I: pbuilder: network access will be disabled during build I: Current time: Sat Dec 27 01:56:59 +14 2025 I: pbuilder-time-stamp: 1766750219 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 gpgv: Signature made Sun May 26 07:54:47 2024 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-4.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-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/657350/tmp/hooks/D01_modify_environment starting debug: Running on ionos15-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 Dec 26 11:57 /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/657350/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/657350/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]="32" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.32(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=42 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=6f1b9bbeab174defb093c5ea59e3a18a 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=657350 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.FiiPtPYP/pbuilderrc_lBfD --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.FiiPtPYP/b2 --logfile b2/build.log psortb_3.0.6+dfsg-4.dsc' SUDO_GID=111 SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://213.165.73.152:3128 I: uname -a Linux i-capture-the-hostname 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/657350/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 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 ... 19969 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} libcom-err2{a} libdata-stag-perl{a} libdebhelper-perl{a} libdevel-stacktrace-perl{a} libelf1t64{a} libexception-class-perl{a} libexpat1{a} libfile-slurp-perl{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgssapi-krb5-2{a} libhmmer2-dev{a} libicu72{a} libio-string-perl{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblmdb0{a} libmagic-mgc{a} libmagic1t64{a} libmbedcrypto16{a} libmbedtls21{a} libmbedx509-7{a} libmodhmm-dev{a} libmodhmm0{a} libnghttp2-14{a} libnsl2{a} libpipeline1{a} libpkgconf3{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-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} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{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} python3.12{a} python3.12-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 krb5-locales 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, 91 newly installed, 0 to remove and 0 not upgraded. Need to get 76.6 MB of archives. After unpacking 271 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libpython3.12-minimal amd64 3.12.7-3 [815 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 python3.12-minimal amd64 3.12.7-3 [2162 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.12.6-1 [26.7 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 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 2024b-3 [255 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.1-1+b1 [23.2 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 12 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libnsl2 amd64 1.3.0-3+b3 [40.6 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-5 [69.3 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libpython3.12-stdlib amd64 3.12.7-3 [1966 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 python3.12 amd64 3.12.7-3 [671 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.12.6-1 [9692 B] Get: 22 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.12.6-1 [27.8 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.2-11 [91.5 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libio-string-perl all 1.08-4 [12.1 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libdata-stag-perl all 0.14-3 [448 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libbio-perl-perl all 1.7.8-1 [2603 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 libclass-data-inheritable-perl all 0.10-1 [8632 B] Get: 42 http://deb.debian.org/debian trixie/main amd64 libdevel-stacktrace-perl all 2.0500-1 [26.4 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libexception-class-perl all 1.45-1 [34.6 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libtest-deep-perl all 1.204-1 [52.9 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 libcapture-tiny-perl all 0.48-2 [24.6 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 libalgorithm-diff-perl all 1.201-1 [43.3 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 libtext-diff-perl all 1.45-2 [27.2 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 libtest-differences-perl all 0.71-1 [17.9 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 libsub-uplevel-perl all 0.2800-3 [14.0 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 libtest-exception-perl all 0.43-3 [16.9 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 libtest-warn-perl all 0.37-2 [14.5 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libtest-most-perl all 0.38-1 [25.1 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 bioperl all 1.7.8-1 [246 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-8 [517 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 60 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.20 [915 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 libfile-slurp-perl all 9999.32-2 [26.7 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-8 [836 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 libhmmer2-dev amd64 2.3.2+dfsg-12+b1 [97.2 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 liblmdb0 amd64 0.9.31-1+b2 [45.2 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 libmbedcrypto16 amd64 3.6.2-3 [355 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 libmbedx509-7 amd64 3.6.2-3 [147 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 libmbedtls21 amd64 3.6.2-3 [234 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 libmodhmm0 amd64 1.0+dfsg-7 [79.8 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 libmodhmm-dev amd64 1.0+dfsg-7 [79.8 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 libsquid1t64 amd64 1.9g+cvs20050121-15.1+b1 [76.9 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 libsquid-dev amd64 1.9g+cvs20050121-15.1+b1 [144 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 libsvm3 amd64 3.24+ds-6+b1 [41.5 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 libsvm-dev amd64 3.24+ds-6+b1 [62.1 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 libsvmloc0 amd64 1.0+dfsg-7 [13.3 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 libsvmloc-dev amd64 1.0+dfsg-7 [12.2 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 libuv1t64 amd64 1.48.0-7 [148 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 ncbi-data all 6.1.20170106+dfsg2-5 [3537 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 ncbi-blast+ amd64 2.16.0+ds-6+b1 [15.2 MB] Get: 88 http://deb.debian.org/debian trixie/main amd64 ncbi-blast+-legacy all 2.16.0+ds-6 [10.4 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 pftools amd64 3.2.12-1 [24.8 MB] Get: 90 http://deb.debian.org/debian trixie/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Fetched 76.6 MB in 1s (63.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19969 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.7-3_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.7-3) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.7-3_amd64.deb ... Unpacking python3.12-minimal (3.12.7-3) ... Setting up libpython3.12-minimal:amd64 (3.12.7-3) ... Setting up libexpat1:amd64 (2.6.4-1) ... Setting up python3.12-minimal (3.12.7-3) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20289 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.6-1_amd64.deb ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:amd64. Preparing to unpack .../12-libnsl2_1.3.0-3+b3_amd64.deb ... Unpacking libnsl2:amd64 (1.3.0-3+b3) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../14-libreadline8t64_8.2-5_amd64.deb ... 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Setting up libpkgconf3:amd64 (1.8.1-4) ... Setting up libtext-diff-perl (1.45-2) ... Setting up autopoint (0.22.5-2) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libk5crypto3:amd64 (1.21.3-3) ... Setting up libgfortran5:amd64 (14.2.0-8) ... Setting up autoconf (2.72-3) ... Setting up libcapture-tiny-perl (0.48-2) ... Setting up dwz (0.15-1+b1) ... Setting up libdata-stag-perl (0.14-3) ... Setting up sensible-utils (0.0.24) ... Setting up pftools (3.2.12-1) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up libsub-uplevel-perl (0.2800-3) ... Setting up netbase (6.4) ... Setting up libdevel-stacktrace-perl (2.0500-1) ... Setting up libkrb5-3:amd64 (1.21.3-3) ... Setting up libbio-perl-perl (1.7.8-1) ... Setting up libmbedcrypto16:amd64 (3.6.2-3) ... Setting up libhmmer2-dev:amd64 (2.3.2+dfsg-12+b1) ... Setting up libmodhmm-dev:amd64 (1.0+dfsg-7) ... Setting up readline-common (8.2-5) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up libsquid1t64:amd64 (1.9g+cvs20050121-15.1+b1) ... Setting up libsvm3:amd64 (3.24+ds-6+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.22.5-2) ... Setting up libtool (2.4.7-8) ... Setting up libtest-warn-perl (0.37-2) ... Setting up libtest-differences-perl (0.71-1) ... Setting up libexception-class-perl (1.45-1) ... Setting up libsquid-dev (1.9g+cvs20050121-15.1+b1) ... 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 libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up libmbedtls21:amd64 (3.6.2-3) ... Setting up libreadline8t64:amd64 (8.2-5) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up libsvmloc-dev:amd64 (1.0+dfsg-7) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Setting up libtest-most-perl (0.38-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libnsl2:amd64 (1.3.0-3+b3) ... Setting up bioperl (1.7.8-1) ... Setting up libpython3.12-stdlib:amd64 (3.12.7-3) ... Setting up python3.12 (3.12.7-3) ... Setting up debhelper (13.20) ... Setting up libpython3-stdlib:amd64 (3.12.6-1) ... Setting up python3 (3.12.6-1) ... Setting up ncbi-blast+ (2.16.0+ds-6+b1) ... Setting up ncbi-blast+-legacy (2.16.0+ds-6) ... Processing triggers for libc-bin (2.40-3) ... 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: user script /srv/workspace/pbuilder/657350/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/657350/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/psortb-3.0.6+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../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 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: 12/27/2025 01:57:52 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: 12/27/2025 01:57:52 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: 12/27/2025 01:57:53 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/5.40.0/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/Module/Null.pm blib/lib/Bio/Tools/PSort/Module/Null.pm cp lib/Bio/Tools/PSort/Module/OMPMotif.pm blib/lib/Bio/Tools/PSort/Module/OMPMotif.pm cp lib/Bio/Tools/PSort/ModuleI.pm blib/lib/Bio/Tools/PSort/ModuleI.pm cp lib/Bio/Tools/PSort/Module/SVMLocApache.pm blib/lib/Bio/Tools/PSort/Module/SVMLocApache.pm cp lib/Bio/Tools/Motif/Match.pm blib/lib/Bio/Tools/Motif/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/Install.pm blib/lib/Bio/Tools/PSort/Install.pm cp lib/Bio/Tools/PSort/Module/Bayesian.pm blib/lib/Bio/Tools/PSort/Module/Bayesian.pm cp lib/Bio/Tools/PSort/Module/SVMLoc.pm blib/lib/Bio/Tools/PSort/Module/SVMLoc.pm cp lib/Bio/Tools/PSort/Module/Rules.pm blib/lib/Bio/Tools/PSort/Module/Rules.pm cp lib/Bio/Tools/PSort/Report/Result.pm blib/lib/Bio/Tools/PSort/Report/Result.pm cp lib/Bio/Tools/PSort/Module/InputI.pm blib/lib/Bio/Tools/PSort/Module/InputI.pm cp lib/Bio/Tools/PSort/Module/AnalysisI.pm blib/lib/Bio/Tools/PSort/Module/AnalysisI.pm cp lib/Bio/Tools/PSort/Module/OutputI.pm blib/lib/Bio/Tools/PSort/Module/OutputI.pm cp lib/Bio/Tools/PSort/Module/Signal.pm blib/lib/Bio/Tools/PSort/Module/Signal.pm cp lib/Bio/Tools/Motif.pm blib/lib/Bio/Tools/Motif.pm cp lib/Bio/Tools/PSort/Pathway.pm blib/lib/Bio/Tools/PSort/Pathway.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/Report.pm blib/lib/Bio/Tools/PSort/Report.pm cp lib/Bio/Tools/PSort/Profile.pm blib/lib/Bio/Tools/PSort/Profile.pm cp lib/Bio/Tools/PSort/Module/Profile.pm blib/lib/Bio/Tools/PSort/Module/Profile.pm cp lib/Bio/Tools/PSort/Module/SCLBlast.pm blib/lib/Bio/Tools/PSort/Module/SCLBlast.pm cp lib/Bio/Tools/PSort/Report/Formatter/html.pm blib/lib/Bio/Tools/PSort/Report/Formatter/html.pm cp lib/Bio/Tools/PSort/Report/Formatter.pm blib/lib/Bio/Tools/PSort/Report/Formatter.pm cp lib/Bio/Tools/PSort/Report/Formatter/terse.pm blib/lib/Bio/Tools/PSort/Report/Formatter/terse.pm cp lib/Bio/Tools/PSort/Module/Motif.pm blib/lib/Bio/Tools/PSort/Module/Motif.pm cp lib/Bio/Tools/PSort.pm blib/lib/Bio/Tools/PSort.pm cp lib/Bio/Tools/Motif/Pattern.pm blib/lib/Bio/Tools/Motif/Pattern.pm cp lib/Bio/Tools/PSort/Profile/Match.pm blib/lib/Bio/Tools/PSort/Profile/Match.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/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/Report.pm ../blib/lib/Algorithm/HMM/Report.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/Hit/Global.pm ../blib/lib/Algorithm/HMM/Hit/Global.pm cp lib/Bio/Tools/Signal.pm blib/lib/Bio/Tools/Signal.pm cp lib/Bio/Tools/Run/HMMTOP.pm blib/lib/Bio/Tools/Run/HMMTOP.pm cp lib/Bio/Tools/Signal/Report.pm blib/lib/Bio/Tools/Signal/Report.pm cp lib/Bio/Tools/SVMLoc.pm blib/lib/Bio/Tools/SVMLoc.pm cp lib/Bio/Tools/PSort/XMLRPC/Client.pm blib/lib/Bio/Tools/PSort/XMLRPC/Client.pm cp lib/Bio/Tools/Run/SCLBlast.pm blib/lib/Bio/Tools/Run/SCLBlast.pm cp lib/Bio/Tools/Run/SCLBlast/Hit.pm blib/lib/Bio/Tools/Run/SCLBlast/Hit.pm cp lib/Bio/Tools/Run/HMMTOP/Report.pm blib/lib/Bio/Tools/Run/HMMTOP/Report.pm cp lib/Bio/Tools/Run/SCLBlast/Report.pm blib/lib/Bio/Tools/Run/SCLBlast/Report.pm cp lib/Bio/Tools/Run/SCLBlastLocal.pm blib/lib/Bio/Tools/Run/SCLBlastLocal.pm cp lib/Bio/Tools/Run/HMMTOP/Helix.pm blib/lib/Bio/Tools/Run/HMMTOP/Helix.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' "/usr/bin/perl" "/usr/share/perl/5.40.0/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 Running Mkbootstrap for SVMLoc () 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.pm ../blib/lib/Bio/Tools/PSort/SVMLoc.pm AutoSplitting ../blib/lib/Bio/Tools/PSort/SVMLoc.pm (../blib/lib/auto/Bio/Tools/PSort/SVMLoc) cp lib/Bio/Tools/PSort/SVMLoc/DataSet.pm ../blib/lib/Bio/Tools/PSort/SVMLoc/DataSet.pm 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' "/usr/bin/perl" "/usr/share/perl/5.40.0/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 Running Mkbootstrap for ModHMM () 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, 1 wallclock secs ( 0.01 usr 0.00 sys + 0.07 cusr 0.00 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, 0 wallclock secs ( 0.01 usr 0.01 sys + 0.18 cusr 0.02 csys = 0.22 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 ( 0.01 usr 0.00 sys + 0.14 cusr 0.00 csys = 0.15 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, 1 wallclock secs ( 0.02 usr 0.00 sys + 0.09 cusr 0.00 csys = 0.11 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/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/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/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/Hit.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/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/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/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/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/PSort.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/SVMLoc.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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/Null.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/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/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/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/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.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/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/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/terse.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/Bio/Tools/Motif/Match.pm 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/Bio::Tools::PSort::Module::InputI.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::Pathway.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/Bio::Tools::Run::HMMTOP.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::PSort::Module::Null.3pm Installing /build/reproducible-path/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::PSort::Module::Profile.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.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::Module::Motif.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::AnalysisI.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::OMPMotif.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::ModHMM.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::SVMLoc.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::Match.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::Module::OutputI.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: user script /srv/workspace/pbuilder/657350/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/657350/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/657350 and its subdirectories I: Current time: Sat Dec 27 01:58:33 +14 2025 I: pbuilder-time-stamp: 1766750313