Mon Dec 14 03:30:41 UTC 2020 I: starting to build psortb/buster/amd64 on jenkins on '2020-12-14 03:30' Mon Dec 14 03:30:41 UTC 2020 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_23/3536/console.log Mon Dec 14 03:30:41 UTC 2020 I: Downloading source for buster/psortb=3.0.6+dfsg-1 --2020-12-14 03:30:41-- http://deb.debian.org/debian/pool/main/p/psortb/psortb_3.0.6+dfsg-1.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2090 (2.0K) Saving to: ‘psortb_3.0.6+dfsg-1.dsc’ 0K .. 100% 176M=0s 2020-12-14 03:30:41 (176 MB/s) - ‘psortb_3.0.6+dfsg-1.dsc’ saved [2090/2090] Mon Dec 14 03:30:41 UTC 2020 I: psortb_3.0.6+dfsg-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: psortb Binary: psortb Architecture: any Version: 3.0.6+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: http://www.psort.org/ Standards-Version: 4.2.1 Vcs-Browser: https://salsa.debian.org/med-team/psortb Vcs-Git: https://salsa.debian.org/med-team/psortb.git Testsuite: autopkgtest-pkg-perl Build-Depends: debhelper (>= 11~), libsvm-dev, bioperl, ncbi-blast+-legacy, libsquid-dev, libhmmer2-dev, libsvmloc-dev, libmodhmm-dev, pkg-config, pftools Package-List: psortb deb science optional arch=any Checksums-Sha1: c47d0ec328df75f2151dd6d5b5840768006519f8 17036876 psortb_3.0.6+dfsg.orig.tar.xz 06cb16f6308d91aa9a153a6a59233ad60d1eb368 6356 psortb_3.0.6+dfsg-1.debian.tar.xz Checksums-Sha256: ed32aa0240bb03daed228b32614a53c146afba6ca66fd087702315d75e23f751 17036876 psortb_3.0.6+dfsg.orig.tar.xz 230b8d540d3c7966df383d811b6227de86deef00f45ba7081b6e6f79e75ead40 6356 psortb_3.0.6+dfsg-1.debian.tar.xz Files: c4feab06d3031fecac1ab90258550209 17036876 psortb_3.0.6+dfsg.orig.tar.xz 2f91955333f5401f5117fe558e3ad1c5 6356 psortb_3.0.6+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAlur5xURHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHniA/+PTweDudDa/6C8QzbEnIMnSESOWXaIkcF M1sJzC3jFEuTK4rU6LupMOPehVqDhbW5uTDR7HQPkHRTsEOORtma3bBUZB8jbLBF cBY+4XLEbFI8KtSszTqpklrWu6jqU7BhjoilG+64o6tbCcBpF0LZhlJRpjaRsXvu YRWuERjurLrGcJPEwBBpVD8S/RyDVXo0g4Mwngc8e4PzFo15UNff0m3SrYJJZQUc bk5ItmDH0OPrQymPDVfW2uYK3Ie4Vjq3CrfhlCyDyWdROhKzq3bAI7FcTagECJxa +yjZX6fsWKuJDaA52wJDxdyxF/S/E0jVKF48QnsXHAfRTlH7D3okP2tKcGu4KrlD tz7IIORJ3UnZwTSLpg3jMoIPEDRHJ59wvxPOcDbHDlgFYbgzLNUccbp1gImvng/O 5W8/DvoCuFCGVY9RfC6gVoiqcXJUbZTxgsSUcgnV2+Vp/XZqTVDAMNgQbdB7IqkG 3wbn+F7hEIPY2ZWYvv08AbT0XH8Pv2iyzhQTg9psB93i+Q02WOlr0daOb4R6IRqM 0Tx3RmQRTllRqsQzBGEG35/XxSjpYNB31PIs4jf9q7yOuZYbWuYmsqOS8b9ENqSE ImiRhH9wEjFx6LlDdURUq+UTw3izrrhOTzMTYzMjW0eDICF/6948Tn6jDgy4Ufzk 4djv671a9Lo= =gCoW -----END PGP SIGNATURE----- Mon Dec 14 03:30:41 UTC 2020 I: Checking whether the package is not for us Mon Dec 14 03:30:41 UTC 2020 I: Starting 1st build on remote node ionos11-amd64.debian.net. Mon Dec 14 03:30:41 UTC 2020 I: Preparing to do remote build '1' on ionos11-amd64.debian.net. Mon Dec 14 03:32:10 UTC 2020 I: Deleting $TMPDIR on ionos11-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Dec 13 15:30:43 -12 2020 I: pbuilder-time-stamp: 1607916643 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-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-1.dsc] I: copying [./psortb_3.0.6+dfsg.orig.tar.xz] I: copying [./psortb_3.0.6+dfsg-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Wed Sep 26 08:07:49 2018 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./psortb_3.0.6+dfsg-1.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-1.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 I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/40557/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' DISTRIBUTION='' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='fdca6046e4da43daae41efd4b6b27080' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='40557' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.LntXQzkPRS/pbuilderrc_SILw --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.LntXQzkPRS/b1 --logfile b1/build.log psortb_3.0.6+dfsg-1.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://78.137.99.97:3128' I: uname -a Linux ionos11-amd64 4.19.0-13-amd64 #1 SMP Debian 4.19.160-2 (2020-11-28) x86_64 GNU/Linux I: ls -l /bin total 5116 -rwxr-xr-x 1 root root 1168776 Apr 17 2019 bash -rwxr-xr-x 3 root root 38984 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 14328 Jul 10 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore -rwxr-xr-x 1 root root 43744 Feb 28 2019 cat -rwxr-xr-x 1 root root 64320 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 64288 Feb 28 2019 chmod -rwxr-xr-x 1 root root 72512 Feb 28 2019 chown -rwxr-xr-x 1 root root 146880 Feb 28 2019 cp -rwxr-xr-x 1 root root 121464 Jan 17 2019 dash -rwxr-xr-x 1 root root 109408 Feb 28 2019 date -rwxr-xr-x 1 root root 76712 Feb 28 2019 dd -rwxr-xr-x 1 root root 93744 Feb 28 2019 df -rwxr-xr-x 1 root root 138856 Feb 28 2019 dir -rwxr-xr-x 1 root root 84288 Jan 9 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname -rwxr-xr-x 1 root root 39520 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 35424 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 68880 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 34896 Apr 22 2020 fusermount -rwxr-xr-x 1 root root 198976 Jan 7 2019 grep -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe -rwxr-xr-x 1 root root 98048 Jan 5 2019 gzip -rwxr-xr-x 1 root root 26696 Sep 26 2018 hostname -rwxr-xr-x 1 root root 68552 Feb 28 2019 ln -rwxr-xr-x 1 root root 56760 Jul 26 2018 login -rwxr-xr-x 1 root root 138856 Feb 28 2019 ls -rwxr-xr-x 1 root root 108624 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 89088 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 68544 Feb 28 2019 mknod -rwxr-xr-x 1 root root 43808 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 43008 Jan 9 2019 more -rwsr-xr-x 1 root root 51280 Jan 9 2019 mount -rwxr-xr-x 1 root root 14408 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 138728 Feb 28 2019 mv lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 39616 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 47776 Feb 28 2019 readlink -rwxr-xr-x 1 root root 68416 Feb 28 2019 rm -rwxr-xr-x 1 root root 47776 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 23312 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Dec 6 20:24 sh -> dash -rwxr-xr-x 1 root root 39552 Feb 28 2019 sleep -rwxr-xr-x 1 root root 80672 Feb 28 2019 stty -rwsr-xr-x 1 root root 63568 Jan 9 2019 su -rwxr-xr-x 1 root root 35488 Feb 28 2019 sync -rwxr-xr-x 1 root root 445560 Apr 23 2019 tar -rwxr-xr-x 1 root root 14440 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 97152 Feb 28 2019 touch -rwxr-xr-x 1 root root 35424 Feb 28 2019 true -rwxr-xr-x 1 root root 14328 Apr 22 2020 ulockmgr_server -rwsr-xr-x 1 root root 34888 Jan 9 2019 umount -rwxr-xr-x 1 root root 39584 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 138856 Feb 28 2019 vdir -rwxr-xr-x 1 root root 34896 Jan 9 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 21 2019 which lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew I: user script /srv/workspace/pbuilder/40557/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 (>= 11~), 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 ... 19195 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 (>= 11~); however: Package debhelper 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} bsdmainutils{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} libbsd0{a} libcapture-tiny-perl{a} libclass-data-inheritable-perl{a} libcroco3{a} libdata-stag-perl{a} libdevel-stacktrace-perl{a} libelf1{a} libexception-class-perl{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libglib2.0-0{a} libhmmer2-dev{a} libicu63{a} libio-string-perl{a} liblmdb0{a} libmagic-mgc{a} libmagic1{a} libmbedcrypto3{a} libmbedtls12{a} libmbedx509-0{a} libmodhmm-dev{a} libmodhmm0{a} libncurses6{a} libpipeline1{a} libpvm3{a} libpython-stdlib{a} libpython2-stdlib{a} libpython2.7-minimal{a} libpython2.7-stdlib{a} libreadline7{a} libsigsegv2{a} libsquid-dev{a} libsquid1{a} libssl1.1{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} mime-support{a} ncbi-blast+{a} ncbi-blast+-legacy{a} ncbi-data{a} pftools{a} pkg-config{a} po-debconf{a} python{a} python-minimal{a} python2{a} python2-minimal{a} python2.7{a} python2.7-minimal{a} readline-common{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: bioperl-run 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 libgpm2 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 pvm shared-mime-info wget xdg-user-dirs 0 packages upgraded, 84 newly installed, 0 to remove and 0 not upgraded. Need to get 47.7 MB of archives. After unpacking 190 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main amd64 libbsd0 amd64 0.9.1-2 [99.5 kB] Get: 2 http://deb.debian.org/debian buster/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get: 3 http://deb.debian.org/debian buster/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get: 4 http://deb.debian.org/debian buster/main amd64 groff-base amd64 1.22.4-3 [916 kB] Get: 5 http://deb.debian.org/debian buster/main amd64 libpipeline1 amd64 1.5.1-2 [31.2 kB] Get: 6 http://deb.debian.org/debian buster/main amd64 man-db amd64 2.8.5-2 [1274 kB] Get: 7 http://deb.debian.org/debian buster/main amd64 libpython2.7-minimal amd64 2.7.16-2+deb10u1 [395 kB] Get: 8 http://deb.debian.org/debian buster/main amd64 python2.7-minimal amd64 2.7.16-2+deb10u1 [1369 kB] Get: 9 http://deb.debian.org/debian buster/main amd64 python2-minimal amd64 2.7.16-1 [41.4 kB] Get: 10 http://deb.debian.org/debian buster/main amd64 python-minimal amd64 2.7.16-1 [21.0 kB] Get: 11 http://deb.debian.org/debian buster/main amd64 libssl1.1 amd64 1.1.1d-0+deb10u3 [1538 kB] Get: 12 http://deb.debian.org/debian buster/main amd64 mime-support all 3.62 [37.2 kB] Get: 13 http://deb.debian.org/debian buster/main amd64 libexpat1 amd64 2.2.6-2+deb10u1 [106 kB] Get: 14 http://deb.debian.org/debian buster/main amd64 readline-common all 7.0-5 [70.6 kB] Get: 15 http://deb.debian.org/debian buster/main amd64 libreadline7 amd64 7.0-5 [151 kB] Get: 16 http://deb.debian.org/debian buster/main amd64 libpython2.7-stdlib amd64 2.7.16-2+deb10u1 [1912 kB] Get: 17 http://deb.debian.org/debian buster/main amd64 python2.7 amd64 2.7.16-2+deb10u1 [305 kB] Get: 18 http://deb.debian.org/debian buster/main amd64 libpython2-stdlib amd64 2.7.16-1 [20.8 kB] Get: 19 http://deb.debian.org/debian buster/main amd64 libpython-stdlib amd64 2.7.16-1 [20.8 kB] Get: 20 http://deb.debian.org/debian buster/main amd64 python2 amd64 2.7.16-1 [41.6 kB] Get: 21 http://deb.debian.org/debian buster/main amd64 python amd64 2.7.16-1 [22.8 kB] Get: 22 http://deb.debian.org/debian buster/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get: 23 http://deb.debian.org/debian buster/main amd64 libmagic-mgc amd64 1:5.35-4+deb10u1 [242 kB] Get: 24 http://deb.debian.org/debian buster/main amd64 libmagic1 amd64 1:5.35-4+deb10u1 [117 kB] Get: 25 http://deb.debian.org/debian buster/main amd64 file amd64 1:5.35-4+deb10u1 [66.4 kB] Get: 26 http://deb.debian.org/debian buster/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get: 27 http://deb.debian.org/debian buster/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get: 28 http://deb.debian.org/debian buster/main amd64 m4 amd64 1.4.18-2 [203 kB] Get: 29 http://deb.debian.org/debian buster/main amd64 autoconf all 2.69-11 [341 kB] Get: 30 http://deb.debian.org/debian buster/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get: 31 http://deb.debian.org/debian buster/main amd64 automake all 1:1.16.1-4 [771 kB] Get: 32 http://deb.debian.org/debian buster/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get: 33 http://deb.debian.org/debian buster/main amd64 libio-string-perl all 1.08-3 [12.3 kB] Get: 34 http://deb.debian.org/debian buster/main amd64 libdata-stag-perl all 0.14-2 [448 kB] Get: 35 http://deb.debian.org/debian buster/main amd64 libbio-perl-perl all 1.7.2-3 [4553 kB] Get: 36 http://deb.debian.org/debian buster/main amd64 libclass-data-inheritable-perl all 0.08-3 [8588 B] Get: 37 http://deb.debian.org/debian buster/main amd64 libdevel-stacktrace-perl all 2.0300-1 [28.0 kB] Get: 38 http://deb.debian.org/debian buster/main amd64 libexception-class-perl all 1.44-1 [32.3 kB] Get: 39 http://deb.debian.org/debian buster/main amd64 libtest-deep-perl all 1.128-1 [48.8 kB] Get: 40 http://deb.debian.org/debian buster/main amd64 libcapture-tiny-perl all 0.48-1 [26.0 kB] Get: 41 http://deb.debian.org/debian buster/main amd64 libalgorithm-diff-perl all 1.19.03-2 [47.9 kB] Get: 42 http://deb.debian.org/debian buster/main amd64 libtext-diff-perl all 1.45-1 [27.7 kB] Get: 43 http://deb.debian.org/debian buster/main amd64 libtest-differences-perl all 0.65-1 [18.1 kB] Get: 44 http://deb.debian.org/debian buster/main amd64 libsub-uplevel-perl all 0.2800-1 [16.3 kB] Get: 45 http://deb.debian.org/debian buster/main amd64 libtest-exception-perl all 0.43-1 [18.7 kB] Get: 46 http://deb.debian.org/debian buster/main amd64 libtest-warn-perl all 0.36-1 [16.2 kB] Get: 47 http://deb.debian.org/debian buster/main amd64 libtest-most-perl all 0.35-1 [24.5 kB] Get: 48 http://deb.debian.org/debian buster/main amd64 bioperl all 1.7.2-3 [418 kB] Get: 49 http://deb.debian.org/debian buster/main amd64 libtool all 2.4.6-9 [547 kB] Get: 50 http://deb.debian.org/debian buster/main amd64 dh-autoreconf all 19 [16.9 kB] Get: 51 http://deb.debian.org/debian buster/main amd64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 52 http://deb.debian.org/debian buster/main amd64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 53 http://deb.debian.org/debian buster/main amd64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 54 http://deb.debian.org/debian buster/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get: 55 http://deb.debian.org/debian buster/main amd64 dwz amd64 0.12-3 [78.0 kB] Get: 56 http://deb.debian.org/debian buster/main amd64 libglib2.0-0 amd64 2.58.3-2+deb10u2 [1258 kB] Get: 57 http://deb.debian.org/debian buster/main amd64 libicu63 amd64 63.1-6+deb10u1 [8300 kB] Get: 58 http://deb.debian.org/debian buster/main amd64 libxml2 amd64 2.9.4+dfsg1-7+deb10u1 [689 kB] Get: 59 http://deb.debian.org/debian buster/main amd64 libcroco3 amd64 0.6.12-3 [145 kB] Get: 60 http://deb.debian.org/debian buster/main amd64 libncurses6 amd64 6.1+20181013-2+deb10u2 [102 kB] Get: 61 http://deb.debian.org/debian buster/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get: 62 http://deb.debian.org/debian buster/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 63 http://deb.debian.org/debian buster/main amd64 po-debconf all 1.0.21 [248 kB] Get: 64 http://deb.debian.org/debian buster/main amd64 debhelper all 12.1.1 [1016 kB] Get: 65 http://deb.debian.org/debian buster/main amd64 libgfortran5 amd64 8.3.0-6 [581 kB] Get: 66 http://deb.debian.org/debian buster/main amd64 libhmmer2-dev amd64 2.3.2+dfsg-6 [101 kB] Get: 67 http://deb.debian.org/debian buster/main amd64 liblmdb0 amd64 0.9.22-1 [45.0 kB] Get: 68 http://deb.debian.org/debian buster/main amd64 libmbedcrypto3 amd64 2.16.0-1 [209 kB] Get: 69 http://deb.debian.org/debian buster/main amd64 libmbedx509-0 amd64 2.16.0-1 [91.4 kB] Get: 70 http://deb.debian.org/debian buster/main amd64 libmbedtls12 amd64 2.16.0-1 [130 kB] Get: 71 http://deb.debian.org/debian buster/main amd64 libmodhmm0 amd64 1.0+dfsg-3 [79.1 kB] Get: 72 http://deb.debian.org/debian buster/main amd64 libmodhmm-dev amd64 1.0+dfsg-3 [79.0 kB] Get: 73 http://deb.debian.org/debian buster/main amd64 libpvm3 amd64 3.4.6-2 [90.1 kB] Get: 74 http://deb.debian.org/debian buster/main amd64 libsquid1 amd64 1.9g+cvs20050121-11 [76.9 kB] Get: 75 http://deb.debian.org/debian buster/main amd64 libsquid-dev amd64 1.9g+cvs20050121-11 [400 kB] Get: 76 http://deb.debian.org/debian buster/main amd64 libsvm3 amd64 3.21+ds-1.2 [41.6 kB] Get: 77 http://deb.debian.org/debian buster/main amd64 libsvm-dev amd64 3.21+ds-1.2 [41.9 kB] Get: 78 http://deb.debian.org/debian buster/main amd64 libsvmloc0 amd64 1.0+dfsg-3 [13.0 kB] Get: 79 http://deb.debian.org/debian buster/main amd64 libsvmloc-dev amd64 1.0+dfsg-3 [11.9 kB] Get: 80 http://deb.debian.org/debian buster/main amd64 ncbi-data all 6.1.20170106+dfsg1-0+deb10u2 [3552 kB] Get: 81 http://deb.debian.org/debian buster/main amd64 ncbi-blast+ amd64 2.8.1-1+deb10u1 [10.9 MB] Get: 82 http://deb.debian.org/debian buster/main amd64 ncbi-blast+-legacy all 2.8.1-1+deb10u1 [10.6 kB] Get: 83 http://deb.debian.org/debian buster/main amd64 pftools amd64 3+dfsg-3 [392 kB] Get: 84 http://deb.debian.org/debian buster/main amd64 pkg-config amd64 0.29-6 [63.5 kB] Fetched 47.7 MB in 1s (32.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0: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 ... 19195 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_amd64.deb ... Unpacking libbsd0:amd64 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../02-libuchardet0_0.0.6-3_amd64.deb ... 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Selecting previously unselected package libcroco3:amd64. Preparing to unpack .../38-libcroco3_0.6.12-3_amd64.deb ... Unpacking libcroco3:amd64 (0.6.12-3) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../39-libncurses6_6.1+20181013-2+deb10u2_amd64.deb ... Unpacking libncurses6:amd64 (6.1+20181013-2+deb10u2) ... Selecting previously unselected package gettext. Preparing to unpack .../40-gettext_0.19.8.1-9_amd64.deb ... Unpacking gettext (0.19.8.1-9) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../41-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 .../42-po-debconf_1.0.21_all.deb ... Unpacking po-debconf (1.0.21) ... Selecting previously unselected package debhelper. Preparing to unpack .../43-debhelper_12.1.1_all.deb ... Unpacking debhelper (12.1.1) ... 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Selecting previously unselected package libmodhmm0:amd64. Preparing to unpack .../50-libmodhmm0_1.0+dfsg-3_amd64.deb ... Unpacking libmodhmm0:amd64 (1.0+dfsg-3) ... Selecting previously unselected package libmodhmm-dev:amd64. Preparing to unpack .../51-libmodhmm-dev_1.0+dfsg-3_amd64.deb ... Unpacking libmodhmm-dev:amd64 (1.0+dfsg-3) ... Selecting previously unselected package libpvm3:amd64. Preparing to unpack .../52-libpvm3_3.4.6-2_amd64.deb ... Unpacking libpvm3:amd64 (3.4.6-2) ... Selecting previously unselected package libsquid1. Preparing to unpack .../53-libsquid1_1.9g+cvs20050121-11_amd64.deb ... Unpacking libsquid1 (1.9g+cvs20050121-11) ... Selecting previously unselected package libsquid-dev. Preparing to unpack .../54-libsquid-dev_1.9g+cvs20050121-11_amd64.deb ... Unpacking libsquid-dev (1.9g+cvs20050121-11) ... Selecting previously unselected package libsvm3. Preparing to unpack .../55-libsvm3_3.21+ds-1.2_amd64.deb ... Unpacking libsvm3 (3.21+ds-1.2) ... 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Setting up gettext-base (0.19.8.1-9) ... Setting up file (1:5.35-4+deb10u1) ... Setting up libmodhmm0:amd64 (1.0+dfsg-3) ... Setting up libicu63:amd64 (63.1-6+deb10u1) ... Setting up libio-string-perl (1.08-3) ... Setting up autotools-dev (20180224.1) ... Setting up libclass-data-inheritable-perl (0.08-3) ... Setting up libtext-diff-perl (1.45-1) ... Setting up libncurses6:amd64 (6.1+20181013-2+deb10u2) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up autopoint (0.19.8.1-9) ... Setting up pkg-config (0.29-6) ... Setting up libgfortran5:amd64 (8.3.0-6) ... Setting up libcapture-tiny-perl (0.48-1) ... Setting up libsquid1 (1.9g+cvs20050121-11) ... Setting up libdata-stag-perl (0.14-2) ... Setting up sensible-utils (0.0.12) ... Setting up pftools (3+dfsg-3) ... Setting up libuchardet0:amd64 (0.0.6-3) ... Setting up libmbedcrypto3:amd64 (2.16.0-1) ... Setting up libsub-uplevel-perl (0.2800-1) ... Setting up libdevel-stacktrace-perl (2.0300-1) ... Setting up libbio-perl-perl (1.7.2-3) ... Setting up libhmmer2-dev (2.3.2+dfsg-6) ... Setting up libmodhmm-dev:amd64 (1.0+dfsg-3) ... Setting up libbsd0:amd64 (0.9.1-2) ... Setting up libelf1:amd64 (0.176-1.1) ... Setting up readline-common (7.0-5) ... Setting up libxml2:amd64 (2.9.4+dfsg1-7+deb10u1) ... Setting up libsvm3 (3.21+ds-1.2) ... Setting up libreadline7:amd64 (7.0-5) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libtool (2.4.6-9) ... Setting up libmbedx509-0:amd64 (2.16.0-1) ... Setting up libtest-warn-perl (0.36-1) ... Setting up libmbedtls12:amd64 (2.16.0-1) ... Setting up libtest-differences-perl (0.65-1) ... Setting up m4 (1.4.18-2) ... Setting up libexception-class-perl (1.44-1) ... Setting up libsquid-dev (1.9g+cvs20050121-11) ... Setting up libpython2.7-stdlib:amd64 (2.7.16-2+deb10u1) ... Setting up libtest-exception-perl (0.43-1) ... Setting up libsvmloc0:amd64 (1.0+dfsg-3) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libsvm-dev (3.21+ds-1.2) ... Setting up libcroco3:amd64 (0.6.12-3) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.19.8.1-9) ... Setting up libsvmloc-dev:amd64 (1.0+dfsg-3) ... Setting up python2.7 (2.7.16-2+deb10u1) ... Setting up libpython2-stdlib:amd64 (2.7.16-1) ... Setting up libtest-most-perl (0.35-1) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up python2 (2.7.16-1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libpython-stdlib:amd64 (2.7.16-1) ... Setting up python (2.7.16-1) ... Setting up bioperl (1.7.2-3) ... Setting up po-debconf (1.0.21) ... Setting up ncbi-blast+ (2.8.1-1+deb10u1) ... Setting up ncbi-blast+-legacy (2.8.1-1+deb10u1) ... Setting up debhelper (12.1.1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Processing triggers for libc-bin (2.28-10) ... 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 Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/psortb-3.0.6+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package psortb dpkg-buildpackage: info: source version 3.0.6+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot 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 build dh build 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 -ffile-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 -ffile-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: 12/13/2020 15:31:14 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 volume: /build/psortb-3.0.6+dfsg/psort/conf/analysis/sclblast/gramneg/sclblast file: /build/psortb-3.0.6+dfsg/psort/conf/analysis/sclblast/gramneg/sclblast.pin file: /build/psortb-3.0.6+dfsg/psort/conf/analysis/sclblast/gramneg/sclblast.phr file: /build/psortb-3.0.6+dfsg/psort/conf/analysis/sclblast/gramneg/sclblast.psq file: /build/psortb-3.0.6+dfsg/psort/conf/analysis/sclblast/gramneg/sclblast.psi file: /build/psortb-3.0.6+dfsg/psort/conf/analysis/sclblast/gramneg/sclblast.psd file: /build/psortb-3.0.6+dfsg/psort/conf/analysis/sclblast/gramneg/sclblast.pog 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: 12/13/2020 15:31:15 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 volume: /build/psortb-3.0.6+dfsg/psort/conf/analysis/sclblast/grampos/sclblast file: /build/psortb-3.0.6+dfsg/psort/conf/analysis/sclblast/grampos/sclblast.pin file: /build/psortb-3.0.6+dfsg/psort/conf/analysis/sclblast/grampos/sclblast.phr file: /build/psortb-3.0.6+dfsg/psort/conf/analysis/sclblast/grampos/sclblast.psq file: /build/psortb-3.0.6+dfsg/psort/conf/analysis/sclblast/grampos/sclblast.psi file: /build/psortb-3.0.6+dfsg/psort/conf/analysis/sclblast/grampos/sclblast.psd file: /build/psortb-3.0.6+dfsg/psort/conf/analysis/sclblast/grampos/sclblast.pog 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: 12/13/2020 15:31:16 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 volume: /build/psortb-3.0.6+dfsg/psort/conf/analysis/sclblast/archaea/sclblast file: /build/psortb-3.0.6+dfsg/psort/conf/analysis/sclblast/archaea/sclblast.pin file: /build/psortb-3.0.6+dfsg/psort/conf/analysis/sclblast/archaea/sclblast.phr file: /build/psortb-3.0.6+dfsg/psort/conf/analysis/sclblast/archaea/sclblast.psq file: /build/psortb-3.0.6+dfsg/psort/conf/analysis/sclblast/archaea/sclblast.psi file: /build/psortb-3.0.6+dfsg/psort/conf/analysis/sclblast/archaea/sclblast.psd file: /build/psortb-3.0.6+dfsg/psort/conf/analysis/sclblast/archaea/sclblast.pog 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/5.28.1/ExtUtils/xsubpp" -C++ -typemap '/usr/share/perl/5.28/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 -ffile-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/5.28/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/Bio/Tools/PSort/Pathway.pm blib/lib/Bio/Tools/PSort/Pathway.pm cp lib/Bio/Tools/PSort/Module/SCLBlast.pm blib/lib/Bio/Tools/PSort/Module/SCLBlast.pm cp lib/Bio/Tools/PSort/Module/Profile.pm blib/lib/Bio/Tools/PSort/Module/Profile.pm cp lib/Bio/Tools/PSort/Install.pm blib/lib/Bio/Tools/PSort/Install.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/Rules.pm blib/lib/Bio/Tools/PSort/Module/Rules.pm cp lib/Bio/Tools/PSort/Module/Signal.pm blib/lib/Bio/Tools/PSort/Module/Signal.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/AnalysisI.pm blib/lib/Bio/Tools/PSort/Module/AnalysisI.pm cp lib/Bio/Tools/PSort/Module/SVMLocApache.pm blib/lib/Bio/Tools/PSort/Module/SVMLocApache.pm cp lib/Bio/Tools/PSort/Module/HMMTOP.pm blib/lib/Bio/Tools/PSort/Module/HMMTOP.pm cp lib/Bio/Tools/Motif/Pattern.pm blib/lib/Bio/Tools/Motif/Pattern.pm cp lib/Bio/Tools/PSort/Module/Motif.pm blib/lib/Bio/Tools/PSort/Module/Motif.pm cp lib/Bio/Tools/PSort/Module/OMPMotif.pm blib/lib/Bio/Tools/PSort/Module/OMPMotif.pm cp lib/Bio/Tools/PSort/Profile.pm blib/lib/Bio/Tools/PSort/Profile.pm cp lib/Bio/Tools/PSort/Module/SVMLoc.pm blib/lib/Bio/Tools/PSort/Module/SVMLoc.pm cp lib/Bio/Tools/PSort.pm blib/lib/Bio/Tools/PSort.pm cp lib/Bio/Tools/PSort/Report/Formatter/html.pm blib/lib/Bio/Tools/PSort/Report/Formatter/html.pm cp lib/Bio/Tools/PSort/Constants.pm blib/lib/Bio/Tools/PSort/Constants.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/Module/ModHMM.pm blib/lib/Bio/Tools/PSort/Module/ModHMM.pm cp lib/Bio/Tools/PSort/Report.pm blib/lib/Bio/Tools/PSort/Report.pm cp lib/Bio/Tools/PSort/Report/Formatter.pm blib/lib/Bio/Tools/PSort/Report/Formatter.pm cp lib/Bio/Tools/PSort/Report/Formatter/long.pm blib/lib/Bio/Tools/PSort/Report/Formatter/long.pm cp lib/Bio/Tools/Motif.pm blib/lib/Bio/Tools/Motif.pm cp lib/Bio/Tools/PSort/Module/Bayesian.pm blib/lib/Bio/Tools/PSort/Module/Bayesian.pm cp lib/Bio/Tools/PSort/Report/Formatter/terse.pm blib/lib/Bio/Tools/PSort/Report/Formatter/terse.pm cp lib/Bio/Tools/PSort/ModuleI.pm blib/lib/Bio/Tools/PSort/ModuleI.pm cp lib/Bio/Tools/PSort/Profile/Match.pm blib/lib/Bio/Tools/PSort/Profile/Match.pm cp lib/Bio/Tools/Motif/Match.pm blib/lib/Bio/Tools/Motif/Match.pm 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/Algorithm/HMM.pm ../blib/lib/Algorithm/HMM.pm AutoSplitting ../blib/lib/Algorithm/HMM.pm (../blib/lib/auto/Algorithm/HMM) cp lib/Bio/Tools/Run/HMMTOP/Helix.pm blib/lib/Bio/Tools/Run/HMMTOP/Helix.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/SCLBlastLocal.pm blib/lib/Bio/Tools/Run/SCLBlastLocal.pm cp lib/Bio/Tools/Run/SCLBlast/Hit.pm blib/lib/Bio/Tools/Run/SCLBlast/Hit.pm cp lib/Bio/Tools/Run/SCLBlast.pm blib/lib/Bio/Tools/Run/SCLBlast.pm cp lib/Bio/Tools/SVMLoc.pm blib/lib/Bio/Tools/SVMLoc.pm cp lib/Bio/Tools/Run/SCLBlast/Report.pm blib/lib/Bio/Tools/Run/SCLBlast/Report.pm cp lib/Bio/Tools/PSort/XMLRPC/Client.pm blib/lib/Bio/Tools/PSort/XMLRPC/Client.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 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 -ffile-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/5.28/CORE" HMM.c hmm-binding.cpp: In member function 'HMMReport* HMM::search(char*)': hmm-binding.cpp:138:15: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] FALSE); ^ rm -f ../blib/arch/auto/Algorithm/HMM/HMM.so x86_64-linux-gnu-gcc -g -O2 -ffile-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/5.28.1/ExtUtils/xsubpp" -C++ -typemap '/usr/share/perl/5.28/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/DataSet.pm ../blib/lib/Bio/Tools/PSort/SVMLoc/DataSet.pm cp lib/Bio/Tools/PSort/SVMLoc.pm ../blib/lib/Bio/Tools/PSort/SVMLoc.pm AutoSplitting ../blib/lib/Bio/Tools/PSort/SVMLoc.pm (../blib/lib/auto/Bio/Tools/PSort/SVMLoc) Please specify prototyping behavior for SVMLoc.xs (see perlxs manual) mv SVMLoc.xsc SVMLoc.c g++ -c -Wall -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -ffile-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/5.28/CORE" SVMLoc.c rm -f ../blib/arch/auto/Bio/Tools/PSort/SVMLoc/SVMLoc.so x86_64-linux-gnu-gcc -g -O2 -ffile-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/5.28.1/ExtUtils/xsubpp" -typemap '/usr/share/perl/5.28/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 -ffile-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/5.28/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 binding.c: In function 'helix_DESTROY': binding.c:52:6: warning: implicit declaration of function 'free' [-Wimplicit-function-declaration] free(hSites->helix); ^~~~ binding.c:52:6: warning: incompatible implicit declaration of built-in function 'free' binding.c:52:6: note: include '' or provide a declaration of 'free' binding.c:4:1: +#include binding.c:52:6: free(hSites->helix); ^~~~ binding.c:55:2: warning: incompatible implicit declaration of built-in function 'free' free(hSites); ^~~~ binding.c:55:2: note: include '' or provide a declaration of 'free' 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 -ffile-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/5.28/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] 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 -ffile-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 0.01 sys + 0.09 cusr 0.02 csys = 0.15 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 ( 0.03 usr 0.01 sys + 0.32 cusr 0.04 csys = 0.40 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 ( 0.03 usr 0.00 sys + 0.32 cusr 0.01 csys = 0.36 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, 1 wallclock secs ( 0.03 usr 0.01 sys + 0.12 cusr 0.02 csys = 0.18 CPU) Result: PASS make[1]: Leaving directory '/build/psortb-3.0.6+dfsg' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot 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/perl5/5.28/auto/Algorithm/HMM/HMM.so Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.28/auto/Bio/Tools/PSort/ModHMM/ModHMM.so Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.28/auto/Bio/Tools/PSort/SVMLoc/SVMLoc.so Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.28/Algorithm/HMM.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.28/Algorithm/HMM/Hit.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.28/Algorithm/HMM/Report.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.28/Algorithm/HMM/Hit/Global.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.28/Algorithm/HMM/Hit/Domain.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.28/auto/Algorithm/HMM/autosplit.ix Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.28/auto/Bio/Tools/PSort/ModHMM/autosplit.ix Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.28/auto/Bio/Tools/PSort/SVMLoc/autosplit.ix Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.28/Bio/Tools/SVMLoc.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.28/Bio/Tools/Signal.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.28/Bio/Tools/Motif.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.28/Bio/Tools/PSort.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.28/Bio/Tools/Signal/Report.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.28/Bio/Tools/Run/HMMTOP.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.28/Bio/Tools/Run/SCLBlast.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.28/Bio/Tools/Run/SCLBlastLocal.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.28/Bio/Tools/Run/SCLBlast/Report.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.28/Bio/Tools/Run/SCLBlast/Hit.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.28/Bio/Tools/Run/HMMTOP/Report.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.28/Bio/Tools/Run/HMMTOP/Helix.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.28/Bio/Tools/Motif/Match.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.28/Bio/Tools/Motif/Pattern.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.28/Bio/Tools/PSort/ModHMM.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.28/Bio/Tools/PSort/SVMLoc.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.28/Bio/Tools/PSort/ModuleI.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.28/Bio/Tools/PSort/Report.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.28/Bio/Tools/PSort/Constants.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.28/Bio/Tools/PSort/Profile.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.28/Bio/Tools/PSort/Install.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.28/Bio/Tools/PSort/Pathway.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.28/Bio/Tools/PSort/SVMLoc/DataSet.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.28/Bio/Tools/PSort/XMLRPC/Client.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.28/Bio/Tools/PSort/Profile/Match.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.28/Bio/Tools/PSort/Report/Formatter.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.28/Bio/Tools/PSort/Report/Result.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.28/Bio/Tools/PSort/Report/Formatter/terse.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.28/Bio/Tools/PSort/Report/Formatter/long.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.28/Bio/Tools/PSort/Report/Formatter/html.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.28/Bio/Tools/PSort/Report/Formatter/normal.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.28/Bio/Tools/PSort/Module/Bayesian.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.28/Bio/Tools/PSort/Module/ModHMM.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.28/Bio/Tools/PSort/Module/Null.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.28/Bio/Tools/PSort/Module/OutputI.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.28/Bio/Tools/PSort/Module/SVMLoc.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.28/Bio/Tools/PSort/Module/OMPMotif.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.28/Bio/Tools/PSort/Module/Motif.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.28/Bio/Tools/PSort/Module/HMMTOP.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.28/Bio/Tools/PSort/Module/SVMLocApache.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.28/Bio/Tools/PSort/Module/AnalysisI.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.28/Bio/Tools/PSort/Module/Signal.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.28/Bio/Tools/PSort/Module/Rules.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.28/Bio/Tools/PSort/Module/InputI.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.28/Bio/Tools/PSort/Module/Profile.pm Installing /build/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.28/Bio/Tools/PSort/Module/SCLBlast.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_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_strip dh_makeshlibs dh_shlibdeps dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.28/auto/Bio/Tools/PSort/SVMLoc/SVMLoc.so was not linked against libsvm.so.3 (it uses none of the library's symbols) dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'psortb' in '../psortb_3.0.6+dfsg-1_amd64.deb'. dpkg-deb: building package 'psortb-dbgsym' in '../psortb-dbgsym_3.0.6+dfsg-1_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../psortb_3.0.6+dfsg-1_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) I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/40557 and its subdirectories I: Current time: Sun Dec 13 15:32:10 -12 2020 I: pbuilder-time-stamp: 1607916730 Mon Dec 14 03:32:11 UTC 2020 I: 1st build successful. Starting 2nd build on remote node ionos15-amd64.debian.net. Mon Dec 14 03:32:11 UTC 2020 I: Preparing to do remote build '2' on ionos15-amd64.debian.net. Mon Dec 14 03:36:00 UTC 2020 I: Deleting $TMPDIR on ionos15-amd64.debian.net. Mon Dec 14 03:36:00 UTC 2020 I: psortb_3.0.6+dfsg-1_amd64.changes: Format: 1.8 Date: Wed, 26 Sep 2018 22:03:35 +0200 Source: psortb Binary: psortb psortb-dbgsym Architecture: amd64 Version: 3.0.6+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: psortb - bacterial localization prediction tool Changes: psortb (3.0.6+dfsg-1) unstable; urgency=medium . * New upstream version * Standards-Version: 4.2.1 Checksums-Sha1: 95b4ac0b8a7a0c7fe0e870d23c1068742bb78237 206536 psortb-dbgsym_3.0.6+dfsg-1_amd64.deb 31e619ba6c4a4e89adb650cf91e15c9b9fb476fa 6320 psortb_3.0.6+dfsg-1_amd64.buildinfo e482ea5dbcbaefc46b83e0ae846fa25928c44b4b 16242080 psortb_3.0.6+dfsg-1_amd64.deb Checksums-Sha256: 16ec196deab2399bbf64d08a97d8024213dbe412e57ef7a5703f6fc8d697fad0 206536 psortb-dbgsym_3.0.6+dfsg-1_amd64.deb 47cbfbbe17d37d7bbd196f547add8af058c95fb52c5348b7b786bbd2c92a7294 6320 psortb_3.0.6+dfsg-1_amd64.buildinfo 180538c8a746b958fc6407c1c3082a5ef18e7411ff055125ba25a713e0d0baed 16242080 psortb_3.0.6+dfsg-1_amd64.deb Files: 1e5f2aeaa5620c297e3a106097f24618 206536 debug optional psortb-dbgsym_3.0.6+dfsg-1_amd64.deb f19f5c10c7a64c22a2c59dc9edd97e4f 6320 science optional psortb_3.0.6+dfsg-1_amd64.buildinfo 1a31e7dc6dbbcc18c32cad218ee7022c 16242080 science optional psortb_3.0.6+dfsg-1_amd64.deb Mon Dec 14 03:36:01 UTC 2020 I: diffoscope 162 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.LntXQzkPRS/psortb_3.0.6+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.LntXQzkPRS/psortb_3.0.6+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.LntXQzkPRS/psortb_3.0.6+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.LntXQzkPRS/b1/psortb_3.0.6+dfsg-1_amd64.changes /srv/reproducible-results/rbuild-debian/tmp.LntXQzkPRS/b2/psortb_3.0.6+dfsg-1_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.899s) 0.899s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.364s) 0.364s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Mon Dec 14 03:36:05 UTC 2020 I: diffoscope 162 found no differences in the changes files, and a .buildinfo file also exists. Mon Dec 14 03:36:05 UTC 2020 I: psortb from buster built successfully and reproducibly on amd64. Mon Dec 14 03:36:07 UTC 2020 I: Submitting .buildinfo files to external archives: Mon Dec 14 03:36:07 UTC 2020 I: Submitting 8.0K b1/psortb_3.0.6+dfsg-1_amd64.buildinfo.asc Mon Dec 14 03:36:08 UTC 2020 I: Submitting 8.0K b2/psortb_3.0.6+dfsg-1_amd64.buildinfo.asc Mon Dec 14 03:36:09 UTC 2020 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon Dec 14 03:36:09 UTC 2020 I: Done submitting .buildinfo files. Mon Dec 14 03:36:09 UTC 2020 I: Removing signed psortb_3.0.6+dfsg-1_amd64.buildinfo.asc files: removed './b1/psortb_3.0.6+dfsg-1_amd64.buildinfo.asc' removed './b2/psortb_3.0.6+dfsg-1_amd64.buildinfo.asc'