I: pbuilder: network access will be disabled during build I: Current time: Wed Oct 27 09:12:27 +14 2021 I: pbuilder-time-stamp: 1635275547 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration 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-2.dsc] I: copying [./psortb_3.0.6+dfsg.orig.tar.xz] I: copying [./psortb_3.0.6+dfsg-2.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.caRgTjAb/trustedkeys.kbx': General error gpgv: Signature made Sat Feb 22 00:54:32 2020 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tillea@rki.de" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./psortb_3.0.6+dfsg-2.dsc 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-2.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/3868752/tmp/hooks/D01_modify_environment starting debug: Running on ionos1-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 Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by 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/3868752/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/3868752/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.1.4(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=15' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=10422e55d5f14c7ab7e4f74711c092c9 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=3868752 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/tmp.ffkFCPohQq/pbuilderrc_MUjK --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.ffkFCPohQq/b2 --logfile b2/build.log psortb_3.0.6+dfsg-2.dsc' SUDO_GID=110 SUDO_UID=105 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://78.137.99.97:3128 I: uname -a Linux i-capture-the-hostname 5.10.0-9-amd64 #1 SMP Debian 5.10.70-1 (2021-09-30) x86_64 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1234376 Aug 5 10:25 bash -rwxr-xr-x 3 root root 38984 Jul 21 2020 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzip2 -rwxr-xr-x 1 root root 18424 Jul 21 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore -rwxr-xr-x 1 root root 43936 Sep 24 2020 cat -rwxr-xr-x 1 root root 72672 Sep 24 2020 chgrp -rwxr-xr-x 1 root root 64448 Sep 24 2020 chmod -rwxr-xr-x 1 root root 72672 Sep 24 2020 chown -rwxr-xr-x 1 root root 151168 Sep 24 2020 cp -rwxr-xr-x 1 root root 125560 Dec 11 2020 dash -rwxr-xr-x 1 root root 113664 Sep 24 2020 date -rwxr-xr-x 1 root root 80968 Sep 24 2020 dd -rwxr-xr-x 1 root root 93936 Sep 24 2020 df -rwxr-xr-x 1 root root 147176 Sep 24 2020 dir -rwxr-xr-x 1 root root 84440 Jul 29 09:09 dmesg lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname -rwxr-xr-x 1 root root 39712 Sep 24 2020 echo -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep -rwxr-xr-x 1 root root 39680 Sep 24 2020 false -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep -rwxr-xr-x 1 root root 69032 Jul 29 09:09 findmnt -rwsr-xr-x 1 root root 34896 Feb 27 2021 fusermount -rwxr-xr-x 1 root root 203072 Nov 10 2020 grep -rwxr-xr-x 2 root root 2346 Mar 3 2021 gunzip -rwxr-xr-x 1 root root 6376 Mar 3 2021 gzexe -rwxr-xr-x 1 root root 98048 Mar 3 2021 gzip -rwxr-xr-x 1 root root 22600 Nov 8 2019 hostname -rwxr-xr-x 1 root root 72840 Sep 24 2020 ln -rwxr-xr-x 1 root root 56952 Feb 8 2020 login -rwxr-xr-x 1 root root 147176 Sep 24 2020 ls -rwxr-xr-x 1 root root 149736 Jul 29 09:09 lsblk -rwxr-xr-x 1 root root 85184 Sep 24 2020 mkdir -rwxr-xr-x 1 root root 76896 Sep 24 2020 mknod -rwxr-xr-x 1 root root 48064 Sep 24 2020 mktemp -rwxr-xr-x 1 root root 59632 Jul 29 09:09 more -rwsr-xr-x 1 root root 55528 Jul 29 09:09 mount -rwxr-xr-x 1 root root 18664 Jul 29 09:09 mountpoint -rwxr-xr-x 1 root root 147080 Sep 24 2020 mv lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 19 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43872 Sep 24 2020 pwd lrwxrwxrwx 1 root root 4 Aug 5 10:25 rbash -> bash -rwxr-xr-x 1 root root 52032 Sep 24 2020 readlink -rwxr-xr-x 1 root root 72704 Sep 24 2020 rm -rwxr-xr-x 1 root root 52032 Sep 24 2020 rmdir -rwxr-xr-x 1 root root 27472 Sep 28 2020 run-parts -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Oct 27 09:12 sh -> bash lrwxrwxrwx 1 root root 4 Oct 22 01:41 sh.distrib -> dash -rwxr-xr-x 1 root root 43808 Sep 24 2020 sleep -rwxr-xr-x 1 root root 84928 Sep 24 2020 stty -rwsr-xr-x 1 root root 71912 Jul 29 09:09 su -rwxr-xr-x 1 root root 39744 Sep 24 2020 sync -rwxr-xr-x 1 root root 531928 Feb 17 2021 tar -rwxr-xr-x 1 root root 14456 Sep 28 2020 tempfile -rwxr-xr-x 1 root root 101408 Sep 24 2020 touch -rwxr-xr-x 1 root root 39680 Sep 24 2020 true -rwxr-xr-x 1 root root 14328 Feb 27 2021 ulockmgr_server -rwsr-xr-x 1 root root 35040 Jul 29 09:09 umount -rwxr-xr-x 1 root root 39744 Sep 24 2020 uname -rwxr-xr-x 2 root root 2346 Mar 3 2021 uncompress -rwxr-xr-x 1 root root 147176 Sep 24 2020 vdir -rwxr-xr-x 1 root root 63744 Jul 29 09:09 wdctl lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 3 2021 zcat -rwxr-xr-x 1 root root 1678 Mar 3 2021 zcmp -rwxr-xr-x 1 root root 5880 Mar 3 2021 zdiff -rwxr-xr-x 1 root root 29 Mar 3 2021 zegrep -rwxr-xr-x 1 root root 29 Mar 3 2021 zfgrep -rwxr-xr-x 1 root root 2081 Mar 3 2021 zforce -rwxr-xr-x 1 root root 7585 Mar 3 2021 zgrep -rwxr-xr-x 1 root root 2206 Mar 3 2021 zless -rwxr-xr-x 1 root root 1842 Mar 3 2021 zmore -rwxr-xr-x 1 root root 4553 Mar 3 2021 znew I: user script /srv/workspace/pbuilder/3868752/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 (= 12), 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 ... 19655 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 (= 12); 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-slurp-perl{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libglib2.0-0{a} libhmmer2-dev{a} libicu67{a} libio-string-perl{a} liblmdb0{a} libmagic-mgc{a} libmagic1{a} libmbedcrypto3{a} libmbedtls12{a} libmbedx509-0{a} libmodhmm-dev{a} libmodhmm0{a} libmpdec3{a} libpipeline1{a} libpython3-stdlib{a} libpython3.9-minimal{a} libpython3.9-stdlib{a} libreadline8{a} libsigsegv2{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} pftools{a} pkg-config{a} po-debconf{a} python3{a} python3-minimal{a} python3.9{a} python3.9-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 libglib2.0-data 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 shared-mime-info wget xdg-user-dirs 0 packages upgraded, 80 newly installed, 0 to remove and 0 not upgraded. Need to get 91.4 MB of archives. After unpacking 285 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main amd64 bsdextrautils amd64 2.36.1-8 [145 kB] Get: 2 http://deb.debian.org/debian bullseye/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 3 http://deb.debian.org/debian bullseye/main amd64 groff-base amd64 1.22.4-6 [936 kB] Get: 4 http://deb.debian.org/debian bullseye/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get: 5 http://deb.debian.org/debian bullseye/main amd64 man-db amd64 2.9.4-2 [1354 kB] Get: 6 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-minimal amd64 3.9.2-1 [801 kB] Get: 7 http://deb.debian.org/debian bullseye/main amd64 libexpat1 amd64 2.2.10-2 [96.9 kB] Get: 8 http://deb.debian.org/debian bullseye/main amd64 python3.9-minimal amd64 3.9.2-1 [1955 kB] Get: 9 http://deb.debian.org/debian bullseye/main amd64 python3-minimal amd64 3.9.2-3 [38.2 kB] Get: 10 http://deb.debian.org/debian bullseye/main amd64 media-types all 4.0.0 [30.3 kB] Get: 11 http://deb.debian.org/debian bullseye/main amd64 libmpdec3 amd64 2.5.1-1 [87.7 kB] Get: 12 http://deb.debian.org/debian bullseye/main amd64 readline-common all 8.1-1 [73.7 kB] Get: 13 http://deb.debian.org/debian bullseye/main amd64 libreadline8 amd64 8.1-1 [169 kB] Get: 14 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-stdlib amd64 3.9.2-1 [1684 kB] Get: 15 http://deb.debian.org/debian bullseye/main amd64 python3.9 amd64 3.9.2-1 [466 kB] Get: 16 http://deb.debian.org/debian bullseye/main amd64 libpython3-stdlib amd64 3.9.2-3 [21.4 kB] Get: 17 http://deb.debian.org/debian bullseye/main amd64 python3 amd64 3.9.2-3 [37.9 kB] Get: 18 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get: 19 http://deb.debian.org/debian bullseye/main amd64 libmagic-mgc amd64 1:5.39-3 [273 kB] Get: 20 http://deb.debian.org/debian bullseye/main amd64 libmagic1 amd64 1:5.39-3 [126 kB] Get: 21 http://deb.debian.org/debian bullseye/main amd64 file amd64 1:5.39-3 [69.1 kB] Get: 22 http://deb.debian.org/debian bullseye/main amd64 gettext-base amd64 0.21-4 [175 kB] Get: 23 http://deb.debian.org/debian bullseye/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get: 24 http://deb.debian.org/debian bullseye/main amd64 m4 amd64 1.4.18-5 [204 kB] Get: 25 http://deb.debian.org/debian bullseye/main amd64 autoconf all 2.69-14 [313 kB] Get: 26 http://deb.debian.org/debian bullseye/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 27 http://deb.debian.org/debian bullseye/main amd64 automake all 1:1.16.3-2 [814 kB] Get: 28 http://deb.debian.org/debian bullseye/main amd64 autopoint all 0.21-4 [510 kB] Get: 29 http://deb.debian.org/debian bullseye/main amd64 libio-string-perl all 1.08-3.1 [11.8 kB] Get: 30 http://deb.debian.org/debian bullseye/main amd64 libdata-stag-perl all 0.14-2 [448 kB] Get: 31 http://deb.debian.org/debian bullseye/main amd64 libbio-perl-perl all 1.7.7-2 [2607 kB] Get: 32 http://deb.debian.org/debian bullseye/main amd64 libclass-data-inheritable-perl all 0.08-3 [8588 B] Get: 33 http://deb.debian.org/debian bullseye/main amd64 libdevel-stacktrace-perl all 2.0400-1 [28.6 kB] Get: 34 http://deb.debian.org/debian bullseye/main amd64 libexception-class-perl all 1.44-1 [32.3 kB] Get: 35 http://deb.debian.org/debian bullseye/main amd64 libtest-deep-perl all 1.130-1 [49.3 kB] Get: 36 http://deb.debian.org/debian bullseye/main amd64 libcapture-tiny-perl all 0.48-1 [26.0 kB] Get: 37 http://deb.debian.org/debian bullseye/main amd64 libalgorithm-diff-perl all 1.201-1 [43.3 kB] Get: 38 http://deb.debian.org/debian bullseye/main amd64 libtext-diff-perl all 1.45-1 [27.7 kB] Get: 39 http://deb.debian.org/debian bullseye/main amd64 libtest-differences-perl all 0.67-1 [18.7 kB] Get: 40 http://deb.debian.org/debian bullseye/main amd64 libsub-uplevel-perl all 0.2800-1.1 [16.5 kB] Get: 41 http://deb.debian.org/debian bullseye/main amd64 libtest-exception-perl all 0.43-1 [18.7 kB] Get: 42 http://deb.debian.org/debian bullseye/main amd64 libtest-warn-perl all 0.36-1 [16.2 kB] Get: 43 http://deb.debian.org/debian bullseye/main amd64 libtest-most-perl all 0.37-1 [24.9 kB] Get: 44 http://deb.debian.org/debian bullseye/main amd64 bioperl all 1.7.7-2 [246 kB] Get: 45 http://deb.debian.org/debian bullseye/main amd64 libdebhelper-perl all 13.3.4 [189 kB] Get: 46 http://deb.debian.org/debian bullseye/main amd64 libtool all 2.4.6-15 [513 kB] Get: 47 http://deb.debian.org/debian bullseye/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 48 http://deb.debian.org/debian bullseye/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 49 http://deb.debian.org/debian bullseye/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 50 http://deb.debian.org/debian bullseye/main amd64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 51 http://deb.debian.org/debian bullseye/main amd64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 52 http://deb.debian.org/debian bullseye/main amd64 libelf1 amd64 0.183-1 [165 kB] Get: 53 http://deb.debian.org/debian bullseye/main amd64 dwz amd64 0.13+20210201-1 [175 kB] Get: 54 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get: 55 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7 [693 kB] Get: 56 http://deb.debian.org/debian bullseye/main amd64 gettext amd64 0.21-4 [1311 kB] Get: 57 http://deb.debian.org/debian bullseye/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 58 http://deb.debian.org/debian bullseye/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 59 http://deb.debian.org/debian bullseye/main amd64 debhelper all 13.3.4 [1049 kB] Get: 60 http://deb.debian.org/debian bullseye/main amd64 libfile-slurp-perl all 9999.32-1 [28.1 kB] Get: 61 http://deb.debian.org/debian bullseye/main amd64 libgfortran5 amd64 10.2.1-6 [727 kB] Get: 62 http://deb.debian.org/debian bullseye/main amd64 libglib2.0-0 amd64 2.66.8-1 [1370 kB] Get: 63 http://deb.debian.org/debian bullseye/main amd64 libhmmer2-dev amd64 2.3.2+dfsg-7 [99.2 kB] Get: 64 http://deb.debian.org/debian bullseye/main amd64 liblmdb0 amd64 0.9.24-1 [45.0 kB] Get: 65 http://deb.debian.org/debian bullseye/main amd64 libmbedcrypto3 amd64 2.16.9-0.1 [219 kB] Get: 66 http://deb.debian.org/debian bullseye/main amd64 libmbedx509-0 amd64 2.16.9-0.1 [109 kB] Get: 67 http://deb.debian.org/debian bullseye/main amd64 libmbedtls12 amd64 2.16.9-0.1 [139 kB] Get: 68 http://deb.debian.org/debian bullseye/main amd64 libmodhmm0 amd64 1.0+dfsg-4 [80.2 kB] Get: 69 http://deb.debian.org/debian bullseye/main amd64 libmodhmm-dev amd64 1.0+dfsg-4 [80.0 kB] Get: 70 http://deb.debian.org/debian bullseye/main amd64 libsquid1 amd64 1.9g+cvs20050121-12 [76.6 kB] Get: 71 http://deb.debian.org/debian bullseye/main amd64 libsquid-dev amd64 1.9g+cvs20050121-12 [145 kB] Get: 72 http://deb.debian.org/debian bullseye/main amd64 libsvm3 amd64 3.24+ds-6 [43.6 kB] Get: 73 http://deb.debian.org/debian bullseye/main amd64 libsvm-dev amd64 3.24+ds-6 [64.2 kB] Get: 74 http://deb.debian.org/debian bullseye/main amd64 libsvmloc0 amd64 1.0+dfsg-4 [13.3 kB] Get: 75 http://deb.debian.org/debian bullseye/main amd64 libsvmloc-dev amd64 1.0+dfsg-4 [12.2 kB] Get: 76 http://deb.debian.org/debian bullseye/main amd64 ncbi-data all 6.1.20170106+dfsg1-9 [3556 kB] Get: 77 http://deb.debian.org/debian bullseye/main amd64 ncbi-blast+ amd64 2.11.0+ds-1 [11.3 MB] Get: 78 http://deb.debian.org/debian bullseye/main amd64 ncbi-blast+-legacy all 2.11.0+ds-1 [13.1 kB] Get: 79 http://deb.debian.org/debian bullseye/main amd64 pftools amd64 3.2.6-1 [45.8 MB] Get: 80 http://deb.debian.org/debian bullseye/main amd64 pkg-config amd64 0.29.2-1 [65.1 kB] Fetched 91.4 MB in 1s (64.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19655 files and directories currently installed.) Preparing to unpack .../0-bsdextrautils_2.36.1-8_amd64.deb ... Unpacking bsdextrautils (2.36.1-8) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../1-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../2-groff-base_1.22.4-6_amd64.deb ... 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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 ... 20522 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.9.2-3_amd64.deb ... Unpacking python3-minimal (3.9.2-3) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_4.0.0_all.deb ... Unpacking media-types (4.0.0) ... Selecting previously unselected package libmpdec3:amd64. 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Selecting previously unselected package python3. (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 ... 20943 files and directories currently installed.) Preparing to unpack .../00-python3_3.9.2-3_amd64.deb ... Unpacking python3 (3.9.2-3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package libmagic-mgc. 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Selecting previously unselected package libxml2:amd64. Preparing to unpack .../38-libxml2_2.9.10+dfsg-6.7_amd64.deb ... Unpacking libxml2:amd64 (2.9.10+dfsg-6.7) ... Selecting previously unselected package gettext. Preparing to unpack .../39-gettext_0.21-4_amd64.deb ... Unpacking gettext (0.21-4) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../40-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../41-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../42-debhelper_13.3.4_all.deb ... Unpacking debhelper (13.3.4) ... Selecting previously unselected package libfile-slurp-perl. Preparing to unpack .../43-libfile-slurp-perl_9999.32-1_all.deb ... Unpacking libfile-slurp-perl (9999.32-1) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../44-libgfortran5_10.2.1-6_amd64.deb ... Unpacking libgfortran5:amd64 (10.2.1-6) ... Selecting previously unselected package libglib2.0-0:amd64. Preparing to unpack .../45-libglib2.0-0_2.66.8-1_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.66.8-1) ... Selecting previously unselected package libhmmer2-dev. Preparing to unpack .../46-libhmmer2-dev_2.3.2+dfsg-7_amd64.deb ... Unpacking libhmmer2-dev (2.3.2+dfsg-7) ... Selecting previously unselected package liblmdb0:amd64. Preparing to unpack .../47-liblmdb0_0.9.24-1_amd64.deb ... Unpacking liblmdb0:amd64 (0.9.24-1) ... Selecting previously unselected package libmbedcrypto3:amd64. Preparing to unpack .../48-libmbedcrypto3_2.16.9-0.1_amd64.deb ... Unpacking libmbedcrypto3:amd64 (2.16.9-0.1) ... Selecting previously unselected package libmbedx509-0:amd64. Preparing to unpack .../49-libmbedx509-0_2.16.9-0.1_amd64.deb ... Unpacking libmbedx509-0:amd64 (2.16.9-0.1) ... Selecting previously unselected package libmbedtls12:amd64. Preparing to unpack .../50-libmbedtls12_2.16.9-0.1_amd64.deb ... Unpacking libmbedtls12:amd64 (2.16.9-0.1) ... Selecting previously unselected package libmodhmm0:amd64. Preparing to unpack .../51-libmodhmm0_1.0+dfsg-4_amd64.deb ... Unpacking libmodhmm0:amd64 (1.0+dfsg-4) ... Selecting previously unselected package libmodhmm-dev:amd64. Preparing to unpack .../52-libmodhmm-dev_1.0+dfsg-4_amd64.deb ... Unpacking libmodhmm-dev:amd64 (1.0+dfsg-4) ... Selecting previously unselected package libsquid1. Preparing to unpack .../53-libsquid1_1.9g+cvs20050121-12_amd64.deb ... Unpacking libsquid1 (1.9g+cvs20050121-12) ... Selecting previously unselected package libsquid-dev. Preparing to unpack .../54-libsquid-dev_1.9g+cvs20050121-12_amd64.deb ... Unpacking libsquid-dev (1.9g+cvs20050121-12) ... Selecting previously unselected package libsvm3:amd64. Preparing to unpack .../55-libsvm3_3.24+ds-6_amd64.deb ... Unpacking libsvm3:amd64 (3.24+ds-6) ... Selecting previously unselected package libsvm-dev:amd64. Preparing to unpack .../56-libsvm-dev_3.24+ds-6_amd64.deb ... Unpacking libsvm-dev:amd64 (3.24+ds-6) ... Selecting previously unselected package libsvmloc0:amd64. Preparing to unpack .../57-libsvmloc0_1.0+dfsg-4_amd64.deb ... Unpacking libsvmloc0:amd64 (1.0+dfsg-4) ... Selecting previously unselected package libsvmloc-dev:amd64. Preparing to unpack .../58-libsvmloc-dev_1.0+dfsg-4_amd64.deb ... Unpacking libsvmloc-dev:amd64 (1.0+dfsg-4) ... Selecting previously unselected package ncbi-data. Preparing to unpack .../59-ncbi-data_6.1.20170106+dfsg1-9_all.deb ... Unpacking ncbi-data (6.1.20170106+dfsg1-9) ... Selecting previously unselected package ncbi-blast+. Preparing to unpack .../60-ncbi-blast+_2.11.0+ds-1_amd64.deb ... Unpacking ncbi-blast+ (2.11.0+ds-1) ... Selecting previously unselected package ncbi-blast+-legacy. Preparing to unpack .../61-ncbi-blast+-legacy_2.11.0+ds-1_all.deb ... Unpacking ncbi-blast+-legacy (2.11.0+ds-1) ... Selecting previously unselected package pftools. Preparing to unpack .../62-pftools_3.2.6-1_amd64.deb ... Unpacking pftools (3.2.6-1) ... Selecting previously unselected package pkg-config. Preparing to unpack .../63-pkg-config_0.29.2-1_amd64.deb ... Unpacking pkg-config (0.29.2-1) ... Setting up media-types (4.0.0) ... Setting up libpipeline1:amd64 (1.5.3-1) ... Setting up liblmdb0:amd64 (0.9.24-1) ... Setting up ncbi-data (6.1.20170106+dfsg1-9) ... Setting up libfile-slurp-perl (9999.32-1) ... Setting up bsdextrautils (2.36.1-8) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libicu67:amd64 (67.1-7) ... Setting up libtest-deep-perl (1.130-1) ... Setting up libmagic-mgc (1:5.39-3) ... Setting up libalgorithm-diff-perl (1.201-1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:amd64 (2.66.8-1) ... No schema files found: doing nothing. Setting up libdebhelper-perl (13.3.4) ... Setting up libmagic1:amd64 (1:5.39-3) ... Setting up gettext-base (0.21-4) ... Setting up file (1:5.39-3) ... Setting up libmodhmm0:amd64 (1.0+dfsg-4) ... Setting up libio-string-perl (1.08-3.1) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libclass-data-inheritable-perl (0.08-3) ... Setting up libtext-diff-perl (1.45-1) ... Setting up libsigsegv2:amd64 (2.13-1) ... Setting up autopoint (0.21-4) ... Setting up pkg-config (0.29.2-1) ... Setting up libgfortran5:amd64 (10.2.1-6) ... Setting up libcapture-tiny-perl (0.48-1) ... Setting up libsquid1 (1.9g+cvs20050121-12) ... Setting up libdata-stag-perl (0.14-2) ... Setting up sensible-utils (0.0.14) ... Setting up pftools (3.2.6-1) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libmpdec3:amd64 (2.5.1-1) ... Setting up libmbedcrypto3:amd64 (2.16.9-0.1) ... Setting up libsub-uplevel-perl (0.2800-1.1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libdevel-stacktrace-perl (2.0400-1) ... Setting up libbio-perl-perl (1.7.7-2) ... Setting up libhmmer2-dev (2.3.2+dfsg-7) ... Setting up libmodhmm-dev:amd64 (1.0+dfsg-4) ... Setting up libelf1:amd64 (0.183-1) ... Setting up readline-common (8.1-1) ... Setting up libxml2:amd64 (2.9.10+dfsg-6.7) ... Setting up libsvm3:amd64 (3.24+ds-6) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up gettext (0.21-4) ... Setting up libtool (2.4.6-15) ... Setting up libmbedx509-0:amd64 (2.16.9-0.1) ... Setting up libtest-warn-perl (0.36-1) ... Setting up libreadline8:amd64 (8.1-1) ... Setting up libmbedtls12:amd64 (2.16.9-0.1) ... Setting up libtest-differences-perl (0.67-1) ... Setting up m4 (1.4.18-5) ... Setting up libexception-class-perl (1.44-1) ... Setting up libsquid-dev (1.9g+cvs20050121-12) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libtest-exception-perl (0.43-1) ... Setting up libsvmloc0:amd64 (1.0+dfsg-4) ... Setting up libsvm-dev:amd64 (3.24+ds-6) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up libpython3.9-stdlib:amd64 (3.9.2-1) ... Setting up libpython3-stdlib:amd64 (3.9.2-3) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libsvmloc-dev:amd64 (1.0+dfsg-4) ... Setting up libtest-most-perl (0.37-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up dh-autoreconf (20) ... Setting up python3.9 (3.9.2-1) ... Setting up bioperl (1.7.7-2) ... Setting up debhelper (13.3.4) ... Setting up python3 (3.9.2-3) ... Setting up ncbi-blast+ (2.11.0+ds-1) ... Setting up ncbi-blast+-legacy (2.11.0+ds-1) ... Processing triggers for libc-bin (2.31-13+deb11u2) ... 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 hostname: Name or service not known I: Running cd /build/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-2_source.changes dpkg-buildpackage: info: source package psortb dpkg-buildpackage: info: source version 3.0.6+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra 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/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/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/psortb-3.0.6+dfsg' cp -a psort/bin/psort psort/bin/psort.debsave dh_auto_configure perl Makefile.PL INSTALLDIRS=vendor "OPTIMIZE=-g -O2 -fdebug-prefix-map=/build/psortb-3.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "LD=x86_64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/build/psortb-3.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/lib] /usr/local/lib We're still not finding hmmer either in your dynamic linker path (/etc/ld.so.conf) or in /usr/local/lib. 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/lib] /usr/local/lib We're still not finding squid either in your dynamic linker path (/etc/ld.so.conf) or in /usr/local/lib. 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/lib] /usr/local/lib We're still not finding svmloc either in your dynamic linker path (/etc/ld.so.conf) or in /usr/local/lib. 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/lib] /usr/local/lib We're still not finding modhmm either in your dynamic linker path (/etc/ld.so.conf) or in /usr/local/lib. 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: 10/27/2021 09:13:04 New DB name: /build/psortb-3.0.6+dfsg/psort/conf/analysis/sclblast/gramneg/sclblast New DB title: sclblast Sequence type: Protein Keep MBits: T Maximum file size: 1000000000B Error: NCBI C++ Exception: T0 "c++/include/corelib/ncbidiag.hpp", line 2143: Error: (CSeqIdException::eFormat) ncbi::objects::CSeq_id::Set() - Malformatted ID 15596049[Extracellular] Program failed, try executing the command manually. Building a new DB, current time: 10/27/2021 09:13:05 New DB name: /build/psortb-3.0.6+dfsg/psort/conf/analysis/sclblast/grampos/sclblast New DB title: sclblast Sequence type: Protein Keep MBits: T Maximum file size: 1000000000B 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: 10/27/2021 09:13:05 New DB name: /build/psortb-3.0.6+dfsg/psort/conf/analysis/sclblast/archaea/sclblast New DB title: sclblast Sequence type: Protein Keep MBits: T Maximum file size: 1000000000B 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/psortb-3.0.6+dfsg' debian/rules override_dh_auto_build make[1]: Entering directory '/build/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 -j15 make[2]: Entering directory '/build/psortb-3.0.6+dfsg' make[3]: Entering directory '/build/psortb-3.0.6+dfsg/algorithm-hmm' Running Mkbootstrap for HMM () "/usr/bin/perl" "/usr/share/perl/5.32.1/ExtUtils/xsubpp" -C++ -typemap '/usr/share/perl/5.32/ExtUtils/typemap' -typemap '/build/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 -fdebug-prefix-map=/build/psortb-3.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"0.02\" -DXS_VERSION=\"0.02\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.32/CORE" hmm-binding.cpp 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/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/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/Bio/Tools/Motif/Match.pm blib/lib/Bio/Tools/Motif/Match.pm cp lib/Bio/Tools/PSort/Module/OMPMotif.pm blib/lib/Bio/Tools/PSort/Module/OMPMotif.pm cp lib/Bio/Tools/PSort/Module/Profile.pm blib/lib/Bio/Tools/PSort/Module/Profile.pm cp lib/Bio/Tools/PSort.pm blib/lib/Bio/Tools/PSort.pm cp lib/Bio/Tools/PSort/Profile.pm blib/lib/Bio/Tools/PSort/Profile.pm cp lib/Bio/Tools/PSort/Constants.pm blib/lib/Bio/Tools/PSort/Constants.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/InputI.pm blib/lib/Bio/Tools/PSort/Module/InputI.pm cp lib/Bio/Tools/PSort/Module/ModHMM.pm blib/lib/Bio/Tools/PSort/Module/ModHMM.pm cp lib/Bio/Tools/PSort/Module/Signal.pm blib/lib/Bio/Tools/PSort/Module/Signal.pm cp lib/Bio/Tools/PSort/Profile/Match.pm blib/lib/Bio/Tools/PSort/Profile/Match.pm cp lib/Bio/Tools/Motif/Pattern.pm blib/lib/Bio/Tools/Motif/Pattern.pm cp lib/Bio/Tools/PSort/Report/Formatter/terse.pm blib/lib/Bio/Tools/PSort/Report/Formatter/terse.pm cp lib/Bio/Tools/PSort/Report/Result.pm blib/lib/Bio/Tools/PSort/Report/Result.pm cp lib/Bio/Tools/PSort/Report/Formatter/normal.pm blib/lib/Bio/Tools/PSort/Report/Formatter/normal.pm cp lib/Bio/Tools/PSort/Report/Formatter.pm blib/lib/Bio/Tools/PSort/Report/Formatter.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/SVMLocApache.pm blib/lib/Bio/Tools/PSort/Module/SVMLocApache.pm cp lib/Bio/Tools/PSort/Module/OutputI.pm blib/lib/Bio/Tools/PSort/Module/OutputI.pm cp lib/Bio/Tools/PSort/Module/Null.pm blib/lib/Bio/Tools/PSort/Module/Null.pm cp lib/Bio/Tools/PSort/Pathway.pm blib/lib/Bio/Tools/PSort/Pathway.pm cp lib/Bio/Tools/PSort/Report/Formatter/long.pm blib/lib/Bio/Tools/PSort/Report/Formatter/long.pm cp lib/Bio/Tools/PSort/Module/AnalysisI.pm blib/lib/Bio/Tools/PSort/Module/AnalysisI.pm cp lib/Bio/Tools/PSort/Module/Rules.pm blib/lib/Bio/Tools/PSort/Module/Rules.pm cp lib/Bio/Tools/Motif.pm blib/lib/Bio/Tools/Motif.pm cp lib/Bio/Tools/PSort/Module/HMMTOP.pm blib/lib/Bio/Tools/PSort/Module/HMMTOP.pm cp lib/Bio/Tools/PSort/ModuleI.pm blib/lib/Bio/Tools/PSort/ModuleI.pm cp lib/Bio/Tools/PSort/Report.pm blib/lib/Bio/Tools/PSort/Report.pm cp lib/Bio/Tools/PSort/Install.pm blib/lib/Bio/Tools/PSort/Install.pm cp lib/Bio/Tools/PSort/Module/Motif.pm blib/lib/Bio/Tools/PSort/Module/Motif.pm cp lib/Bio/Tools/PSort/Module/SCLBlast.pm blib/lib/Bio/Tools/PSort/Module/SCLBlast.pm cp lib/Bio/Tools/SVMLoc.pm blib/lib/Bio/Tools/SVMLoc.pm cp lib/Bio/Tools/Run/HMMTOP.pm blib/lib/Bio/Tools/Run/HMMTOP.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/SCLBlastLocal.pm blib/lib/Bio/Tools/Run/SCLBlastLocal.pm cp lib/Bio/Tools/Signal.pm blib/lib/Bio/Tools/Signal.pm cp lib/Bio/Tools/Run/HMMTOP/Report.pm blib/lib/Bio/Tools/Run/HMMTOP/Report.pm cp lib/Bio/Tools/Run/SCLBlast/Hit.pm blib/lib/Bio/Tools/Run/SCLBlast/Hit.pm cp lib/Bio/Tools/Signal/Report.pm blib/lib/Bio/Tools/Signal/Report.pm cp lib/Bio/Tools/Run/SCLBlast.pm blib/lib/Bio/Tools/Run/SCLBlast.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 -fdebug-prefix-map=/build/psortb-3.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"0.02\" -DXS_VERSION=\"0.02\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.32/CORE" HMM.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 -fdebug-prefix-map=/build/psortb-3.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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++ -L/usr/local/lib -lhmmer -lsquid \ chmod 755 ../blib/arch/auto/Algorithm/HMM/HMM.so Manifying 5 pod documents make[3]: Leaving directory '/build/psortb-3.0.6+dfsg/algorithm-hmm' make[3]: Entering directory '/build/psortb-3.0.6+dfsg/bio-tools-psort-svmloc' Running Mkbootstrap for SVMLoc () "/usr/bin/perl" "/usr/share/perl/5.32.1/ExtUtils/xsubpp" -C++ -typemap '/usr/share/perl/5.32/ExtUtils/typemap' -typemap '/build/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.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 -fdebug-prefix-map=/build/psortb-3.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"0.01\" -DXS_VERSION=\"0.01\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.32/CORE" SVMLoc.c rm -f ../blib/arch/auto/Bio/Tools/PSort/SVMLoc/SVMLoc.so x86_64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/build/psortb-3.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 \ -L/usr/local/lib -lsvmloc -lm -lsvm -lstdc++ \ chmod 755 ../blib/arch/auto/Bio/Tools/PSort/SVMLoc/SVMLoc.so Manifying 2 pod documents make[3]: Leaving directory '/build/psortb-3.0.6+dfsg/bio-tools-psort-svmloc' make[3]: Entering directory '/build/psortb-3.0.6+dfsg/bio-tools-psort-modhmm' Running Mkbootstrap for ModHMM () "/usr/bin/perl" "/usr/share/perl/5.32.1/ExtUtils/xsubpp" -typemap '/usr/share/perl/5.32/ExtUtils/typemap' -typemap '/build/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 -fdebug-prefix-map=/build/psortb-3.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"0.01\" -DXS_VERSION=\"0.01\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.32/CORE" binding.c chmod 644 "ModHMM.bs" binding.c: In function 'helix_DESTROY': binding.c:52:6: warning: implicit declaration of function 'free' [-Wimplicit-function-declaration] 52 | free(hSites->helix); | ^~~~ binding.c:52:6: warning: incompatible implicit declaration of built-in function 'free' binding.c:4:1: note: include '' or provide a declaration of 'free' 3 | #include "modhmm0.92b/structs.h" +++ |+#include 4 | binding.c:55:2: warning: incompatible implicit declaration of built-in function 'free' 55 | free(hSites); | ^~~~ binding.c:55:2: note: include '' or provide a declaration of 'free' "/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 -fdebug-prefix-map=/build/psortb-3.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"0.01\" -DXS_VERSION=\"0.01\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.32/CORE" modhmm.c modhmm.c: In function 'XS_Bio__Tools__PSort__ModHMM_find_helices': modhmm.c:179:11: warning: implicit declaration of function 'find_helices'; did you mean 'get_helices'? [-Wimplicit-function-declaration] 179 | RETVAL = find_helices(seq, hmmfile, repfile, path); | ^~~~~~~~~~~~ | get_helices rm -f ../blib/arch/auto/Bio/Tools/PSort/ModHMM/ModHMM.so x86_64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/build/psortb-3.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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++ -L/usr/local/lib -lmodhmm \ chmod 755 ../blib/arch/auto/Bio/Tools/PSort/ModHMM/ModHMM.so Manifying 1 pod document make[3]: Leaving directory '/build/psortb-3.0.6+dfsg/bio-tools-psort-modhmm' Manifying 18 pod documents make[2]: Leaving directory '/build/psortb-3.0.6+dfsg' make[1]: Leaving directory '/build/psortb-3.0.6+dfsg' dh_auto_test make -j15 test TEST_VERBOSE=1 make[1]: Entering directory '/build/psortb-3.0.6+dfsg' make[2]: Entering directory '/build/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/psortb-3.0.6+dfsg/algorithm-hmm' make[2]: Entering directory '/build/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/psortb-3.0.6+dfsg/bio-tools-psort-svmloc' make[2]: Entering directory '/build/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/psortb-3.0.6+dfsg/bio-tools-psort-modhmm' make[2]: Entering directory '/build/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 ( 0.03 usr 0.00 sys + 0.09 cusr 0.00 csys = 0.12 CPU) Result: PASS make[2]: Leaving directory '/build/psortb-3.0.6+dfsg/algorithm-hmm' make[2]: Entering directory '/build/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 + 0.29 cusr 0.01 csys = 0.32 CPU) Result: PASS make[2]: Leaving directory '/build/psortb-3.0.6+dfsg/bio-tools-psort-svmloc' make[2]: Entering directory '/build/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 + 0.24 cusr 0.03 csys = 0.30 CPU) Result: PASS make[2]: Leaving directory '/build/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 ( 0.02 usr 0.00 sys + 0.09 cusr 0.03 csys = 0.14 CPU) Result: PASS make[1]: Leaving directory '/build/psortb-3.0.6+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install make -j15 install DESTDIR=/build/psortb-3.0.6\+dfsg/debian/psortb AM_UPDATE_INFO_DIR=no PREFIX=/usr make[1]: Entering directory '/build/psortb-3.0.6+dfsg' make[2]: Entering directory '/build/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/psortb-3.0.6+dfsg/algorithm-hmm' make[2]: Entering directory '/build/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/psortb-3.0.6+dfsg/bio-tools-psort-svmloc' make[2]: Entering directory '/build/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/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/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/auto/Algorithm/HMM/HMM.so Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/auto/Bio/Tools/PSort/ModHMM/ModHMM.so Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/auto/Bio/Tools/PSort/SVMLoc/SVMLoc.so Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Algorithm/HMM.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Algorithm/HMM/Report.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Algorithm/HMM/Hit.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Algorithm/HMM/Hit/Global.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Algorithm/HMM/Hit/Domain.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/auto/Algorithm/HMM/autosplit.ix Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/auto/Bio/Tools/PSort/ModHMM/autosplit.ix Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/auto/Bio/Tools/PSort/SVMLoc/autosplit.ix Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/Signal.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/SVMLoc.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/Motif.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/Signal/Report.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/Run/SCLBlast.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/Run/SCLBlastLocal.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/Run/HMMTOP.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/Run/HMMTOP/Helix.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/Run/HMMTOP/Report.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/Run/SCLBlast/Hit.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/Run/SCLBlast/Report.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/ModHMM.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/SVMLoc.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/Install.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/Report.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/ModuleI.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/Pathway.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/Constants.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/Profile.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/SVMLoc/DataSet.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/XMLRPC/Client.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/Report/Formatter.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/Report/Result.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/Report/Formatter/long.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/Report/Formatter/html.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/Report/Formatter/normal.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/Report/Formatter/terse.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/Profile/Match.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/Module/SCLBlast.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/Module/Motif.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/Module/HMMTOP.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/Module/Rules.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/Module/AnalysisI.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/Module/Null.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/Module/OutputI.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/Module/SVMLocApache.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/Module/Signal.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/Module/ModHMM.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/Module/InputI.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/Module/SVMLoc.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/Module/Bayesian.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/Module/Profile.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/Module/OMPMotif.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/Motif/Pattern.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/Motif/Match.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::Signal.3pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::SVMLoc.3pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::Run::HMMTOP.3pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::PSort::Profile::Match.3pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::PSort::Profile.3pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::PSort::Pathway.3pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::PSort::ModuleI.3pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::PSort::Module::Profile.3pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::PSort::Module::OutputI.3pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::PSort::Module::OMPMotif.3pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::PSort::Module::Null.3pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::PSort::Module::Motif.3pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::PSort::Module::InputI.3pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::PSort::Module::AnalysisI.3pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::PSort.3pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::Motif::Pattern.3pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::Motif::Match.3pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::Motif.3pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::PSort::ModHMM.3pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::PSort::SVMLoc::DataSet.3pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::PSort::SVMLoc.3pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Algorithm::HMM::Report.3pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Algorithm::HMM::Hit::Global.3pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Algorithm::HMM::Hit::Domain.3pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Algorithm::HMM::Hit.3pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Algorithm::HMM.3pm make[1]: Leaving directory '/build/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/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/psortb-3.0.6+dfsg' dh_missing dh_dwz dh_strip dh_makeshlibs dh_shlibdeps dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'psortb-dbgsym' in '../psortb-dbgsym_3.0.6+dfsg-2_amd64.deb'. dpkg-deb: building package 'psortb' in '../psortb_3.0.6+dfsg-2_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../psortb_3.0.6+dfsg-2_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/3868752/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/3868752/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/3868752 and its subdirectories I: Current time: Wed Oct 27 09:13:50 +14 2021 I: pbuilder-time-stamp: 1635275630