Diff of the two buildlogs:
--
--- b1/build.log 2021-08-11 22:29:03.959852397 +0000
+++ b2/build.log 2021-08-11 22:32:40.131792170 +0000
@@ -1,6 +1,6 @@
I: pbuilder: network access will be disabled during build
-I: Current time: Wed Aug 11 10:22:10 -12 2021
-I: pbuilder-time-stamp: 1628720530
+I: Current time: Thu Aug 12 12:29:19 +14 2021
+I: pbuilder-time-stamp: 1628720959
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz]
I: copying local configuration
@@ -16,8 +16,8 @@
I: copying [./kallisto_0.46.2+dfsg-2.debian.tar.xz]
I: Extracting source
gpgv: unknown type of key resource 'trustedkeys.kbx'
-gpgv: keyblock resource '/tmp/dpkg-verify-sig.u1QgH7uX/trustedkeys.kbx': General error
-gpgv: Signature made Fri May 15 17:26:02 2020 -12
+gpgv: keyblock resource '/tmp/dpkg-verify-sig.2oBMnNxA/trustedkeys.kbx': General error
+gpgv: Signature made Sat May 16 19:26:02 2020 +14
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
@@ -32,135 +32,169 @@
dpkg-source: info: applying Check_busOptions.seq_length_before_accessing.patch
I: Not using root during the build.
I: Installing the build-deps
-I: user script /srv/workspace/pbuilder/29247/tmp/hooks/D02_print_environment starting
+I: user script /srv/workspace/pbuilder/26973/tmp/hooks/D01_modify_environment starting
+debug: Running on virt32b.
+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/26973/tmp/hooks/D01_modify_environment finished
+I: user script /srv/workspace/pbuilder/26973/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,-fixfilepath parallel=5'
- DISTRIBUTION=''
- HOME='/root'
- HOST_ARCH='armhf'
+ 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]="arm-unknown-linux-gnueabihf")
+ 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=armhf
+ DEBIAN_FRONTEND=noninteractive
+ DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=4'
+ DIRSTACK=()
+ DISTRIBUTION=
+ EUID=0
+ FUNCNAME=([0]="Echo" [1]="main")
+ GROUPS=()
+ HOME=/root
+ HOSTNAME=i-capture-the-hostname
+ HOSTTYPE=arm
+ HOST_ARCH=armhf
IFS='
'
- INVOCATION_ID='4df7e2cfe7da4839a6c8afc635738831'
- 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='29247'
- PS1='# '
- PS2='> '
+ INVOCATION_ID=27d47a49d13645ceac0a2f95a96bd6ed
+ 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=26973
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.4DPiG1SaWk/pbuilderrc_dwUG --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.4DPiG1SaWk/b1 --logfile b1/build.log kallisto_0.46.2+dfsg-2.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://10.0.0.15:8000/'
+ 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.4DPiG1SaWk/pbuilderrc_zAyC --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.4DPiG1SaWk/b2 --logfile b2/build.log --extrapackages usrmerge kallisto_0.46.2+dfsg-2.dsc'
+ SUDO_GID=112
+ SUDO_UID=106
+ SUDO_USER=jenkins
+ TERM=unknown
+ TZ=/usr/share/zoneinfo/Etc/GMT-14
+ UID=0
+ USER=root
+ _='I: set'
+ http_proxy=http://10.0.0.15:8000/
I: uname -a
- Linux ff64a 5.10.0-8-arm64 #1 SMP Debian 5.10.46-4 (2021-08-03) aarch64 GNU/Linux
+ Linux i-capture-the-hostname 5.10.0-8-armmp-lpae #1 SMP Debian 5.10.46-4 (2021-08-03) armv7l GNU/Linux
I: ls -l /bin
total 3580
- -rwxr-xr-x 1 root root 816764 Aug 4 08:25 bash
- -rwxr-xr-x 3 root root 26052 Jul 20 2020 bunzip2
- -rwxr-xr-x 3 root root 26052 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 26052 Jul 20 2020 bzip2
- -rwxr-xr-x 1 root root 9636 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 26668 Sep 22 2020 cat
- -rwxr-xr-x 1 root root 43104 Sep 22 2020 chgrp
- -rwxr-xr-x 1 root root 38984 Sep 22 2020 chmod
- -rwxr-xr-x 1 root root 43112 Sep 22 2020 chown
- -rwxr-xr-x 1 root root 92616 Sep 22 2020 cp
- -rwxr-xr-x 1 root root 75524 Dec 10 2020 dash
- -rwxr-xr-x 1 root root 75880 Sep 22 2020 date
- -rwxr-xr-x 1 root root 55436 Sep 22 2020 dd
- -rwxr-xr-x 1 root root 59912 Sep 22 2020 df
- -rwxr-xr-x 1 root root 96764 Sep 22 2020 dir
- -rwxr-xr-x 1 root root 55012 Jul 28 07:09 dmesg
- lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname
- lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname
- -rwxr-xr-x 1 root root 22508 Sep 22 2020 echo
- -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep
- -rwxr-xr-x 1 root root 22496 Sep 22 2020 false
- -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep
- -rwxr-xr-x 1 root root 47492 Jul 28 07:09 findmnt
- -rwsr-xr-x 1 root root 26076 Feb 26 04:12 fusermount
- -rwxr-xr-x 1 root root 124508 Nov 9 2020 grep
- -rwxr-xr-x 2 root root 2346 Mar 2 11:30 gunzip
- -rwxr-xr-x 1 root root 6376 Mar 2 11:30 gzexe
- -rwxr-xr-x 1 root root 64212 Mar 2 11:30 gzip
- -rwxr-xr-x 1 root root 13784 Nov 6 2019 hostname
- -rwxr-xr-x 1 root root 43180 Sep 22 2020 ln
- -rwxr-xr-x 1 root root 35068 Feb 7 2020 login
- -rwxr-xr-x 1 root root 96764 Sep 22 2020 ls
- -rwxr-xr-x 1 root root 99940 Jul 28 07:09 lsblk
- -rwxr-xr-x 1 root root 51408 Sep 22 2020 mkdir
- -rwxr-xr-x 1 root root 43184 Sep 22 2020 mknod
- -rwxr-xr-x 1 root root 30780 Sep 22 2020 mktemp
- -rwxr-xr-x 1 root root 34408 Jul 28 07:09 more
- -rwsr-xr-x 1 root root 34400 Jul 28 07:09 mount
- -rwxr-xr-x 1 root root 9824 Jul 28 07:09 mountpoint
- -rwxr-xr-x 1 root root 88524 Sep 22 2020 mv
- lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname
- lrwxrwxrwx 1 root root 14 Apr 18 03:38 pidof -> /sbin/killall5
- -rwxr-xr-x 1 root root 26652 Sep 22 2020 pwd
- lrwxrwxrwx 1 root root 4 Aug 4 08:25 rbash -> bash
- -rwxr-xr-x 1 root root 30740 Sep 22 2020 readlink
- -rwxr-xr-x 1 root root 43104 Sep 22 2020 rm
- -rwxr-xr-x 1 root root 30732 Sep 22 2020 rmdir
- -rwxr-xr-x 1 root root 14144 Sep 27 2020 run-parts
- -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed
- lrwxrwxrwx 1 root root 4 Aug 9 21:28 sh -> dash
- -rwxr-xr-x 1 root root 22532 Sep 22 2020 sleep
- -rwxr-xr-x 1 root root 55360 Sep 22 2020 stty
- -rwsr-xr-x 1 root root 46704 Jul 28 07:09 su
- -rwxr-xr-x 1 root root 22532 Sep 22 2020 sync
- -rwxr-xr-x 1 root root 340872 Feb 16 21:55 tar
- -rwxr-xr-x 1 root root 9808 Sep 27 2020 tempfile
- -rwxr-xr-x 1 root root 67696 Sep 22 2020 touch
- -rwxr-xr-x 1 root root 22496 Sep 22 2020 true
- -rwxr-xr-x 1 root root 9636 Feb 26 04:12 ulockmgr_server
- -rwsr-xr-x 1 root root 22108 Jul 28 07:09 umount
- -rwxr-xr-x 1 root root 22520 Sep 22 2020 uname
- -rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress
- -rwxr-xr-x 1 root root 96764 Sep 22 2020 vdir
- -rwxr-xr-x 1 root root 38512 Jul 28 07:09 wdctl
- lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname
- -rwxr-xr-x 1 root root 1984 Mar 2 11:30 zcat
- -rwxr-xr-x 1 root root 1678 Mar 2 11:30 zcmp
- -rwxr-xr-x 1 root root 5880 Mar 2 11:30 zdiff
- -rwxr-xr-x 1 root root 29 Mar 2 11:30 zegrep
- -rwxr-xr-x 1 root root 29 Mar 2 11:30 zfgrep
- -rwxr-xr-x 1 root root 2081 Mar 2 11:30 zforce
- -rwxr-xr-x 1 root root 7585 Mar 2 11:30 zgrep
- -rwxr-xr-x 1 root root 2206 Mar 2 11:30 zless
- -rwxr-xr-x 1 root root 1842 Mar 2 11:30 zmore
- -rwxr-xr-x 1 root root 4553 Mar 2 11:30 znew
-I: user script /srv/workspace/pbuilder/29247/tmp/hooks/D02_print_environment finished
+ -rwxr-xr-x 1 root root 816764 Aug 5 10:25 bash
+ -rwxr-xr-x 3 root root 26052 Jul 21 2020 bunzip2
+ -rwxr-xr-x 3 root root 26052 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 26052 Jul 21 2020 bzip2
+ -rwxr-xr-x 1 root root 9636 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 26668 Sep 23 2020 cat
+ -rwxr-xr-x 1 root root 43104 Sep 23 2020 chgrp
+ -rwxr-xr-x 1 root root 38984 Sep 23 2020 chmod
+ -rwxr-xr-x 1 root root 43112 Sep 23 2020 chown
+ -rwxr-xr-x 1 root root 92616 Sep 23 2020 cp
+ -rwxr-xr-x 1 root root 75524 Dec 11 2020 dash
+ -rwxr-xr-x 1 root root 75880 Sep 23 2020 date
+ -rwxr-xr-x 1 root root 55436 Sep 23 2020 dd
+ -rwxr-xr-x 1 root root 59912 Sep 23 2020 df
+ -rwxr-xr-x 1 root root 96764 Sep 23 2020 dir
+ -rwxr-xr-x 1 root root 55012 Jul 29 09:09 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 22508 Sep 23 2020 echo
+ -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep
+ -rwxr-xr-x 1 root root 22496 Sep 23 2020 false
+ -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep
+ -rwxr-xr-x 1 root root 47492 Jul 29 09:09 findmnt
+ -rwsr-xr-x 1 root root 26076 Feb 27 06:12 fusermount
+ -rwxr-xr-x 1 root root 124508 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 64212 Mar 3 13:30 gzip
+ -rwxr-xr-x 1 root root 13784 Nov 8 2019 hostname
+ -rwxr-xr-x 1 root root 43180 Sep 23 2020 ln
+ -rwxr-xr-x 1 root root 35068 Feb 8 2020 login
+ -rwxr-xr-x 1 root root 96764 Sep 23 2020 ls
+ -rwxr-xr-x 1 root root 99940 Jul 29 09:09 lsblk
+ -rwxr-xr-x 1 root root 51408 Sep 23 2020 mkdir
+ -rwxr-xr-x 1 root root 43184 Sep 23 2020 mknod
+ -rwxr-xr-x 1 root root 30780 Sep 23 2020 mktemp
+ -rwxr-xr-x 1 root root 34408 Jul 29 09:09 more
+ -rwsr-xr-x 1 root root 34400 Jul 29 09:09 mount
+ -rwxr-xr-x 1 root root 9824 Jul 29 09:09 mountpoint
+ -rwxr-xr-x 1 root root 88524 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 26652 Sep 23 2020 pwd
+ lrwxrwxrwx 1 root root 4 Aug 5 10:25 rbash -> bash
+ -rwxr-xr-x 1 root root 30740 Sep 23 2020 readlink
+ -rwxr-xr-x 1 root root 43104 Sep 23 2020 rm
+ -rwxr-xr-x 1 root root 30732 Sep 23 2020 rmdir
+ -rwxr-xr-x 1 root root 14144 Sep 28 2020 run-parts
+ -rwxr-xr-x 1 root root 76012 Dec 23 2018 sed
+ lrwxrwxrwx 1 root root 4 Aug 12 12:29 sh -> bash
+ lrwxrwxrwx 1 root root 4 Aug 11 23:26 sh.distrib -> dash
+ -rwxr-xr-x 1 root root 22532 Sep 23 2020 sleep
+ -rwxr-xr-x 1 root root 55360 Sep 23 2020 stty
+ -rwsr-xr-x 1 root root 46704 Jul 29 09:09 su
+ -rwxr-xr-x 1 root root 22532 Sep 23 2020 sync
+ -rwxr-xr-x 1 root root 340872 Feb 17 23:55 tar
+ -rwxr-xr-x 1 root root 9808 Sep 28 2020 tempfile
+ -rwxr-xr-x 1 root root 67696 Sep 23 2020 touch
+ -rwxr-xr-x 1 root root 22496 Sep 23 2020 true
+ -rwxr-xr-x 1 root root 9636 Feb 27 06:12 ulockmgr_server
+ -rwsr-xr-x 1 root root 22108 Jul 29 09:09 umount
+ -rwxr-xr-x 1 root root 22520 Sep 23 2020 uname
+ -rwxr-xr-x 2 root root 2346 Mar 3 13:30 uncompress
+ -rwxr-xr-x 1 root root 96764 Sep 23 2020 vdir
+ -rwxr-xr-x 1 root root 38512 Jul 29 09:09 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/26973/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
@@ -275,7 +309,7 @@
Get: 71 http://deb.debian.org/debian bullseye/main armhf libhts3 armhf 1.11-4 [332 kB]
Get: 72 http://deb.debian.org/debian bullseye/main armhf liblzma-dev armhf 5.2.5-2 [220 kB]
Get: 73 http://deb.debian.org/debian bullseye/main armhf libhts-dev armhf 1.11-4 [3819 kB]
-Fetched 35.7 MB in 4s (9891 kB/s)
+Fetched 35.7 MB in 4s (10.1 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package bsdextrautils.
(Reading database ...
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(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 19398 files and directories currently installed.)
@@ -583,8 +617,45 @@
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 armhf libnumber-compare-perl all 0.03-1.1 [6956 B]
+Get:2 http://deb.debian.org/debian bullseye/main armhf libtext-glob-perl all 0.11-1 [8888 B]
+Get:3 http://deb.debian.org/debian bullseye/main armhf libfile-find-rule-perl all 0.34-1 [30.6 kB]
+Get:4 http://deb.debian.org/debian bullseye/main armhf usrmerge all 25 [13.0 kB]
+debconf: delaying package configuration, since apt-utils is not installed
+Fetched 59.5 kB in 0s (1222 kB/s)
+Selecting previously unselected package libnumber-compare-perl.
+(Reading database ...
(Reading database ... 5%
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(Reading database ... 24844 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/kallisto-0.46.2+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../kallisto_0.46.2+dfsg-2_source.changes
+hostname: Name or service not known
+I: Running cd /build/kallisto-0.46.2+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../kallisto_0.46.2+dfsg-2_source.changes
dpkg-buildpackage: info: source package kallisto
dpkg-buildpackage: info: source version 0.46.2+dfsg-2
dpkg-buildpackage: info: source distribution unstable
@@ -636,7 +707,7 @@
-- Build files have been written to: /build/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf
make[1]: Leaving directory '/build/kallisto-0.46.2+dfsg'
dh_auto_build
- cd obj-arm-linux-gnueabihf && make -j5 "INSTALL=install --strip-program=true" VERBOSE=1
+ cd obj-arm-linux-gnueabihf && make -j4 "INSTALL=install --strip-program=true" VERBOSE=1
make[1]: Entering directory '/build/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf'
/usr/bin/cmake -S/build/kallisto-0.46.2+dfsg -B/build/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /build/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles /build/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf//CMakeFiles/progress.marks
@@ -651,22 +722,18 @@
make[3]: Leaving directory '/build/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf'
make -f src/CMakeFiles/kallisto_core.dir/build.make src/CMakeFiles/kallisto_core.dir/build
make[3]: Entering directory '/build/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf'
-[ 9%] Building CXX object src/CMakeFiles/kallisto_core.dir/BUSData.cpp.o
+[ 4%] Building CXX object src/CMakeFiles/kallisto_core.dir/BUSData.cpp.o
+cd /build/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/kallisto-0.46.2+dfsg/src -g -O2 -fdebug-prefix-map=/build/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/BUSData.cpp.o -c /build/kallisto-0.46.2+dfsg/src/BUSData.cpp
[ 9%] Building CXX object src/CMakeFiles/kallisto_core.dir/BUSTools.cpp.o
cd /build/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/kallisto-0.46.2+dfsg/src -g -O2 -fdebug-prefix-map=/build/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/BUSTools.cpp.o -c /build/kallisto-0.46.2+dfsg/src/BUSTools.cpp
-cd /build/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/kallisto-0.46.2+dfsg/src -g -O2 -fdebug-prefix-map=/build/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/BUSData.cpp.o -c /build/kallisto-0.46.2+dfsg/src/BUSData.cpp
-[ 14%] Building CXX object src/CMakeFiles/kallisto_core.dir/H5Writer.cpp.o
+[ 14%] Building CXX object src/CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o
+cd /build/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/kallisto-0.46.2+dfsg/src -g -O2 -fdebug-prefix-map=/build/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o -c /build/kallisto-0.46.2+dfsg/src/Bootstrap.cpp
[ 19%] Building CXX object src/CMakeFiles/kallisto_core.dir/GeneModel.cpp.o
-cd /build/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/kallisto-0.46.2+dfsg/src -g -O2 -fdebug-prefix-map=/build/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/H5Writer.cpp.o -c /build/kallisto-0.46.2+dfsg/src/H5Writer.cpp
cd /build/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/kallisto-0.46.2+dfsg/src -g -O2 -fdebug-prefix-map=/build/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/GeneModel.cpp.o -c /build/kallisto-0.46.2+dfsg/src/GeneModel.cpp
-[ 23%] Building CXX object src/CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o
-cd /build/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/kallisto-0.46.2+dfsg/src -g -O2 -fdebug-prefix-map=/build/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o -c /build/kallisto-0.46.2+dfsg/src/Bootstrap.cpp
+[ 23%] Building CXX object src/CMakeFiles/kallisto_core.dir/H5Writer.cpp.o
+cd /build/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/kallisto-0.46.2+dfsg/src -g -O2 -fdebug-prefix-map=/build/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/H5Writer.cpp.o -c /build/kallisto-0.46.2+dfsg/src/H5Writer.cpp
[ 28%] Building CXX object src/CMakeFiles/kallisto_core.dir/Kmer.cpp.o
cd /build/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/kallisto-0.46.2+dfsg/src -g -O2 -fdebug-prefix-map=/build/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/Kmer.cpp.o -c /build/kallisto-0.46.2+dfsg/src/Kmer.cpp
-[ 33%] Building CXX object src/CMakeFiles/kallisto_core.dir/KmerIndex.cpp.o
-cd /build/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/kallisto-0.46.2+dfsg/src -g -O2 -fdebug-prefix-map=/build/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/KmerIndex.cpp.o -c /build/kallisto-0.46.2+dfsg/src/KmerIndex.cpp
-[ 38%] Building CXX object src/CMakeFiles/kallisto_core.dir/KmerIterator.cpp.o
-cd /build/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/kallisto-0.46.2+dfsg/src -g -O2 -fdebug-prefix-map=/build/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/KmerIterator.cpp.o -c /build/kallisto-0.46.2+dfsg/src/KmerIterator.cpp
In file included from /build/kallisto-0.46.2+dfsg/src/KmerIndex.h:18,
from /build/kallisto-0.46.2+dfsg/src/GeneModel.h:10,
from /build/kallisto-0.46.2+dfsg/src/GeneModel.cpp:1:
@@ -679,15 +746,8 @@
/build/kallisto-0.46.2+dfsg/src/GeneModel.h:66:105: warning: left shift count >= width of type [-Wshift-count-overflow]
66 | return std::hash<TranscriptAlignment>()(x.first) ^ (std::hash<TranscriptAlignment>()(x.second)<<32);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~
-[ 42%] Building CXX object src/CMakeFiles/kallisto_core.dir/Merge.cpp.o
-cd /build/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/kallisto-0.46.2+dfsg/src -g -O2 -fdebug-prefix-map=/build/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/Merge.cpp.o -c /build/kallisto-0.46.2+dfsg/src/Merge.cpp
-In file included from /build/kallisto-0.46.2+dfsg/src/KmerIndex.h:18,
- from /build/kallisto-0.46.2+dfsg/src/Bootstrap.h:7,
- from /build/kallisto-0.46.2+dfsg/src/Bootstrap.cpp:1:
-/build/kallisto-0.46.2+dfsg/src/KmerHashTable.h: In member function 'size_t KmerHashTable<T, Hash>::rndup(size_t)':
-/build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow]
- 240 | v |= v >> 32;
- | ~~^~~~~
+[ 33%] Building CXX object src/CMakeFiles/kallisto_core.dir/KmerIndex.cpp.o
+cd /build/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/kallisto-0.46.2+dfsg/src -g -O2 -fdebug-prefix-map=/build/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/KmerIndex.cpp.o -c /build/kallisto-0.46.2+dfsg/src/KmerIndex.cpp
In file included from /build/kallisto-0.46.2+dfsg/src/KmerIndex.h:18,
from /build/kallisto-0.46.2+dfsg/src/GeneModel.h:10,
from /build/kallisto-0.46.2+dfsg/src/GeneModel.cpp:1:
@@ -698,8 +758,15 @@
/build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow]
240 | v |= v >> 32;
| ~~^~~~~
-[ 47%] Building CXX object src/CMakeFiles/kallisto_core.dir/MinCollector.cpp.o
-cd /build/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/kallisto-0.46.2+dfsg/src -g -O2 -fdebug-prefix-map=/build/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/MinCollector.cpp.o -c /build/kallisto-0.46.2+dfsg/src/MinCollector.cpp
+In file included from /build/kallisto-0.46.2+dfsg/src/KmerIndex.h:18,
+ from /build/kallisto-0.46.2+dfsg/src/Bootstrap.h:7,
+ from /build/kallisto-0.46.2+dfsg/src/Bootstrap.cpp:1:
+/build/kallisto-0.46.2+dfsg/src/KmerHashTable.h: In member function 'size_t KmerHashTable<T, Hash>::rndup(size_t)':
+/build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow]
+ 240 | v |= v >> 32;
+ | ~~^~~~~
+[ 38%] Building CXX object src/CMakeFiles/kallisto_core.dir/KmerIterator.cpp.o
+cd /build/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/kallisto-0.46.2+dfsg/src -g -O2 -fdebug-prefix-map=/build/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/KmerIterator.cpp.o -c /build/kallisto-0.46.2+dfsg/src/KmerIterator.cpp
In file included from /build/kallisto-0.46.2+dfsg/src/PlaintextWriter.h:13,
from /build/kallisto-0.46.2+dfsg/src/Bootstrap.cpp:2:
/build/kallisto-0.46.2+dfsg/src/GeneModel.h: In member function 'std::size_t std::hash<std::pair<TranscriptAlignment, TranscriptAlignment> >::operator()(const std::pair<TranscriptAlignment, TranscriptAlignment>&) const':
@@ -707,12 +774,6 @@
66 | return std::hash<TranscriptAlignment>()(x.first) ^ (std::hash<TranscriptAlignment>()(x.second)<<32);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~
In file included from /build/kallisto-0.46.2+dfsg/src/KmerIndex.h:18,
- from /build/kallisto-0.46.2+dfsg/src/KmerIndex.cpp:1:
-/build/kallisto-0.46.2+dfsg/src/KmerHashTable.h: In member function 'size_t KmerHashTable<T, Hash>::rndup(size_t)':
-/build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow]
- 240 | v |= v >> 32;
- | ~~^~~~~
-In file included from /build/kallisto-0.46.2+dfsg/src/KmerIndex.h:18,
from /build/kallisto-0.46.2+dfsg/src/Bootstrap.h:7,
from /build/kallisto-0.46.2+dfsg/src/Bootstrap.cpp:1:
/build/kallisto-0.46.2+dfsg/src/KmerHashTable.h: In instantiation of 'size_t KmerHashTable<T, Hash>::rndup(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]':
@@ -723,32 +784,13 @@
240 | v |= v >> 32;
| ~~^~~~~
In file included from /build/kallisto-0.46.2+dfsg/src/KmerIndex.h:18,
- from /build/kallisto-0.46.2+dfsg/src/MinCollector.h:11,
- from /build/kallisto-0.46.2+dfsg/src/MinCollector.cpp:1:
-/build/kallisto-0.46.2+dfsg/src/KmerHashTable.h: In member function 'size_t KmerHashTable<T, Hash>::rndup(size_t)':
-/build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow]
- 240 | v |= v >> 32;
- | ~~^~~~~
-In file included from /build/kallisto-0.46.2+dfsg/src/KmerIndex.h:18,
- from /build/kallisto-0.46.2+dfsg/src/Merge.cpp:11:
+ from /build/kallisto-0.46.2+dfsg/src/KmerIndex.cpp:1:
/build/kallisto-0.46.2+dfsg/src/KmerHashTable.h: In member function 'size_t KmerHashTable<T, Hash>::rndup(size_t)':
/build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow]
240 | v |= v >> 32;
| ~~^~~~~
-/build/kallisto-0.46.2+dfsg/src/KmerHashTable.h: In instantiation of 'size_t KmerHashTable<T, Hash>::rndup(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]':
-/build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:218:13: required from 'void KmerHashTable<T, Hash>::reserve(size_t, bool) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]'
-/build/kallisto-0.46.2+dfsg/src/KmerIndex.cpp:848:32: required from here
-/build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow]
-/build/kallisto-0.46.2+dfsg/src/KmerHashTable.h: In instantiation of 'size_t KmerHashTable<T, Hash>::rndup(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]':
-/build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:125:13: required from 'void KmerHashTable<T, Hash>::init_table(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]'
-/build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:92:5: required from 'KmerHashTable<T, Hash>::KmerHashTable(const Hash&) [with T = KmerEntry; Hash = KmerHash]'
-/build/kallisto-0.46.2+dfsg/src/KmerIndex.h:96:106: required from here
-/build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow]
-/build/kallisto-0.46.2+dfsg/src/KmerHashTable.h: In instantiation of 'size_t KmerHashTable<T, Hash>::rndup(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]':
-/build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:125:13: required from 'void KmerHashTable<T, Hash>::init_table(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]'
-/build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:92:5: required from 'KmerHashTable<T, Hash>::KmerHashTable(const Hash&) [with T = KmerEntry; Hash = KmerHash]'
-/build/kallisto-0.46.2+dfsg/src/KmerIndex.h:96:106: required from here
-/build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow]
+[ 42%] Building CXX object src/CMakeFiles/kallisto_core.dir/Merge.cpp.o
+cd /build/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/kallisto-0.46.2+dfsg/src -g -O2 -fdebug-prefix-map=/build/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/Merge.cpp.o -c /build/kallisto-0.46.2+dfsg/src/Merge.cpp
In file included from /usr/include/c++/10/vector:72,
from /build/kallisto-0.46.2+dfsg/src/KmerIndex.h:7,
from /build/kallisto-0.46.2+dfsg/src/Bootstrap.h:7,
@@ -768,10 +810,37 @@
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
+/build/kallisto-0.46.2+dfsg/src/KmerHashTable.h: In instantiation of 'size_t KmerHashTable<T, Hash>::rndup(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]':
+/build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:218:13: required from 'void KmerHashTable<T, Hash>::reserve(size_t, bool) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]'
+/build/kallisto-0.46.2+dfsg/src/KmerIndex.cpp:848:32: required from here
+/build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow]
+In file included from /build/kallisto-0.46.2+dfsg/src/KmerIndex.h:18,
+ from /build/kallisto-0.46.2+dfsg/src/Merge.cpp:11:
+/build/kallisto-0.46.2+dfsg/src/KmerHashTable.h: In member function 'size_t KmerHashTable<T, Hash>::rndup(size_t)':
+/build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow]
+ 240 | v |= v >> 32;
+ | ~~^~~~~
+[ 47%] Building CXX object src/CMakeFiles/kallisto_core.dir/MinCollector.cpp.o
+cd /build/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/kallisto-0.46.2+dfsg/src -g -O2 -fdebug-prefix-map=/build/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/MinCollector.cpp.o -c /build/kallisto-0.46.2+dfsg/src/MinCollector.cpp
+/build/kallisto-0.46.2+dfsg/src/KmerHashTable.h: In instantiation of 'size_t KmerHashTable<T, Hash>::rndup(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]':
+/build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:125:13: required from 'void KmerHashTable<T, Hash>::init_table(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]'
+/build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:92:5: required from 'KmerHashTable<T, Hash>::KmerHashTable(const Hash&) [with T = KmerEntry; Hash = KmerHash]'
+/build/kallisto-0.46.2+dfsg/src/KmerIndex.h:96:106: required from here
+/build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow]
[ 52%] Building CXX object src/CMakeFiles/kallisto_core.dir/PlaintextWriter.cpp.o
cd /build/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/kallisto-0.46.2+dfsg/src -g -O2 -fdebug-prefix-map=/build/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/PlaintextWriter.cpp.o -c /build/kallisto-0.46.2+dfsg/src/PlaintextWriter.cpp
-[ 57%] Building CXX object src/CMakeFiles/kallisto_core.dir/ProcessReads.cpp.o
-cd /build/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/kallisto-0.46.2+dfsg/src -g -O2 -fdebug-prefix-map=/build/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/ProcessReads.cpp.o -c /build/kallisto-0.46.2+dfsg/src/ProcessReads.cpp
+In file included from /build/kallisto-0.46.2+dfsg/src/KmerIndex.h:18,
+ from /build/kallisto-0.46.2+dfsg/src/MinCollector.h:11,
+ from /build/kallisto-0.46.2+dfsg/src/MinCollector.cpp:1:
+/build/kallisto-0.46.2+dfsg/src/KmerHashTable.h: In member function 'size_t KmerHashTable<T, Hash>::rndup(size_t)':
+/build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow]
+ 240 | v |= v >> 32;
+ | ~~^~~~~
+/build/kallisto-0.46.2+dfsg/src/KmerHashTable.h: In instantiation of 'size_t KmerHashTable<T, Hash>::rndup(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]':
+/build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:125:13: required from 'void KmerHashTable<T, Hash>::init_table(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]'
+/build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:92:5: required from 'KmerHashTable<T, Hash>::KmerHashTable(const Hash&) [with T = KmerEntry; Hash = KmerHash]'
+/build/kallisto-0.46.2+dfsg/src/KmerIndex.h:96:106: required from here
+/build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow]
In file included from /build/kallisto-0.46.2+dfsg/src/KmerIndex.h:18,
from /build/kallisto-0.46.2+dfsg/src/PlaintextWriter.h:12,
from /build/kallisto-0.46.2+dfsg/src/PlaintextWriter.cpp:1:
@@ -779,12 +848,6 @@
/build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow]
240 | v |= v >> 32;
| ~~^~~~~
-In file included from /build/kallisto-0.46.2+dfsg/src/PlaintextWriter.h:13,
- from /build/kallisto-0.46.2+dfsg/src/PlaintextWriter.cpp:1:
-/build/kallisto-0.46.2+dfsg/src/GeneModel.h: In member function 'std::size_t std::hash<std::pair<TranscriptAlignment, TranscriptAlignment> >::operator()(const std::pair<TranscriptAlignment, TranscriptAlignment>&) const':
-/build/kallisto-0.46.2+dfsg/src/GeneModel.h:66:105: warning: left shift count >= width of type [-Wshift-count-overflow]
- 66 | return std::hash<TranscriptAlignment>()(x.first) ^ (std::hash<TranscriptAlignment>()(x.second)<<32);
- | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~
In file included from /usr/include/c++/10/vector:72,
from /build/kallisto-0.46.2+dfsg/src/KmerIndex.h:7,
from /build/kallisto-0.46.2+dfsg/src/KmerIndex.cpp:1:
@@ -792,6 +855,12 @@
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Kmer>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
+In file included from /build/kallisto-0.46.2+dfsg/src/PlaintextWriter.h:13,
+ from /build/kallisto-0.46.2+dfsg/src/PlaintextWriter.cpp:1:
+/build/kallisto-0.46.2+dfsg/src/GeneModel.h: In member function 'std::size_t std::hash<std::pair<TranscriptAlignment, TranscriptAlignment> >::operator()(const std::pair<TranscriptAlignment, TranscriptAlignment>&) const':
+/build/kallisto-0.46.2+dfsg/src/GeneModel.h:66:105: warning: left shift count >= width of type [-Wshift-count-overflow]
+ 66 | return std::hash<TranscriptAlignment>()(x.first) ^ (std::hash<TranscriptAlignment>()(x.second)<<32);
+ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~
In file included from /build/kallisto-0.46.2+dfsg/src/KmerIndex.h:18,
from /build/kallisto-0.46.2+dfsg/src/PlaintextWriter.h:12,
from /build/kallisto-0.46.2+dfsg/src/PlaintextWriter.cpp:1:
@@ -802,8 +871,35 @@
/build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow]
240 | v |= v >> 32;
| ~~^~~~~
-[ 61%] Building CXX object src/CMakeFiles/kallisto_core.dir/PseudoBam.cpp.o
-cd /build/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/kallisto-0.46.2+dfsg/src -g -O2 -fdebug-prefix-map=/build/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/PseudoBam.cpp.o -c /build/kallisto-0.46.2+dfsg/src/PseudoBam.cpp
+/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {Kmer}; _Tp = Kmer; _Alloc = std::allocator<Kmer>]':
+/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Kmer>::iterator' changed in GCC 7.1
+In file included from /usr/include/c++/10/vector:67,
+ from /build/kallisto-0.46.2+dfsg/src/KmerIndex.h:7,
+ from /build/kallisto-0.46.2+dfsg/src/KmerIndex.cpp:1:
+/usr/include/c++/10/bits/stl_vector.h: In member function 'void KmerIndex::BuildDeBruijnGraph(const ProgramOptions&, const std::vector<std::__cxx11::basic_string<char> >&)':
+/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Kmer*, std::vector<Kmer> >' changed in GCC 7.1
+ 1198 | _M_realloc_insert(end(), __x);
+ | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
+/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Kmer*, std::vector<Kmer> >' changed in GCC 7.1
+ 1198 | _M_realloc_insert(end(), __x);
+ | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
+/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Kmer*, std::vector<Kmer> >' changed in GCC 7.1
+ 1198 | _M_realloc_insert(end(), __x);
+ | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
+In file included from /usr/include/c++/10/vector:72,
+ from /build/kallisto-0.46.2+dfsg/src/KmerIndex.h:7,
+ from /build/kallisto-0.46.2+dfsg/src/KmerIndex.cpp:1:
+/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Kmer*, std::vector<Kmer> >' changed in GCC 7.1
+ 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
+ | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+In file included from /usr/include/c++/10/vector:67,
+ from /build/kallisto-0.46.2+dfsg/src/KmerIndex.h:7,
+ from /build/kallisto-0.46.2+dfsg/src/KmerIndex.cpp:1:
+/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Kmer*, std::vector<Kmer> >' changed in GCC 7.1
+ 1198 | _M_realloc_insert(end(), __x);
+ | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
+[ 57%] Building CXX object src/CMakeFiles/kallisto_core.dir/ProcessReads.cpp.o
+cd /build/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/kallisto-0.46.2+dfsg/src -g -O2 -fdebug-prefix-map=/build/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/ProcessReads.cpp.o -c /build/kallisto-0.46.2+dfsg/src/ProcessReads.cpp
In file included from /build/kallisto-0.46.2+dfsg/src/KmerIndex.h:18,
from /build/kallisto-0.46.2+dfsg/src/MinCollector.h:11,
from /build/kallisto-0.46.2+dfsg/src/ProcessReads.h:18,
@@ -812,6 +908,14 @@
/build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow]
240 | v |= v >> 32;
| ~~^~~~~
+In file included from /usr/include/c++/10/vector:72,
+ from /build/kallisto-0.46.2+dfsg/src/Merge.cpp:5:
+/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
+/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' changed in GCC 7.1
+ 426 | vector<_Tp, _Alloc>::
+ | ^~~~~~~~~~~~~~~~~~~
+[ 61%] Building CXX object src/CMakeFiles/kallisto_core.dir/PseudoBam.cpp.o
+cd /build/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/kallisto-0.46.2+dfsg/src -g -O2 -fdebug-prefix-map=/build/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/PseudoBam.cpp.o -c /build/kallisto-0.46.2+dfsg/src/PseudoBam.cpp
In file included from /build/kallisto-0.46.2+dfsg/src/PseudoBam.h:13,
from /build/kallisto-0.46.2+dfsg/src/ProcessReads.h:21,
from /build/kallisto-0.46.2+dfsg/src/ProcessReads.cpp:22:
@@ -832,33 +936,6 @@
/build/kallisto-0.46.2+dfsg/src/GeneModel.h:66:105: warning: left shift count >= width of type [-Wshift-count-overflow]
66 | return std::hash<TranscriptAlignment>()(x.first) ^ (std::hash<TranscriptAlignment>()(x.second)<<32);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~
-/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {Kmer}; _Tp = Kmer; _Alloc = std::allocator<Kmer>]':
-/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Kmer>::iterator' changed in GCC 7.1
-In file included from /usr/include/c++/10/vector:67,
- from /build/kallisto-0.46.2+dfsg/src/KmerIndex.h:7,
- from /build/kallisto-0.46.2+dfsg/src/KmerIndex.cpp:1:
-/usr/include/c++/10/bits/stl_vector.h: In member function 'void KmerIndex::BuildDeBruijnGraph(const ProgramOptions&, const std::vector<std::__cxx11::basic_string<char> >&)':
-/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Kmer*, std::vector<Kmer> >' changed in GCC 7.1
- 1198 | _M_realloc_insert(end(), __x);
- | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
-/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Kmer*, std::vector<Kmer> >' changed in GCC 7.1
- 1198 | _M_realloc_insert(end(), __x);
- | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
-/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Kmer*, std::vector<Kmer> >' changed in GCC 7.1
- 1198 | _M_realloc_insert(end(), __x);
- | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
-In file included from /usr/include/c++/10/vector:72,
- from /build/kallisto-0.46.2+dfsg/src/KmerIndex.h:7,
- from /build/kallisto-0.46.2+dfsg/src/KmerIndex.cpp:1:
-/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Kmer*, std::vector<Kmer> >' changed in GCC 7.1
- 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
- | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from /usr/include/c++/10/vector:67,
- from /build/kallisto-0.46.2+dfsg/src/KmerIndex.h:7,
- from /build/kallisto-0.46.2+dfsg/src/KmerIndex.cpp:1:
-/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Kmer*, std::vector<Kmer> >' changed in GCC 7.1
- 1198 | _M_realloc_insert(end(), __x);
- | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /build/kallisto-0.46.2+dfsg/src/KmerIndex.h:18,
from /build/kallisto-0.46.2+dfsg/src/PseudoBam.h:12,
from /build/kallisto-0.46.2+dfsg/src/PseudoBam.cpp:3:
@@ -869,12 +946,6 @@
/build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow]
240 | v |= v >> 32;
| ~~^~~~~
-In file included from /usr/include/c++/10/vector:72,
- from /build/kallisto-0.46.2+dfsg/src/Merge.cpp:5:
-/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
-/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' changed in GCC 7.1
- 426 | vector<_Tp, _Alloc>::
- | ^~~~~~~~~~~~~~~~~~~
In file included from /build/kallisto-0.46.2+dfsg/src/KmerIndex.h:18,
from /build/kallisto-0.46.2+dfsg/src/MinCollector.h:11,
from /build/kallisto-0.46.2+dfsg/src/ProcessReads.h:18,
@@ -914,26 +985,31 @@
/build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow]
240 | v |= v >> 32;
| ~~^~~~~
-In file included from /build/kallisto-0.46.2+dfsg/src/KmerIndex.h:18,
- from /build/kallisto-0.46.2+dfsg/src/MinCollector.h:11,
- from /build/kallisto-0.46.2+dfsg/src/ProcessReads.h:18,
- from /build/kallisto-0.46.2+dfsg/src/main.cpp:17:
-/build/kallisto-0.46.2+dfsg/src/KmerHashTable.h: In member function 'size_t KmerHashTable<T, Hash>::rndup(size_t)':
-/build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow]
- 240 | v |= v >> 32;
- | ~~^~~~~
/build/kallisto-0.46.2+dfsg/src/KmerHashTable.h: In instantiation of 'size_t KmerHashTable<T, Hash>::rndup(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]':
/build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:125:13: required from 'void KmerHashTable<T, Hash>::init_table(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]'
/build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:92:5: required from 'KmerHashTable<T, Hash>::KmerHashTable(const Hash&) [with T = KmerEntry; Hash = KmerHash]'
/build/kallisto-0.46.2+dfsg/src/KmerIndex.h:96:106: required from here
/build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow]
-In file included from /build/kallisto-0.46.2+dfsg/src/PseudoBam.h:13,
- from /build/kallisto-0.46.2+dfsg/src/ProcessReads.h:21,
- from /build/kallisto-0.46.2+dfsg/src/main.cpp:17:
-/build/kallisto-0.46.2+dfsg/src/GeneModel.h: In member function 'std::size_t std::hash<std::pair<TranscriptAlignment, TranscriptAlignment> >::operator()(const std::pair<TranscriptAlignment, TranscriptAlignment>&) const':
-/build/kallisto-0.46.2+dfsg/src/GeneModel.h:66:105: warning: left shift count >= width of type [-Wshift-count-overflow]
- 66 | return std::hash<TranscriptAlignment>()(x.first) ^ (std::hash<TranscriptAlignment>()(x.second)<<32);
- | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~
+In file included from /usr/include/c++/10/bits/stl_algo.h:61,
+ from /usr/include/c++/10/algorithm:62,
+ from /build/kallisto-0.46.2+dfsg/src/ProcessReads.h:9,
+ from /build/kallisto-0.46.2+dfsg/src/ProcessReads.cpp:22:
+/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<long long unsigned int, long long unsigned int>*, std::vector<std::pair<long long unsigned int, long long unsigned int> > >; _Distance = int; _Tp = std::pair<long long unsigned int, long long unsigned int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<MasterProcessor::processAln(const EMAlgorithm&, bool)::<lambda(std::pair<long long unsigned int, long long unsigned int>, std::pair<long long unsigned int, long long unsigned int>)> >]':
+/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, long long unsigned int>*, std::vector<std::pair<long long unsigned int, long long unsigned int> > >' changed in GCC 7.1
+ 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
+ | ^~~~~~~~~~~~~
+In file included from /usr/include/c++/10/algorithm:62,
+ from /build/kallisto-0.46.2+dfsg/src/ProcessReads.h:9,
+ from /build/kallisto-0.46.2+dfsg/src/ProcessReads.cpp:22:
+/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<long long unsigned int, long long unsigned int>*, std::vector<std::pair<long long unsigned int, long long unsigned int> > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<MasterProcessor::processAln(const EMAlgorithm&, bool)::<lambda(std::pair<long long unsigned int, long long unsigned int>, std::pair<long long unsigned int, long long unsigned int>)> >]':
+/usr/include/c++/10/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, long long unsigned int>*, std::vector<std::pair<long long unsigned int, long long unsigned int> > >' changed in GCC 7.1
+ 1819 | __unguarded_linear_insert(_RandomAccessIterator __last,
+ | ^~~~~~~~~~~~~~~~~~~~~~~~~
+/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<long long unsigned int, long long unsigned int>*, std::vector<std::pair<long long unsigned int, long long unsigned int> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<MasterProcessor::processAln(const EMAlgorithm&, bool)::<lambda(std::pair<long long unsigned int, long long unsigned int>, std::pair<long long unsigned int, long long unsigned int>)> >]':
+/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, long long unsigned int>*, std::vector<std::pair<long long unsigned int, long long unsigned int> > >' changed in GCC 7.1
+ 1839 | __insertion_sort(_RandomAccessIterator __first,
+ | ^~~~~~~~~~~~~~~~
+/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, long long unsigned int>*, std::vector<std::pair<long long unsigned int, long long unsigned int> > >' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /build/kallisto-0.46.2+dfsg/src/KmerIndex.h:7,
from /build/kallisto-0.46.2+dfsg/src/weights.h:4,
@@ -969,6 +1045,10 @@
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
+/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<long long unsigned int, long long unsigned int>*, std::vector<std::pair<long long unsigned int, long long unsigned int> > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<MasterProcessor::processAln(const EMAlgorithm&, bool)::<lambda(std::pair<long long unsigned int, long long unsigned int>, std::pair<long long unsigned int, long long unsigned int>)> >]':
+/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, long long unsigned int>*, std::vector<std::pair<long long unsigned int, long long unsigned int> > >' changed in GCC 7.1
+ 1945 | __introsort_loop(_RandomAccessIterator __first,
+ | ^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /build/kallisto-0.46.2+dfsg/src/KmerIndex.h:7,
from /build/kallisto-0.46.2+dfsg/src/weights.h:4,
@@ -977,6 +1057,18 @@
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, long long unsigned int>*, std::vector<std::pair<long long unsigned int, long long unsigned int> > >' changed in GCC 7.1
+/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, long long unsigned int>*, std::vector<std::pair<long long unsigned int, long long unsigned int> > >' changed in GCC 7.1
+ 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
+ | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+In file included from /build/kallisto-0.46.2+dfsg/src/KmerIndex.h:18,
+ from /build/kallisto-0.46.2+dfsg/src/MinCollector.h:11,
+ from /build/kallisto-0.46.2+dfsg/src/ProcessReads.h:18,
+ from /build/kallisto-0.46.2+dfsg/src/main.cpp:17:
+/build/kallisto-0.46.2+dfsg/src/KmerHashTable.h: In member function 'size_t KmerHashTable<T, Hash>::rndup(size_t)':
+/build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow]
+ 240 | v |= v >> 32;
+ | ~~^~~~~
In file included from /usr/include/c++/10/vector:72,
from /build/kallisto-0.46.2+dfsg/src/KmerIndex.h:7,
from /build/kallisto-0.46.2+dfsg/src/weights.h:4,
@@ -985,25 +1077,23 @@
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
+In file included from /build/kallisto-0.46.2+dfsg/src/PseudoBam.h:13,
+ from /build/kallisto-0.46.2+dfsg/src/ProcessReads.h:21,
+ from /build/kallisto-0.46.2+dfsg/src/main.cpp:17:
+/build/kallisto-0.46.2+dfsg/src/GeneModel.h: In member function 'std::size_t std::hash<std::pair<TranscriptAlignment, TranscriptAlignment> >::operator()(const std::pair<TranscriptAlignment, TranscriptAlignment>&) const':
+/build/kallisto-0.46.2+dfsg/src/GeneModel.h:66:105: warning: left shift count >= width of type [-Wshift-count-overflow]
+ 66 | return std::hash<TranscriptAlignment>()(x.first) ^ (std::hash<TranscriptAlignment>()(x.second)<<32);
+ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~
/usr/include/c++/10/bits/vector.tcc: In function 'WeightMap calc_weights(const std::vector<int>&, const EcMap&, const std::vector<double>&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from /usr/include/c++/10/bits/stl_algo.h:61,
- from /usr/include/c++/10/algorithm:62,
- from /build/kallisto-0.46.2+dfsg/src/ProcessReads.h:9,
- from /build/kallisto-0.46.2+dfsg/src/ProcessReads.cpp:22:
-/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<long long unsigned int, long long unsigned int>*, std::vector<std::pair<long long unsigned int, long long unsigned int> > >; _Distance = int; _Tp = std::pair<long long unsigned int, long long unsigned int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<MasterProcessor::processAln(const EMAlgorithm&, bool)::<lambda(std::pair<long long unsigned int, long long unsigned int>, std::pair<long long unsigned int, long long unsigned int>)> >]':
-/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, long long unsigned int>*, std::vector<std::pair<long long unsigned int, long long unsigned int> > >' changed in GCC 7.1
- 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
- | ^~~~~~~~~~~~~
-In file included from /usr/include/c++/10/algorithm:62,
- from /build/kallisto-0.46.2+dfsg/src/ProcessReads.h:9,
- from /build/kallisto-0.46.2+dfsg/src/ProcessReads.cpp:22:
-/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<long long unsigned int, long long unsigned int>*, std::vector<std::pair<long long unsigned int, long long unsigned int> > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<MasterProcessor::processAln(const EMAlgorithm&, bool)::<lambda(std::pair<long long unsigned int, long long unsigned int>, std::pair<long long unsigned int, long long unsigned int>)> >]':
-/usr/include/c++/10/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, long long unsigned int>*, std::vector<std::pair<long long unsigned int, long long unsigned int> > >' changed in GCC 7.1
- 1819 | __unguarded_linear_insert(_RandomAccessIterator __last,
- | ^~~~~~~~~~~~~~~~~~~~~~~~~
+In file included from /usr/include/c++/10/vector:67,
+ from /build/kallisto-0.46.2+dfsg/src/Merge.cpp:5:
+/usr/include/c++/10/bits/stl_vector.h: In function 'bool MergeBatchDirectories(const ProgramOptions&, int&, int64_t&, int64_t&, int64_t&, int&)':
+/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
+ 1198 | _M_realloc_insert(end(), __x);
+ | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /build/kallisto-0.46.2+dfsg/src/KmerIndex.h:18,
from /build/kallisto-0.46.2+dfsg/src/MinCollector.h:11,
from /build/kallisto-0.46.2+dfsg/src/ProcessReads.h:18,
@@ -1015,19 +1105,6 @@
/build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow]
240 | v |= v >> 32;
| ~~^~~~~
-/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<long long unsigned int, long long unsigned int>*, std::vector<std::pair<long long unsigned int, long long unsigned int> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<MasterProcessor::processAln(const EMAlgorithm&, bool)::<lambda(std::pair<long long unsigned int, long long unsigned int>, std::pair<long long unsigned int, long long unsigned int>)> >]':
-/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, long long unsigned int>*, std::vector<std::pair<long long unsigned int, long long unsigned int> > >' changed in GCC 7.1
- 1839 | __insertion_sort(_RandomAccessIterator __first,
- | ^~~~~~~~~~~~~~~~
-/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, long long unsigned int>*, std::vector<std::pair<long long unsigned int, long long unsigned int> > >' changed in GCC 7.1
-/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<long long unsigned int, long long unsigned int>*, std::vector<std::pair<long long unsigned int, long long unsigned int> > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<MasterProcessor::processAln(const EMAlgorithm&, bool)::<lambda(std::pair<long long unsigned int, long long unsigned int>, std::pair<long long unsigned int, long long unsigned int>)> >]':
-/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, long long unsigned int>*, std::vector<std::pair<long long unsigned int, long long unsigned int> > >' changed in GCC 7.1
- 1945 | __introsort_loop(_RandomAccessIterator __first,
- | ^~~~~~~~~~~~~~~~
-/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, long long unsigned int>*, std::vector<std::pair<long long unsigned int, long long unsigned int> > >' changed in GCC 7.1
-/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, long long unsigned int>*, std::vector<std::pair<long long unsigned int, long long unsigned int> > >' changed in GCC 7.1
- 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
- | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /build/kallisto-0.46.2+dfsg/src/ProcessReads.h:7,
from /build/kallisto-0.46.2+dfsg/src/ProcessReads.cpp:22:
@@ -1037,12 +1114,6 @@
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const BUSData&}; _Tp = BUSData; _Alloc = std::allocator<BUSData>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<BUSData>::iterator' changed in GCC 7.1
-In file included from /usr/include/c++/10/vector:67,
- from /build/kallisto-0.46.2+dfsg/src/Merge.cpp:5:
-/usr/include/c++/10/bits/stl_vector.h: In function 'bool MergeBatchDirectories(const ProgramOptions&, int&, int64_t&, int64_t&, int64_t&, int&)':
-/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
- 1198 | _M_realloc_insert(end(), __x);
- | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair<long long unsigned int, long long unsigned int>}; _Tp = std::pair<long long unsigned int, long long unsigned int>; _Alloc = std::allocator<std::pair<long long unsigned int, long long unsigned int> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<std::pair<long long unsigned int, long long unsigned int> >::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {PseudoAlignmentInfo}; _Tp = PseudoAlignmentInfo; _Alloc = std::allocator<PseudoAlignmentInfo>]':
@@ -1114,14 +1185,6 @@
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<bam1_t*, std::vector<bam1_t> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
-In file included from /usr/include/c++/10/vector:72,
- from /usr/include/c++/10/bits/random.h:34,
- from /usr/include/c++/10/random:49,
- from /build/kallisto-0.46.2+dfsg/src/main.cpp:3:
-/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = std::pair<double, double>; _Alloc = std::allocator<std::pair<double, double> >]':
-/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<std::pair<double, double> >::iterator' changed in GCC 7.1
- 509 | vector<_Tp, _Alloc>::
- | ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void MasterProcessor::update(const std::vector<int>&, const std::vector<std::vector<int> >&, std::vector<std::pair<int, std::__cxx11::basic_string<char> > >&, std::vector<std::pair<std::vector<int>, std::__cxx11::basic_string<char> > >&, int, std::vector<int>&, std::vector<int>&, const PseudoAlignmentBatch&, std::vector<BUSData>&, std::vector<std::pair<BUSData, std::vector<int> > >, int*, int*, int, int)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BUSData*, std::vector<BUSData> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
@@ -1154,6 +1217,14 @@
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<bam1_t*, std::vector<bam1_t> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
+In file included from /usr/include/c++/10/vector:72,
+ from /usr/include/c++/10/bits/random.h:34,
+ from /usr/include/c++/10/random:49,
+ from /build/kallisto-0.46.2+dfsg/src/main.cpp:3:
+/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = std::pair<double, double>; _Alloc = std::allocator<std::pair<double, double> >]':
+/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<std::pair<double, double> >::iterator' changed in GCC 7.1
+ 509 | vector<_Tp, _Alloc>::
+ | ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair<int, double>}; _Tp = std::pair<int, double>; _Alloc = std::allocator<std::pair<int, double> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<std::pair<int, double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
@@ -1272,7 +1343,7 @@
create-stamp debian/debhelper-build-stamp
dh_prep
dh_auto_install
- cd obj-arm-linux-gnueabihf && make -j5 install DESTDIR=/build/kallisto-0.46.2\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true"
+ cd obj-arm-linux-gnueabihf && make -j4 install DESTDIR=/build/kallisto-0.46.2\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true"
make[1]: Entering directory '/build/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf'
/usr/bin/cmake -S/build/kallisto-0.46.2+dfsg -B/build/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /build/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles /build/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf//CMakeFiles/progress.marks
@@ -1325,9 +1396,9 @@
dh_gencontrol
dh_md5sums
dh_builddeb
-dpkg-deb: building package 'kallisto-examples' in '../kallisto-examples_0.46.2+dfsg-2_all.deb'.
dpkg-deb: building package 'kallisto' in '../kallisto_0.46.2+dfsg-2_armhf.deb'.
dpkg-deb: building package 'kallisto-dbgsym' in '../kallisto-dbgsym_0.46.2+dfsg-2_armhf.deb'.
+dpkg-deb: building package 'kallisto-examples' in '../kallisto-examples_0.46.2+dfsg-2_all.deb'.
dpkg-genbuildinfo --build=binary
dpkg-genchanges --build=binary >../kallisto_0.46.2+dfsg-2_armhf.changes
dpkg-genchanges: info: binary-only upload (no source code included)
@@ -1335,12 +1406,14 @@
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/26973/tmp/hooks/B01_cleanup starting
+I: user script /srv/workspace/pbuilder/26973/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/29247 and its subdirectories
-I: Current time: Wed Aug 11 10:28:59 -12 2021
-I: pbuilder-time-stamp: 1628720939
+I: removing directory /srv/workspace/pbuilder/26973 and its subdirectories
+I: Current time: Thu Aug 12 12:32:36 +14 2021
+I: pbuilder-time-stamp: 1628721156