Diff of the two buildlogs:
--
--- b1/build.log 2023-05-17 22:02:19.667915285 +0000
+++ b2/build.log 2023-05-17 22:12:19.549619326 +0000
@@ -1,6 +1,6 @@
I: pbuilder: network access will be disabled during build
-I: Current time: Wed May 17 09:59:15 -12 2023
-I: pbuilder-time-stamp: 1684360755
+I: Current time: Thu May 18 12:02:30 +14 2023
+I: pbuilder-time-stamp: 1684360950
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz]
I: copying local configuration
@@ -16,7 +16,7 @@
I: copying [./proda_1.0.orig.tar.gz]
I: copying [./proda_1.0-13.debian.tar.xz]
I: Extracting source
-gpgv: Signature made Mon Nov 23 08:10:25 2020 -12
+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
@@ -33,135 +33,167 @@
dpkg-source: info: applying hardening.patch
I: Not using root during the build.
I: Installing the build-deps
-I: user script /srv/workspace/pbuilder/9665/tmp/hooks/D02_print_environment starting
+I: user script /srv/workspace/pbuilder/23903/tmp/hooks/D01_modify_environment starting
+debug: Running on virt32a.
+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 May 18 12:03 /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/23903/tmp/hooks/D01_modify_environment finished
+I: user script /srv/workspace/pbuilder/23903/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='armhf'
- DEBIAN_FRONTEND='noninteractive'
- DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=5 '
- DISTRIBUTION='bookworm'
- HOME='/root'
- HOST_ARCH='armhf'
+ BASH=/bin/sh
+ BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath
+ BASH_ALIASES=()
+ BASH_ARGC=()
+ BASH_ARGV=()
+ BASH_CMDS=()
+ BASH_LINENO=([0]="12" [1]="0")
+ BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:.
+ BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment")
+ BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf")
+ BASH_VERSION='5.2.15(1)-release'
+ BUILDDIR=/build
+ BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
+ BUILDUSERNAME=pbuilder2
+ BUILD_ARCH=armhf
+ DEBIAN_FRONTEND=noninteractive
+ DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 '
+ DIRSTACK=()
+ DISTRIBUTION=bookworm
+ EUID=0
+ FUNCNAME=([0]="Echo" [1]="main")
+ GROUPS=()
+ HOME=/root
+ HOSTNAME=i-capture-the-hostname
+ HOSTTYPE=arm
+ HOST_ARCH=armhf
IFS='
'
- INVOCATION_ID='f59978e34ab6463fb58b5bc1f37f82a3'
- 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='9665'
- PS1='# '
- PS2='> '
+ INVOCATION_ID=cafae018f7b44681866119c538ef2208
+ LANG=C
+ LANGUAGE=it_CH:it
+ LC_ALL=C
+ MACHTYPE=arm-unknown-linux-gnueabihf
+ MAIL=/var/mail/root
+ OPTERR=1
+ OPTIND=1
+ OSTYPE=linux-gnueabihf
+ 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=23903
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.xiRfUhxc/pbuilderrc_iGoH --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.xiRfUhxc/b1 --logfile b1/build.log proda_1.0-13.dsc'
- SUDO_GID='114'
- SUDO_UID='109'
- SUDO_USER='jenkins'
- TERM='unknown'
- TZ='/usr/share/zoneinfo/Etc/GMT+12'
- USER='root'
- _='/usr/bin/systemd-run'
- http_proxy='http://10.0.0.15:3142/'
+ 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.xiRfUhxc/pbuilderrc_XdzV --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.xiRfUhxc/b2 --logfile b2/build.log --extrapackages usrmerge proda_1.0-13.dsc'
+ SUDO_GID=113
+ SUDO_UID=107
+ SUDO_USER=jenkins
+ TERM=unknown
+ TZ=/usr/share/zoneinfo/Etc/GMT-14
+ UID=0
+ USER=root
+ _='I: set'
+ http_proxy=http://10.0.0.15:3142/
I: uname -a
- Linux ff64a 5.10.0-23-arm64 #1 SMP Debian 5.10.179-1 (2023-05-12) aarch64 GNU/Linux
+ Linux i-capture-the-hostname 5.10.0-23-armmp-lpae #1 SMP Debian 5.10.179-1 (2023-05-12) armv7l GNU/Linux
I: ls -l /bin
total 5072
- -rwxr-xr-x 1 root root 838488 Apr 23 09:24 bash
- -rwxr-xr-x 3 root root 67144 Sep 18 2022 bunzip2
- -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzcat
- lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff
- -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff
- lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep
- -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe
- lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep
- -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep
- -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzip2
- -rwxr-xr-x 1 root root 67112 Sep 18 2022 bzip2recover
- lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore
- -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore
- -rwxr-xr-x 1 root root 67632 Sep 20 2022 cat
- -rwxr-xr-x 1 root root 67676 Sep 20 2022 chgrp
- -rwxr-xr-x 1 root root 67644 Sep 20 2022 chmod
- -rwxr-xr-x 1 root root 67684 Sep 20 2022 chown
- -rwxr-xr-x 1 root root 133532 Sep 20 2022 cp
- -rwxr-xr-x 1 root root 132868 Jan 5 01:20 dash
- -rwxr-xr-x 1 root root 133220 Sep 20 2022 date
- -rwxr-xr-x 1 root root 67732 Sep 20 2022 dd
- -rwxr-xr-x 1 root root 68104 Sep 20 2022 df
- -rwxr-xr-x 1 root root 133632 Sep 20 2022 dir
- -rwxr-xr-x 1 root root 59128 Mar 22 21:02 dmesg
- lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname
- lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname
- -rwxr-xr-x 1 root root 67560 Sep 20 2022 echo
- -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep
- -rwxr-xr-x 1 root root 67548 Sep 20 2022 false
- -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep
- -rwxr-xr-x 1 root root 55748 Mar 22 21:02 findmnt
- -rwsr-xr-x 1 root root 26208 Mar 22 20:15 fusermount
- -rwxr-xr-x 1 root root 128608 Jan 24 02:43 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 64220 Apr 9 2022 gzip
- -rwxr-xr-x 1 root root 67032 Dec 19 01:33 hostname
- -rwxr-xr-x 1 root root 67720 Sep 20 2022 ln
- -rwxr-xr-x 1 root root 35132 Mar 22 21:51 login
- -rwxr-xr-x 1 root root 133632 Sep 20 2022 ls
- -rwxr-xr-x 1 root root 136808 Mar 22 21:02 lsblk
- -rwxr-xr-x 1 root root 67800 Sep 20 2022 mkdir
- -rwxr-xr-x 1 root root 67764 Sep 20 2022 mknod
- -rwxr-xr-x 1 root root 67596 Sep 20 2022 mktemp
- -rwxr-xr-x 1 root root 38504 Mar 22 21:02 more
- -rwsr-xr-x 1 root root 38496 Mar 22 21:02 mount
- -rwxr-xr-x 1 root root 9824 Mar 22 21:02 mountpoint
- -rwxr-xr-x 1 root root 133532 Sep 20 2022 mv
- lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname
- lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5
- -rwxr-xr-x 1 root root 67608 Sep 20 2022 pwd
- lrwxrwxrwx 1 root root 4 Apr 23 09:24 rbash -> bash
- -rwxr-xr-x 1 root root 67600 Sep 20 2022 readlink
- -rwxr-xr-x 1 root root 67672 Sep 20 2022 rm
- -rwxr-xr-x 1 root root 67600 Sep 20 2022 rmdir
- -rwxr-xr-x 1 root root 67400 Nov 2 2022 run-parts
- -rwxr-xr-x 1 root root 133372 Jan 5 07:55 sed
- lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash
- -rwxr-xr-x 1 root root 67584 Sep 20 2022 sleep
- -rwxr-xr-x 1 root root 67644 Sep 20 2022 stty
- -rwsr-xr-x 1 root root 50800 Mar 22 21:02 su
- -rwxr-xr-x 1 root root 67584 Sep 20 2022 sync
- -rwxr-xr-x 1 root root 336764 Apr 6 02:25 tar
- -rwxr-xr-x 1 root root 67144 Nov 2 2022 tempfile
- -rwxr-xr-x 1 root root 133224 Sep 20 2022 touch
- -rwxr-xr-x 1 root root 67548 Sep 20 2022 true
- -rwxr-xr-x 1 root root 9768 Mar 22 20:15 ulockmgr_server
- -rwsr-xr-x 1 root root 22108 Mar 22 21:02 umount
- -rwxr-xr-x 1 root root 67572 Sep 20 2022 uname
- -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress
- -rwxr-xr-x 1 root root 133632 Sep 20 2022 vdir
- -rwxr-xr-x 1 root root 42608 Mar 22 21:02 wdctl
- lrwxrwxrwx 1 root root 8 Dec 19 01:33 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 6460 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 8103 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/9665/tmp/hooks/D02_print_environment finished
+ -rwxr-xr-x 1 root root 838488 Apr 24 11:24 bash
+ -rwxr-xr-x 3 root root 67144 Sep 19 2022 bunzip2
+ -rwxr-xr-x 3 root root 67144 Sep 19 2022 bzcat
+ lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff
+ -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff
+ lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep
+ -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe
+ lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep
+ -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep
+ -rwxr-xr-x 3 root root 67144 Sep 19 2022 bzip2
+ -rwxr-xr-x 1 root root 67112 Sep 19 2022 bzip2recover
+ lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore
+ -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore
+ -rwxr-xr-x 1 root root 67632 Sep 21 2022 cat
+ -rwxr-xr-x 1 root root 67676 Sep 21 2022 chgrp
+ -rwxr-xr-x 1 root root 67644 Sep 21 2022 chmod
+ -rwxr-xr-x 1 root root 67684 Sep 21 2022 chown
+ -rwxr-xr-x 1 root root 133532 Sep 21 2022 cp
+ -rwxr-xr-x 1 root root 132868 Jan 6 03:20 dash
+ -rwxr-xr-x 1 root root 133220 Sep 21 2022 date
+ -rwxr-xr-x 1 root root 67732 Sep 21 2022 dd
+ -rwxr-xr-x 1 root root 68104 Sep 21 2022 df
+ -rwxr-xr-x 1 root root 133632 Sep 21 2022 dir
+ -rwxr-xr-x 1 root root 59128 Mar 23 23:02 dmesg
+ lrwxrwxrwx 1 root root 8 Dec 20 03:33 dnsdomainname -> hostname
+ lrwxrwxrwx 1 root root 8 Dec 20 03:33 domainname -> hostname
+ -rwxr-xr-x 1 root root 67560 Sep 21 2022 echo
+ -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep
+ -rwxr-xr-x 1 root root 67548 Sep 21 2022 false
+ -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep
+ -rwxr-xr-x 1 root root 55748 Mar 23 23:02 findmnt
+ -rwsr-xr-x 1 root root 26208 Mar 23 22:15 fusermount
+ -rwxr-xr-x 1 root root 128608 Jan 25 04:43 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 64220 Apr 10 2022 gzip
+ -rwxr-xr-x 1 root root 67032 Dec 20 03:33 hostname
+ -rwxr-xr-x 1 root root 67720 Sep 21 2022 ln
+ -rwxr-xr-x 1 root root 35132 Mar 23 23:51 login
+ -rwxr-xr-x 1 root root 133632 Sep 21 2022 ls
+ -rwxr-xr-x 1 root root 136808 Mar 23 23:02 lsblk
+ -rwxr-xr-x 1 root root 67800 Sep 21 2022 mkdir
+ -rwxr-xr-x 1 root root 67764 Sep 21 2022 mknod
+ -rwxr-xr-x 1 root root 67596 Sep 21 2022 mktemp
+ -rwxr-xr-x 1 root root 38504 Mar 23 23:02 more
+ -rwsr-xr-x 1 root root 38496 Mar 23 23:02 mount
+ -rwxr-xr-x 1 root root 9824 Mar 23 23:02 mountpoint
+ -rwxr-xr-x 1 root root 133532 Sep 21 2022 mv
+ lrwxrwxrwx 1 root root 8 Dec 20 03:33 nisdomainname -> hostname
+ lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5
+ -rwxr-xr-x 1 root root 67608 Sep 21 2022 pwd
+ lrwxrwxrwx 1 root root 4 Apr 24 11:24 rbash -> bash
+ -rwxr-xr-x 1 root root 67600 Sep 21 2022 readlink
+ -rwxr-xr-x 1 root root 67672 Sep 21 2022 rm
+ -rwxr-xr-x 1 root root 67600 Sep 21 2022 rmdir
+ -rwxr-xr-x 1 root root 67400 Nov 3 2022 run-parts
+ -rwxr-xr-x 1 root root 133372 Jan 6 09:55 sed
+ lrwxrwxrwx 1 root root 9 May 18 12:03 sh -> /bin/bash
+ -rwxr-xr-x 1 root root 67584 Sep 21 2022 sleep
+ -rwxr-xr-x 1 root root 67644 Sep 21 2022 stty
+ -rwsr-xr-x 1 root root 50800 Mar 23 23:02 su
+ -rwxr-xr-x 1 root root 67584 Sep 21 2022 sync
+ -rwxr-xr-x 1 root root 336764 Apr 7 04:25 tar
+ -rwxr-xr-x 1 root root 67144 Nov 3 2022 tempfile
+ -rwxr-xr-x 1 root root 133224 Sep 21 2022 touch
+ -rwxr-xr-x 1 root root 67548 Sep 21 2022 true
+ -rwxr-xr-x 1 root root 9768 Mar 23 22:15 ulockmgr_server
+ -rwsr-xr-x 1 root root 22108 Mar 23 23:02 umount
+ -rwxr-xr-x 1 root root 67572 Sep 21 2022 uname
+ -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress
+ -rwxr-xr-x 1 root root 133632 Sep 21 2022 vdir
+ -rwxr-xr-x 1 root root 42608 Mar 23 23:02 wdctl
+ lrwxrwxrwx 1 root root 8 Dec 20 03:33 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 6460 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 8103 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/23903/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
@@ -227,7 +259,7 @@
Get: 28 http://deb.debian.org/debian bookworm/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 29 http://deb.debian.org/debian bookworm/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get: 30 http://deb.debian.org/debian bookworm/main armhf debhelper all 13.11.4 [942 kB]
-Fetched 18.0 MB in 2s (10.8 MB/s)
+Fetched 18.0 MB in 23s (769 kB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package sensible-utils.
(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 ... 19329 files and directories currently installed.)
@@ -361,8 +393,19 @@
Writing extended state information...
Building tag database...
-> Finished parsing the build-deps
+Reading package lists...
+Building dependency tree...
+Reading state information...
+usrmerge is already the newest version (35).
+0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
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 && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../proda_1.0-13_source.changes
+I: user script /srv/workspace/pbuilder/23903/tmp/hooks/A99_set_merged_usr starting
+Re-configuring usrmerge...
+removed '/etc/unsupported-skip-usrmerge-conversion'
+The system has been successfully converted.
+I: user script /srv/workspace/pbuilder/23903/tmp/hooks/A99_set_merged_usr finished
+hostname: Name or service not known
+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 && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../proda_1.0-13_source.changes
dpkg-buildpackage: info: source package proda
dpkg-buildpackage: info: source version 1.0-13
dpkg-buildpackage: info: source distribution unstable
@@ -372,7 +415,7 @@
debian/rules clean
dh clean
dh_auto_clean
- make -j5 clean
+ make -j4 clean
make[1]: Entering directory '/build/proda-1.0'
rm -f *.o
make[1]: Leaving directory '/build/proda-1.0'
@@ -383,14 +426,13 @@
dh_autoreconf
dh_auto_configure
dh_auto_build
- make -j5 "INSTALL=install --strip-program=true"
+ make -j4 "INSTALL=install --strip-program=true"
make[1]: Entering directory '/build/proda-1.0'
g++ -g -O2 -ffile-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 -ffile-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
g++ -g -O2 -ffile-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 Block.o Block.cc
g++ -g -O2 -ffile-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 Consistency.o Consistency.cc
g++ -g -O2 -ffile-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 GlobalAlign.o GlobalAlign.cc
-g++ -g -O2 -ffile-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 LocalAlign.o LocalAlign.cc
In file included from Matrix.h:12,
from GlobalAlign.h:11,
from GlobalAlign.cc:7:
@@ -407,21 +449,6 @@
62 | const int GetNumCols() const;
| ^~~~~
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 Types.h:12,
from Block.h:10,
from Block.cc:6:
@@ -454,28 +481,6 @@
ScoreMatrix.h:104:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers]
104 | const int GetNumCols() const {
| ^~~~~
-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 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;
- | ^~~~~
-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 ScoreMatrix.h:12,
from Matrix.h:13,
from SparseMatrix.h:12,
@@ -487,6 +492,15 @@
Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers]
52 | const int GetID () const;
| ^~~~~
+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 {
+ | ^~~~~
ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers]
88 | const int GetNumLayers() const {
| ^~~~~
@@ -505,6 +519,19 @@
Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers]
116 | const int GetNumCols() 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;
+ | ^~~~~
+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;
+ | ^~~~~
SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers]
57 | const int GetRowSize (int layer, int row) const;
| ^~~~~
@@ -560,60 +587,23 @@
MultiSequence.h:49:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers]
49 | const int GetLength() const;
| ^~~~~
-In file included from ScoreMatrix.h:12,
- from Matrix.h:13:
-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;
- | ^~~~~
-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 {
+g++ -g -O2 -ffile-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 LocalAlign.o LocalAlign.cc
+g++ -g -O2 -ffile-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 Main.o Main.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;
| ^~~~~
-Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers]
- 100 | const int GetNumLayers() const {
+SparseMatrix.h:60:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers]
+ 60 | const int GetNumLayers() const;
| ^~~~~
-Matrix.h:108:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers]
- 108 | const int GetNumRows() const {
+SparseMatrix.h:61:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers]
+ 61 | const int GetNumRows() const;
| ^~~~~
-Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers]
- 116 | const int GetNumCols() const {
+SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers]
+ 62 | const int GetNumCols() const;
| ^~~~~
-g++ -g -O2 -ffile-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 Main.o Main.cc
-LocalAlign.cc: In static member function 'static AlignedFragment* LocalAlign::ComputeLocalAlignment(const Sequence&, const Sequence&, const Matrix&, float*)':
-LocalAlign.cc:68:17: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
- 68 | delete nullX;
- | ^~~~~
-LocalAlign.cc:22:38: note: returned from 'void* operator new [](std::size_t)'
- 22 | float *nullX = new float[rows];
- | ^
-LocalAlign.cc:69:17: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
- 69 | delete nullY;
- | ^~~~~
-LocalAlign.cc:23:38: note: returned from 'void* operator new [](std::size_t)'
- 23 | float *nullY = new float[cols];
- | ^
-LocalAlign.cc:73:25: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
- 73 | delete traceback;
- | ^~~~~~~~~
-LocalAlign.cc:19:65: note: returned from 'void* operator new [](std::size_t)'
- 19 | TracebackType *traceback = new TracebackType[rows * cols];
- | ^
-LocalAlign.cc:121:10: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
- 121 | delete s2;
- | ^~
-LocalAlign.cc:99:34: note: returned from 'void* operator new [](std::size_t)'
- 99 | int *s2 = new int[besty - c + 1];
- | ^
-g++ -g -O2 -ffile-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 -ffile-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
GlobalAlign.cc: In static member function 'static float GlobalAlign::ComputeAlignmentScore(const MultiSequence&, int, SparseMatrix**)':
GlobalAlign.cc:226:10: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
226 | delete scores;
@@ -621,7 +611,7 @@
GlobalAlign.cc:191:35: note: returned from 'void* operator new [](std::size_t)'
191 | float *scores = new float[length];
| ^
-g++ -g -O2 -ffile-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 -ffile-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
In file included from Sequence.h:11:
In constructor 'Fragment::Fragment(int, int, int, int)',
inlined from 'Block::Block(std::vector<AlignedFragment>&, MultiSequence*, bool, Block*)' at Block.cc:104:51:
@@ -692,19 +682,31 @@
Block.cc:60:41: note: returned from 'void* operator new [](std::size_t)'
60 | int *bad = new int[afrags.size()];//fragments that cannot be a seed
| ^
-In file included from Matrix.h:12,
- 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;
+In file included from ScoreMatrix.h:12,
+ from Matrix.h:13:
+Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers]
+ 51 | const int GetLength () const;
| ^~~~~
-SparseMatrix.h:60:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers]
- 60 | const int GetNumLayers() const;
+Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers]
+ 52 | const int GetID () const;
| ^~~~~
-SparseMatrix.h:61:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers]
- 61 | const int GetNumRows() const;
+ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers]
+ 88 | const int GetNumLayers() const {
| ^~~~~
-SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers]
- 62 | const int GetNumCols() 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.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 MultiSequence.h:12,
from Main.cc:12:
@@ -714,6 +716,13 @@
Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers]
52 | const int GetID () const;
| ^~~~~
+Block.cc: In member function 'int Block::AdjustAFragmentList(AVECT&, Matrix*, float)':
+Block.cc:369:16: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
+ 369 | delete used;
+ | ^~~~
+Block.cc:331:34: note: returned from 'void* operator new [](std::size_t)'
+ 331 | int *used = new int[asize];
+ | ^
In file included from Matrix.h:12,
from Types.h:12,
from Block.h:10,
@@ -768,6 +777,38 @@
Tree.h:45:5: warning: type qualifiers ignored on function return type [-Wignored-qualifiers]
45 | const int GetNumSequences() const;
| ^~~~~
+LocalAlign.cc: In static member function 'static AlignedFragment* LocalAlign::ComputeLocalAlignment(const Sequence&, const Sequence&, const Matrix&, float*)':
+LocalAlign.cc:68:17: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
+ 68 | delete nullX;
+ | ^~~~~
+LocalAlign.cc:22:38: note: returned from 'void* operator new [](std::size_t)'
+ 22 | float *nullX = new float[rows];
+ | ^
+LocalAlign.cc:69:17: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
+ 69 | delete nullY;
+ | ^~~~~
+LocalAlign.cc:23:38: note: returned from 'void* operator new [](std::size_t)'
+ 23 | float *nullY = new float[cols];
+ | ^
+LocalAlign.cc:73:25: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
+ 73 | delete traceback;
+ | ^~~~~~~~~
+LocalAlign.cc:19:65: note: returned from 'void* operator new [](std::size_t)'
+ 19 | TracebackType *traceback = new TracebackType[rows * cols];
+ | ^
+LocalAlign.cc:121:10: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
+ 121 | delete s2;
+ | ^~
+LocalAlign.cc:99:34: note: returned from 'void* operator new [](std::size_t)'
+ 99 | int *s2 = new int[besty - c + 1];
+ | ^
+Block.cc: In member function 'int Block::AdjustAFragmentList(AVECT&, int, Matrix*, float)':
+Block.cc:426:16: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
+ 426 | delete used;
+ | ^~~~
+Block.cc:387:34: note: returned from 'void* operator new [](std::size_t)'
+ 387 | int *used = new int[asize];
+ | ^
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]
@@ -776,13 +817,7 @@
Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers]
52 | const int GetID () const;
| ^~~~~
-Block.cc: In member function 'int Block::AdjustAFragmentList(AVECT&, Matrix*, float)':
-Block.cc:369:16: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
- 369 | delete used;
- | ^~~~
-Block.cc:331:34: note: returned from 'void* operator new [](std::size_t)'
- 331 | int *used = new int[asize];
- | ^
+g++ -g -O2 -ffile-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
In file included from Matrix.h:12,
from Types.h:12,
from ProbModel.h:11,
@@ -818,13 +853,100 @@
Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers]
116 | const int GetNumCols() const {
| ^~~~~
-Block.cc: In member function 'int Block::AdjustAFragmentList(AVECT&, int, Matrix*, float)':
-Block.cc:426:16: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
- 426 | delete used;
- | ^~~~
-Block.cc:387:34: note: returned from 'void* operator new [](std::size_t)'
- 387 | int *used = new int[asize];
- | ^
+g++ -g -O2 -ffile-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
+Main.cc: In function 'void RunLocalAligner(int, char**)':
+Main.cc:339:57: warning: 'fasta' may be used uninitialized [-Wmaybe-uninitialized]
+ 339 | seqs->WriteFASTA(fasta,block,result,start,end);
+ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+Main.cc:214:9: note: 'fasta' was declared here
+ 214 | FILE *fasta;
+ | ^~~~~
+Main.cc:291:34: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
+ 291 | delete used;
+ | ^~~~
+Main.cc:284:48: note: returned from 'void* operator new [](std::size_t)'
+ 284 | int *used = new int[m];
+ | ^
+In file included from Matrix.h:12,
+ 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;
+ | ^~~~~
+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;
+ | ^~~~~
+Main.cc: In function 'int main(int, char**)':
+Main.cc:111:10: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
+ 111 | delete filenames;
+ | ^~~~~~~~~
+Main.cc:61:38: note: returned from 'void* operator new [](std::size_t)'
+ 61 | string *filenames = new string[argc];
+ | ^
+g++ -g -O2 -ffile-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
+PairAligner.cc: In member function 'void PairAligner::ConsistencyCheck(AVECT&)':
+PairAligner.cc:178:64: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
+ 178 | delete l_map;
+ | ^~~~~
+PairAligner.cc:169:98: note: returned from 'void* operator new [](std::size_t)'
+ 169 | int *l_map = new int[(xLen+1)* (yLen + 1)];
+ | ^
+PairAligner.cc: In member function 'void PairAligner::FastPairAlign(AVECT&)':
+PairAligner.cc:206:24: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
+ 206 | delete s1;delete s2;
+ | ^~
+PairAligner.cc:200:39: note: returned from 'void* operator new [](std::size_t)'
+ 200 | int *s1 = new int[xLen];
+ | ^
+PairAligner.cc:206:34: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
+ 206 | delete s1;delete s2;
+ | ^~
+PairAligner.cc:201:39: note: returned from 'void* operator new [](std::size_t)'
+ 201 | int *s2 = new int[xLen];
+ | ^
+PairAligner.cc: In member function 'void PairAligner::PairAlign(AVECT&)':
+PairAligner.cc:281:24: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
+ 281 | delete s1;delete s2;
+ | ^~
+PairAligner.cc:275:39: note: returned from 'void* operator new [](std::size_t)'
+ 275 | int *s1 = new int[xLen];
+ | ^
+PairAligner.cc:281:34: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
+ 281 | delete s1;delete s2;
+ | ^~
+PairAligner.cc:276:39: note: returned from 'void* operator new [](std::size_t)'
+ 276 | int *s2 = new int[xLen];
+ | ^
+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;
+ | ^~~~~
+g++ -g -O2 -ffile-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
+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;
+ | ^~~~~
+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 Matrix.h:13:
Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers]
@@ -862,27 +984,6 @@
Matrix.cc:186:13: warning: variable 'pos' set but not used [-Wunused-but-set-variable]
186 | int pos = 0;
| ^~~
-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;
- | ^~~~~
-Main.cc: In function 'void RunLocalAligner(int, char**)':
-Main.cc:339:57: warning: 'fasta' may be used uninitialized [-Wmaybe-uninitialized]
- 339 | seqs->WriteFASTA(fasta,block,result,start,end);
- | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-Main.cc:214:9: note: 'fasta' was declared here
- 214 | FILE *fasta;
- | ^~~~~
-Main.cc:291:34: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
- 291 | delete used;
- | ^~~~
-Main.cc:284:48: note: returned from 'void* operator new [](std::size_t)'
- 284 | int *used = new int[m];
- | ^
In file included from Matrix.h:12,
from Types.h:12,
from Block.h:10,
@@ -942,87 +1043,7 @@
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 {
| ^~~~~
-g++ -g -O2 -ffile-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
-PairAligner.cc: In member function 'void PairAligner::ConsistencyCheck(AVECT&)':
-PairAligner.cc:178:64: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
- 178 | delete l_map;
- | ^~~~~
-PairAligner.cc:169:98: note: returned from 'void* operator new [](std::size_t)'
- 169 | int *l_map = new int[(xLen+1)* (yLen + 1)];
- | ^
-g++ -g -O2 -ffile-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
-Main.cc: In function 'int main(int, char**)':
-Main.cc:111:10: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
- 111 | delete filenames;
- | ^~~~~~~~~
-Main.cc:61:38: note: returned from 'void* operator new [](std::size_t)'
- 61 | string *filenames = new string[argc];
- | ^
-PairAligner.cc: In member function 'void PairAligner::FastPairAlign(AVECT&)':
-PairAligner.cc:206:24: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
- 206 | delete s1;delete s2;
- | ^~
-PairAligner.cc:200:39: note: returned from 'void* operator new [](std::size_t)'
- 200 | int *s1 = new int[xLen];
- | ^
-PairAligner.cc:206:34: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
- 206 | delete s1;delete s2;
- | ^~
-PairAligner.cc:201:39: note: returned from 'void* operator new [](std::size_t)'
- 201 | int *s2 = new int[xLen];
- | ^
g++ -g -O2 -ffile-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
-PairAligner.cc: In member function 'void PairAligner::PairAlign(AVECT&)':
-PairAligner.cc:281:24: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
- 281 | delete s1;delete s2;
- | ^~
-PairAligner.cc:275:39: note: returned from 'void* operator new [](std::size_t)'
- 275 | int *s1 = new int[xLen];
- | ^
-PairAligner.cc:281:34: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
- 281 | delete s1;delete s2;
- | ^~
-PairAligner.cc:276:39: note: returned from 'void* operator new [](std::size_t)'
- 276 | int *s2 = new int[xLen];
- | ^
-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;
- | ^~~~~
-SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers]
- 62 | const int GetNumCols() const;
- | ^~~~~
-g++ -g -O2 -ffile-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 -ffile-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
-MultiSequence.cc: In member function 'void MultiSequence::WriteFASTA(FILE*, Block*, MultiSequence*, int, int)':
-MultiSequence.cc:757:16: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
- 757 | delete map;
- | ^~~
-MultiSequence.cc:702:40: note: returned from 'void* operator new [](std::size_t)'
- 702 | int *map = new int[numSequences];
- | ^
-MultiSequence.cc: In member function 'void MultiSequence::FindBlock(Block&, int&, int&, int)':
-MultiSequence.cc:633:16: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
- 633 | delete map;
- | ^~~
-MultiSequence.cc:534:50: note: returned from 'void* operator new [](std::size_t)'
- 534 | int **map = new pint[numSequences];
- | ^
-MultiSequence.cc:634:16: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
- 634 | delete data;
- | ^~~~
-MultiSequence.cc:513:51: note: returned from 'void* operator new [](std::size_t)'
- 513 | const char **data = new pchar[numSequences];
- | ^
In file included from ScoreMatrix.h:12,
from Matrix.h:13:
Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers]
@@ -1049,7 +1070,28 @@
Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers]
116 | const int GetNumCols() const {
| ^~~~~
-g++ -g -O2 -ffile-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 -ffile-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
+MultiSequence.cc: In member function 'void MultiSequence::WriteFASTA(FILE*, Block*, MultiSequence*, int, int)':
+MultiSequence.cc:757:16: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
+ 757 | delete map;
+ | ^~~
+MultiSequence.cc:702:40: note: returned from 'void* operator new [](std::size_t)'
+ 702 | int *map = new int[numSequences];
+ | ^
+MultiSequence.cc: In member function 'void MultiSequence::FindBlock(Block&, int&, int&, int)':
+MultiSequence.cc:633:16: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
+ 633 | delete map;
+ | ^~~
+MultiSequence.cc:534:50: note: returned from 'void* operator new [](std::size_t)'
+ 534 | int **map = new pint[numSequences];
+ | ^
+MultiSequence.cc:634:16: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
+ 634 | delete data;
+ | ^~~~
+MultiSequence.cc:513:51: note: returned from 'void* operator new [](std::size_t)'
+ 513 | const char **data = new pchar[numSequences];
+ | ^
+g++ -g -O2 -ffile-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
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]
@@ -1105,7 +1147,12 @@
Sequence.cc:129:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers]
129 | const int Sequence::GetID () const {
| ^~~~~
+g++ -g -O2 -ffile-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 -ffile-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
+Utilities.cc: In function 'int GetData(FILE*, char*&, const char*, const char*)':
+Utilities.cc:55:30: warning: comparison is always true due to limited range of data type [-Wtype-limits]
+ 55 | while ((ch = fgetc (file)) != EOF){
+ | ^
In file included from ScoreMatrix.h:12,
from Matrix.h:13,
from SparseMatrix.h:12,
@@ -1173,10 +1220,13 @@
SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers]
62 | const int GetNumCols() const;
| ^~~~~
-Utilities.cc: In function 'int GetData(FILE*, char*&, const char*, const char*)':
-Utilities.cc:55:30: warning: comparison is always true due to limited range of data type [-Wtype-limits]
- 55 | while ((ch = fgetc (file)) != EOF){
- | ^
+ProbModel.cc: In member function 'AlignedFragment* ProbModel::Viterbi(const Sequence&, const Sequence&, int*)':
+ProbModel.cc:866:10: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
+ 866 | delete s2;
+ | ^~
+ProbModel.cc:843:34: note: returned from 'void* operator new [](std::size_t)'
+ 843 | int *s2 = new int[besty - c + 1];
+ | ^
In file included from ScoreMatrix.h:12,
from Matrix.h:13:
Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers]
@@ -1228,13 +1278,6 @@
Tree.cc:42:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers]
42 | const int Tree::TreeNode::GetNumSequences() const {
| ^~~~~
-ProbModel.cc: In member function 'AlignedFragment* ProbModel::Viterbi(const Sequence&, const Sequence&, int*)':
-ProbModel.cc:866:10: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
- 866 | delete s2;
- | ^~
-ProbModel.cc:843:34: note: returned from 'void* operator new [](std::size_t)'
- 843 | int *s2 = new int[besty - c + 1];
- | ^
ProbModel.cc: In member function 'void ProbModel::ViterbiUpdate(ScoreMatrix*, Matrix*, const Sequence&, const Sequence&, int*, AlignedFragment*, int)':
ProbModel.cc:1239:10: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
1239 | delete buf;
@@ -1282,12 +1325,14 @@
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/23903/tmp/hooks/B01_cleanup starting
+I: user script /srv/workspace/pbuilder/23903/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/9665 and its subdirectories
-I: Current time: Wed May 17 10:02:15 -12 2023
-I: pbuilder-time-stamp: 1684360935
+I: removing directory /srv/workspace/pbuilder/23903 and its subdirectories
+I: Current time: Thu May 18 12:12:15 +14 2023
+I: pbuilder-time-stamp: 1684361535