I: pbuilder: network access will be disabled during build
I: Current time: Wed Jun 7 21:19:14 +14 2023
I: pbuilder-time-stamp: 1686122354
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: Copying source file
I: copying [provean_1.1.5+ds-2.dsc]
I: copying [./provean_1.1.5+ds.orig.tar.xz]
I: copying [./provean_1.1.5+ds-2.debian.tar.xz]
I: Extracting source
gpgv: Signature made Thu May 19 00:00:00 2022 +14
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./provean_1.1.5+ds-2.dsc: no acceptable signature found
dpkg-source: info: extracting provean in provean-1.1.5+ds
dpkg-source: info: unpacking provean_1.1.5+ds.orig.tar.xz
dpkg-source: info: unpacking provean_1.1.5+ds-2.debian.tar.xz
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/733948/tmp/hooks/D01_modify_environment starting
debug: Running on ionos1-amd64.
I: Changing host+domainname to test build reproducibility
I: Adding a custom variable just for the fun of it...
I: Changing /bin/sh to bash
'/bin/sh' -> '/bin/bash'
lrwxrwxrwx 1 root root 9 Jun 7 21:19 /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/733948/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/733948/tmp/hooks/D02_print_environment starting
I: set
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]="x86_64-pc-linux-gnu")
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=amd64
DEBIAN_FRONTEND=noninteractive
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15 '
DIRSTACK=()
DISTRIBUTION=bookworm
EUID=0
FUNCNAME=([0]="Echo" [1]="main")
GROUPS=()
HOME=/root
HOSTNAME=i-capture-the-hostname
HOSTTYPE=x86_64
HOST_ARCH=amd64
IFS='
'
INVOCATION_ID=2d8a658a70414c9584e28e049d0bc479
LANG=C
LANGUAGE=et_EE:et
LC_ALL=C
MACHTYPE=x86_64-pc-linux-gnu
MAIL=/var/mail/root
OPTERR=1
OPTIND=1
OSTYPE=linux-gnu
PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path
PBCURRENTCOMMANDLINEOPERATION=build
PBUILDER_OPERATION=build
PBUILDER_PKGDATADIR=/usr/share/pbuilder
PBUILDER_PKGLIBDIR=/usr/lib/pbuilder
PBUILDER_SYSCONFDIR=/etc
PIPESTATUS=([0]="0")
POSIXLY_CORRECT=y
PPID=733948
PS4='+ '
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.IZQjIH0U/pbuilderrc_IZCM --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.IZQjIH0U/b2 --logfile b2/build.log --extrapackages usrmerge provean_1.1.5+ds-2.dsc'
SUDO_GID=110
SUDO_UID=105
SUDO_USER=jenkins
TERM=unknown
TZ=/usr/share/zoneinfo/Etc/GMT-14
UID=0
USER=root
_='I: set'
http_proxy=http://78.137.99.97:3128
I: uname -a
Linux i-capture-the-hostname 5.10.0-23-amd64 #1 SMP Debian 5.10.179-1 (2023-05-12) x86_64 GNU/Linux
I: ls -l /bin
total 5632
-rwxr-xr-x 1 root root 1265648 Apr 24 11:23 bash
-rwxr-xr-x 3 root root 39224 Sep 19 2022 bunzip2
-rwxr-xr-x 3 root root 39224 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 39224 Sep 19 2022 bzip2
-rwxr-xr-x 1 root root 14568 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 44016 Sep 21 2022 cat
-rwxr-xr-x 1 root root 68656 Sep 21 2022 chgrp
-rwxr-xr-x 1 root root 64496 Sep 21 2022 chmod
-rwxr-xr-x 1 root root 72752 Sep 21 2022 chown
-rwxr-xr-x 1 root root 151152 Sep 21 2022 cp
-rwxr-xr-x 1 root root 125640 Jan 6 03:20 dash
-rwxr-xr-x 1 root root 121904 Sep 21 2022 date
-rwxr-xr-x 1 root root 89240 Sep 21 2022 dd
-rwxr-xr-x 1 root root 102200 Sep 21 2022 df
-rwxr-xr-x 1 root root 151344 Sep 21 2022 dir
-rwxr-xr-x 1 root root 88656 Mar 24 00:02 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 43856 Sep 21 2022 echo
-rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep
-rwxr-xr-x 1 root root 35664 Sep 21 2022 false
-rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep
-rwxr-xr-x 1 root root 85600 Mar 24 00:02 findmnt
-rwsr-xr-x 1 root root 35128 Mar 23 22:35 fusermount
-rwxr-xr-x 1 root root 203152 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 98136 Apr 10 2022 gzip
-rwxr-xr-x 1 root root 22680 Dec 20 03:33 hostname
-rwxr-xr-x 1 root root 72824 Sep 21 2022 ln
-rwxr-xr-x 1 root root 53024 Mar 24 02:40 login
-rwxr-xr-x 1 root root 151344 Sep 21 2022 ls
-rwxr-xr-x 1 root root 207168 Mar 24 00:02 lsblk
-rwxr-xr-x 1 root root 97552 Sep 21 2022 mkdir
-rwxr-xr-x 1 root root 72912 Sep 21 2022 mknod
-rwxr-xr-x 1 root root 43952 Sep 21 2022 mktemp
-rwxr-xr-x 1 root root 59712 Mar 24 00:02 more
-rwsr-xr-x 1 root root 59704 Mar 24 00:02 mount
-rwxr-xr-x 1 root root 18744 Mar 24 00:02 mountpoint
-rwxr-xr-x 1 root root 142968 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 43952 Sep 21 2022 pwd
lrwxrwxrwx 1 root root 4 Apr 24 11:23 rbash -> bash
-rwxr-xr-x 1 root root 52112 Sep 21 2022 readlink
-rwxr-xr-x 1 root root 72752 Sep 21 2022 rm
-rwxr-xr-x 1 root root 56240 Sep 21 2022 rmdir
-rwxr-xr-x 1 root root 27560 Nov 3 2022 run-parts
-rwxr-xr-x 1 root root 126424 Jan 6 09:55 sed
lrwxrwxrwx 1 root root 9 Jun 7 21:19 sh -> /bin/bash
-rwxr-xr-x 1 root root 43888 Sep 21 2022 sleep
-rwxr-xr-x 1 root root 85008 Sep 21 2022 stty
-rwsr-xr-x 1 root root 72000 Mar 24 00:02 su
-rwxr-xr-x 1 root root 39824 Sep 21 2022 sync
-rwxr-xr-x 1 root root 531984 Apr 7 04:25 tar
-rwxr-xr-x 1 root root 14520 Nov 3 2022 tempfile
-rwxr-xr-x 1 root root 109616 Sep 21 2022 touch
-rwxr-xr-x 1 root root 35664 Sep 21 2022 true
-rwxr-xr-x 1 root root 14568 Mar 23 22:35 ulockmgr_server
-rwsr-xr-x 1 root root 35128 Mar 24 00:02 umount
-rwxr-xr-x 1 root root 43888 Sep 21 2022 uname
-rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress
-rwxr-xr-x 1 root root 151344 Sep 21 2022 vdir
-rwxr-xr-x 1 root root 72024 Mar 24 00:02 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/733948/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: amd64
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
This package was created automatically by pbuilder to satisfy the
build-dependencies of the package being currently built.
Depends: cd-hit, debhelper-compat (= 13), ncbi-blast+
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19591 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
pbuilder-satisfydepends-dummy depends on cd-hit; however:
Package cd-hit is not installed.
pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however:
Package debhelper-compat is not installed.
pbuilder-satisfydepends-dummy depends on ncbi-blast+; however:
Package ncbi-blast+ is not installed.
Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} cd-hit{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libicu72{a} liblmdb0{a} libmagic-mgc{a} libmagic1{a} libmbedcrypto7{a} libmbedtls14{a} libmbedx509-1{a} libpcre3{a} libpipeline1{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} ncbi-blast+{a} ncbi-data{a} po-debconf{a} python3{a} python3-minimal{a} python3.11{a} python3.11-minimal{a} readline-common{a} sensible-utils{a}
The following packages are RECOMMENDED but will NOT be installed:
ca-certificates curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget
0 packages upgraded, 49 newly installed, 0 to remove and 0 not upgraded.
Need to get 41.4 MB of archives. After unpacking 176 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6 [813 kB]
Get: 2 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB]
Get: 3 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6 [2064 kB]
Get: 4 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB]
Get: 5 http://deb.debian.org/debian bookworm/main amd64 media-types all 10.0.0 [26.1 kB]
Get: 6 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB]
Get: 7 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB]
Get: 8 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6 [1796 kB]
Get: 9 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6 [572 kB]
Get: 10 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B]
Get: 11 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB]
Get: 12 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB]
Get: 13 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB]
Get: 14 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB]
Get: 15 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB]
Get: 16 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB]
Get: 17 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB]
Get: 18 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB]
Get: 19 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB]
Get: 20 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB]
Get: 21 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB]
Get: 22 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB]
Get: 23 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB]
Get: 24 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get: 25 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB]
Get: 26 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB]
Get: 27 http://deb.debian.org/debian bookworm/main amd64 cd-hit amd64 4.8.1-4 [522 kB]
Get: 28 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB]
Get: 29 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB]
Get: 30 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB]
Get: 31 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 32 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B]
Get: 33 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get: 34 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get: 35 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB]
Get: 36 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB]
Get: 37 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB]
Get: 38 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.2 [687 kB]
Get: 39 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB]
Get: 40 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 41 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 42 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB]
Get: 43 http://deb.debian.org/debian bookworm/main amd64 liblmdb0 amd64 0.9.24-1 [45.0 kB]
Get: 44 http://deb.debian.org/debian bookworm/main amd64 libmbedcrypto7 amd64 2.28.3-1 [277 kB]
Get: 45 http://deb.debian.org/debian bookworm/main amd64 libmbedx509-1 amd64 2.28.3-1 [128 kB]
Get: 46 http://deb.debian.org/debian bookworm/main amd64 libmbedtls14 amd64 2.28.3-1 [163 kB]
Get: 47 http://deb.debian.org/debian bookworm/main amd64 libpcre3 amd64 2:8.39-15 [341 kB]
Get: 48 http://deb.debian.org/debian bookworm/main amd64 ncbi-data all 6.1.20170106+dfsg1-10 [3557 kB]
Get: 49 http://deb.debian.org/debian bookworm/main amd64 ncbi-blast+ amd64 2.12.0+ds-3+b1 [11.9 MB]
Fetched 41.4 MB in 2s (23.1 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package libpython3.11-minimal:amd64.
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Preparing to unpack .../libpython3.11-minimal_3.11.2-6_amd64.deb ...
Unpacking libpython3.11-minimal:amd64 (3.11.2-6) ...
Selecting previously unselected package libexpat1:amd64.
Preparing to unpack .../libexpat1_2.5.0-1_amd64.deb ...
Unpacking libexpat1:amd64 (2.5.0-1) ...
Selecting previously unselected package python3.11-minimal.
Preparing to unpack .../python3.11-minimal_3.11.2-6_amd64.deb ...
Unpacking python3.11-minimal (3.11.2-6) ...
Setting up libpython3.11-minimal:amd64 (3.11.2-6) ...
Setting up libexpat1:amd64 (2.5.0-1) ...
Setting up python3.11-minimal (3.11.2-6) ...
Selecting previously unselected package python3-minimal.
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Preparing to unpack .../0-python3-minimal_3.11.2-1+b1_amd64.deb ...
Unpacking python3-minimal (3.11.2-1+b1) ...
Selecting previously unselected package media-types.
Preparing to unpack .../1-media-types_10.0.0_all.deb ...
Unpacking media-types (10.0.0) ...
Selecting previously unselected package readline-common.
Preparing to unpack .../2-readline-common_8.2-1.3_all.deb ...
Unpacking readline-common (8.2-1.3) ...
Selecting previously unselected package libreadline8:amd64.
Preparing to unpack .../3-libreadline8_8.2-1.3_amd64.deb ...
Unpacking libreadline8:amd64 (8.2-1.3) ...
Selecting previously unselected package libpython3.11-stdlib:amd64.
Preparing to unpack .../4-libpython3.11-stdlib_3.11.2-6_amd64.deb ...
Unpacking libpython3.11-stdlib:amd64 (3.11.2-6) ...
Selecting previously unselected package python3.11.
Preparing to unpack .../5-python3.11_3.11.2-6_amd64.deb ...
Unpacking python3.11 (3.11.2-6) ...
Selecting previously unselected package libpython3-stdlib:amd64.
Preparing to unpack .../6-libpython3-stdlib_3.11.2-1+b1_amd64.deb ...
Unpacking libpython3-stdlib:amd64 (3.11.2-1+b1) ...
Setting up python3-minimal (3.11.2-1+b1) ...
Selecting previously unselected package python3.
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Preparing to unpack .../00-python3_3.11.2-1+b1_amd64.deb ...
Unpacking python3 (3.11.2-1+b1) ...
Selecting previously unselected package sensible-utils.
Preparing to unpack .../01-sensible-utils_0.0.17+nmu1_all.deb ...
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usrmerge is already the newest version (35).
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I: Building the package
I: user script /srv/workspace/pbuilder/733948/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/733948/tmp/hooks/A99_set_merged_usr finished
hostname: Name or service not known
I: Running cd /build/provean-1.1.5+ds/ && 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 > ../provean_1.1.5+ds-2_source.changes
dpkg-buildpackage: info: source package provean
dpkg-buildpackage: info: source version 1.1.5+ds-2
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andreas Tille <tille@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture amd64
debian/rules clean
dh clean
dh_clean
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
configure.ac:2: installing './install-sh'
configure.ac:2: installing './missing'
src/Makefile.am: installing './depcomp'
dh_auto_configure
./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a race-free mkdir -p... /usr/bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C++... yes
checking whether g++ accepts -g... yes
checking for g++ option to enable C++11 features... none needed
checking whether make supports the include directive... yes (GNU style)
checking dependency style of g++... none
checking for psiblast... /usr/bin/psiblast
checking for cd-hit... /usr/bin/cd-hit
checking for blastdbcmd... /usr/bin/blastdbcmd
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating scripts/Makefile
config.status: creating examples/Makefile
config.status: creating config.h
config.status: executing depfiles commands
dh_auto_build
make -j15
make[1]: Entering directory '/build/provean-1.1.5+ds'
make all-recursive
make[2]: Entering directory '/build/provean-1.1.5+ds'
Making all in src
make[3]: Entering directory '/build/provean-1.1.5+ds/src'
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/provean-1.1.5+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o provean.o provean.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/provean-1.1.5+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Common.o Common.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/provean-1.1.5+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Options.o Options.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/provean-1.1.5+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o SequenceDB.o SequenceDB.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/provean-1.1.5+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ScoreMatrix.o ScoreMatrix.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/provean-1.1.5+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Sequence.o Sequence.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/provean-1.1.5+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Tables.o Tables.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/provean-1.1.5+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Variant.o Variant.cpp
Sequence.cpp: In member function 'bool Sequence::SetSequenceFromFastaFile(const char*, std::string)':
Sequence.cpp:100:38: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
100 | fgets(buf, sizeof(buf), fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~
SequenceDB.cpp: In member function 'int SequenceDB::SetSequencesFromFastaFile(std::string)':
SequenceDB.cpp:295:38: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
295 | fgets(buf, sizeof(buf), fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~
SequenceDB.cpp: In member function 'int SequenceDB::SetOnlySequencesFromFastaFile(std::string)':
SequenceDB.cpp:652:38: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
652 | fgets(buf, sizeof(buf), fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~
SequenceDB.cpp: In member function 'int SequenceDB::ClusterAndSelectFromFastaFile(std::string)':
SequenceDB.cpp:737:35: warning: '.help' directive writing 5 bytes into a region of size between 1 and 65536 [-Wformat-overflow=]
737 | sprintf(help_filename, "%s.help", output_prefix);
| ^~~~~
In file included from /usr/include/stdio.h:906,
from /usr/include/c++/12/cstdio:42,
from /usr/include/c++/12/ext/string_conversions.h:43,
from /usr/include/c++/12/bits/basic_string.h:3960,
from /usr/include/c++/12/string:53,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/ostream:38,
from /usr/include/c++/12/iostream:39,
from SequenceDB.cpp:17:
In function 'int sprintf(char*, const char*, ...)',
inlined from 'int SequenceDB::ClusterAndSelectFromFastaFile(std::string)' at SequenceDB.cpp:737:9:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 6 and 65541 bytes into a destination of size 65536
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
SequenceDB.cpp: In member function 'int SequenceDB::ClusterAndSelectFromFastaFile(std::string)':
SequenceDB.cpp:738:41: warning: '%s' directive writing up to 65535 bytes into a region of size 65530 [-Wformat-overflow=]
738 | sprintf(cdhit_command, "%s -h > %s",
| ^~
739 | p_options_->cdhit_command_.c_str(),
740 | help_filename);
| ~~~~~~~~~~~~~
In function 'int sprintf(char*, const char*, ...)',
inlined from 'int SequenceDB::ClusterAndSelectFromFastaFile(std::string)' at SequenceDB.cpp:738:9:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 7 or more bytes (assuming 65542) into a destination of size 65536
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
SequenceDB.cpp: In member function 'int SequenceDB::ClusterAndSelectFromFastaFile(std::string)':
SequenceDB.cpp:776:53: warning: '%s' directive writing up to 65535 bytes into a region of size 65528 [-Wformat-overflow=]
776 | sprintf(cdhit_command, "%s -i %s -o %s.cluster -c %.2f -s %.1f -n 5 -l %d -bak 1 > %s.log",
| ^~
......
779 | output_prefix,
| ~~~~~~~~~~~~~
SequenceDB.cpp:776:40: note: assuming directive output of 4 bytes
776 | sprintf(cdhit_command, "%s -i %s -o %s.cluster -c %.2f -s %.1f -n 5 -l %d -bak 1 > %s.log",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SequenceDB.cpp:776:40: note: using the range [-2147483648, 2147483647] for directive argument
In function 'int sprintf(char*, const char*, ...)',
inlined from 'int SequenceDB::ClusterAndSelectFromFastaFile(std::string)' at SequenceDB.cpp:776:10:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 55 or more bytes (assuming 131126) into a destination of size 65536
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
SequenceDB.cpp: In member function 'int SequenceDB::ClusterAndSelectFromFastaFile(std::string)':
SequenceDB.cpp:785:53: warning: '%s' directive writing up to 65535 bytes into a region of size 65528 [-Wformat-overflow=]
785 | sprintf(cdhit_command, "%s -i %s -o %s.cluster -c %.2f -s %.1f -n 5 -l %d > %s.log",
| ^~
......
788 | output_prefix,
| ~~~~~~~~~~~~~
SequenceDB.cpp:785:40: note: assuming directive output of 4 bytes
785 | sprintf(cdhit_command, "%s -i %s -o %s.cluster -c %.2f -s %.1f -n 5 -l %d > %s.log",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SequenceDB.cpp:785:40: note: using the range [-2147483648, 2147483647] for directive argument
In function 'int sprintf(char*, const char*, ...)',
inlined from 'int SequenceDB::ClusterAndSelectFromFastaFile(std::string)' at SequenceDB.cpp:785:10:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 48 or more bytes (assuming 131119) into a destination of size 65536
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
SequenceDB.cpp: In member function 'int SequenceDB::ClusterAndSelectFromFastaFile(std::string)':
SequenceDB.cpp:830:38: warning: '.cluster.bak.clstr' directive writing 18 bytes into a region of size between 1 and 65536 [-Wformat-overflow=]
830 | sprintf(cluster_filename, "%s.cluster.bak.clstr", output_prefix);
| ^~~~~~~~~~~~~~~~~~
In function 'int sprintf(char*, const char*, ...)',
inlined from 'int SequenceDB::ClusterAndSelectFromFastaFile(std::string)' at SequenceDB.cpp:830:9:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 19 and 65554 bytes into a destination of size 65536
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
SequenceDB.cpp: In member function 'int SequenceDB::ClusterAndSelectFromFastaFile(std::string)':
SequenceDB.cpp:804:42: warning: '.log' directive writing 4 bytes into a region of size between 1 and 65536 [-Wformat-overflow=]
804 | sprintf(log_filename, "%s.log", output_prefix);
| ^~~~
In function 'int sprintf(char*, const char*, ...)',
inlined from 'int SequenceDB::ClusterAndSelectFromFastaFile(std::string)' at SequenceDB.cpp:804:10:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 65540 bytes into a destination of size 65536
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
SequenceDB.cpp: In member function 'void SequenceDB::RunBlast(std::string, std::string, std::string)':
SequenceDB.cpp:1552:47: warning: '%s' directive writing up to 65535 bytes into a region of size 65524 [-Wformat-overflow=]
1552 | sprintf(blast_command, "%s -version > %s", p_options_->psiblast_command_.c_str(), blast_help);
| ^~ ~~~~~~~~~~
In function 'int sprintf(char*, const char*, ...)',
inlined from 'void SequenceDB::RunBlast(std::string, std::string, std::string)' at SequenceDB.cpp:1552:9:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 13 or more bytes (assuming 65548) into a destination of size 65536
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/provean-1.1.5+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -o provean provean.o Common.o Options.o SequenceDB.o ScoreMatrix.o Sequence.o Tables.o Variant.o
make[3]: Leaving directory '/build/provean-1.1.5+ds/src'
Making all in scripts
make[3]: Entering directory '/build/provean-1.1.5+ds/scripts'
sed -e 's,\[@\]PSIBLAST\[@\],/usr/bin/psiblast,g' -e 's,\[@\]CDHIT\[@\],/usr/bin/cd-hit,g' -e 's,\[@\]BLASTDB\[@\],,g' -e 's,\[@\]BLASTDBCMD\[@\],/usr/bin/blastdbcmd,g' -e 's,\[@\]VERSION\[@\],1.1.5,g' < ./provean.sh.in > provean.sh
chmod +x provean.sh
make[3]: Leaving directory '/build/provean-1.1.5+ds/scripts'
Making all in examples
make[3]: Entering directory '/build/provean-1.1.5+ds/examples'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/build/provean-1.1.5+ds/examples'
make[3]: Entering directory '/build/provean-1.1.5+ds'
make[3]: Leaving directory '/build/provean-1.1.5+ds'
make[2]: Leaving directory '/build/provean-1.1.5+ds'
make[1]: Leaving directory '/build/provean-1.1.5+ds'
dh_auto_test
make -j15 check "TESTSUITEFLAGS=-j15 --verbose" VERBOSE=1
make[1]: Entering directory '/build/provean-1.1.5+ds'
Making check in src
make[2]: Entering directory '/build/provean-1.1.5+ds/src'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/build/provean-1.1.5+ds/src'
Making check in scripts
make[2]: Entering directory '/build/provean-1.1.5+ds/scripts'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/build/provean-1.1.5+ds/scripts'
Making check in examples
make[2]: Entering directory '/build/provean-1.1.5+ds/examples'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/build/provean-1.1.5+ds/examples'
make[2]: Entering directory '/build/provean-1.1.5+ds'
make[2]: Leaving directory '/build/provean-1.1.5+ds'
make[1]: Leaving directory '/build/provean-1.1.5+ds'
create-stamp debian/debhelper-build-stamp
dh_prep
dh_auto_install --destdir=debian/provean/
make -j15 install DESTDIR=/build/provean-1.1.5\+ds/debian/provean AM_UPDATE_INFO_DIR=no
make[1]: Entering directory '/build/provean-1.1.5+ds'
Making install in src
make[2]: Entering directory '/build/provean-1.1.5+ds/src'
make[3]: Entering directory '/build/provean-1.1.5+ds/src'
make[3]: Nothing to be done for 'install-data-am'.
/usr/bin/mkdir -p '/build/provean-1.1.5+ds/debian/provean/usr/bin'
/usr/bin/install -c provean '/build/provean-1.1.5+ds/debian/provean/usr/bin'
make[3]: Leaving directory '/build/provean-1.1.5+ds/src'
make[2]: Leaving directory '/build/provean-1.1.5+ds/src'
Making install in scripts
make[2]: Entering directory '/build/provean-1.1.5+ds/scripts'
make[3]: Entering directory '/build/provean-1.1.5+ds/scripts'
/usr/bin/mkdir -p '/build/provean-1.1.5+ds/debian/provean/usr/bin'
make[3]: Nothing to be done for 'install-data-am'.
/usr/bin/install -c provean.sh '/build/provean-1.1.5+ds/debian/provean/usr/bin'
make[3]: Leaving directory '/build/provean-1.1.5+ds/scripts'
make[2]: Leaving directory '/build/provean-1.1.5+ds/scripts'
Making install in examples
make[2]: Entering directory '/build/provean-1.1.5+ds/examples'
make[3]: Entering directory '/build/provean-1.1.5+ds/examples'
make[3]: Nothing to be done for 'install-exec-am'.
/usr/bin/mkdir -p '/build/provean-1.1.5+ds/debian/provean/usr/share/data/provean/examples'
/usr/bin/install -c -m 644 P04637.fasta P04637.var '/build/provean-1.1.5+ds/debian/provean/usr/share/data/provean/examples'
make[3]: Leaving directory '/build/provean-1.1.5+ds/examples'
make[2]: Leaving directory '/build/provean-1.1.5+ds/examples'
make[2]: Entering directory '/build/provean-1.1.5+ds'
make[3]: Entering directory '/build/provean-1.1.5+ds'
make[3]: Nothing to be done for 'install-exec-am'.
/usr/bin/mkdir -p '/build/provean-1.1.5+ds/debian/provean/usr/share/doc/provean'
/usr/bin/install -c -m 644 README LICENSE '/build/provean-1.1.5+ds/debian/provean/usr/share/doc/provean'
make[3]: Leaving directory '/build/provean-1.1.5+ds'
make[2]: Leaving directory '/build/provean-1.1.5+ds'
make[1]: Leaving directory '/build/provean-1.1.5+ds'
debian/rules override_dh_install
make[1]: Entering directory '/build/provean-1.1.5+ds'
dh_install
rm debian/provean/usr/bin/provean.sh
make[1]: Leaving directory '/build/provean-1.1.5+ds'
dh_installdocs
dh_installchangelogs
dh_installman
dh_perl
dh_link
dh_strip_nondeterminism
dh_compress
dh_fixperms
dh_missing
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dh_installdeb
dh_gencontrol
dh_md5sums
dh_builddeb
dpkg-deb: building package 'provean-dbgsym' in '../provean-dbgsym_1.1.5+ds-2_amd64.deb'.
dpkg-deb: building package 'provean' in '../provean_1.1.5+ds-2_amd64.deb'.
dpkg-genbuildinfo --build=binary -O../provean_1.1.5+ds-2_amd64.buildinfo
dpkg-genchanges --build=binary -O../provean_1.1.5+ds-2_amd64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
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/733948/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/733948/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/733948 and its subdirectories
I: Current time: Wed Jun 7 21:22:24 +14 2023
I: pbuilder-time-stamp: 1686122544