I: pbuilder: network access will be disabled during build
I: Current time: Wed Aug  6 14:43:29 -12 2025
I: pbuilder-time-stamp: 1754534609
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: Copying source file
I: copying [psortb_3.0.6+dfsg-3.dsc]
I: copying [./psortb_3.0.6+dfsg.orig.tar.xz]
I: copying [./psortb_3.0.6+dfsg-3.debian.tar.xz]
I: Extracting source
gpgv: Signature made Sun Apr 24 08:35:50 2022 -12
gpgv:                using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA
gpgv:                issuer "emollier@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./psortb_3.0.6+dfsg-3.dsc: no acceptable signature found
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-3.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
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/2476591/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='arm64'
  DEBIAN_FRONTEND='noninteractive'
  DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 '
  DISTRIBUTION='bookworm'
  HOME='/root'
  HOST_ARCH='arm64'
  IFS=' 	
  '
  INVOCATION_ID='907548bef2334932b09a96f45e0cfc09'
  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='2476591'
  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.qWPKVI2A/pbuilderrc_gG2X --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.qWPKVI2A/b1 --logfile b1/build.log psortb_3.0.6+dfsg-3.dsc'
  SUDO_GID='109'
  SUDO_UID='104'
  SUDO_USER='jenkins'
  TERM='unknown'
  TZ='/usr/share/zoneinfo/Etc/GMT+12'
  USER='root'
  _='/usr/bin/systemd-run'
  http_proxy='http://192.168.101.4:3128'
I: uname -a
  Linux codethink01-arm64 6.1.0-22-cloud-arm64 #1 SMP Debian 6.1.94-1 (2024-06-21) aarch64 GNU/Linux
I: ls -l /bin
  total 7104
  -rwxr-xr-x 1 root root 1346480 Mar 29  2024 bash
  -rwxr-xr-x 3 root root   67728 Sep 18  2022 bunzip2
  -rwxr-xr-x 3 root root   67728 Sep 18  2022 bzcat
  lrwxrwxrwx 1 root root       6 Sep 18  2022 bzcmp -> bzdiff
  -rwxr-xr-x 1 root root    2225 Sep 18  2022 bzdiff
  lrwxrwxrwx 1 root root       6 Sep 18  2022 bzegrep -> bzgrep
  -rwxr-xr-x 1 root root    4893 Nov 27  2021 bzexe
  lrwxrwxrwx 1 root root       6 Sep 18  2022 bzfgrep -> bzgrep
  -rwxr-xr-x 1 root root    3775 Sep 18  2022 bzgrep
  -rwxr-xr-x 3 root root   67728 Sep 18  2022 bzip2
  -rwxr-xr-x 1 root root   67664 Sep 18  2022 bzip2recover
  lrwxrwxrwx 1 root root       6 Sep 18  2022 bzless -> bzmore
  -rwxr-xr-x 1 root root    1297 Sep 18  2022 bzmore
  -rwxr-xr-x 1 root root   68536 Sep 20  2022 cat
  -rwxr-xr-x 1 root root   68616 Sep 20  2022 chgrp
  -rwxr-xr-x 1 root root   68552 Sep 20  2022 chmod
  -rwxr-xr-x 1 root root   68632 Sep 20  2022 chown
  -rwxr-xr-x 1 root root  200264 Sep 20  2022 cp
  -rwxr-xr-x 1 root root  133640 Jan  5  2023 dash
  -rwxr-xr-x 1 root root  134144 Sep 20  2022 date
  -rwxr-xr-x 1 root root  134248 Sep 20  2022 dd
  -rwxr-xr-x 1 root root  134888 Sep 20  2022 df
  -rwxr-xr-x 1 root root  200440 Sep 20  2022 dir
  -rwxr-xr-x 1 root root  141720 Mar 27  2024 dmesg
  lrwxrwxrwx 1 root root       8 Dec 19  2022 dnsdomainname -> hostname
  lrwxrwxrwx 1 root root       8 Dec 19  2022 domainname -> hostname
  -rwxr-xr-x 1 root root   68408 Sep 20  2022 echo
  -rwxr-xr-x 1 root root      41 Jan 24  2023 egrep
  -rwxr-xr-x 1 root root   68384 Sep 20  2022 false
  -rwxr-xr-x 1 root root      41 Jan 24  2023 fgrep
  -rwxr-xr-x 1 root root  134584 Mar 27  2024 findmnt
  -rwsr-xr-x 1 root root   67744 Mar 22  2023 fusermount
  -rwxr-xr-x 1 root root  198880 Jan 24  2023 grep
  -rwxr-xr-x 2 root root    2346 Apr  9  2022 gunzip
  -rwxr-xr-x 1 root root    6447 Apr  9  2022 gzexe
  -rwxr-xr-x 1 root root   93752 Apr  9  2022 gzip
  -rwxr-xr-x 1 root root   67592 Dec 19  2022 hostname
  -rwxr-xr-x 1 root root   68664 Sep 20  2022 ln
  -rwxr-xr-x 1 root root   69208 Mar 22  2023 login
  -rwxr-xr-x 1 root root  200440 Sep 20  2022 ls
  -rwxr-xr-x 1 root root  264360 Mar 27  2024 lsblk
  -rwxr-xr-x 1 root root  134384 Sep 20  2022 mkdir
  -rwxr-xr-x 1 root root   68768 Sep 20  2022 mknod
  -rwxr-xr-x 1 root root   68472 Sep 20  2022 mktemp
  -rwxr-xr-x 1 root root   67752 Mar 27  2024 more
  -rwsr-xr-x 1 root root   67744 Mar 27  2024 mount
  -rwxr-xr-x 1 root root   67744 Mar 27  2024 mountpoint
  -rwxr-xr-x 1 root root  134728 Sep 20  2022 mv
  lrwxrwxrwx 1 root root       8 Dec 19  2022 nisdomainname -> hostname
  lrwxrwxrwx 1 root root      14 Apr  2  2023 pidof -> /sbin/killall5
  -rwxr-xr-x 1 root root   68496 Sep 20  2022 pwd
  lrwxrwxrwx 1 root root       4 Mar 29  2024 rbash -> bash
  -rwxr-xr-x 1 root root   68456 Sep 20  2022 readlink
  -rwxr-xr-x 1 root root   68592 Sep 20  2022 rm
  -rwxr-xr-x 1 root root   68480 Sep 20  2022 rmdir
  -rwxr-xr-x 1 root root   68392 Jul 28  2023 run-parts
  -rwxr-xr-x 1 root root  134536 Jan  5  2023 sed
  lrwxrwxrwx 1 root root       4 Jan  5  2023 sh -> dash
  -rwxr-xr-x 1 root root   68432 Sep 20  2022 sleep
  -rwxr-xr-x 1 root root  134088 Sep 20  2022 stty
  -rwsr-xr-x 1 root root  133312 Mar 27  2024 su
  -rwxr-xr-x 1 root root   68448 Sep 20  2022 sync
  -rwxr-xr-x 1 root root  539896 Jan 19  2024 tar
  -rwxr-xr-x 1 root root   67904 Jul 28  2023 tempfile
  -rwxr-xr-x 1 root root  134160 Sep 20  2022 touch
  -rwxr-xr-x 1 root root   68384 Sep 20  2022 true
  -rwxr-xr-x 1 root root   67664 Mar 22  2023 ulockmgr_server
  -rwsr-xr-x 1 root root   67744 Mar 27  2024 umount
  -rwxr-xr-x 1 root root   68416 Sep 20  2022 uname
  -rwxr-xr-x 2 root root    2346 Apr  9  2022 uncompress
  -rwxr-xr-x 1 root root  200440 Sep 20  2022 vdir
  -rwxr-xr-x 1 root root  133312 Mar 27  2024 wdctl
  lrwxrwxrwx 1 root root       8 Dec 19  2022 ypdomainname -> hostname
  -rwxr-xr-x 1 root root    1984 Apr  9  2022 zcat
  -rwxr-xr-x 1 root root    1678 Apr  9  2022 zcmp
  -rwxr-xr-x 1 root root    6460 Apr  9  2022 zdiff
  -rwxr-xr-x 1 root root      29 Apr  9  2022 zegrep
  -rwxr-xr-x 1 root root      29 Apr  9  2022 zfgrep
  -rwxr-xr-x 1 root root    2081 Apr  9  2022 zforce
  -rwxr-xr-x 1 root root    8103 Apr  9  2022 zgrep
  -rwxr-xr-x 1 root root    2206 Apr  9  2022 zless
  -rwxr-xr-x 1 root root    1842 Apr  9  2022 zmore
  -rwxr-xr-x 1 root root    4577 Apr  9  2022 znew
I: user script /srv/workspace/pbuilder/2476591/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: arm64
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, pkg-config, 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 ... 19569 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 pkg-config; however:
  Package pkg-config 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} libelf1{a} libexception-class-perl{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libhmmer2-dev{a} libicu72{a} libio-string-perl{a} liblmdb0{a} libmagic-mgc{a} libmagic1{a} libmbedcrypto7{a} libmbedtls14{a} libmbedx509-1{a} libmodhmm-dev{a} libmodhmm0{a} libpcre3{a} libpipeline1{a} libpkgconf3{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8{a} libsquid-dev{a} libsquid1{a} libsub-override-perl{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} libxml2{a} m4{a} man-db{a} media-types{a} ncbi-blast+{a} ncbi-blast+-legacy{a} ncbi-data{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} python3{a} python3-minimal{a} python3.11{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} 
The following packages are RECOMMENDED but will NOT be installed:
  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, 78 newly installed, 0 to remove and 0 not upgraded.
Need to get 43.4 MB of archives. After unpacking 190 MB will be used.
The following packages have unmet dependencies:
 pbuilder-satisfydepends-dummy : Depends: pftools which is a virtual package and is not provided by any available package

Unable to resolve dependencies!  Giving up...
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} libelf1{a} libexception-class-perl{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libhmmer2-dev{a} libicu72{a} libio-string-perl{a} liblmdb0{a} libmagic-mgc{a} libmagic1{a} libmbedcrypto7{a} libmbedtls14{a} libmbedx509-1{a} libmodhmm-dev{a} libmodhmm0{a} libpcre3{a} libpipeline1{a} libpkgconf3{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8{a} libsquid-dev{a} libsquid1{a} libsub-override-perl{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} libxml2{a} m4{a} man-db{a} media-types{a} ncbi-blast+{a} ncbi-blast+-legacy{a} ncbi-data{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} python3{a} python3-minimal{a} python3.11{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} 
The following packages are RECOMMENDED but will NOT be installed:
  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, 78 newly installed, 0 to remove and 0 not upgraded.
Need to get 43.4 MB of archives. After unpacking 190 MB will be used.
Abort.
E: pbuilder-satisfydepends failed.
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/2476591 and its subdirectories