Sun Mar 2 20:42:43 UTC 2025 I: starting to build psortb/trixie/amd64 on jenkins on '2025-03-02 20:42'
Sun Mar 2 20:42:43 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_6/34097/console.log
Sun Mar 2 20:42:43 UTC 2025 I: Downloading source for trixie/psortb=3.0.6+dfsg-4
--2025-03-02 20:42:43-- http://deb.debian.org/debian/pool/main/p/psortb/psortb_3.0.6%2bdfsg-4.dsc
Connecting to 46.16.76.132:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 2254 (2.2K) [text/prs.lines.tag]
Saving to: ‘psortb_3.0.6+dfsg-4.dsc’
0K .. 100% 304M=0s
2025-03-02 20:42:44 (304 MB/s) - ‘psortb_3.0.6+dfsg-4.dsc’ saved [2254/2254]
Sun Mar 2 20:42:44 UTC 2025 I: psortb_3.0.6+dfsg-4.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: psortb
Binary: psortb
Architecture: any
Version: 3.0.6+dfsg-4
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>, Étienne Mollier <emollier@debian.org>
Homepage: https://www.psort.org/
Standards-Version: 4.7.0
Vcs-Browser: https://salsa.debian.org/med-team/psortb
Vcs-Git: https://salsa.debian.org/med-team/psortb.git
Testsuite: autopkgtest-pkg-perl
Build-Depends: debhelper-compat (= 13), libsvm-dev, bioperl, ncbi-blast+-legacy, libsquid-dev, libhmmer2-dev, libsvmloc-dev, libmodhmm-dev, pkgconf, pftools
Package-List:
psortb deb science optional arch=any
Checksums-Sha1:
c47d0ec328df75f2151dd6d5b5840768006519f8 17036876 psortb_3.0.6+dfsg.orig.tar.xz
c10819ffb3b3d31ca99a66f9768493ed46e5a541 7480 psortb_3.0.6+dfsg-4.debian.tar.xz
Checksums-Sha256:
ed32aa0240bb03daed228b32614a53c146afba6ca66fd087702315d75e23f751 17036876 psortb_3.0.6+dfsg.orig.tar.xz
fc09ccbf18a26cefd75e8c6030e192878b94b251a6a3206614931820ef6344d0 7480 psortb_3.0.6+dfsg-4.debian.tar.xz
Files:
c4feab06d3031fecac1ab90258550209 17036876 psortb_3.0.6+dfsg.orig.tar.xz
dbe47096a741a5132191480aa07bb7d4 7480 psortb_3.0.6+dfsg-4.debian.tar.xz
Dgit: 4806a2aae47b085aac7d4851a89b803020876c96 debian archive/debian/3.0.6+dfsg-4 https://git.dgit.debian.org/psortb
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Sun Mar 2 20:42:44 UTC 2025 I: Checking whether the package is not for us
Sun Mar 2 20:42:44 UTC 2025 I: Starting 1st build on remote node ionos5-amd64.debian.net.
Sun Mar 2 20:42:44 UTC 2025 I: Preparing to do remote build '1' on ionos5-amd64.debian.net.
Sun Mar 2 20:43:59 UTC 2025 I: Deleting $TMPDIR on ionos5-amd64.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Sat Apr 4 15:05:45 -12 2026
I: pbuilder-time-stamp: 1775358345
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/trixie-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 [psortb_3.0.6+dfsg-4.dsc]
I: copying [./psortb_3.0.6+dfsg.orig.tar.xz]
I: copying [./psortb_3.0.6+dfsg-4.debian.tar.xz]
I: Extracting source
dpkg-source: warning: cannot verify inline signature for ./psortb_3.0.6+dfsg-4.dsc: unsupported subcommand
dpkg-source: info: extracting psortb in psortb-3.0.6+dfsg
dpkg-source: info: unpacking psortb_3.0.6+dfsg.orig.tar.xz
dpkg-source: info: unpacking psortb_3.0.6+dfsg-4.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying biosquid_includes.patch
dpkg-source: info: applying fix_hmmer_interface.patch
dpkg-source: info: applying fix_build_Algorithm-SVM.patch
dpkg-source: info: applying remove-bundled-party-libsvm.patch
dpkg-source: info: applying path_to_conf.patch
dpkg-source: info: applying fix_module_path.patch
dpkg-source: info: applying add_missing_header.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/1903626/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build/reproducible-path'
BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
BUILDUSERNAME='pbuilder1'
BUILD_ARCH='amd64'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 '
DISTRIBUTION='trixie'
HOME='/root'
HOST_ARCH='amd64'
IFS='
'
INVOCATION_ID='5a31ba13309e4f668dfca8ed7bfb127f'
LANG='C'
LANGUAGE='en_US:en'
LC_ALL='C'
MAIL='/var/mail/root'
OPTIND='1'
PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
PBCURRENTCOMMANDLINEOPERATION='build'
PBUILDER_OPERATION='build'
PBUILDER_PKGDATADIR='/usr/share/pbuilder'
PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
PBUILDER_SYSCONFDIR='/etc'
PPID='1903626'
PS1='# '
PS2='> '
PS4='+ '
PWD='/'
SHELL='/bin/bash'
SHLVL='2'
SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.7cldvroz/pbuilderrc_lbqg --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.7cldvroz/b1 --logfile b1/build.log psortb_3.0.6+dfsg-4.dsc'
SUDO_GID='110'
SUDO_UID='105'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://213.165.73.152:3128'
I: uname -a
Linux ionos5-amd64 6.12.9+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.9-1~bpo12+1 (2025-01-19) x86_64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/1903626/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), libsvm-dev, bioperl, ncbi-blast+-legacy, libsquid-dev, libhmmer2-dev, libsvmloc-dev, libmodhmm-dev, pkgconf, pftools
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19802 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 libsvm-dev; however:
Package libsvm-dev is not installed.
pbuilder-satisfydepends-dummy depends on bioperl; however:
Package bioperl is not installed.
pbuilder-satisfydepends-dummy depends on ncbi-blast+-legacy; however:
Package ncbi-blast+-legacy is not installed.
pbuilder-satisfydepends-dummy depends on libsquid-dev; however:
Package libsquid-dev is not installed.
pbuilder-satisfydepends-dummy depends on libhmmer2-dev; however:
Package libhmmer2-dev is not installed.
pbuilder-satisfydepends-dummy depends on libsvmloc-dev; however:
Package libsvmloc-dev is not installed.
pbuilder-satisfydepends-dummy depends on libmodhmm-dev; however:
Package libmodhmm-dev is not installed.
pbuilder-satisfydepends-dummy depends on pkgconf; however:
Package pkgconf is not installed.
pbuilder-satisfydepends-dummy depends on pftools; however:
Package pftools 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} bioperl{a} bsdextrautils{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} libalgorithm-diff-perl{a} libarchive-zip-perl{a} libbio-perl-perl{a} libcapture-tiny-perl{a} libclass-data-inheritable-perl{a} libdata-stag-perl{a} libdebhelper-perl{a} libdevel-stacktrace-perl{a} libelf1t64{a} libexception-class-perl{a} libexpat1{a} libffi8{a} libfile-slurp-perl{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libhmmer2-dev{a} libicu72{a} libio-string-perl{a} liblmdb0{a} libmagic-mgc{a} libmagic1t64{a} libmbedcrypto16{a} libmbedtls21{a} libmbedx509-7{a} libmodhmm-dev{a} libmodhmm0{a} libnghttp2-14{a} libpipeline1{a} libpkgconf3{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} libsquid-dev{a} libsquid1t64{a} libsub-uplevel-perl{a} libsvm-dev{a} libsvm3{a} libsvmloc-dev{a} libsvmloc0{a} libtest-deep-perl{a} libtest-differences-perl{a} libtest-exception-perl{a} libtest-most-perl{a} libtest-warn-perl{a} libtext-diff-perl{a} libtool{a} libuchardet0{a} libunistring5{a} libuv1t64{a} libxml2{a} m4{a} man-db{a} media-types{a} ncbi-blast+{a} ncbi-blast+-legacy{a} ncbi-data{a} netbase{a} pftools{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} python3{a} python3-minimal{a} python3.13{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} tzdata{a}
The following packages are RECOMMENDED but will NOT be installed:
bioperl-run ca-certificates curl libace-perl libalgorithm-diff-xs-perl libalgorithm-munkres-perl libapache-dbi-perl libarchive-cpio-perl libarray-compare-perl libbio-asn1-entrezgene-perl libbio-perl-run-perl libcache-cache-perl libclone-perl libconvert-binary-c-perl libdbd-mysql-perl libdbd-pg-perl libdbd-sqlite3-perl libdbi-perl libgd-perl libgraph-perl libgraphviz-perl libhtml-parser-perl libhtml-tableextract-perl libhttp-message-perl liblist-moreutils-perl libltdl-dev libmail-sendmail-perl libmldbm-perl libpostscript-perl libset-scalar-perl libsoap-lite-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-graph-perl libsvg-perl 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 libyaml-perl lynx perl-doc perl-tk wget
0 packages upgraded, 84 newly installed, 0 to remove and 0 not upgraded.
Need to get 76.8 MB of archives. After unpacking 270 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian trixie/main amd64 libpython3.13-minimal amd64 3.13.2-1 [859 kB]
Get: 2 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB]
Get: 3 http://deb.debian.org/debian trixie/main amd64 python3.13-minimal amd64 3.13.2-1 [2205 kB]
Get: 4 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.13.2-1 [27.1 kB]
Get: 5 http://deb.debian.org/debian trixie/main amd64 media-types all 12.0.0 [28.9 kB]
Get: 6 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB]
Get: 7 http://deb.debian.org/debian trixie/main amd64 tzdata all 2025a-2 [259 kB]
Get: 8 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB]
Get: 9 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-6 [69.4 kB]
Get: 10 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-6 [169 kB]
Get: 11 http://deb.debian.org/debian trixie/main amd64 libpython3.13-stdlib amd64 3.13.2-1 [1979 kB]
Get: 12 http://deb.debian.org/debian trixie/main amd64 python3.13 amd64 3.13.2-1 [745 kB]
Get: 13 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.13.2-1 [10.0 kB]
Get: 14 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.13.2-1 [28.1 kB]
Get: 15 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB]
Get: 16 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB]
Get: 17 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB]
Get: 18 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB]
Get: 19 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-1 [243 kB]
Get: 20 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB]
Get: 21 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-7 [1185 kB]
Get: 22 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.4-5 [92.4 kB]
Get: 23 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB]
Get: 24 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB]
Get: 25 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-5 [294 kB]
Get: 26 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB]
Get: 27 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get: 28 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-3 [862 kB]
Get: 29 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-1 [770 kB]
Get: 30 http://deb.debian.org/debian trixie/main amd64 libio-string-perl all 1.08-4 [12.1 kB]
Get: 31 http://deb.debian.org/debian trixie/main amd64 libdata-stag-perl all 0.14-3 [448 kB]
Get: 32 http://deb.debian.org/debian trixie/main amd64 libbio-perl-perl all 1.7.8-1 [2603 kB]
Get: 33 http://deb.debian.org/debian trixie/main amd64 libclass-data-inheritable-perl all 0.10-1 [8632 B]
Get: 34 http://deb.debian.org/debian trixie/main amd64 libdevel-stacktrace-perl all 2.0500-1 [26.4 kB]
Get: 35 http://deb.debian.org/debian trixie/main amd64 libexception-class-perl all 1.45-1 [34.6 kB]
Get: 36 http://deb.debian.org/debian trixie/main amd64 libtest-deep-perl all 1.204-1 [52.9 kB]
Get: 37 http://deb.debian.org/debian trixie/main amd64 libcapture-tiny-perl all 0.50-1 [24.6 kB]
Get: 38 http://deb.debian.org/debian trixie/main amd64 libalgorithm-diff-perl all 1.201-1 [43.3 kB]
Get: 39 http://deb.debian.org/debian trixie/main amd64 libtext-diff-perl all 1.45-2 [27.2 kB]
Get: 40 http://deb.debian.org/debian trixie/main amd64 libtest-differences-perl all 0.71-1 [17.9 kB]
Get: 41 http://deb.debian.org/debian trixie/main amd64 libsub-uplevel-perl all 0.2800-3 [14.0 kB]
Get: 42 http://deb.debian.org/debian trixie/main amd64 libtest-exception-perl all 0.43-3 [16.9 kB]
Get: 43 http://deb.debian.org/debian trixie/main amd64 libtest-warn-perl all 0.37-2 [14.5 kB]
Get: 44 http://deb.debian.org/debian trixie/main amd64 libtest-most-perl all 0.38-1 [25.1 kB]
Get: 45 http://deb.debian.org/debian trixie/main amd64 bioperl all 1.7.8-1 [246 kB]
Get: 46 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 47 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-3 [539 kB]
Get: 48 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB]
Get: 49 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 50 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 51 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 52 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB]
Get: 53 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB]
Get: 54 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-1 [476 kB]
Get: 55 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-6 [9421 kB]
Get: 56 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b2 [699 kB]
Get: 57 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-1 [1680 kB]
Get: 58 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 59 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 60 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.1 [920 kB]
Get: 61 http://deb.debian.org/debian trixie/main amd64 libfile-slurp-perl all 9999.32-2 [26.7 kB]
Get: 62 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-16 [836 kB]
Get: 63 http://deb.debian.org/debian trixie/main amd64 libhmmer2-dev amd64 2.3.2+dfsg-12+b2 [97.4 kB]
Get: 64 http://deb.debian.org/debian trixie/main amd64 liblmdb0 amd64 0.9.31-1+b2 [45.2 kB]
Get: 65 http://deb.debian.org/debian trixie/main amd64 libmbedcrypto16 amd64 3.6.2-3 [355 kB]
Get: 66 http://deb.debian.org/debian trixie/main amd64 libmbedx509-7 amd64 3.6.2-3 [147 kB]
Get: 67 http://deb.debian.org/debian trixie/main amd64 libmbedtls21 amd64 3.6.2-3 [234 kB]
Get: 68 http://deb.debian.org/debian trixie/main amd64 libmodhmm0 amd64 1.0+dfsg-7 [79.8 kB]
Get: 69 http://deb.debian.org/debian trixie/main amd64 libmodhmm-dev amd64 1.0+dfsg-7 [79.8 kB]
Get: 70 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB]
Get: 71 http://deb.debian.org/debian trixie/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB]
Get: 72 http://deb.debian.org/debian trixie/main amd64 libsquid1t64 amd64 1.9g+cvs20050121-15.1+b2 [76.8 kB]
Get: 73 http://deb.debian.org/debian trixie/main amd64 libsquid-dev amd64 1.9g+cvs20050121-15.1+b2 [145 kB]
Get: 74 http://deb.debian.org/debian trixie/main amd64 libsvm3 amd64 3.24+ds-6+b1 [41.5 kB]
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Get: 79 http://deb.debian.org/debian trixie/main amd64 ncbi-data all 6.1.20170106+dfsg2-5 [3537 kB]
Get: 80 http://deb.debian.org/debian trixie/main amd64 ncbi-blast+ amd64 2.16.0+ds-6+b1 [15.2 MB]
Get: 81 http://deb.debian.org/debian trixie/main amd64 ncbi-blast+-legacy all 2.16.0+ds-6 [10.4 kB]
Get: 82 http://deb.debian.org/debian trixie/main amd64 pftools amd64 3.2.12-1 [24.8 MB]
Get: 83 http://deb.debian.org/debian trixie/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB]
Get: 84 http://deb.debian.org/debian trixie/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB]
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Setting up pkgconf:amd64 (1.8.1-4) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
Setting up libmbedx509-7:amd64 (3.6.2-3) ...
Setting up libtest-exception-perl (0.43-3) ...
Setting up libsvmloc0:amd64 (1.0+dfsg-7) ...
Setting up libsvm-dev:amd64 (3.24+ds-6+b1) ...
Setting up libmbedtls21:amd64 (3.6.2-3) ...
Setting up libreadline8t64:amd64 (8.2-6) ...
Setting up dh-strip-nondeterminism (1.14.1-2) ...
Setting up groff-base (1.23.0-7) ...
Setting up libpython3.13-stdlib:amd64 (3.13.2-1) ...
Setting up libpython3-stdlib:amd64 (3.13.2-1) ...
Setting up libsvmloc-dev:amd64 (1.0+dfsg-7) ...
Setting up python3.13 (3.13.2-1) ...
Setting up libtest-most-perl (0.38-1) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up python3 (3.13.2-1) ...
Setting up man-db (2.13.0-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up ncbi-blast+ (2.16.0+ds-6+b1) ...
Setting up bioperl (1.7.8-1) ...
Setting up ncbi-blast+-legacy (2.16.0+ds-6) ...
Setting up debhelper (13.24.1) ...
Processing triggers for libc-bin (2.40-7) ...
Reading package lists...
Building dependency tree...
Reading state information...
Reading extended state information...
Initializing package states...
Writing extended state information...
Building tag database...
-> Finished parsing the build-deps
I: Building the package
I: Running cd /build/reproducible-path/psortb-3.0.6+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../psortb_3.0.6+dfsg-4_source.changes
dpkg-buildpackage: info: source package psortb
dpkg-buildpackage: info: source version 3.0.6+dfsg-4
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
debian/rules override_dh_auto_clean
make[1]: Entering directory '/build/reproducible-path/psortb-3.0.6+dfsg'
dh_auto_clean
if [ -x psort/bin/psort.debsave ] ; then \
mv psort/bin/psort.debsave psort/bin/psort ; \
fi
make[1]: Leaving directory '/build/reproducible-path/psortb-3.0.6+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/reproducible-path/psortb-3.0.6+dfsg'
cp -a psort/bin/psort psort/bin/psort.debsave
dh_auto_configure
/usr/bin/perl Makefile.PL INSTALLDIRS=vendor "OPTIMIZE=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/psortb-3.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2" "LD=x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/psortb-3.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now"
External Module XML::RPC, XML Based RPC client, is not installed on this computer.
The XML::RPC in PSortb needs it for making calls to remote PSortb servers, if you don't plan to do this, ignore this warning
We think we've found blastall, please enter the path if this isn't correct [/usr/bin/] /usr/bin/
We think we've found pfscan, please enter the path if this isn't correct [/usr/bin/] /usr/bin/
Where do you plan to install the psort configuration files? [/usr/local/psortb] /usr/local/psortb
Checking if your kit is complete...
Looks good
hmmer was not found in the dynamic linker path, is there somewhere else we should check? [/usr/local/lib64] /usr/local/lib64
We're still not finding hmmer either in your dynamic linker path (/etc/ld.so.conf) or
in /usr/local/lib64.
Do you want to continue anyways? [Y/n] [Y] Y
squid was not found in the dynamic linker path, is there somewhere else we should check? [/usr/local/lib64] /usr/local/lib64
We're still not finding squid either in your dynamic linker path (/etc/ld.so.conf) or
in /usr/local/lib64.
Do you want to continue anyways? [Y/n] [Y] Y
Checking if your kit is complete...
Looks good
Writing MYMETA.yml and MYMETA.json
svmloc was not found in the dynamic linker path, is there somewhere else we should check? [/usr/local/lib64] /usr/local/lib64
We're still not finding svmloc either in your dynamic linker path (/etc/ld.so.conf) or
in /usr/local/lib64.
Do you want to continue anyways? [Y/n] [Y] Y
Checking if your kit is complete...
Looks good
Writing MYMETA.yml and MYMETA.json
modhmm was not found in the dynamic linker path, is there somewhere else we should check? [/usr/local/lib64] /usr/local/lib64
We're still not finding modhmm either in your dynamic linker path (/etc/ld.so.conf) or
in /usr/local/lib64.
Do you want to continue anyways? [Y/n] [Y] Y
Writing MYMETA.yml and MYMETA.json
Generating a Unix-style Makefile
Writing Makefile for Bio::Tools::PSort
Writing MYMETA.yml and MYMETA.json
Updating psort/bin/psort with path hints
Making sclblast databases
Building a new DB, current time: 04/04/2026 15:06:26
New DB name: /build/reproducible-path/psortb-3.0.6+dfsg/psort/conf/analysis/sclblast/gramneg/sclblast
New DB title: sclblast
Sequence type: Protein
Keep MBits: T
Maximum file size: 3000000000B
BLAST Database creation error: Error: Duplicate seq_ids are found:
LCL|6226665
Program failed, try executing the command manually.
Building a new DB, current time: 04/04/2026 15:06:26
New DB name: /build/reproducible-path/psortb-3.0.6+dfsg/psort/conf/analysis/sclblast/grampos/sclblast
New DB title: sclblast
Sequence type: Protein
Keep MBits: T
Maximum file size: 3000000000B
BLAST Database creation error: Error: Duplicate seq_ids are found:
LCL|145559529
Program failed, try executing the command manually.
Building a new DB, current time: 04/04/2026 15:06:26
New DB name: /build/reproducible-path/psortb-3.0.6+dfsg/psort/conf/analysis/sclblast/archaea/sclblast
New DB title: sclblast
Sequence type: Protein
Keep MBits: T
Maximum file size: 3000000000B
FASTA-Reader: Ignoring invalid residues at position(s): On line 46049: 38
FASTA-Reader: Ignoring invalid residues at position(s): On line 87237: 23
FASTA-Reader: Title ends with at least 50 valid amino acid characters. Was the sequence accidentally put in the title line?
FASTA-Reader: Ignoring invalid residues at position(s): On line 87252: 4
FASTA-Reader: Ignoring invalid residues at position(s): On line 87263: 8
BLAST Database creation error: Error: Duplicate seq_ids are found:
LCL|15596641
Program failed, try executing the command manually.
Ready for make, next steps you must run:
$ make
$ make test
$ make install
RECOMMENDED:
cp -r psort /usr/local/psortb
PSortb will then be available at /usr/local/psortb/bin/psort or in your path depending on your configuration
make[1]: Leaving directory '/build/reproducible-path/psortb-3.0.6+dfsg'
debian/rules override_dh_auto_build
make[1]: Entering directory '/build/reproducible-path/psortb-3.0.6+dfsg'
# hack around the issue that configure injects wrong root dir /usr/local/psortb
mv psort/bin/psort.debsave psort/bin/psort
dh_auto_build
make -j42
make[2]: Entering directory '/build/reproducible-path/psortb-3.0.6+dfsg'
make[3]: Entering directory '/build/reproducible-path/psortb-3.0.6+dfsg/algorithm-hmm'
Running Mkbootstrap for HMM ()
"/usr/bin/perl" "/usr/share/perl/5.40.1/ExtUtils/xsubpp" -C++ -typemap '/usr/share/perl/5.40/ExtUtils/typemap' -typemap '/build/reproducible-path/psortb-3.0.6+dfsg/algorithm-hmm/typemap' HMM.xs > HMM.xsc
g++ -c -Isrc/include `pkg-config --cflags libsquid` `pkg-config --cflags libhmmer2` -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/psortb-3.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"0.02\" -DXS_VERSION=\"0.02\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE" hmm-binding.cpp
cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++
chmod 644 "HMM.bs"
"/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- HMM.bs ../blib/arch/auto/Algorithm/HMM/HMM.bs 644
cp lib/Bio/Tools/PSort/Pathway.pm blib/lib/Bio/Tools/PSort/Pathway.pm
cp lib/Bio/Tools/PSort/Report/Formatter/terse.pm blib/lib/Bio/Tools/PSort/Report/Formatter/terse.pm
cp lib/Bio/Tools/Motif/Pattern.pm blib/lib/Bio/Tools/Motif/Pattern.pm
cp lib/Bio/Tools/PSort/Module/OMPMotif.pm blib/lib/Bio/Tools/PSort/Module/OMPMotif.pm
cp lib/Bio/Tools/PSort/Module/SVMLoc.pm blib/lib/Bio/Tools/PSort/Module/SVMLoc.pm
cp lib/Bio/Tools/PSort/Module/Bayesian.pm blib/lib/Bio/Tools/PSort/Module/Bayesian.pm
cp lib/Bio/Tools/PSort/Profile/Match.pm blib/lib/Bio/Tools/PSort/Profile/Match.pm
cp lib/Bio/Tools/PSort/Report/Formatter/long.pm blib/lib/Bio/Tools/PSort/Report/Formatter/long.pm
cp lib/Bio/Tools/PSort/Profile.pm blib/lib/Bio/Tools/PSort/Profile.pm
cp lib/Bio/Tools/PSort/Module/Signal.pm blib/lib/Bio/Tools/PSort/Module/Signal.pm
cp lib/Bio/Tools/PSort/Module/AnalysisI.pm blib/lib/Bio/Tools/PSort/Module/AnalysisI.pm
cp lib/Bio/Tools/PSort.pm blib/lib/Bio/Tools/PSort.pm
cp lib/Bio/Tools/PSort/Report.pm blib/lib/Bio/Tools/PSort/Report.pm
cp lib/Bio/Tools/PSort/Module/Null.pm blib/lib/Bio/Tools/PSort/Module/Null.pm
cp lib/Bio/Tools/PSort/Module/Profile.pm blib/lib/Bio/Tools/PSort/Module/Profile.pm
cp lib/Bio/Tools/PSort/Module/HMMTOP.pm blib/lib/Bio/Tools/PSort/Module/HMMTOP.pm
cp lib/Bio/Tools/PSort/Constants.pm blib/lib/Bio/Tools/PSort/Constants.pm
cp lib/Bio/Tools/PSort/Install.pm blib/lib/Bio/Tools/PSort/Install.pm
cp lib/Bio/Tools/PSort/ModuleI.pm blib/lib/Bio/Tools/PSort/ModuleI.pm
cp lib/Bio/Tools/PSort/Module/Motif.pm blib/lib/Bio/Tools/PSort/Module/Motif.pm
cp lib/Bio/Tools/Motif/Match.pm blib/lib/Bio/Tools/Motif/Match.pm
cp lib/Bio/Tools/PSort/Module/InputI.pm blib/lib/Bio/Tools/PSort/Module/InputI.pm
cp lib/Bio/Tools/PSort/Module/SVMLocApache.pm blib/lib/Bio/Tools/PSort/Module/SVMLocApache.pm
cp lib/Bio/Tools/PSort/Report/Formatter/normal.pm blib/lib/Bio/Tools/PSort/Report/Formatter/normal.pm
cp lib/Bio/Tools/PSort/Module/OutputI.pm blib/lib/Bio/Tools/PSort/Module/OutputI.pm
cp lib/Bio/Tools/PSort/Report/Result.pm blib/lib/Bio/Tools/PSort/Report/Result.pm
cp lib/Bio/Tools/PSort/Report/Formatter/html.pm blib/lib/Bio/Tools/PSort/Report/Formatter/html.pm
cp lib/Bio/Tools/PSort/Module/Rules.pm blib/lib/Bio/Tools/PSort/Module/Rules.pm
cp lib/Bio/Tools/PSort/Report/Formatter.pm blib/lib/Bio/Tools/PSort/Report/Formatter.pm
cp lib/Bio/Tools/PSort/Module/SCLBlast.pm blib/lib/Bio/Tools/PSort/Module/SCLBlast.pm
cp lib/Bio/Tools/Motif.pm blib/lib/Bio/Tools/Motif.pm
cp lib/Bio/Tools/PSort/Module/ModHMM.pm blib/lib/Bio/Tools/PSort/Module/ModHMM.pm
cp lib/Algorithm/HMM.pm ../blib/lib/Algorithm/HMM.pm
AutoSplitting ../blib/lib/Algorithm/HMM.pm (../blib/lib/auto/Algorithm/HMM)
cp lib/Algorithm/HMM/Hit/Global.pm ../blib/lib/Algorithm/HMM/Hit/Global.pm
cp lib/Algorithm/HMM/Hit/Domain.pm ../blib/lib/Algorithm/HMM/Hit/Domain.pm
cp lib/Algorithm/HMM/Hit.pm ../blib/lib/Algorithm/HMM/Hit.pm
cp lib/Algorithm/HMM/Report.pm ../blib/lib/Algorithm/HMM/Report.pm
cp lib/Bio/Tools/Run/SCLBlast.pm blib/lib/Bio/Tools/Run/SCLBlast.pm
cp lib/Bio/Tools/Signal.pm blib/lib/Bio/Tools/Signal.pm
cp lib/Bio/Tools/Run/HMMTOP/Helix.pm blib/lib/Bio/Tools/Run/HMMTOP/Helix.pm
cp lib/Bio/Tools/Signal/Report.pm blib/lib/Bio/Tools/Signal/Report.pm
cp lib/Bio/Tools/PSort/XMLRPC/Client.pm blib/lib/Bio/Tools/PSort/XMLRPC/Client.pm
cp lib/Bio/Tools/Run/SCLBlast/Report.pm blib/lib/Bio/Tools/Run/SCLBlast/Report.pm
cp lib/Bio/Tools/Run/SCLBlast/Hit.pm blib/lib/Bio/Tools/Run/SCLBlast/Hit.pm
cp lib/Bio/Tools/Run/HMMTOP.pm blib/lib/Bio/Tools/Run/HMMTOP.pm
cp lib/Bio/Tools/Run/HMMTOP/Report.pm blib/lib/Bio/Tools/Run/HMMTOP/Report.pm
cp lib/Bio/Tools/Run/SCLBlastLocal.pm blib/lib/Bio/Tools/Run/SCLBlastLocal.pm
cp lib/Bio/Tools/SVMLoc.pm blib/lib/Bio/Tools/SVMLoc.pm
Please specify prototyping behavior for HMM.xs (see perlxs manual)
mv HMM.xsc HMM.c
g++ -c -Isrc/include `pkg-config --cflags libsquid` `pkg-config --cflags libhmmer2` -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/psortb-3.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"0.02\" -DXS_VERSION=\"0.02\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE" HMM.c
cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++
hmm-binding.cpp: In member function 'HMMReport* HMM::search(char*)':
hmm-binding.cpp:136:71: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
136 | PostprocessSignificantHit(ghit, dhit, trace, model, dseq, seqlen, "SEQ",
| ^~~~~
rm -f ../blib/arch/auto/Algorithm/HMM/HMM.so
x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/psortb-3.0.6+dfsg=. -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 HMM.o hmm-binding.o -o ../blib/arch/auto/Algorithm/HMM/HMM.so \
-lm -lpthread -lstdc++ -lhmmer -lsquid \
chmod 755 ../blib/arch/auto/Algorithm/HMM/HMM.so
Manifying 5 pod documents
make[3]: Leaving directory '/build/reproducible-path/psortb-3.0.6+dfsg/algorithm-hmm'
make[3]: Entering directory '/build/reproducible-path/psortb-3.0.6+dfsg/bio-tools-psort-svmloc'
Running Mkbootstrap for SVMLoc ()
"/usr/bin/perl" "/usr/share/perl/5.40.1/ExtUtils/xsubpp" -C++ -typemap '/usr/share/perl/5.40/ExtUtils/typemap' -typemap '/build/reproducible-path/psortb-3.0.6+dfsg/bio-tools-psort-svmloc/typemap' SVMLoc.xs > SVMLoc.xsc
chmod 644 "SVMLoc.bs"
"/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- SVMLoc.bs ../blib/arch/auto/Bio/Tools/PSort/SVMLoc/SVMLoc.bs 644
cp lib/Bio/Tools/PSort/SVMLoc/DataSet.pm ../blib/lib/Bio/Tools/PSort/SVMLoc/DataSet.pm
cp lib/Bio/Tools/PSort/SVMLoc.pm ../blib/lib/Bio/Tools/PSort/SVMLoc.pm
AutoSplitting ../blib/lib/Bio/Tools/PSort/SVMLoc.pm (../blib/lib/auto/Bio/Tools/PSort/SVMLoc)
Please specify prototyping behavior for SVMLoc.xs (see perlxs manual)
mv SVMLoc.xsc SVMLoc.c
g++ -c -Wall -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/psortb-3.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"0.01\" -DXS_VERSION=\"0.01\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE" SVMLoc.c
cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++
rm -f ../blib/arch/auto/Bio/Tools/PSort/SVMLoc/SVMLoc.so
x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/psortb-3.0.6+dfsg=. -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 SVMLoc.o -o ../blib/arch/auto/Bio/Tools/PSort/SVMLoc/SVMLoc.so \
-lsvmloc -lm -lsvm -lstdc++ \
chmod 755 ../blib/arch/auto/Bio/Tools/PSort/SVMLoc/SVMLoc.so
Manifying 2 pod documents
make[3]: Leaving directory '/build/reproducible-path/psortb-3.0.6+dfsg/bio-tools-psort-svmloc'
make[3]: Entering directory '/build/reproducible-path/psortb-3.0.6+dfsg/bio-tools-psort-modhmm'
Running Mkbootstrap for ModHMM ()
"/usr/bin/perl" "/usr/share/perl/5.40.1/ExtUtils/xsubpp" -typemap '/usr/share/perl/5.40/ExtUtils/typemap' -typemap '/build/reproducible-path/psortb-3.0.6+dfsg/bio-tools-psort-modhmm/typemap' modhmm.xs > modhmm.xsc
cc -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/psortb-3.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"0.01\" -DXS_VERSION=\"0.01\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE" binding.c
chmod 644 "ModHMM.bs"
"/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- ModHMM.bs ../blib/arch/auto/Bio/Tools/PSort/ModHMM/ModHMM.bs 644
cp lib/Bio/Tools/PSort/ModHMM.pm ../blib/lib/Bio/Tools/PSort/ModHMM.pm
AutoSplitting ../blib/lib/Bio/Tools/PSort/ModHMM.pm (../blib/lib/auto/Bio/Tools/PSort/ModHMM)
mv modhmm.xsc modhmm.c
cc -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/psortb-3.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"0.01\" -DXS_VERSION=\"0.01\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE" modhmm.c
rm -f ../blib/arch/auto/Bio/Tools/PSort/ModHMM/ModHMM.so
x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/psortb-3.0.6+dfsg=. -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 modhmm.o binding.o -o ../blib/arch/auto/Bio/Tools/PSort/ModHMM/ModHMM.so \
-lm -lstdc++ -lmodhmm \
chmod 755 ../blib/arch/auto/Bio/Tools/PSort/ModHMM/ModHMM.so
Manifying 1 pod document
make[3]: Leaving directory '/build/reproducible-path/psortb-3.0.6+dfsg/bio-tools-psort-modhmm'
Manifying 18 pod documents
make[2]: Leaving directory '/build/reproducible-path/psortb-3.0.6+dfsg'
make[1]: Leaving directory '/build/reproducible-path/psortb-3.0.6+dfsg'
dh_auto_test
make -j42 test TEST_VERBOSE=1
make[1]: Entering directory '/build/reproducible-path/psortb-3.0.6+dfsg'
make[2]: Entering directory '/build/reproducible-path/psortb-3.0.6+dfsg/algorithm-hmm'
"/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- HMM.bs ../blib/arch/auto/Algorithm/HMM/HMM.bs 644
Manifying 5 pod documents
make[2]: Leaving directory '/build/reproducible-path/psortb-3.0.6+dfsg/algorithm-hmm'
make[2]: Entering directory '/build/reproducible-path/psortb-3.0.6+dfsg/bio-tools-psort-svmloc'
"/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- SVMLoc.bs ../blib/arch/auto/Bio/Tools/PSort/SVMLoc/SVMLoc.bs 644
Manifying 2 pod documents
make[2]: Leaving directory '/build/reproducible-path/psortb-3.0.6+dfsg/bio-tools-psort-svmloc'
make[2]: Entering directory '/build/reproducible-path/psortb-3.0.6+dfsg/bio-tools-psort-modhmm'
"/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- ModHMM.bs ../blib/arch/auto/Bio/Tools/PSort/ModHMM/ModHMM.bs 644
Manifying 1 pod document
make[2]: Leaving directory '/build/reproducible-path/psortb-3.0.6+dfsg/bio-tools-psort-modhmm'
make[2]: Entering directory '/build/reproducible-path/psortb-3.0.6+dfsg/algorithm-hmm'
"/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- HMM.bs ../blib/arch/auto/Algorithm/HMM/HMM.bs 644
PERL_DL_NONLAZY=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(1, '../blib/lib', '../blib/arch')" t/*.t
t/hmm.t ..
1..5
ok 1 - use Algorithm::HMM;
ok 2
Creating new Algorithm::HMM
ok 3 - Ensuring we could load a model
Saving model...
ok 4 - Testing saving a model
Loading saved model...
ok 5 - Testing reloading a model
ok
All tests successful.
Files=1, Tests=5, 0 wallclock secs ( 0.02 usr 0.00 sys + 0.05 cusr 0.01 csys = 0.08 CPU)
Result: PASS
make[2]: Leaving directory '/build/reproducible-path/psortb-3.0.6+dfsg/algorithm-hmm'
make[2]: Entering directory '/build/reproducible-path/psortb-3.0.6+dfsg/bio-tools-psort-svmloc'
"/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- SVMLoc.bs ../blib/arch/auto/Bio/Tools/PSort/SVMLoc/SVMLoc.bs 644
PERL_DL_NONLAZY=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(1, '../blib/lib', '../blib/arch')" t/*.t
t/svmloc.t ..
1..15
ok 1 - use Bio::Tools::PSort::SVMLoc;
ok 2 - use Bio::Tools::PSort::SVMLoc::DataSet;
ok 3 - Loaded SVMLoc
Creating new Bio::Tools::PSort::SVMLoc
ok 4 - Creating SVMLoc object
Checking predictions on loaded model
ok 5 - Classify seq 1
ok 6 - Classify seq 2
ok 7 - Classify seq 3
Creating second Bio::Tools::PSort::SVMLoc
ok 8 - Creating SVMLoc object 2
Creating new Bio::Tools::PSort::SVMLoc::DataSet objects
ok 9 - Dataset 1 created
ok 10 - Dataset 2 created
ok 11 - Dataset 3 created
Adding attributes to Bio::Tools::PSort::SVMLoc::DataSet objects
ok 12
Checking predictions on second loaded model
ok 13 - Classify seq 1 on model 2
ok 14 - Classify seq 2 on model 2
ok 15 - Classify seq 3 on model 2
Everything looks ok!
ok
All tests successful.
Files=1, Tests=15, 1 wallclock secs ( 0.02 usr 0.00 sys + 0.17 cusr 0.02 csys = 0.21 CPU)
Result: PASS
make[2]: Leaving directory '/build/reproducible-path/psortb-3.0.6+dfsg/bio-tools-psort-svmloc'
make[2]: Entering directory '/build/reproducible-path/psortb-3.0.6+dfsg/bio-tools-psort-modhmm'
"/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- ModHMM.bs ../blib/arch/auto/Bio/Tools/PSort/ModHMM/ModHMM.bs 644
PERL_DL_NONLAZY=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(1, '../blib/lib', '../blib/arch')" t/*.t
t/modhmm.t ..
1..4
ok 1 - use Bio::Tools::PSort::ModHMM;
ok 2 - Loading ModHMM
Running sequence through Bio::Tools::PSort::ModHMM
ok 3 - Running sequence through ModHMM
Retreiving TM helix sites
ok 4 - Retreiving TM helix sites
ok
All tests successful.
Files=1, Tests=4, 0 wallclock secs ( 0.02 usr 0.01 sys + 0.12 cusr 0.02 csys = 0.17 CPU)
Result: PASS
make[2]: Leaving directory '/build/reproducible-path/psortb-3.0.6+dfsg/bio-tools-psort-modhmm'
PERL_DL_NONLAZY=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(1, 'blib/lib', 'blib/arch')" t/*.t
t/psort.t ..
1..2
ok 1 - PSort module loaded
Creating new Bio::Tools::PSort
ok 2 - PSort object made
ok
All tests successful.
Files=1, Tests=2, 0 wallclock secs ( 0.01 usr 0.00 sys + 0.08 cusr 0.00 csys = 0.09 CPU)
Result: PASS
make[1]: Leaving directory '/build/reproducible-path/psortb-3.0.6+dfsg'
create-stamp debian/debhelper-build-stamp
dh_prep
dh_auto_install --destdir=debian/psortb/
make -j42 install DESTDIR=/build/reproducible-path/psortb-3.0.6\+dfsg/debian/psortb AM_UPDATE_INFO_DIR=no PREFIX=/usr
make[1]: Entering directory '/build/reproducible-path/psortb-3.0.6+dfsg'
make[2]: Entering directory '/build/reproducible-path/psortb-3.0.6+dfsg/algorithm-hmm'
"/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- HMM.bs ../blib/arch/auto/Algorithm/HMM/HMM.bs 644
Manifying 5 pod documents
make[2]: Leaving directory '/build/reproducible-path/psortb-3.0.6+dfsg/algorithm-hmm'
make[2]: Entering directory '/build/reproducible-path/psortb-3.0.6+dfsg/bio-tools-psort-svmloc'
"/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- SVMLoc.bs ../blib/arch/auto/Bio/Tools/PSort/SVMLoc/SVMLoc.bs 644
Manifying 2 pod documents
make[2]: Leaving directory '/build/reproducible-path/psortb-3.0.6+dfsg/bio-tools-psort-svmloc'
make[2]: Entering directory '/build/reproducible-path/psortb-3.0.6+dfsg/bio-tools-psort-modhmm'
"/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- ModHMM.bs ../blib/arch/auto/Bio/Tools/PSort/ModHMM/ModHMM.bs 644
Manifying 1 pod document
make[2]: Leaving directory '/build/reproducible-path/psortb-3.0.6+dfsg/bio-tools-psort-modhmm'
Manifying 18 pod documents
Files found in blib/arch: installing files in blib/lib into architecture dependent library tree
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/auto/Bio/Tools/PSort/SVMLoc/SVMLoc.so
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/auto/Bio/Tools/PSort/ModHMM/ModHMM.so
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/auto/Algorithm/HMM/HMM.so
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/auto/Bio/Tools/PSort/SVMLoc/autosplit.ix
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/auto/Bio/Tools/PSort/ModHMM/autosplit.ix
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/auto/Algorithm/HMM/autosplit.ix
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/Signal.pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/SVMLoc.pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/Motif.pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort.pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/Install.pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/Constants.pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/Profile.pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/ModHMM.pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/ModuleI.pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/SVMLoc.pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/Pathway.pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/Report.pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/Report/Formatter.pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/Report/Result.pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/Report/Formatter/html.pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/Report/Formatter/long.pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/Report/Formatter/normal.pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/Report/Formatter/terse.pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/SVMLoc/DataSet.pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/Profile/Match.pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/XMLRPC/Client.pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/Module/AnalysisI.pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/Module/SVMLocApache.pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/Module/Profile.pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/Module/OutputI.pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/Module/Signal.pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/Module/ModHMM.pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/Module/InputI.pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/Module/OMPMotif.pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/Module/HMMTOP.pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/Module/SVMLoc.pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/Module/Rules.pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/Module/Motif.pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/Module/SCLBlast.pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/Module/Bayesian.pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/Module/Null.pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/Signal/Report.pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/Run/HMMTOP.pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/Run/SCLBlast.pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/Run/SCLBlastLocal.pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/Run/SCLBlast/Report.pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/Run/SCLBlast/Hit.pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/Run/HMMTOP/Helix.pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/Run/HMMTOP/Report.pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/Motif/Match.pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/Motif/Pattern.pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Algorithm/HMM.pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Algorithm/HMM/Report.pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Algorithm/HMM/Hit.pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Algorithm/HMM/Hit/Domain.pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Algorithm/HMM/Hit/Global.pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::PSort::Module::Motif.3pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::PSort::Profile::Match.3pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::Motif.3pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Algorithm::HMM::Hit::Domain.3pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::PSort::SVMLoc::DataSet.3pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::PSort::Module::AnalysisI.3pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::PSort::Module::OMPMotif.3pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::PSort::Profile.3pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Algorithm::HMM.3pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::PSort::Module::OutputI.3pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::Run::HMMTOP.3pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::PSort::ModuleI.3pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::Motif::Pattern.3pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::PSort::Module::Null.3pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Algorithm::HMM::Hit::Global.3pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::PSort::Pathway.3pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::Signal.3pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::PSort::Module::InputI.3pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Algorithm::HMM::Report.3pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::PSort.3pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Algorithm::HMM::Hit.3pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::Motif::Match.3pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::SVMLoc.3pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::PSort::ModHMM.3pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::PSort::SVMLoc.3pm
Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::PSort::Module::Profile.3pm
make[1]: Leaving directory '/build/reproducible-path/psortb-3.0.6+dfsg'
dh_install
dh_installdocs
dh_installchangelogs
dh_installman
dh_lintian
dh_perl
dh_link
dh_strip_nondeterminism
dh_compress
debian/rules override_dh_fixperms
make[1]: Entering directory '/build/reproducible-path/psortb-3.0.6+dfsg'
dh_fixperms
chmod +x debian/psortb/usr/lib/psort/conf/analysis/signal/archaea/check-sig
make[1]: Leaving directory '/build/reproducible-path/psortb-3.0.6+dfsg'
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 'psortb' in '../psortb_3.0.6+dfsg-4_amd64.deb'.
dpkg-deb: building package 'psortb-dbgsym' in '../psortb-dbgsym_3.0.6+dfsg-4_amd64.deb'.
dpkg-genbuildinfo --build=binary -O../psortb_3.0.6+dfsg-4_amd64.buildinfo
dpkg-genchanges --build=binary -O../psortb_3.0.6+dfsg-4_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: 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/1903626 and its subdirectories
I: Current time: Sat Apr 4 15:06:58 -12 2026
I: pbuilder-time-stamp: 1775358418
Sun Mar 2 20:44:00 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos11-amd64.debian.net.
Sun Mar 2 20:44:00 UTC 2025 I: Preparing to do remote build '2' on ionos11-amd64.debian.net.
Sun Mar 2 20:50:19 UTC 2025 I: Deleting $TMPDIR on ionos11-amd64.debian.net.
Sun Mar 2 20:50:20 UTC 2025 I: psortb_3.0.6+dfsg-4_amd64.changes:
Format: 1.8
Date: Sun, 26 May 2024 09:32:14 +0200
Source: psortb
Binary: psortb psortb-dbgsym
Architecture: amd64
Version: 3.0.6+dfsg-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Étienne Mollier <emollier@debian.org>
Description:
psortb - bacterial localization prediction tool
Closes: 1070459
Changes:
psortb (3.0.6+dfsg-4) unstable; urgency=medium
.
[ Andreas Tille ]
* Add missing header file
Closes: #1070459
* Standards-Version: 4.7.0 (routine-update)
.
[ Étienne Mollier ]
* add_missing_header.patch: supplement to finish fixing ftbfs.
* d/control: add myself to uploaders.
* d/control: migrate to pkgconf.
Checksums-Sha1:
9e781dfca5a9a7270c1f0b2213662aa310a2d534 159780 psortb-dbgsym_3.0.6+dfsg-4_amd64.deb
8999a6ae2769b7feeb6a61507bfe902bc469282c 6635 psortb_3.0.6+dfsg-4_amd64.buildinfo
2de19511779a3c9c71350fc41718c7f89efc1a17 16375428 psortb_3.0.6+dfsg-4_amd64.deb
Checksums-Sha256:
b804ad1ed321bcf9c5db1f23501979c25211516b2a16c270f8774cdd61a2ff8f 159780 psortb-dbgsym_3.0.6+dfsg-4_amd64.deb
933c062089406550e2305b35e3402440489a9a97cf3b03c84c223497207f5a2a 6635 psortb_3.0.6+dfsg-4_amd64.buildinfo
23a1158dabba9939ad58eb6c87f4c7b8e4b8f5419e4694a06f95d2dc4c2deee2 16375428 psortb_3.0.6+dfsg-4_amd64.deb
Files:
5b85a8828e4533d9fd243839f7f9a41a 159780 debug optional psortb-dbgsym_3.0.6+dfsg-4_amd64.deb
8095f283aded36ece81d1e11810d3d9c 6635 science optional psortb_3.0.6+dfsg-4_amd64.buildinfo
5f968359d8223d44aa1812a63977843f 16375428 science optional psortb_3.0.6+dfsg-4_amd64.deb
Sun Mar 2 20:50:20 UTC 2025 I: diffoscope 289 will be used to compare the two builds:
Running as unit: rb-diffoscope-amd64_6-34097.service
# Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.7cldvroz/psortb_3.0.6+dfsg-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.7cldvroz/psortb_3.0.6+dfsg-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.7cldvroz/psortb_3.0.6+dfsg-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.7cldvroz/b1/psortb_3.0.6+dfsg-4_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.7cldvroz/b2/psortb_3.0.6+dfsg-4_amd64.changes
## command (total time: 0.000s)
0.000s 1 call cmp (internal)
## has_same_content_as (total time: 0.000s)
0.000s 1 call diffoscope.comparators.binary.FilesystemFile
## main (total time: 0.003s)
0.003s 2 calls outputs
0.000s 1 call cleanup
Finished with result: success
Main processes terminated with: code=exited/status=0
Service runtime: 229ms
CPU time consumed: 228ms
Sun Mar 2 20:50:22 UTC 2025 I: diffoscope 289 found no differences in the changes files, and a .buildinfo file also exists.
Sun Mar 2 20:50:22 UTC 2025 I: psortb from trixie built successfully and reproducibly on amd64.
Sun Mar 2 20:50:24 UTC 2025 I: Submitting .buildinfo files to external archives:
Sun Mar 2 20:50:24 UTC 2025 I: Submitting 8.0K b1/psortb_3.0.6+dfsg-4_amd64.buildinfo.asc
Sun Mar 2 20:50:25 UTC 2025 I: Submitting 8.0K b2/psortb_3.0.6+dfsg-4_amd64.buildinfo.asc
Sun Mar 2 20:50:27 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Sun Mar 2 20:50:27 UTC 2025 I: Done submitting .buildinfo files.
Sun Mar 2 20:50:27 UTC 2025 I: Removing signed psortb_3.0.6+dfsg-4_amd64.buildinfo.asc files:
removed './b1/psortb_3.0.6+dfsg-4_amd64.buildinfo.asc'
removed './b2/psortb_3.0.6+dfsg-4_amd64.buildinfo.asc'