 100 | const int GetNumLayers() const { + | ^~~~~ +Matrix.h:108:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 108 | const int GetNumRows() const { + | ^~~~~ +Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 116 | const int GetNumCols() const { + | ^~~~~ +In file included from Main.cc:18: +Tree.h:44:5: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 44 | const bool GetIsLeaf() const; + | ^~~~~ +Tree.h:45:5: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 45 | const int GetNumSequences() const; + | ^~~~~ +In file included from MultiSequence.cc:10: +MultiSequence.h:24:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 24 | const int AutoDetectFileFormat (const char *filename) const; + | ^~~~~ +MultiSequence.h:28:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 28 | const char ComputeAnnotation (const char *data, const int size) const; | ^~~~~ MultiSequence.h:48:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 48 | const int GetNumSequences() const; @@ -971,6 +967,18 @@ MultiSequence.h:49:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 49 | const int GetLength() const; | ^~~~~ +MultiSequence.cc:86:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 86 | const int MultiSequence::GetNumSequences() const { + | ^~~~~ +MultiSequence.cc:94:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 94 | const int MultiSequence::GetLength() const { + | ^~~~~ +MultiSequence.cc:130:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 130 | const int MultiSequence::AutoDetectFileFormat (const char *filename) const { + | ^~~~~ +MultiSequence.cc:388:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 388 | const char MultiSequence::ComputeAnnotation (const char *data, const int size) const { + | ^~~~~ In file included from ScoreMatrix.h:12, from Matrix.h:13, from Types.h:12, @@ -997,8 +1005,7 @@ | ^~~~~ In file included from Types.h:12, from ProbModel.h:11, - from PairAligner.h:11, - from PairAligner.cc:9: + from ProbModel.cc:8: Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 100 | const int GetNumLayers() const { | ^~~~~ @@ -1008,9 +1015,111 @@ Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 116 | const int GetNumCols() const { | ^~~~~ +Main.cc: In function 'void RunLocalAligner(int, char**)': +Main.cc:339:22: warning: 'fasta' may be used uninitialized in this function [-Wmaybe-uninitialized] + 339 | seqs->WriteFASTA(fasta,block,result,start,end); + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -fdebug-prefix-map=/build/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Score.o Score.cc +g++ -g -O2 -fdebug-prefix-map=/build/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o ScoreMatrix.o ScoreMatrix.cc +g++ -g -O2 -fdebug-prefix-map=/build/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Sequence.o Sequence.cc +g++ -g -O2 -fdebug-prefix-map=/build/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o SparseMatrix.o SparseMatrix.cc +g++ -g -O2 -fdebug-prefix-map=/build/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Tree.o Tree.cc +g++ -g -O2 -fdebug-prefix-map=/build/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Utilities.o Utilities.cc +In file included from Sequence.h:11, + from ScoreMatrix.h:12, + from Matrix.h:13, + from Types.h:12, + from Block.h:10, + from Block.cc:6: +AlignedFragment.h: In constructor 'Block::Block(std::vector&, MultiSequence*, bool, Block*)': +AlignedFragment.h:66:66: warning: 'best_end' may be used uninitialized in this function [-Wmaybe-uninitialized] + 66 | {begin = f.begin; length = f.length; multiply = f.multiply;end = f.end;id = f.id;return *this;} + | ~~~~^~~~~~~ +Block.cc:58:49: note: 'best_end' was declared here + 58 | int best,best_id, best_pos, multi,end,bfrag,bk,best_end; + | ^~~~~~~~ +Block.cc:130:13: warning: 'bk' may be used uninitialized in this function [-Wmaybe-uninitialized] + 130 | bad[bfrag]=bk; + | ~~~~~~~~~~^~~ +Block.cc:130:7: warning: 'bfrag' may be used uninitialized in this function [-Wmaybe-uninitialized] + 130 | bad[bfrag]=bk; + | ^~~~~ +In file included from Sequence.h:11, + from ScoreMatrix.h:12, + from Matrix.h:13, + from Types.h:12, + from Block.h:10, + from Block.cc:6: +AlignedFragment.h:66:10: warning: 'best_pos' may be used uninitialized in this function [-Wmaybe-uninitialized] + 66 | {begin = f.begin; length = f.length; multiply = f.multiply;end = f.end;id = f.id;return *this;} + | ~~~~~~^~~~~~~~~ +Block.cc:58:20: note: 'best_pos' was declared here + 58 | int best,best_id, best_pos, multi,end,bfrag,bk,best_end; + | ^~~~~~~~ +In file included from Sequence.h:11, + from ScoreMatrix.h:12, + from Matrix.h:13, + from Types.h:12, + from Block.h:10, + from Block.cc:6: +AlignedFragment.h:66:77: warning: 'best_id' may be used uninitialized in this function [-Wmaybe-uninitialized] + 66 | {begin = f.begin; length = f.length; multiply = f.multiply;end = f.end;id = f.id;return *this;} + | ~~~^~~~~~ +Block.cc:58:11: note: 'best_id' was declared here + 58 | int best,best_id, best_pos, multi,end,bfrag,bk,best_end; + | ^~~~~~~ +In file included from Matrix.h:12, + from Tree.h:9, + from Tree.cc:6: +SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 57 | const int GetRowSize (int layer, int row) const; + | ^~~~~ +SparseMatrix.h:60:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 60 | const int GetNumLayers() const; + | ^~~~~ +SparseMatrix.h:61:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 61 | const int GetNumRows() const; + | ^~~~~ +SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 62 | const int GetNumCols() const; + | ^~~~~ +In file included from ScoreMatrix.h:12, + from ScoreMatrix.cc:7: +Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 51 | const int GetLength () const; + | ^~~~~ +Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 52 | const int GetID () const; + | ^~~~~ +In file included from ScoreMatrix.cc:7: +ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 88 | const int GetNumLayers() const { + | ^~~~~ +ScoreMatrix.h:96:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 96 | const int GetNumRows() const { + | ^~~~~ +ScoreMatrix.h:104:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 104 | const int GetNumCols() const { + | ^~~~~ +In file included from Matrix.h:12, + from Types.h:12, + from ProbModel.h:11, + from ScoreMatrix.cc:8: +SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 57 | const int GetRowSize (int layer, int row) const; + | ^~~~~ +SparseMatrix.h:60:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 60 | const int GetNumLayers() const; + | ^~~~~ +SparseMatrix.h:61:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 61 | const int GetNumRows() const; + | ^~~~~ +SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 62 | const int GetNumCols() const; + | ^~~~~ In file included from Types.h:12, from ProbModel.h:11, - from ProbModel.cc:8: + from ScoreMatrix.cc:8: Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 100 | const int GetNumLayers() const { | ^~~~~ @@ -1020,20 +1129,53 @@ Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 116 | const int GetNumCols() const { | ^~~~~ -MultiSequence.cc:86:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 86 | const int MultiSequence::GetNumSequences() const { - | ^~~~~ -MultiSequence.cc:94:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 94 | const int MultiSequence::GetLength() const { +In file included from Sequence.cc:8: +Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 51 | const int GetLength () const; + | ^~~~~ +Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 52 | const int GetID () const; + | ^~~~~ +Sequence.cc:121:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 121 | const int Sequence::GetLength () const { | ^~~~~ -MultiSequence.cc:130:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 130 | const int MultiSequence::AutoDetectFileFormat (const char *filename) const { +Sequence.cc:129:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 129 | const int Sequence::GetID () const { | ^~~~~ -In file included from Matrix.h:12, - from Types.h:12, - from Block.h:10, - from MultiSequence.h:13, - from Main.cc:12: +In file included from ScoreMatrix.h:12, + from Matrix.h:13, + from SparseMatrix.h:12, + from SparseMatrix.cc:6: +Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 51 | const int GetLength () const; + | ^~~~~ +Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 52 | const int GetID () const; + | ^~~~~ +In file included from Matrix.h:13, + from SparseMatrix.h:12, + from SparseMatrix.cc:6: +ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 88 | const int GetNumLayers() const { + | ^~~~~ +ScoreMatrix.h:96:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 96 | const int GetNumRows() const { + | ^~~~~ +ScoreMatrix.h:104:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 104 | const int GetNumCols() const { + | ^~~~~ +In file included from SparseMatrix.h:12, + from SparseMatrix.cc:6: +Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 100 | const int GetNumLayers() const { + | ^~~~~ +Matrix.h:108:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 108 | const int GetNumRows() const { + | ^~~~~ +Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 116 | const int GetNumCols() const { + | ^~~~~ +In file included from SparseMatrix.cc:6: SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 57 | const int GetRowSize (int layer, int row) const; | ^~~~~ @@ -1046,33 +1188,31 @@ SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 62 | const int GetNumCols() const; | ^~~~~ -In file included from Tree.h:10, +SparseMatrix.cc:199:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 199 | const int SparseMatrix::GetRowSize (int layer, int row) const { + | ^~~~~ +SparseMatrix.cc:209:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 209 | const int SparseMatrix::GetNumLayers() const { + | ^~~~~ +SparseMatrix.cc:217:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 217 | const int SparseMatrix::GetNumRows() const { + | ^~~~~ +SparseMatrix.cc:225:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 225 | const int SparseMatrix::GetNumCols() const { + | ^~~~~ +In file included from ScoreMatrix.h:12, + from Matrix.h:13, + from Tree.h:9, from Tree.cc:6: -MultiSequence.h:24:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 24 | const int AutoDetectFileFormat (const char *filename) const; - | ^~~~~ -MultiSequence.h:28:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 28 | const char ComputeAnnotation (const char *data, const int size) const; - | ^~~~~ -MultiSequence.h:48:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 48 | const int GetNumSequences() const; - | ^~~~~ -MultiSequence.h:49:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 49 | const int GetLength() const; - | ^~~~~ -In file included from GlobalAlign.h:12, - from GlobalAlign.cc:7: -MultiSequence.h:24:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 24 | const int AutoDetectFileFormat (const char *filename) const; +Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 51 | const int GetLength () const; | ^~~~~ -MultiSequence.h:28:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 28 | const char ComputeAnnotation (const char *data, const int size) const; +Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 52 | const int GetID () const; | ^~~~~ In file included from Matrix.h:13, - from Types.h:12, - from Block.h:10, - from MultiSequence.h:13, - from Main.cc:12: + from Tree.h:9, + from Tree.cc:6: ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 88 | const int GetNumLayers() const { | ^~~~~ @@ -1082,23 +1222,8 @@ ScoreMatrix.h:104:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 104 | const int GetNumCols() const { | ^~~~~ -MultiSequence.h:48:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 48 | const int GetNumSequences() const; - | ^~~~~ -MultiSequence.h:49:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 49 | const int GetLength() const; - | ^~~~~ -In file included from Tree.cc:6: -Tree.h:44:5: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 44 | const bool GetIsLeaf() const; - | ^~~~~ -Tree.h:45:5: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 45 | const int GetNumSequences() const; - | ^~~~~ -In file included from Types.h:12, - from Block.h:10, - from MultiSequence.h:13, - from Main.cc:12: +In file included from Tree.h:9, + from Tree.cc:6: Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 100 | const int GetNumLayers() const { | ^~~~~ @@ -1108,16 +1233,8 @@ Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 116 | const int GetNumCols() const { | ^~~~~ -Tree.cc:34:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 34 | const bool Tree::TreeNode::GetIsLeaf() const { - | ^~~~~ -Tree.cc:42:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 42 | const int Tree::TreeNode::GetNumSequences() const { - | ^~~~~ -MultiSequence.cc:388:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 388 | const char MultiSequence::ComputeAnnotation (const char *data, const int size) const { - | ^~~~~ -In file included from Main.cc:12: +In file included from Tree.h:10, + from Tree.cc:6: MultiSequence.h:24:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 24 | const int AutoDetectFileFormat (const char *filename) const; | ^~~~~ @@ -1130,64 +1247,19 @@ MultiSequence.h:49:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 49 | const int GetLength() const; | ^~~~~ -Block.cc: In constructor 'Block::Block(std::vector&, MultiSequence*, bool, Block*)': -Block.cc:58:36: warning: variable 'end' set but not used [-Wunused-but-set-variable] - 58 | int best,best_id, best_pos, multi,end,bfrag,bk,best_end; - | ^~~ -In file included from Main.cc:18: +In file included from Tree.cc:6: Tree.h:44:5: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 44 | const bool GetIsLeaf() const; | ^~~~~ Tree.h:45:5: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 45 | const int GetNumSequences() const; | ^~~~~ -Main.cc: In function 'void RunLocalAligner(int, char**)': -Main.cc:339:22: warning: 'fasta' may be used uninitialized in this function [-Wmaybe-uninitialized] - 339 | seqs->WriteFASTA(fasta,block,result,start,end); - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from Sequence.h:11, - from ScoreMatrix.h:12, - from Matrix.h:13, - from Types.h:12, - from Block.h:10, - from Block.cc:6: -AlignedFragment.h: In constructor 'Block::Block(std::vector&, MultiSequence*, bool, Block*)': -AlignedFragment.h:66:66: warning: 'best_end' may be used uninitialized in this function [-Wmaybe-uninitialized] - 66 | {begin = f.begin; length = f.length; multiply = f.multiply;end = f.end;id = f.id;return *this;} - | ~~~~^~~~~~~ -Block.cc:58:49: note: 'best_end' was declared here - 58 | int best,best_id, best_pos, multi,end,bfrag,bk,best_end; - | ^~~~~~~~ -Block.cc:130:13: warning: 'bk' may be used uninitialized in this function [-Wmaybe-uninitialized] - 130 | bad[bfrag]=bk; - | ~~~~~~~~~~^~~ -Block.cc:130:7: warning: 'bfrag' may be used uninitialized in this function [-Wmaybe-uninitialized] - 130 | bad[bfrag]=bk; - | ^~~~~ -In file included from Sequence.h:11, - from ScoreMatrix.h:12, - from Matrix.h:13, - from Types.h:12, - from Block.h:10, - from Block.cc:6: -AlignedFragment.h:66:10: warning: 'best_pos' may be used uninitialized in this function [-Wmaybe-uninitialized] - 66 | {begin = f.begin; length = f.length; multiply = f.multiply;end = f.end;id = f.id;return *this;} - | ~~~~~~^~~~~~~~~ -Block.cc:58:20: note: 'best_pos' was declared here - 58 | int best,best_id, best_pos, multi,end,bfrag,bk,best_end; - | ^~~~~~~~ -In file included from Sequence.h:11, - from ScoreMatrix.h:12, - from Matrix.h:13, - from Types.h:12, - from Block.h:10, - from Block.cc:6: -AlignedFragment.h:66:77: warning: 'best_id' may be used uninitialized in this function [-Wmaybe-uninitialized] - 66 | {begin = f.begin; length = f.length; multiply = f.multiply;end = f.end;id = f.id;return *this;} - | ~~~^~~~~~ -Block.cc:58:11: note: 'best_id' was declared here - 58 | int best,best_id, best_pos, multi,end,bfrag,bk,best_end; - | ^~~~~~~ +Tree.cc:34:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 34 | const bool Tree::TreeNode::GetIsLeaf() const { + | ^~~~~ +Tree.cc:42:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 42 | const int Tree::TreeNode::GetNumSequences() const { + | ^~~~~ g++ -g -O2 -fdebug-prefix-map=/build/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -lm AlignedFragment.o Assert.o Block.o Consistency.o GlobalAlign.o LocalAlign.o Main.o PairAligner.o Matrix.o MultiSequence.o ProbModel.o Score.o ScoreMatrix.o Sequence.o SparseMatrix.o Tree.o Utilities.o -o proda -Wl,-z,relro -Wl,-z,now make[1]: Leaving directory '/build/proda-1.0' dh_auto_test @@ -1212,20 +1284,21 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'proda' in '../proda_1.0-13_i386.deb'. dpkg-deb: building package 'proda-dbgsym' in '../proda-dbgsym_1.0-13_i386.deb'. +dpkg-deb: building package 'proda' in '../proda_1.0-13_i386.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../proda_1.0-13_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -I: copying local configuration +I: user script /srv/workspace/pbuilder/17593/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/17593/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/2582 and its subdirectories -I: Current time: Tue Jul 19 14:23:46 -12 2022 -I: pbuilder-time-stamp: 1658283826 +I: removing directory /srv/workspace/pbuilder/17593 and its subdirectories +I: Current time: Thu Jun 17 10:04:36 +14 2021 +I: pbuilder-time-stamp: 1623873876