I: pbuilder: network access will be disabled during build
I: Current time: Fri May 19 10:19:57 +14 2023
I: pbuilder-time-stamp: 1684441197
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 [pbdagcon_0.3+git20180411.c14c422+dfsg-8.dsc]
I: copying [./pbdagcon_0.3+git20180411.c14c422+dfsg.orig.tar.xz]
I: copying [./pbdagcon_0.3+git20180411.c14c422+dfsg-8.debian.tar.xz]
I: Extracting source
gpgv: Signature made Thu Mar 10 19:34:27 2022 +14
gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1
gpgv: issuer "nilesh@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./pbdagcon_0.3+git20180411.c14c422+dfsg-8.dsc: no acceptable signature found
dpkg-source: info: extracting pbdagcon in pbdagcon-0.3+git20180411.c14c422+dfsg
dpkg-source: info: unpacking pbdagcon_0.3+git20180411.c14c422+dfsg.orig.tar.xz
dpkg-source: info: unpacking pbdagcon_0.3+git20180411.c14c422+dfsg-8.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying compiler-flags.patch
dpkg-source: info: applying 2to3.patch
dpkg-source: info: applying libdata_libpbihdf.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/283060/tmp/hooks/D01_modify_environment starting
debug: Running on ionos11-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 May 19 10:20 /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/283060/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/283060/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=bf5939be36d845dfb280ce1cc50a03e0
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=283060
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.DI0FX5Cc/pbuilderrc_S1v5 --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.DI0FX5Cc/b2 --logfile b2/build.log --extrapackages usrmerge pbdagcon_0.3+git20180411.c14c422+dfsg-8.dsc'
SUDO_GID=111
SUDO_UID=106
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 May 19 10:20 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/283060/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: debhelper-compat (= 13), python3:any, zlib1g-dev, libhdf5-dev, libboost-dev, libtclap-dev, libpbseq-dev (>= 5.3.5+dfsg-4~), libpbbam-dev, libpbdata-dev (>= 5.3.5+dfsg-4~), libpbcopper-dev, libpbihdf-dev (>= 5.3.5+dfsg-4~), googletest
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19596 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 debhelper-compat (= 13); however:
Package debhelper-compat is not installed.
pbuilder-satisfydepends-dummy depends on python3:any.
pbuilder-satisfydepends-dummy depends on zlib1g-dev; however:
Package zlib1g-dev is not installed.
pbuilder-satisfydepends-dummy depends on libhdf5-dev; however:
Package libhdf5-dev is not installed.
pbuilder-satisfydepends-dummy depends on libboost-dev; however:
Package libboost-dev is not installed.
pbuilder-satisfydepends-dummy depends on libtclap-dev; however:
Package libtclap-dev is not installed.
pbuilder-satisfydepends-dummy depends on libpbseq-dev (>= 5.3.5+dfsg-4~); however:
Package libpbseq-dev is not installed.
pbuilder-satisfydepends-dummy depends on libpbbam-dev; however:
Package libpbbam-dev is not installed.
pbuilder-satisfydepends-dummy depends on libpbdata-dev (>= 5.3.5+dfsg-4~); however:
Package libpbdata-dev is not installed.
pbuilder-satisfydepends-dummy depends on libpbcopper-dev; however:
Package libpbcopper-dev is not installed.
pbuilder-satisfydepends-dummy depends on libpbihdf-dev (>= 5.3.5+dfsg-4~); however:
Package libpbihdf-dev is not installed.
pbuilder-satisfydepends-dummy depends on googletest; however:
Package googletest 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} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} googletest{a} groff-base{a} hdf5-helpers{a} intltool-debian{a} libaec-dev{a} libaec0{a} libarchive-zip-perl{a} libblasr-dev{a} libblasr5.3.5{a} libboost-dev{a} libboost1.74-dev{a} libbrotli1{a} libcurl3-gnutls{a} libcurl4{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libhdf5-103-1{a} libhdf5-cpp-103-1{a} libhdf5-dev{a} libhdf5-fortran-102{a} libhdf5-hl-100{a} libhdf5-hl-cpp-100{a} libhdf5-hl-fortran-100{a} libhts-dev{a} libhts3{a} libhtscodecs2{a} libicu72{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libldap-2.5-0{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libpbbam-dev{a} libpbbam2.1.0{a} libpbcopper-dev{a} libpbcopper2.0.0{a} libpbdata-dev{a} libpbihdf-dev{a} libpbseq-dev{a} libpipeline1{a} libpsl5{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1{a} libssl-dev{a} libsub-override-perl{a} libsz2{a} libtclap-dev{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} po-debconf{a} python3{a} python3-minimal{a} python3.11{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} zlib1g-dev{a}
The following packages are RECOMMENDED but will NOT be installed:
ca-certificates curl libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget
0 packages upgraded, 88 newly installed, 0 to remove and 0 not upgraded.
Need to get 57.0 MB of archives. After unpacking 339 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 libdebhelper-perl all 13.11.4 [81.2 kB]
Get: 28 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB]
Get: 29 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB]
Get: 30 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 31 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B]
Get: 32 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get: 33 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get: 34 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB]
Get: 35 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB]
Get: 36 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB]
Get: 37 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.2 [687 kB]
Get: 38 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB]
Get: 39 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 40 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 41 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB]
Get: 42 http://deb.debian.org/debian bookworm/main amd64 googletest all 1.12.1-0.2 [506 kB]
Get: 43 http://deb.debian.org/debian bookworm/main amd64 hdf5-helpers amd64 1.10.8+repack1-1 [27.9 kB]
Get: 44 http://deb.debian.org/debian bookworm/main amd64 libaec0 amd64 1.0.6-1+b1 [21.1 kB]
Get: 45 http://deb.debian.org/debian bookworm/main amd64 libsz2 amd64 1.0.6-1+b1 [7804 B]
Get: 46 http://deb.debian.org/debian bookworm/main amd64 libaec-dev amd64 1.0.6-1+b1 [19.9 kB]
Get: 47 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB]
Get: 48 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB]
Get: 49 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB]
Get: 50 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB]
Get: 51 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.52.0-1 [72.3 kB]
Get: 52 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB]
Get: 53 http://deb.debian.org/debian bookworm/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB]
Get: 54 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB]
Get: 55 http://deb.debian.org/debian bookworm/main amd64 libcurl4 amd64 7.88.1-9 [386 kB]
Get: 56 http://deb.debian.org/debian bookworm/main amd64 libhdf5-103-1 amd64 1.10.8+repack1-1 [1237 kB]
Get: 57 http://deb.debian.org/debian bookworm/main amd64 libhdf5-cpp-103-1 amd64 1.10.8+repack1-1 [128 kB]
Get: 58 http://deb.debian.org/debian bookworm/main amd64 libcurl3-gnutls amd64 7.88.1-9 [381 kB]
Get: 59 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB]
Get: 60 http://deb.debian.org/debian bookworm/main amd64 libhtscodecs2 amd64 1.3.0-4 [87.5 kB]
Get: 61 http://deb.debian.org/debian bookworm/main amd64 libhts3 amd64 1.16+ds-3 [430 kB]
Get: 62 http://deb.debian.org/debian bookworm/main amd64 libpbcopper2.0.0 amd64 2.0.0+dfsg-2 [606 kB]
Get: 63 http://deb.debian.org/debian bookworm/main amd64 libpbbam2.1.0 amd64 2.1.0+dfsg-2 [762 kB]
Get: 64 http://deb.debian.org/debian bookworm/main amd64 libblasr5.3.5 amd64 5.3.5+dfsg-4+b2 [1094 kB]
Get: 65 http://deb.debian.org/debian bookworm/main amd64 libpbcopper-dev amd64 2.0.0+dfsg-2 [920 kB]
Get: 66 http://deb.debian.org/debian bookworm/main amd64 libpbdata-dev amd64 5.3.5+dfsg-4+b2 [41.6 kB]
Get: 67 http://deb.debian.org/debian bookworm/main amd64 libblasr-dev amd64 5.3.5+dfsg-4+b2 [2073 kB]
Get: 68 http://deb.debian.org/debian bookworm/main amd64 libboost1.74-dev amd64 1.74.0+ds1-20 [9510 kB]
Get: 69 http://deb.debian.org/debian bookworm/main amd64 libboost-dev amd64 1.74.0.3 [4548 B]
Get: 70 http://deb.debian.org/debian bookworm/main amd64 libcurl4-gnutls-dev amd64 7.88.1-9 [481 kB]
Get: 71 http://deb.debian.org/debian bookworm/main amd64 libdeflate-dev amd64 1.14-1 [53.3 kB]
Get: 72 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12.2.0-14 [793 kB]
Get: 73 http://deb.debian.org/debian bookworm/main amd64 libhdf5-fortran-102 amd64 1.10.8+repack1-1 [93.3 kB]
Get: 74 http://deb.debian.org/debian bookworm/main amd64 libhdf5-hl-100 amd64 1.10.8+repack1-1 [67.8 kB]
Get: 75 http://deb.debian.org/debian bookworm/main amd64 libhdf5-hl-fortran-100 amd64 1.10.8+repack1-1 [44.5 kB]
Get: 76 http://deb.debian.org/debian bookworm/main amd64 libhdf5-hl-cpp-100 amd64 1.10.8+repack1-1 [25.5 kB]
Get: 77 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB]
Get: 78 http://deb.debian.org/debian bookworm/main amd64 libjpeg62-turbo amd64 1:2.1.5-2 [166 kB]
Get: 79 http://deb.debian.org/debian bookworm/main amd64 libjpeg62-turbo-dev amd64 1:2.1.5-2 [290 kB]
Get: 80 http://deb.debian.org/debian bookworm/main amd64 libjpeg-dev amd64 1:2.1.5-2 [71.8 kB]
Get: 81 http://deb.debian.org/debian bookworm/main amd64 libssl-dev amd64 3.0.8-1 [2427 kB]
Get: 82 http://deb.debian.org/debian bookworm/main amd64 libhdf5-dev amd64 1.10.8+repack1-1 [2615 kB]
Get: 83 http://deb.debian.org/debian bookworm/main amd64 liblzma-dev amd64 5.4.1-0.2 [260 kB]
Get: 84 http://deb.debian.org/debian bookworm/main amd64 libhts-dev amd64 1.16+ds-3 [1601 kB]
Get: 85 http://deb.debian.org/debian bookworm/main amd64 libpbbam-dev amd64 2.1.0+dfsg-2 [88.8 kB]
Get: 86 http://deb.debian.org/debian bookworm/main amd64 libpbihdf-dev amd64 5.3.5+dfsg-4+b2 [48.0 kB]
Get: 87 http://deb.debian.org/debian bookworm/main amd64 libpbseq-dev amd64 5.3.5+dfsg-4+b2 [5784 B]
Get: 88 http://deb.debian.org/debian bookworm/main amd64 libtclap-dev amd64 1.2.5-1+b1 [3360 kB]
Fetched 57.0 MB in 2s (24.6 MB/s)
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Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg-10) ...
Setting up autotools-dev (20220109.1) ...
Setting up libjpeg62-turbo:amd64 (1:2.1.5-2) ...
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Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ...
Setting up libssl-dev:amd64 (3.0.8-1) ...
Setting up autopoint (0.21-12) ...
Setting up libpbcopper-dev:amd64 (2.0.0+dfsg-2) ...
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Setting up libssh2-1:amd64 (1.10.0-3+b1) ...
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Setting up libsz2:amd64 (1.0.6-1+b1) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
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Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-5) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
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Not building database; man-db/auto-update is not 'true'.
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Setting up libhdf5-cpp-103-1:amd64 (1.10.8+repack1-1) ...
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update-alternatives: using /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode
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Reading package lists...
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-> Finished parsing the build-deps
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usrmerge is already the newest version (35).
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
I: Building the package
I: user script /srv/workspace/pbuilder/283060/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/283060/tmp/hooks/A99_set_merged_usr finished
hostname: Name or service not known
I: Running cd /build/pbdagcon-0.3+git20180411.c14c422+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 > ../pbdagcon_0.3+git20180411.c14c422+dfsg-8_source.changes
dpkg-buildpackage: info: source package pbdagcon
dpkg-buildpackage: info: source version 0.3+git20180411.c14c422+dfsg-8
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Nilesh Patra <nilesh@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture amd64
debian/rules clean
dh clean
dh_auto_clean
make -j15 clean
make[1]: Entering directory '/build/pbdagcon-0.3+git20180411.c14c422+dfsg'
make -C src/cpp clean
make[2]: Entering directory '/build/pbdagcon-0.3+git20180411.c14c422+dfsg/src/cpp'
rm -f *.d
rm -f *.o
rm -f pbdagcon
rm -f dazcon
make[2]: Leaving directory '/build/pbdagcon-0.3+git20180411.c14c422+dfsg/src/cpp'
make -C test/cpp clean
make[2]: Entering directory '/build/pbdagcon-0.3+git20180411.c14c422+dfsg/test/cpp'
rm -f .//*.o
rm -f *.o
rm -f test_*
make[2]: Leaving directory '/build/pbdagcon-0.3+git20180411.c14c422+dfsg/test/cpp'
make[1]: Leaving directory '/build/pbdagcon-0.3+git20180411.c14c422+dfsg'
dh_clean
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
debian/rules override_dh_auto_configure
make[1]: Entering directory '/build/pbdagcon-0.3+git20180411.c14c422+dfsg'
./configure.py --shared
uname -s
uname='Linux'
writing to '/build/pbdagcon-0.3+git20180411.c14c422+dfsg/defines.mk'
"""
DALIGNER_INCLUDE ?= ${DALIGNER_SRC}
DALIGNER_SRC ?= /build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/daligner-include
DAZZ_DB_INCLUDE ?= ${DAZZ_DB_SRC}
DAZZ_DB_SRC ?= /build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include
GTEST_INCLUDE ?= /usr/src/googletest/googletest/include
GTEST_SRC ?= /usr/src/googletest/googletest/src
HDF5_LIB ?= /usr/lib/x86_64-linux-gnu/hdf5/serial
HDF5_LIBFLAGS ?= -lhdf5_cpp -lhdf5
HTSLIB_LIBS ?= -lhts
LIBBLASR_INCLUDE ?= /usr/include/pbseq/alignment
LIBBLASR_LIBFLAGS ?= -lblasr
LIBPBDATA_INCLUDE ?= /usr/include/pbseq/pbdata
LIBPBIHDF_INCLUDE ?= /usr/include/pbseq/hdf
PBBAM_INCLUDE ?= /usr/include/pbseq
PBBAM_LIBFLAGS ?= -lpbbam
PTHREAD_LIBFLAGS ?= -lpthread
ZLIB_LIBFLAGS ?= -lz
LDLIBS+=-lrt
"""
make[1]: Leaving directory '/build/pbdagcon-0.3+git20180411.c14c422+dfsg'
dh_auto_build
make -j15 "INSTALL=install --strip-program=true"
make[1]: Entering directory '/build/pbdagcon-0.3+git20180411.c14c422+dfsg'
make -C src/cpp
make[2]: Entering directory '/build/pbdagcon-0.3+git20180411.c14c422+dfsg/src/cpp'
g++ -g -O2 -ffile-prefix-map=/build/pbdagcon-0.3+git20180411.c14c422+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wuninitialized -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/daligner-include -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -isystem.//third-party -c -o Alignment.o Alignment.cpp
g++ -g -O2 -ffile-prefix-map=/build/pbdagcon-0.3+git20180411.c14c422+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wuninitialized -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/daligner-include -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -isystem.//third-party -c -o AlnGraphBoost.o AlnGraphBoost.cpp
g++ -g -O2 -ffile-prefix-map=/build/pbdagcon-0.3+git20180411.c14c422+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wuninitialized -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/daligner-include -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -isystem.//third-party -c -o BlasrM5AlnProvider.o BlasrM5AlnProvider.cpp
g++ -g -O2 -ffile-prefix-map=/build/pbdagcon-0.3+git20180411.c14c422+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wuninitialized -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/daligner-include -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -isystem.//third-party -c -o main.o main.cpp
g++ -g -O2 -ffile-prefix-map=/build/pbdagcon-0.3+git20180411.c14c422+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wuninitialized -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/daligner-include -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -isystem.//third-party -c -o SimpleAligner.o SimpleAligner.cpp
cc -g -O2 -ffile-prefix-map=/build/pbdagcon-0.3+git20180411.c14c422+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wextra -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/daligner-include -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -isystem.//third-party -c -o DB.o /build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include/DB.c
cc -g -O2 -ffile-prefix-map=/build/pbdagcon-0.3+git20180411.c14c422+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wextra -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/daligner-include -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -isystem.//third-party -c -o QV.o /build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include/QV.c
cc -g -O2 -ffile-prefix-map=/build/pbdagcon-0.3+git20180411.c14c422+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wextra -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/daligner-include -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -isystem.//third-party -c -o align.o /build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/daligner-include/align.c
g++ -g -O2 -ffile-prefix-map=/build/pbdagcon-0.3+git20180411.c14c422+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wuninitialized -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/daligner-include -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -isystem.//third-party -c -o DazAlnProvider.o DazAlnProvider.cpp
g++ -g -O2 -ffile-prefix-map=/build/pbdagcon-0.3+git20180411.c14c422+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wuninitialized -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/daligner-include -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -isystem.//third-party -c -o dazcon.o dazcon.cpp
/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include/DB.c: In function 'Open_QVs':
/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include/DB.c:2415:16: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
2415 | (void) fscanf(istub,DB_NFILE,&nfiles);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include/DB.c:2419:20: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
2419 | { (void) fscanf(istub,DB_FDATA,&last,fname,prolog);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include/DB.c:2424:20: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
2424 | { (void) fscanf(istub,DB_FDATA,&last,fname,prolog);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o dazcon Alignment.o AlnGraphBoost.o DB.o QV.o align.o DazAlnProvider.o dazcon.o -Wl,-z,relro -L /usr/lib/x86_64-linux-gnu/hdf5/serial -lrt -lblasr -lpbbam -lhdf5_cpp -lhdf5 -lhts -lz -lpthread
g++ -o pbdagcon Alignment.o AlnGraphBoost.o BlasrM5AlnProvider.o main.o SimpleAligner.o -Wl,-z,relro -L /usr/lib/x86_64-linux-gnu/hdf5/serial -lrt -lblasr -lpbbam -lhdf5_cpp -lhdf5 -lhts -lz -lpthread
make[2]: Leaving directory '/build/pbdagcon-0.3+git20180411.c14c422+dfsg/src/cpp'
make[1]: Leaving directory '/build/pbdagcon-0.3+git20180411.c14c422+dfsg'
dh_auto_test
make -j15 check
make[1]: Entering directory '/build/pbdagcon-0.3+git20180411.c14c422+dfsg'
make -C src/cpp
make[2]: Entering directory '/build/pbdagcon-0.3+git20180411.c14c422+dfsg/src/cpp'
make[2]: Nothing to be done for 'all'.
make[2]: Leaving directory '/build/pbdagcon-0.3+git20180411.c14c422+dfsg/src/cpp'
make -C test/cpp
make[2]: Entering directory '/build/pbdagcon-0.3+git20180411.c14c422+dfsg/test/cpp'
g++ -g -O2 -ffile-prefix-map=/build/pbdagcon-0.3+git20180411.c14c422+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -Wall -Wextra -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -I. -I./ -I.//../../src/cpp -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/daligner-include -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -I/usr/src/googletest/googletest/include -Ithird-party -isystem /usr/src/googletest/googletest/include -isystem /usr/src/googletest/googletest/src/.. -c -o gtest-all.o /usr/src/googletest/googletest/src/gtest-all.cc
g++ -g -O2 -ffile-prefix-map=/build/pbdagcon-0.3+git20180411.c14c422+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -Wall -Wextra -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -I. -I./ -I.//../../src/cpp -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/daligner-include -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -I/usr/src/googletest/googletest/include -Ithird-party -isystem /usr/src/googletest/googletest/include -isystem /usr/src/googletest/googletest/src/.. -c -o gtest_main.o /usr/src/googletest/googletest/src/gtest_main.cc
g++ -g -O2 -ffile-prefix-map=/build/pbdagcon-0.3+git20180411.c14c422+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I. -I./ -I.//../../src/cpp -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/daligner-include -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -I/usr/src/googletest/googletest/include -Ithird-party -c -o AlnGraphBoost.o .//../../src/cpp/AlnGraphBoost.cpp
g++ -g -O2 -ffile-prefix-map=/build/pbdagcon-0.3+git20180411.c14c422+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I. -I./ -I.//../../src/cpp -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/daligner-include -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -I/usr/src/googletest/googletest/include -Ithird-party -c -o Alignment.o .//../../src/cpp/Alignment.cpp
g++ -g -O2 -ffile-prefix-map=/build/pbdagcon-0.3+git20180411.c14c422+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I. -I./ -I.//../../src/cpp -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/daligner-include -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -I/usr/src/googletest/googletest/include -Ithird-party -c -o SimpleAligner.o .//../../src/cpp/SimpleAligner.cpp
g++ -g -O2 -ffile-prefix-map=/build/pbdagcon-0.3+git20180411.c14c422+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I. -I./ -I.//../../src/cpp -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/daligner-include -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -I/usr/src/googletest/googletest/include -Ithird-party -c -o AlnGraphBoostTest.o AlnGraphBoostTest.cpp
mkdir xml
g++ -g -O2 -ffile-prefix-map=/build/pbdagcon-0.3+git20180411.c14c422+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I. -I./ -I.//../../src/cpp -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/daligner-include -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -I/usr/src/googletest/googletest/include -Ithird-party -c -o AlignmentTest.o AlignmentTest.cpp
g++ -g -O2 -ffile-prefix-map=/build/pbdagcon-0.3+git20180411.c14c422+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I. -I./ -I.//../../src/cpp -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/daligner-include -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -I/usr/src/googletest/googletest/include -Ithird-party -c -o SimpleAlignerTest.o SimpleAlignerTest.cpp
cc -g -O2 -ffile-prefix-map=/build/pbdagcon-0.3+git20180411.c14c422+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I. -I./ -I.//../../src/cpp -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/daligner-include -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -I/usr/src/googletest/googletest/include -Ithird-party -c -o DB.o /build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include/DB.c
cc -g -O2 -ffile-prefix-map=/build/pbdagcon-0.3+git20180411.c14c422+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I. -I./ -I.//../../src/cpp -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/daligner-include -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -I/usr/src/googletest/googletest/include -Ithird-party -c -o QV.o /build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include/QV.c
cc -g -O2 -ffile-prefix-map=/build/pbdagcon-0.3+git20180411.c14c422+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I. -I./ -I.//../../src/cpp -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/daligner-include -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -I/usr/src/googletest/googletest/include -Ithird-party -c -o align.o /build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/daligner-include/align.c
g++ -g -O2 -ffile-prefix-map=/build/pbdagcon-0.3+git20180411.c14c422+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I. -I./ -I.//../../src/cpp -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/daligner-include -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -I/usr/src/googletest/googletest/include -Ithird-party -c -o DazAlnProvider.o .//../../src/cpp/DazAlnProvider.cpp
g++ -g -O2 -ffile-prefix-map=/build/pbdagcon-0.3+git20180411.c14c422+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I. -I./ -I.//../../src/cpp -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/daligner-include -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -I/usr/src/googletest/googletest/include -Ithird-party -c -o TargetHitTest.o TargetHitTest.cpp
/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include/DB.c: In function 'Open_QVs':
/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include/DB.c:2415:16: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
2415 | (void) fscanf(istub,DB_NFILE,&nfiles);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include/DB.c:2419:20: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
2419 | { (void) fscanf(istub,DB_FDATA,&last,fname,prolog);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include/DB.c:2424:20: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
2424 | { (void) fscanf(istub,DB_FDATA,&last,fname,prolog);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o test-alngraph gtest-all.o gtest_main.o AlnGraphBoost.o Alignment.o SimpleAligner.o AlnGraphBoostTest.o -Wl,-z,relro -L /usr/lib/x86_64-linux-gnu/hdf5/serial -lrt -lblasr -lpbbam -lhdf5_cpp -lhdf5 -lhts -lz -lpthread
g++ -o test-alignment gtest-all.o gtest_main.o AlnGraphBoost.o Alignment.o SimpleAligner.o AlignmentTest.o -Wl,-z,relro -L /usr/lib/x86_64-linux-gnu/hdf5/serial -lrt -lblasr -lpbbam -lhdf5_cpp -lhdf5 -lhts -lz -lpthread
g++ -o test-simple_aligner gtest-all.o gtest_main.o AlnGraphBoost.o Alignment.o SimpleAligner.o SimpleAlignerTest.o -Wl,-z,relro -L /usr/lib/x86_64-linux-gnu/hdf5/serial -lrt -lblasr -lpbbam -lhdf5_cpp -lhdf5 -lhts -lz -lpthread
g++ -o test-target_hit gtest-all.o gtest_main.o DB.o QV.o align.o Alignment.o DazAlnProvider.o TargetHitTest.o -Wl,-z,relro -L /usr/lib/x86_64-linux-gnu/hdf5/serial -lrt -lblasr -lpbbam -lhdf5_cpp -lhdf5 -lhts -lz -lpthread
LD_LIBRARY_PATH=::::/usr/lib/x86_64-linux-gnu/hdf5/serial::: PBDAGCON_TEST_DATA_DIR=./ ./test-target_hit --gtest_output=xml:xml/test-target_hit.xml
Running main() from /usr/src/googletest/googletest/src/gtest_main.cc
[==========] Running 3 tests from 1 test suite.
[----------] Global test environment set-up.
[----------] 3 tests from TargetHitTest
[ RUN ] TargetHitTest.single_overlap_perfect
[ OK ] TargetHitTest.single_overlap_perfect (0 ms)
[ RUN ] TargetHitTest.single_overlap_inaccurate
[ OK ] TargetHitTest.single_overlap_inaccurate (0 ms)
[ RUN ] TargetHitTest.multi_overlap_inaccurate
[ OK ] TargetHitTest.multi_overlap_inaccurate (0 ms)
[----------] 3 tests from TargetHitTest (0 ms total)
[----------] Global test environment tear-down
[==========] 3 tests from 1 test suite ran. (0 ms total)
[ PASSED ] 3 tests.
LD_LIBRARY_PATH=::::/usr/lib/x86_64-linux-gnu/hdf5/serial::: PBDAGCON_TEST_DATA_DIR=./ ./test-alngraph --gtest_output=xml:xml/test-alngraph.xml
LD_LIBRARY_PATH=::::/usr/lib/x86_64-linux-gnu/hdf5/serial::: PBDAGCON_TEST_DATA_DIR=./ ./test-simple_aligner --gtest_output=xml:xml/test-simple_aligner.xml
Running main() from /usr/src/googletest/googletest/src/gtest_main.cc
[==========] Running 2 tests from 1 test suite.
[----------] Global test environment set-up.
[----------] 2 tests from AlnGraphBoostTest
[ RUN ] AlnGraphBoostTest.RawConsensus
[ OK ] AlnGraphBoostTest.RawConsensus (0 ms)
[ RUN ] AlnGraphBoostTest.DanglingNodes
[ OK ] AlnGraphBoostTest.DanglingNodes (0 ms)
[----------] 2 tests from AlnGraphBoostTest (0 ms total)
[----------] Global test environment tear-down
[==========] 2 tests from 1 test suite ran. (4 ms total)
[ PASSED ] 2 tests.
Running main() from /usr/src/googletest/googletest/src/gtest_main.cc
[==========] Running 1 test from 1 test suite.
[----------] Global test environment set-up.
[----------] 1 test from SimpleAligner
[ RUN ] SimpleAligner.align
[ OK ] SimpleAligner.align (0 ms)
[----------] 1 test from SimpleAligner (0 ms total)
[----------] Global test environment tear-down
[==========] 1 test from 1 test suite ran. (0 ms total)
[ PASSED ] 1 test.
LD_LIBRARY_PATH=::::/usr/lib/x86_64-linux-gnu/hdf5/serial::: PBDAGCON_TEST_DATA_DIR=./ ./test-alignment --gtest_output=xml:xml/test-alignment.xml
Running main() from /usr/src/googletest/googletest/src/gtest_main.cc
[==========] Running 4 tests from 1 test suite.
[----------] Global test environment set-up.
[----------] 4 tests from Alignment
[ RUN ] Alignment.Normalize
[ OK ] Alignment.Normalize (0 ms)
[ RUN ] Alignment.ParseBasic
[ OK ] Alignment.ParseBasic (0 ms)
[ RUN ] Alignment.ParseQuery
[ OK ] Alignment.ParseQuery (0 ms)
[ RUN ] Alignment.Trim
[ OK ] Alignment.Trim (0 ms)
[----------] 4 tests from Alignment (0 ms total)
[----------] Global test environment tear-down
[==========] 4 tests from 1 test suite ran. (0 ms total)
[ PASSED ] 4 tests.
make[2]: Leaving directory '/build/pbdagcon-0.3+git20180411.c14c422+dfsg/test/cpp'
make[1]: Leaving directory '/build/pbdagcon-0.3+git20180411.c14c422+dfsg'
create-stamp debian/debhelper-build-stamp
dh_prep
dh_auto_install --destdir=debian/pbdagcon/
dh_install
dh_installdocs
dh_installchangelogs
dh_installexamples
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 'pbdagcon-dbgsym' in '../pbdagcon-dbgsym_0.3+git20180411.c14c422+dfsg-8_amd64.deb'.
dpkg-deb: building package 'pbdagcon' in '../pbdagcon_0.3+git20180411.c14c422+dfsg-8_amd64.deb'.
dpkg-genbuildinfo --build=binary -O../pbdagcon_0.3+git20180411.c14c422+dfsg-8_amd64.buildinfo
dpkg-genchanges --build=binary -O../pbdagcon_0.3+git20180411.c14c422+dfsg-8_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/283060/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/283060/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/283060 and its subdirectories
I: Current time: Fri May 19 10:25:34 +14 2023
I: pbuilder-time-stamp: 1684441534