I: pbuilder: network access will be disabled during build
I: Current time: Sat Mar 15 13:12:35 +14 2025
I: pbuilder-time-stamp: 1741993955
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/unstable-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 [libbio-db-hts-perl_3.01-5.dsc]
I: copying [./libbio-db-hts-perl_3.01.orig.tar.gz]
I: copying [./libbio-db-hts-perl_3.01-5.debian.tar.xz]
I: Extracting source
dpkg-source: warning: cannot verify inline signature for ./libbio-db-hts-perl_3.01-5.dsc: unsupported subcommand
dpkg-source: info: extracting libbio-db-hts-perl in libbio-db-hts-perl-3.01
dpkg-source: info: unpacking libbio-db-hts-perl_3.01.orig.tar.gz
dpkg-source: info: unpacking libbio-db-hts-perl_3.01-5.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying find_htslib.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/1426694/tmp/hooks/D01_modify_environment starting
debug: Running on infom01-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 Mar 14 23:12 /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/1426694/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/1426694/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]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu")
BASH_VERSION='5.2.37(1)-release'
BUILDDIR=/build/reproducible-path
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=12 '
DIRSTACK=()
DISTRIBUTION=unstable
EUID=0
FUNCNAME=([0]="Echo" [1]="main")
GROUPS=()
HOME=/root
HOSTNAME=i-capture-the-hostname
HOSTTYPE=x86_64
HOST_ARCH=amd64
IFS='
'
INVOCATION_ID=71db7ca5e7ae416a9a521623a84adaed
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=1426694
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.tTnZP3I2/pbuilderrc_Huc7 --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.tTnZP3I2/b2 --logfile b2/build.log libbio-db-hts-perl_3.01-5.dsc'
SUDO_GID=109
SUDO_UID=104
SUDO_USER=jenkins
TERM=unknown
TZ=/usr/share/zoneinfo/Etc/GMT-14
UID=0
USER=root
_='I: set'
I: uname -a
Linux i-capture-the-hostname 6.1.0-31-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/1426694/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), libbio-perl-perl, libextutils-cbuilder-perl, libextutils-pkgconfig-perl, libhts-dev, libmodule-build-perl, perl
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19785 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 libbio-perl-perl; however:
Package libbio-perl-perl is not installed.
pbuilder-satisfydepends-dummy depends on libextutils-pkgconfig-perl; however:
Package libextutils-pkgconfig-perl is not installed.
pbuilder-satisfydepends-dummy depends on libhts-dev; however:
Package libhts-dev is not installed.
pbuilder-satisfydepends-dummy depends on libmodule-build-perl; however:
Package libmodule-build-perl 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} comerr-dev{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} krb5-multidev{a} libarchive-zip-perl{a} libbio-perl-perl{a} libbrotli-dev{a} libbrotli1{a} libbz2-dev{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libdata-stag-perl{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1t64{a} libevent-2.1-7t64{a} libextutils-pkgconfig-perl{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgnutls30t64{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libicu76{a} libidn2-0{a} libidn2-dev{a} libio-string-perl{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} libldap-dev{a} libldap2{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libmodule-build-perl{a} libnghttp2-14{a} libnghttp2-dev{a} libnghttp3-9{a} libnghttp3-dev{a} libngtcp2-16{a} libngtcp2-crypto-gnutls-dev{a} libngtcp2-crypto-gnutls8{a} libngtcp2-dev{a} libp11-kit-dev{a} libp11-kit0{a} libpipeline1{a} libpkgconf3{a} libpsl-dev{a} libpsl5t64{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libtasn1-6{a} libtasn1-6-dev{a} libtool{a} libuchardet0{a} libunbound8{a} libunistring5{a} libxml2{a} libzstd-dev{a} m4{a} man-db{a} nettle-dev{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a}
The following packages are RECOMMENDED but will NOT be installed:
bioperl-run bzip2-doc ca-certificates curl krb5-locales libace-perl libalgorithm-munkres-perl libarchive-cpio-perl libarray-compare-perl libbio-asn1-entrezgene-perl libbio-perl-run-perl libclone-perl libconvert-binary-c-perl libdbd-mysql-perl libdbd-pg-perl libdbd-sqlite3-perl libgd-perl libgraph-perl libgraphviz-perl libhtml-parser-perl libhtml-tableextract-perl libldap-common liblist-moreutils-perl libltdl-dev libmail-sendmail-perl libmldbm-perl libmodule-signature-perl libpod-readme-perl libpostscript-perl libsasl2-modules libset-scalar-perl libsoap-lite-perl libsoftware-license-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-graph-perl libsvg-perl libtasn1-doc liburi-perl libwww-perl libxml-dom-xpath-perl libxml-libxml-perl libxml-libxslt-perl libxml-parser-perl libxml-perl libxml-sax-perl libxml-sax-writer-perl libxml-simple-perl libxml-twig-perl libxml-writer-perl lynx perl-tk publicsuffix wget
0 packages upgraded, 100 newly installed, 0 to remove and 0 not upgraded.
Need to get 43.7 MB of archives. After unpacking 157 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB]
Get: 2 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-2 [337 kB]
Get: 3 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-2 [109 kB]
Get: 4 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-2 [43.5 kB]
Get: 5 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-1 [243 kB]
Get: 6 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB]
Get: 7 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-7 [1185 kB]
Get: 8 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.4-5 [92.4 kB]
Get: 9 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB]
Get: 10 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB]
Get: 11 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-7 [294 kB]
Get: 12 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB]
Get: 13 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get: 14 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-3 [862 kB]
Get: 15 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-1 [770 kB]
Get: 16 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-1 [24.0 kB]
Get: 17 http://deb.debian.org/debian unstable/main amd64 comerr-dev amd64 2.1-1.47.2-1 [55.7 kB]
Get: 18 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 19 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-4 [539 kB]
Get: 20 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB]
Get: 21 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 22 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 23 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 24 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB]
Get: 25 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB]
Get: 26 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-1 [476 kB]
Get: 27 http://deb.debian.org/debian unstable/main amd64 libicu76 amd64 76.1-3 [9721 kB]
Get: 28 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.3+b1 [699 kB]
Get: 29 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-1 [1680 kB]
Get: 30 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 31 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 32 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.1 [920 kB]
Get: 33 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB]
Get: 34 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB]
Get: 35 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B]
Get: 36 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB]
Get: 37 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB]
Get: 38 http://deb.debian.org/debian unstable/main amd64 libgssrpc4t64 amd64 1.21.3-5 [60.0 kB]
Get: 39 http://deb.debian.org/debian unstable/main amd64 libkadm5clnt-mit12 amd64 1.21.3-5 [42.5 kB]
Get: 40 http://deb.debian.org/debian unstable/main amd64 libkdb5-10t64 amd64 1.21.3-5 [42.6 kB]
Get: 41 http://deb.debian.org/debian unstable/main amd64 libkadm5srv-mit12 amd64 1.21.3-5 [54.2 kB]
Get: 42 http://deb.debian.org/debian unstable/main amd64 krb5-multidev amd64 1.21.3-5 [126 kB]
Get: 43 http://deb.debian.org/debian unstable/main amd64 libio-string-perl all 1.08-4 [12.1 kB]
Get: 44 http://deb.debian.org/debian unstable/main amd64 libdata-stag-perl all 0.14-3 [448 kB]
Get: 45 http://deb.debian.org/debian unstable/main amd64 libbio-perl-perl all 1.7.8-1 [2603 kB]
Get: 46 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB]
Get: 47 http://deb.debian.org/debian unstable/main amd64 libbrotli-dev amd64 1.1.0-2+b7 [316 kB]
Get: 48 http://deb.debian.org/debian unstable/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB]
Get: 49 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.8-1 [109 kB]
Get: 50 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB]
Get: 51 http://deb.debian.org/debian unstable/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB]
Get: 52 http://deb.debian.org/debian unstable/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB]
Get: 53 http://deb.debian.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.9-2 [1464 kB]
Get: 54 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB]
Get: 55 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB]
Get: 56 http://deb.debian.org/debian unstable/main amd64 libldap2 amd64 2.6.9+dfsg-2 [194 kB]
Get: 57 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB]
Get: 58 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.8.0-1 [67.7 kB]
Get: 59 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.11.0-1 [131 kB]
Get: 60 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.11.0-1 [29.3 kB]
Get: 61 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB]
Get: 62 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB]
Get: 63 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB]
Get: 64 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.12.1-3 [365 kB]
Get: 65 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB]
Get: 66 http://deb.debian.org/debian unstable/main amd64 libunbound8 amd64 1.22.0-1+b1 [598 kB]
Get: 67 http://deb.debian.org/debian unstable/main amd64 libgnutls-dane0t64 amd64 3.8.9-2 [455 kB]
Get: 68 http://deb.debian.org/debian unstable/main amd64 libgnutls-openssl27t64 amd64 3.8.9-2 [455 kB]
Get: 69 http://deb.debian.org/debian unstable/main amd64 libidn2-dev amd64 2.3.8-1 [102 kB]
Get: 70 http://deb.debian.org/debian unstable/main amd64 libp11-kit-dev amd64 0.25.5-3 [208 kB]
Get: 71 http://deb.debian.org/debian unstable/main amd64 libtasn1-6-dev amd64 4.20.0-2 [99.2 kB]
Get: 72 http://deb.debian.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-3 [329 kB]
Get: 73 http://deb.debian.org/debian unstable/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-3 [642 kB]
Get: 74 http://deb.debian.org/debian unstable/main amd64 nettle-dev amd64 3.10.1-1 [1318 kB]
Get: 75 http://deb.debian.org/debian unstable/main amd64 libgnutls28-dev amd64 3.8.9-2 [1401 kB]
Get: 76 http://deb.debian.org/debian unstable/main amd64 libkrb5-dev amd64 1.21.3-5 [16.1 kB]
Get: 77 http://deb.debian.org/debian unstable/main amd64 libldap-dev amd64 2.6.9+dfsg-2 [311 kB]
Get: 78 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB]
Get: 79 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB]
Get: 80 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB]
Get: 81 http://deb.debian.org/debian unstable/main amd64 libnghttp2-dev amd64 1.64.0-1 [115 kB]
Get: 82 http://deb.debian.org/debian unstable/main amd64 libnghttp3-dev amd64 1.8.0-1 [91.3 kB]
Get: 83 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.11.0-1 [34.0 kB]
Get: 84 http://deb.debian.org/debian unstable/main amd64 libngtcp2-dev amd64 1.11.0-1 [179 kB]
Get: 85 http://deb.debian.org/debian unstable/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB]
Get: 86 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB]
Get: 87 http://deb.debian.org/debian unstable/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-2+b5 [68.0 kB]
Get: 88 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.4.1-1 [2787 kB]
Get: 89 http://deb.debian.org/debian unstable/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB]
Get: 90 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.7+dfsg-1 [371 kB]
Get: 91 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.12.1-3 [480 kB]
Get: 92 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.23-1+b1 [47.5 kB]
Get: 93 http://deb.debian.org/debian unstable/main amd64 libdeflate-dev amd64 1.23-1+b1 [56.0 kB]
Get: 94 http://deb.debian.org/debian unstable/main amd64 pkg-config amd64 1.8.1-4 [14.0 kB]
Get: 95 http://deb.debian.org/debian unstable/main amd64 libextutils-pkgconfig-perl all 1.16-3 [9928 B]
Get: 96 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.1-2 [95.8 kB]
Get: 97 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.21+ds-1 [463 kB]
Get: 98 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.6.4-1 [323 kB]
Get: 99 http://deb.debian.org/debian unstable/main amd64 libhts-dev amd64 1.21+ds-1 [1733 kB]
Get: 100 http://deb.debian.org/debian unstable/main amd64 libmodule-build-perl all 0.423400-2 [252 kB]
Fetched 43.7 MB in 0s (106 MB/s)
Preconfiguring packages ...
Selecting previously unselected package sensible-utils.
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update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode
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Not building database; man-db/auto-update is not 'true'.
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Reading package lists...
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-> Finished parsing the build-deps
I: Building the package
I: user script /srv/workspace/pbuilder/1426694/tmp/hooks/A99_set_merged_usr starting
Not re-configuring usrmerge for unstable
I: user script /srv/workspace/pbuilder/1426694/tmp/hooks/A99_set_merged_usr finished
hostname: Name or service not known
I: Running cd /build/reproducible-path/libbio-db-hts-perl-3.01/ && 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 > ../libbio-db-hts-perl_3.01-5_source.changes
dpkg-buildpackage: info: source package libbio-db-hts-perl
dpkg-buildpackage: info: source version 3.01-5
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Étienne Mollier <emollier@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
debian/rules override_dh_auto_configure
make[1]: Entering directory '/build/reproducible-path/libbio-db-hts-perl-3.01'
# Nudge configure steps to locate htslib, as for some reason it
# fails to find the htslb on its own with the logic provided in
# Build.PL.
dh_auto_configure -- \
--htslib-includedir \
/usr/include \
--htslib-libdir \
/usr/lib/x86_64-linux-gnu
/usr/bin/perl Build.PL --installdirs vendor --config "optimize=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libbio-db-hts-perl-3.01=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2" --config "ld=x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libbio-db-hts-perl-3.01=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now" --htslib-includedir /usr/include --htslib-libdir /usr/lib/x86_64-linux-gnu
Created MYMETA.yml and MYMETA.json
Creating new 'Build' script for 'Bio-DB-HTS' version '3.01'
make[1]: Leaving directory '/build/reproducible-path/libbio-db-hts-perl-3.01'
dh_auto_build
/usr/bin/perl Build
Building Bio-DB-HTS
x86_64-linux-gnu-gcc -I/usr/include -I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE '-DVERSION="3.01"' '-DXS_VERSION="3.01"' -fPIC '-D_IOLIB=2' '-D_FILE_OFFSET_BITS=64' -Wno-error -Wno-unused-result -c -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE '-D_FILE_OFFSET_BITS=64' -g -O2 '-Werror=implicit-function-declaration' '-ffile-prefix-map=/build/reproducible-path/libbio-db-hts-perl-3.01=.' -fstack-protector-strong -fstack-clash-protection -Wformat '-Werror=format-security' -fcf-protection -g -O2 '-Werror=implicit-function-declaration' '-ffile-prefix-map=/build/reproducible-path/libbio-db-hts-perl-3.01=.' -fstack-protector-strong -fstack-clash-protection -Wformat '-Werror=format-security' -fcf-protection -Wdate-time '-D_FORTIFY_SOURCE=2' -o lib/Bio/DB/HTS.o lib/Bio/DB/HTS.c
lib/Bio/DB/HTS.xs: In function 'XS_Bio__DB__HTS__VCF__Header_fmt_text':
lib/Bio/DB/HTS.xs:1769:5: warning: 'bcf_hdr_fmt_text' is deprecated: use bcf_hdr_format() instead [-Wdeprecated-declarations]
1769 | RETVAL = newSVpv(bcf_hdr_fmt_text(header, is_bcf, &len), 0);
| ^~~~~~
In file included from lib/Bio/DB/HTS.xs:59:
/usr/include/htslib/vcf.h:591:11: note: declared here
591 | char *bcf_hdr_fmt_text(const bcf_hdr_t *hdr, int is_bcf, int *len)
| ^~~~~~~~~~~~~~~~
lib/Bio/DB/HTS.xs: In function 'XS_Bio__DB__HTS__VCF__Row_print':
lib/Bio/DB/HTS.xs:1785:13: warning: format '%d' expects argument of type 'int', but argument 2 has type 'hts_pos_t' {aka 'long int'} [-Wformat=]
1785 | printf("position:%d\t", (row->pos+1));
| ^~~~~~~~~~~~~~~ ~~~~~~~~~~~~
| |
| hts_pos_t {aka long int}
ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/HTS/HTS.bs')
x86_64-linux-gnu-gcc -g -O2 '-Werror=implicit-function-declaration' '-ffile-prefix-map=/build/reproducible-path/libbio-db-hts-perl-3.01=.' -fstack-protector-strong -fstack-clash-protection -Wformat '-Werror=format-security' -fcf-protection -Wl,-z,relro -Wl,-z,now -shared -L/usr/local/lib -fstack-protector-strong -o blib/arch/auto/Bio/DB/HTS/HTS.so lib/Bio/DB/HTS.o -L/usr/lib/x86_64-linux-gnu -lhts -lpthread -lz
x86_64-linux-gnu-gcc -I/usr/include -I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE '-DVERSION="3.01"' '-DXS_VERSION="3.01"' -fPIC '-D_IOLIB=2' '-D_FILE_OFFSET_BITS=64' -Wno-error -Wno-unused-result -c -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE '-D_FILE_OFFSET_BITS=64' -g -O2 '-Werror=implicit-function-declaration' '-ffile-prefix-map=/build/reproducible-path/libbio-db-hts-perl-3.01=.' -fstack-protector-strong -fstack-clash-protection -Wformat '-Werror=format-security' -fcf-protection -g -O2 '-Werror=implicit-function-declaration' '-ffile-prefix-map=/build/reproducible-path/libbio-db-hts-perl-3.01=.' -fstack-protector-strong -fstack-clash-protection -Wformat '-Werror=format-security' -fcf-protection -Wdate-time '-D_FORTIFY_SOURCE=2' -o lib/Bio/DB/HTS/Faidx.o lib/Bio/DB/HTS/Faidx.c
ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/HTS/Faidx/Faidx.bs')
x86_64-linux-gnu-gcc -g -O2 '-Werror=implicit-function-declaration' '-ffile-prefix-map=/build/reproducible-path/libbio-db-hts-perl-3.01=.' -fstack-protector-strong -fstack-clash-protection -Wformat '-Werror=format-security' -fcf-protection -Wl,-z,relro -Wl,-z,now -shared -L/usr/local/lib -fstack-protector-strong -o blib/arch/auto/Bio/DB/HTS/Faidx/Faidx.so lib/Bio/DB/HTS/Faidx.o -L/usr/lib/x86_64-linux-gnu -lhts -lpthread -lz
dh_auto_test
/usr/bin/perl Build test --verbose 1
t/00load.t .......
ok 1 - use Bio::DB::HTS;
ok 2 - use Bio::DB::HTS::Tabix;
ok 3 - use Bio::DB::HTS::Tabix::Iterator;
ok 4 - use Bio::DB::HTS::Kseq;
1..4
ok
t/01bam.t ........
1..452
# Running under perl version 5.040001 for linux
# Current time local: Fri Mar 14 23:13:22 2025
# Current time GMT: Fri Mar 14 23:13:22 2025
# Using Test.pm version 1.31
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t/02faidx.t ......
1..15
ok 1 - use Bio::DB::HTS;
ok 2 - use Bio::DB::HTS::Faidx;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
# 230218
ok 13 - length of I
ok 14 - has sequence I
ok 15 - Does not have sequence II
ok
t/03cram.t .......
1..139
# Running under perl version 5.040001 for linux
# Current time local: Fri Mar 14 23:13:23 2025
# Current time GMT: Fri Mar 14 23:13:23 2025
# Using Test.pm version 1.31
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t/04tabix.t ......
1..21
ok 1 - use Bio::DB::HTS::Tabix;
ok 2 - \#CHROM FROM TO GERP
ok 3 - \#CHROM FROM TO GERP
ok 4 - can query a region
ok 5 - can get a value from the iterator
ok 6 - row value is correct
ok 7 - correct number of values come back from the iterator
ok 8 - A reference of type 'ARRAY' isa 'ARRAY'
ok 9 - seqnames are correct
ok 10 - can query a region with ':' in chr
ok 11 - can get a value from the iterator
ok 12 - row value is correct with ':' in chr
ok 13 - can query a region with ':' in chr, no end
ok 14 - can get a value from the iterator
ok 15 - row value is correct with ':' in chr, no end
ok 16 - can query a region with ':' in chr, no coord
ok 17 - can get a value from the iterator
ok 18 - row value is correct with ':' in chr, no coord
ok 19 - querying non existent chrom
ok 20 - \#\#fileformat=VCFv4.2
ok 21 - \#\#reference=human_b36_both.fasta
ok
t/05vcf.t ........
1..177
ok 1 - use Bio::DB::HTS::VCF;
ok 2 - use Bio::DB::HTS::VCF::Row;
ok 3 - use Bio::DB::HTS::VCF::RowPtr;
ok 4 - use Bio::DB::HTS::VCF::Header;
ok 5 - use Bio::DB::HTS::VCF::HeaderPtr;
ok 6 - Chromosome value read
ok 7 - Chromosome value read
ok 8 - Position value read
ok 9 - Quality value read
ok 10 - Quality value read
ok 11 - ID value read
ok 12 - Number of alleles value read
ok 13 - A reference of type 'ARRAY' isa 'ARRAY'
ok 14 - alleles are correct
ok 15 - VCF file open
ok 16 - correct number of variants identified in file
ok 17 - Header formatted string
ok 18 - VCF Header version matches
ok 19 - Number of samples
ok 20 - sample names correct
ok 21 - Number of seqnames
ok 22
ok 23 - sequence names correct
ok 24 - Next row
ok 25 - Chromosome value read
ok 26 - Position value read
ok 27 - ID value read
ok 28 - Num Filters OK
ok 29 - Actual Filter present
ok 30 - PASS filter absent
ok 31 - Variant type matches
ok 32 - info read correctly
ok 33 - A reference of type 'ARRAY' isa 'ARRAY'
ok 34 - info flag read correctly
ok 35 - info flag type correct
ok 36 - A reference of type 'ARRAY' isa 'ARRAY'
ok 37 - info float read correctly
ok 38 - info float type correct
ok 39 - A reference of type 'ARRAY' isa 'ARRAY'
ok 40 - info string read correctly
ok 41 - info String type correct
ok 42 - A reference of type 'ARRAY' isa 'ARRAY'
ok 43 - info ints read correctly
ok 44 - info int type correct
ok 45 - format int read
ok 46 - format int read
ok 47 - format id not present
ok 48 - format read
ok 49 - Next row
ok 50 - Chromosome value read
ok 51 - Position value read
ok 52 - Quality value read
ok 53 - Reference value read
ok 54 - Num Alleles
ok 55 - Is SNP
ok 56 - A reference of type 'ARRAY' isa 'ARRAY'
ok 57 - alleles are correct
ok 58 - Num Filters OK
ok 59 - PASS Filter present
ok 60 - Actual Filter absent
ok 61 - Made up filter not existing
ok 62 - info read correctly
ok 63 - format int read
ok 64 - format int read
ok 65 - format id not present
ok 66 - format read
ok 67 - Next row
ok 68 - Chromosome value read
ok 69 - int format type correct
ok 70 - format int read
ok 71 - format int read
ok 72 - format int read
# !!! Not sure this is correct !!!
ok 73 - format int read
ok 74 - format read
ok 75 - A reference of type 'ARRAY' isa 'ARRAY'
ok 76 - genotypes read correctly
ok 77 - format id not found
ok 78 - info id not found
ok 79 - info read correctly
ok 80 - can query a region
ok 81 - can get a value from the iterator
ok 82 - chr
ok 83 - position
ok 84 - id
ok 85 - reference
ok 86 - info
ok 87 - info
ok 88 - info
ok 89 - info
ok 90 - can get a value from the iterator
ok 91 - chr
ok 92 - position
ok 93 - id
ok 94 - reference
ok 95 - info
ok 96 - no more results
ok 97 - BCF file open
ok 98 - correct number of variants identified in file
ok 99 - Header formatted string
ok 100 - VCF Header version matches
ok 101 - Number of samples
ok 102 - sample names correct
ok 103 - Number of seqnames
ok 104 - sequence names correct
ok 105 - Next row
ok 106 - Chromosome value read
ok 107 - Position value read
ok 108 - ID value read
ok 109 - Num Filters OK
ok 110 - Actual Filter present
ok 111 - PASS filter absent
ok 112 - Variant type matches
ok 113 - info read correctly
ok 114 - A reference of type 'ARRAY' isa 'ARRAY'
ok 115 - info flag read correctly
ok 116 - info flag type correct
ok 117 - A reference of type 'ARRAY' isa 'ARRAY'
ok 118 - info float read correctly
ok 119 - info float type correct
ok 120 - A reference of type 'ARRAY' isa 'ARRAY'
ok 121 - info string read correctly
ok 122 - info String type correct
ok 123 - A reference of type 'ARRAY' isa 'ARRAY'
ok 124 - info ints read correctly
ok 125 - info int type correct
ok 126 - format int read
ok 127 - format int read
ok 128 - format ID not present
ok 129 - format read
ok 130 - Next row
ok 131 - Chromosome value read
ok 132 - Position value read
ok 133 - Quality value read
ok 134 - Reference value read
ok 135 - Num Alleles
ok 136 - Is SNP
ok 137 - A reference of type 'ARRAY' isa 'ARRAY'
ok 138 - alleles are correct
ok 139 - Num Filters OK
ok 140 - PASS Filter present
ok 141 - Actual Filter absent
ok 142 - Made up filter not existing
ok 143 - info read correctly
ok 144 - format int read
ok 145 - format int read
ok 146 - format ID not present
ok 147 - format read
ok 148 - Next row
ok 149 - Chromosome value read
ok 150 - int format type correct
ok 151 - format int read
ok 152 - format int read
ok 153 - format int read
# !!! Not sure this is correct !!!
ok 154 - format int read
ok 155 - format read
ok 156 - A reference of type 'ARRAY' isa 'ARRAY'
ok 157 - genotypes read correctly
ok 158 - format id not found
ok 159 - info id not found
ok 160 - info read correctly
ok 161 - can query a region
ok 162 - can get a value from the iterator
ok 163 - chr
ok 164 - position
ok 165 - id
ok 166 - reference
ok 167 - info
ok 168 - info
ok 169 - info
ok 170 - info
ok 171 - can get a value from the iterator
ok 172 - chr
ok 173 - position
ok 174 - id
ok 175 - reference
ok 176 - info
ok 177 - no more results
ok
t/06kseq.t .......
ok 1 - correct num. seqs in bug2335
ok 2 - sample sequence obtained
ok 3 - seq matches bug2335
ok 4 - desc matches bug2335
ok 5 - name matches bug2335
ok 6 - qual matches bug2335
ok 7 - Checking qual and seq lengths are the same in bug2335
ok 8 - Checking qual and seq lengths are the same using object methods in bug2335
ok 9 - correct num. seqs in evil_wrapping
ok 10 - sample sequence obtained
ok 11 - seq matches evil_wrapping
ok 12 - desc matches evil_wrapping
ok 13 - name matches evil_wrapping
ok 14 - qual matches evil_wrapping
ok 15 - Checking qual and seq lengths are the same in evil_wrapping
ok 16 - Checking qual and seq lengths are the same using object methods in evil_wrapping
ok 17 - correct num. seqs in example
ok 18 - sample sequence obtained
ok 19 - seq matches example
ok 20 - desc matches example
ok 21 - name matches example
ok 22 - qual matches example
ok 23 - Checking qual and seq lengths are the same in example
ok 24 - Checking qual and seq lengths are the same using object methods in example
ok 25 - correct num. seqs in illumina_faked
ok 26 - sample sequence obtained
ok 27 - seq matches illumina_faked
ok 28 - desc matches illumina_faked
ok 29 - name matches illumina_faked
ok 30 - qual matches illumina_faked
ok 31 - Checking qual and seq lengths are the same in illumina_faked
ok 32 - Checking qual and seq lengths are the same using object methods in illumina_faked
ok 33 - correct num. seqs in sanger_93
ok 34 - sample sequence obtained
ok 35 - seq matches sanger_93
ok 36 - desc matches sanger_93
ok 37 - name matches sanger_93
ok 38 - qual matches sanger_93
ok 39 - Checking qual and seq lengths are the same in sanger_93
ok 40 - Checking qual and seq lengths are the same using object methods in sanger_93
ok 41 - correct num. seqs in sanger_faked
ok 42 - sample sequence obtained
ok 43 - seq matches sanger_faked
ok 44 - desc matches sanger_faked
ok 45 - name matches sanger_faked
ok 46 - qual matches sanger_faked
ok 47 - Checking qual and seq lengths are the same in sanger_faked
ok 48 - Checking qual and seq lengths are the same using object methods in sanger_faked
ok 49 - correct num. seqs in solexa_example
ok 50 - sample sequence obtained
ok 51 - seq matches solexa_example
ok 52 - desc matches solexa_example
ok 53 - name matches solexa_example
ok 54 - qual matches solexa_example
ok 55 - Checking qual and seq lengths are the same in solexa_example
ok 56 - Checking qual and seq lengths are the same using object methods in solexa_example
ok 57 - correct num. seqs in solexa_faked
ok 58 - sample sequence obtained
ok 59 - seq matches solexa_faked
ok 60 - desc matches solexa_faked
ok 61 - name matches solexa_faked
ok 62 - qual matches solexa_faked
ok 63 - Checking qual and seq lengths are the same in solexa_faked
ok 64 - Checking qual and seq lengths are the same using object methods in solexa_faked
ok 65 - correct num. seqs in test1_sanger
ok 66 - sample sequence obtained
ok 67 - seq matches test1_sanger
ok 68 - desc matches test1_sanger
ok 69 - name matches test1_sanger
ok 70 - qual matches test1_sanger
ok 71 - Checking qual and seq lengths are the same in test1_sanger
ok 72 - Checking qual and seq lengths are the same using object methods in test1_sanger
ok 73 - correct num. seqs in test2_solexa
ok 74 - sample sequence obtained
ok 75 - seq matches test2_solexa
ok 76 - desc matches test2_solexa
ok 77 - name matches test2_solexa
ok 78 - qual matches test2_solexa
ok 79 - Checking qual and seq lengths are the same in test2_solexa
ok 80 - Checking qual and seq lengths are the same using object methods in test2_solexa
ok 81 - correct num. seqs in test3_illumina
ok 82 - sample sequence obtained
ok 83 - seq matches test3_illumina
ok 84 - desc matches test3_illumina
ok 85 - name matches test3_illumina
ok 86 - qual matches test3_illumina
ok 87 - Checking qual and seq lengths are the same in test3_illumina
ok 88 - Checking qual and seq lengths are the same using object methods in test3_illumina
ok 89 - correct num. seqs in tricky
ok 90 - sample sequence obtained
ok 91 - seq matches tricky
ok 92 - desc matches tricky
ok 93 - name matches tricky
ok 94 - qual matches tricky
ok 95 - Checking qual and seq lengths are the same in tricky
ok 96 - Checking qual and seq lengths are the same using object methods in tricky
ok 97 - correct num. seqs in zero_qual
ok 98 - sample sequence obtained
ok 99 - seq matches zero_qual
ok 100 - desc matches zero_qual
ok 101 - name matches zero_qual
ok 102 - qual matches zero_qual
ok 103 - Checking qual and seq lengths are the same in zero_qual
ok 104 - Checking qual and seq lengths are the same using object methods in zero_qual
1..104
ok
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Destination address required
t/07cramwrite.t ..
1..22
# Running under perl version 5.040001 for linux
# Current time local: Fri Mar 14 23:13:26 2025
# Current time GMT: Fri Mar 14 23:13:26 2025
# Using Test.pm version 1.31
ok 1
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok
t/08bamwrite.t ...
1..22
# Running under perl version 5.040001 for linux
# Current time local: Fri Mar 14 23:13:26 2025
# Current time GMT: Fri Mar 14 23:13:26 2025
# Using Test.pm version 1.31
ok 1
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok
t/09sam.t ........
ok 1
ok 2 # skip Cannot test header reading for htslib < 1.5
ok 3 # skip Cannot test header reading for htslib < 1.5
ok 4 # skip Cannot test header reading for htslib < 1.5
ok 5 # skip Cannot test header reading for htslib < 1.5
ok 6 # skip Cannot test header reading for htslib < 1.5
ok 7 # skip Cannot test header reading for htslib < 1.5
ok 8 # skip Cannot test header reading for htslib < 1.5
ok 9 # skip Cannot test header reading for htslib < 1.5
ok 10 # skip Cannot test header reading for htslib < 1.5
ok 11 # skip Cannot test header reading for htslib < 1.5
ok 12
ok 13
ok 14 # skip Cannot test iterating over alignments for htslib < 1.5
ok 15 # skip Cannot test iterating over alignments for htslib < 1.5
ok 16 # skip Cannot test iterating over alignments for htslib < 1.5
ok 17 # skip Cannot test iterating over alignments for htslib < 1.5
ok 18
ok 19
ok 20
ok 21
ok 22 - An object of class 'Bio::PrimarySeq' isa 'Bio::PrimarySeq'
ok 23
1..23
ok
t/10leak.t ....... skipped: require Test::LeakTrace
All tests successful.
Files=11, Tests=979, 4 wallclock secs ( 0.05 usr 0.01 sys + 3.86 cusr 0.22 csys = 4.14 CPU)
Result: PASS
create-stamp debian/debhelper-build-stamp
dh_prep
dh_auto_install --destdir=debian/libbio-db-hts-perl/
/usr/bin/perl Build install --destdir /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl --create_packlist 0
Building Bio-DB-HTS
Files found in blib/arch: installing files in blib/lib into architecture dependent library tree
Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/x86_64-linux-gnu/perl5/5.40/auto/Bio/DB/HTS/HTS.so
Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/x86_64-linux-gnu/perl5/5.40/auto/Bio/DB/HTS/HTS.bs
Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/x86_64-linux-gnu/perl5/5.40/auto/Bio/DB/HTS/Faidx/Faidx.so
Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/x86_64-linux-gnu/perl5/5.40/auto/Bio/DB/HTS/Faidx/Faidx.bs
Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm
Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Faidx.pm
Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Target.pm
Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/ReadIterator.pm
Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Constants.pm
Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/VCF.pm
Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Pileup.pm
Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Alignment.pm
Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/ConfigData.pm
Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Tabix.pm
Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Segment.pm
Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/AlignWrapper.pm
Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Query.pm
Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Kseq.pm
Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/PileupWrapper.pm
Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/FetchIterator.pm
Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Tabix/Iterator.pm
Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/VCF/Header.pm
Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/VCF/Iterator.pm
Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/VCF/RowPtr.pm
Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/VCF/HeaderPtr.pm
Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/VCF/Row.pm
Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Kseq/Iterator.pod
Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Kseq/Record.pm
Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::PileupWrapper.3pm
Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::VCF.3pm
Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::FetchIterator.3pm
Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::Query.3pm
Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::Target.3pm
Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::Kseq::Record.3pm
Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::Segment.3pm
Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::AlignWrapper.3pm
Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::ConfigData.3pm
Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::Tabix.3pm
Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::Kseq::Iterator.3pm
Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::Alignment.3pm
Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::Kseq.3pm
Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::Constants.3pm
Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::ReadIterator.3pm
Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::Pileup.3pm
Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::Faidx.3pm
Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::Tabix::Iterator.3pm
Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::VCF::Iterator.3pm
Installing /build/reproducible-path/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS.3pm
dh_installdocs
dh_installchangelogs
dh_installman
dh_lintian
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
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 from: /lib64/ld-linux-x86-64.so.2
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 to: /lib64/ld-linux-x86-64.so.2.usr-is-merged
dh_installdeb
dh_gencontrol
dh_md5sums
dh_builddeb
dpkg-deb: building package 'libbio-db-hts-perl-dbgsym' in '../libbio-db-hts-perl-dbgsym_3.01-5_amd64.deb'.
dpkg-deb: building package 'libbio-db-hts-perl' in '../libbio-db-hts-perl_3.01-5_amd64.deb'.
dpkg-genbuildinfo --build=binary -O../libbio-db-hts-perl_3.01-5_amd64.buildinfo
dpkg-genchanges --build=binary -O../libbio-db-hts-perl_3.01-5_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/1426694/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/1426694/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/1426694 and its subdirectories
I: Current time: Sat Mar 15 13:13:29 +14 2025
I: pbuilder-time-stamp: 1741994009