sbuild (Debian sbuild) 0.85.10 (30 May 2024) on carme.larted.org.uk +==============================================================================+ | psortb 3.0.6+dfsg-4+b1 (amd64) Sat, 14 Sep 2024 17:23:44 +0000 | +==============================================================================+ Package: psortb Version: 3.0.6+dfsg-4+b1 Source Version: 3.0.6+dfsg-4 Distribution: perl-5.40 Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/perl-5.40-amd64-debomatic-265c8ee1-a5fd-41ef-81d1-84b5afe43ef6' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup psortb_3.0.6+dfsg-4 perl-5.40 amd64 ---------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup psortb_3.0.6+dfsg-4 perl-5.40 amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: NOTICE: Log filtering will replace 'build/psortb-i9cCh5/resolver-dClKRt' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.40 InRelease [3042 B] Hit:2 http://localhost:3142/debian sid InRelease Get:1 file:/srv/reprepro perl-5.40 InRelease [3042 B] Hit:3 http://deb.debian.org/debian unstable InRelease Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/psortb_3.0.6+dfsg-4.dsc exists in /srv/debomatic/incoming; copying to chroot I: NOTICE: Log filtering will replace 'build/psortb-i9cCh5/psortb-3.0.6+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/psortb-i9cCh5' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), libsvm-dev, bioperl, ncbi-blast+-legacy, libsquid-dev, libhmmer2-dev, libsvmloc-dev, libmodhmm-dev, pkgconf, pftools, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), libsvm-dev, bioperl, ncbi-blast+-legacy, libsquid-dev, libhmmer2-dev, libsvmloc-dev, libmodhmm-dev, pkgconf, pftools, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [609 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [735 B] Get:5 copy:/<>/apt_archive ./ Packages [767 B] Fetched 2111 B in 0s (0 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bioperl bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz fakeroot file gettext gettext-base groff-base intltool-debian libalgorithm-diff-perl libarchive-zip-perl libbio-perl-perl libcapture-tiny-perl libclass-data-inheritable-perl libcom-err2 libdata-stag-perl libdebhelper-perl libdevel-stacktrace-perl libelf1t64 libexception-class-perl libexpat1 libfakeroot libfile-slurp-perl libfile-stripnondeterminism-perl libgfortran5 libgssapi-krb5-2 libhmmer2-dev libicu72 libio-string-perl libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblmdb0 libmagic-mgc libmagic1t64 libmbedcrypto7t64 libmbedtls14t64 libmbedx509-1t64 libmodhmm-dev libmodhmm0 libnghttp2-14 libnsl2 libpipeline1 libpkgconf3 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib libsquid-dev libsquid1t64 libsub-uplevel-perl libsvm-dev libsvm3 libsvmloc-dev libsvmloc0 libtest-deep-perl libtest-differences-perl libtest-exception-perl libtest-most-perl libtest-warn-perl libtext-diff-perl libtirpc-common libtirpc3t64 libtool libuchardet0 libuv1t64 libxml2 m4 man-db media-types ncbi-blast+ ncbi-blast+-legacy ncbi-data netbase pftools pkgconf pkgconf-bin po-debconf python3 python3-minimal python3.12 python3.12-minimal sensible-utils tzdata Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libxml-sax-expatxs-perl krb5-doc krb5-user biosquid libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python3.12-venv python3.12-doc binfmt-support Recommended packages: bioperl-run perl-doc libhttp-message-perl libwww-perl libcache-cache-perl libbio-perl-run-perl libdbi-perl libgd-gd2-perl libapache-dbi-perl liburi-perl libxml-simple-perl libyaml-perl libace-perl liblist-moreutils-perl libxml-twig-perl libset-scalar-perl curl | wget | lynx libalgorithm-diff-xs-perl bioperl-run | libbio-perl-run-perl libalgorithm-munkres-perl libarray-compare-perl libbio-asn1-entrezgene-perl libclone-perl libconvert-binary-c-perl libdbd-sqlite3-perl libdbd-mysql-perl libdbd-pg-perl libgd-perl libgraph-perl libgraphviz-perl libhtml-parser-perl libhtml-tableextract-perl libpostscript-perl libsoap-lite-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-perl libsvg-graph-perl libxml-dom-xpath-perl libxml-parser-perl libxml-sax-perl libxml-sax-writer-perl libxml-writer-perl libxml-libxml-perl perl-tk libgd-gd2-perl | libgd-gd2-noxpm-perl libxml-libxslt-perl libmldbm-perl libxml-perl libarchive-cpio-perl krb5-locales libltdl-dev libmail-sendmail-perl ca-certificates The following NEW packages will be installed: autoconf automake autopoint autotools-dev bioperl bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz fakeroot file gettext gettext-base groff-base intltool-debian libalgorithm-diff-perl libarchive-zip-perl libbio-perl-perl libcapture-tiny-perl libclass-data-inheritable-perl libcom-err2 libdata-stag-perl libdebhelper-perl libdevel-stacktrace-perl libelf1t64 libexception-class-perl libexpat1 libfakeroot libfile-slurp-perl libfile-stripnondeterminism-perl libgfortran5 libgssapi-krb5-2 libhmmer2-dev libicu72 libio-string-perl libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblmdb0 libmagic-mgc libmagic1t64 libmbedcrypto7t64 libmbedtls14t64 libmbedx509-1t64 libmodhmm-dev libmodhmm0 libnghttp2-14 libnsl2 libpipeline1 libpkgconf3 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib libsquid-dev libsquid1t64 libsub-uplevel-perl libsvm-dev libsvm3 libsvmloc-dev libsvmloc0 libtest-deep-perl libtest-differences-perl libtest-exception-perl libtest-most-perl libtest-warn-perl libtext-diff-perl libtirpc-common libtirpc3t64 libtool libuchardet0 libuv1t64 libxml2 m4 man-db media-types ncbi-blast+ ncbi-blast+-legacy ncbi-data netbase pftools pkgconf pkgconf-bin po-debconf python3 python3-minimal python3.12 python3.12-minimal sbuild-build-depends-main-dummy sensible-utils tzdata 0 upgraded, 92 newly installed, 0 to remove and 0 not upgraded. Need to get 76.3 MB of archives. After this operation, 270 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [948 B] Get:2 http://deb.debian.org/debian unstable/main amd64 libpython3.12-minimal amd64 3.12.6-1 [814 kB] Get:3 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.3-1 [105 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 python3.12-minimal amd64 3.12.6-1 [2168 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.12.5-1+b1 [27.0 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 tzdata all 2024a-4 [255 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.1-1 [22.9 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get:12 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get:13 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get:14 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3 [82.7 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 libnsl2 amd64 1.3.0-3+b2 [40.3 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 libpython3.12-stdlib amd64 3.12.6-1 [1963 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 python3.12 amd64 3.12.6-1 [669 kB] Get:20 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.12.5-1+b1 [9884 B] Get:21 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.12.5-1+b1 [27.9 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get:23 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get:24 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB] Get:26 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get:27 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.2-8 [97.3 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get:31 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get:33 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amd64 libtest-deep-perl all 1.204-1 [52.9 kB] Get:44 http://deb.debian.org/debian unstable/main amd64 libcapture-tiny-perl all 0.48-2 [24.6 kB] Get:45 http://deb.debian.org/debian unstable/main amd64 libalgorithm-diff-perl all 1.201-1 [43.3 kB] Get:46 http://deb.debian.org/debian unstable/main amd64 libtext-diff-perl all 1.45-2 [27.2 kB] Get:47 http://deb.debian.org/debian unstable/main amd64 libtest-differences-perl all 0.71-1 [17.9 kB] Get:48 http://deb.debian.org/debian unstable/main amd64 libsub-uplevel-perl all 0.2800-3 [14.0 kB] Get:49 http://deb.debian.org/debian unstable/main amd64 libtest-exception-perl all 0.43-3 [16.9 kB] Get:50 http://deb.debian.org/debian unstable/main amd64 libtest-warn-perl all 0.37-2 [14.5 kB] Get:51 http://deb.debian.org/debian unstable/main amd64 libtest-most-perl all 0.38-1 [25.1 kB] Get:52 http://deb.debian.org/debian unstable/main amd64 bioperl all 1.7.8-1 [246 kB] Get:53 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.20 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intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:65 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:66 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.20 [915 kB] Get:67 http://deb.debian.org/debian unstable/main amd64 libfakeroot amd64 1.36-1 [29.1 kB] Get:68 http://deb.debian.org/debian unstable/main amd64 fakeroot amd64 1.36-1 [75.1 kB] Get:69 http://deb.debian.org/debian unstable/main amd64 libfile-slurp-perl all 9999.32-2 [26.7 kB] Get:70 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.2.0-4 [837 kB] Get:71 http://deb.debian.org/debian unstable/main amd64 libhmmer2-dev amd64 2.3.2+dfsg-12 [96.7 kB] Get:72 http://deb.debian.org/debian unstable/main amd64 liblmdb0 amd64 0.9.31-1+b1 [44.8 kB] Get:73 http://deb.debian.org/debian unstable/main amd64 libmbedcrypto7t64 amd64 2.28.8-1 [284 kB] Get:74 http://deb.debian.org/debian unstable/main amd64 libmbedx509-1t64 amd64 2.28.8-1 [131 kB] Get:75 http://deb.debian.org/debian unstable/main amd64 libmbedtls14t64 amd64 2.28.8-1 [167 kB] Get:76 http://deb.debian.org/debian unstable/main amd64 libmodhmm0 amd64 1.0+dfsg-7 [79.8 kB] Get:77 http://deb.debian.org/debian unstable/main amd64 libmodhmm-dev amd64 1.0+dfsg-7 [79.8 kB] Get:78 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.63.0-1 [74.8 kB] Get:79 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-3 [36.2 kB] Get:80 http://deb.debian.org/debian unstable/main amd64 libsquid1t64 amd64 1.9g+cvs20050121-15.1 [76.1 kB] Get:81 http://deb.debian.org/debian unstable/main amd64 libsquid-dev amd64 1.9g+cvs20050121-15.1 [144 kB] Get:82 http://deb.debian.org/debian unstable/main amd64 libsvm3 amd64 3.24+ds-6+b1 [41.5 kB] Get:83 http://deb.debian.org/debian unstable/main amd64 libsvm-dev amd64 3.24+ds-6+b1 [62.1 kB] Get:84 http://deb.debian.org/debian unstable/main amd64 libsvmloc0 amd64 1.0+dfsg-7 [13.3 kB] Get:85 http://deb.debian.org/debian unstable/main amd64 libsvmloc-dev amd64 1.0+dfsg-7 [12.2 kB] Get:86 http://deb.debian.org/debian unstable/main amd64 libuv1t64 amd64 1.48.0-6 [148 kB] Get:87 http://deb.debian.org/debian unstable/main amd64 ncbi-data all 6.1.20170106+dfsg2-4 [3540 kB] Get:88 http://deb.debian.org/debian unstable/main amd64 ncbi-blast+ amd64 2.16.0+ds-6 [15.2 MB] Get:89 http://deb.debian.org/debian unstable/main amd64 ncbi-blast+-legacy all 2.16.0+ds-6 [10.4 kB] Get:90 http://deb.debian.org/debian unstable/main amd64 pftools amd64 3.2.12-1 [24.8 MB] Get:91 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-3 [29.9 kB] Get:92 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-3 [26.1 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 76.3 MB in 1s (95.4 MB/s) Selecting previously unselected package libpython3.12-minimal:amd64. (Reading database ... 22986 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.6-1_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.6-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.3-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.3-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.6-1_amd64.deb ... Unpacking python3.12-minimal (3.12.6-1) ... Setting up libpython3.12-minimal:amd64 (3.12.6-1) ... Setting up libexpat1:amd64 (2.6.3-1) ... Setting up python3.12-minimal (3.12.6-1) ... Selecting previously unselected package python3-minimal. (Reading database ... 23306 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.5-1+b1_amd64.deb ... Unpacking python3-minimal (3.12.5-1+b1) ... Selecting previously unselected package media-types. 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Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up liblmdb0:amd64 (0.9.31-1+b1) ... Setting up ncbi-data (6.1.20170106+dfsg2-4) ... Setting up libkeyutils1:amd64 (1.6.3-3) ... Setting up libfile-slurp-perl (9999.32-2) ... Setting up libicu72:amd64 (72.1-5) ... Setting up bsdextrautils (2.40.2-8) ... Setting up libmbedcrypto7t64:amd64 (2.28.8-1) ... Setting up libtest-deep-perl (1.204-1) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libalgorithm-diff-perl (1.201-1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libdebhelper-perl (13.20) ... Setting up libuv1t64:amd64 (1.48.0-6) ... Setting up libmagic1t64:amd64 (1:5.45-3) ... Setting up libnghttp2-14:amd64 (1.63.0-1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libcom-err2:amd64 (1.47.1-1) ... Setting up file (1:5.45-3) ... Setting up libmodhmm0:amd64 (1.0+dfsg-7) ... Setting up libfakeroot:amd64 (1.36-1) ... Setting up libelf1t64:amd64 (0.191-2) ... Setting up libkrb5support0:amd64 (1.21.3-3) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Sep 14 17:24:08 UTC 2024. Universal Time is now: Sat Sep 14 17:24:08 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up fakeroot (1.36-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Setting up libio-string-perl (1.08-4) ... Setting up autotools-dev (20220109.1) ... Setting up libclass-data-inheritable-perl (0.08-3) ... Setting up libpkgconf3:amd64 (1.8.1-3) ... Setting up libtext-diff-perl (1.45-2) ... Setting up autopoint (0.22.5-2) ... Setting up pkgconf-bin (1.8.1-3) ... Setting up libk5crypto3:amd64 (1.21.3-3) ... Setting up libgfortran5:amd64 (14.2.0-4) ... Setting up autoconf (2.72-3) ... Setting up libcapture-tiny-perl (0.48-2) ... Setting up dwz (0.15-1+b1) ... Setting up libdata-stag-perl (0.14-3) ... Setting up sensible-utils (0.0.24) ... Setting up pftools (3.2.12-1) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up libsub-uplevel-perl (0.2800-3) ... Setting up netbase (6.4) ... Configuration file '/etc/protocols' ==> File on system created by you or by a script. ==> File also in package provided by package maintainer. ==> Using current old file as you requested. Configuration file '/etc/services' ==> File on system created by you or by a script. ==> File also in package provided by package maintainer. ==> Using current old file as you requested. Setting up libdevel-stacktrace-perl (2.0500-1) ... Setting up libkrb5-3:amd64 (1.21.3-3) ... Setting up libbio-perl-perl (1.7.8-1) ... Setting up libhmmer2-dev:amd64 (2.3.2+dfsg-12) ... Setting up libmodhmm-dev:amd64 (1.0+dfsg-7) ... Setting up libxml2:amd64 (2.12.7+dfsg-3+b1) ... Setting up libsquid1t64:amd64 (1.9g+cvs20050121-15.1) ... Setting up libsvm3:amd64 (3.24+ds-6+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.22.5-2) ... Setting up libmbedx509-1t64:amd64 (2.28.8-1) ... Setting up libtool (2.4.7-7) ... Setting up libtest-warn-perl (0.37-2) ... Setting up libtest-differences-perl (0.71-1) ... Setting up libexception-class-perl (1.45-1) ... Setting up libsquid-dev (1.9g+cvs20050121-15.1) ... Setting up pkgconf:amd64 (1.8.1-3) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libtest-exception-perl (0.43-3) ... Setting up libsvmloc0:amd64 (1.0+dfsg-7) ... Setting up libsvm-dev:amd64 (3.24+ds-6+b1) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up libmbedtls14t64:amd64 (2.28.8-1) ... Setting up groff-base (1.23.0-5) ... Setting up libsvmloc-dev:amd64 (1.0+dfsg-7) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3) ... Setting up libtest-most-perl (0.38-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libnsl2:amd64 (1.3.0-3+b2) ... Setting up bioperl (1.7.8-1) ... Setting up libpython3.12-stdlib:amd64 (3.12.6-1) ... Setting up python3.12 (3.12.6-1) ... Setting up debhelper (13.20) ... Setting up libpython3-stdlib:amd64 (3.12.5-1+b1) ... Setting up python3 (3.12.5-1+b1) ... Setting up ncbi-blast+ (2.16.0+ds-6) ... Setting up ncbi-blast+-legacy (2.16.0+ds-6) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.40-2) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 6.9.7-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.9.7-1 (2024-06-27) amd64 (x86_64) Toolchain package versions: binutils_2.43.1-4 dpkg-dev_1.22.11 g++-13_13.3.0-6 g++-14_14.2.0-4 gcc-13_13.3.0-6 gcc-14_14.2.0-4 libc6-dev_2.40-2 libstdc++-13-dev_13.3.0-6 libstdc++-14-dev_14.2.0-4 libstdc++6_14.2.0-4 linux-libc-dev_6.10.9-1 Package versions: adduser_3.137 apt_2.9.8 autoconf_2.72-3 automake_1:1.16.5-1.3 autopoint_0.22.5-2 autotools-dev_20220109.1 base-files_13.5 base-passwd_3.6.4 bash_5.2.32-1+b1 binutils_2.43.1-4 binutils-common_2.43.1-4 binutils-x86-64-linux-gnu_2.43.1-4 bioperl_1.7.8-1 bsdextrautils_2.40.2-8 bsdutils_1:2.40.2-8 build-essential_12.10 bzip2_1.0.8-6 coreutils_9.4-3.1 cpp_4:14.1.0-2 cpp-13_13.3.0-6 cpp-13-x86-64-linux-gnu_13.3.0-6 cpp-14_14.2.0-4 cpp-14-x86-64-linux-gnu_14.2.0-4 cpp-x86-64-linux-gnu_4:14.1.0-2 dash_0.5.12-9 debconf_1.5.87 debhelper_13.20 debian-archive-keyring_2023.4 debianutils_5.20 dh-autoreconf_20 dh-strip-nondeterminism_1.14.0-1 diffutils_1:3.10-1 dirmngr_2.2.43-8+b1 dpkg_1.22.11 dpkg-dev_1.22.11 dwz_0.15-1+b1 eatmydata_131-2 fakeroot_1.36-1 file_1:5.45-3 findutils_4.10.0-3 g++_4:14.1.0-2 g++-13_13.3.0-6 g++-13-x86-64-linux-gnu_13.3.0-6 g++-14_14.2.0-4 g++-14-x86-64-linux-gnu_14.2.0-4 g++-x86-64-linux-gnu_4:14.1.0-2 gcc_4:14.1.0-2 gcc-13_13.3.0-6 gcc-13-base_13.3.0-6 gcc-13-x86-64-linux-gnu_13.3.0-6 gcc-14_14.2.0-4 gcc-14-base_14.2.0-4 gcc-14-x86-64-linux-gnu_14.2.0-4 gcc-x86-64-linux-gnu_4:14.1.0-2 gettext_0.22.5-2 gettext-base_0.22.5-2 gnupg_2.2.43-8 gnupg-l10n_2.2.43-8 gnupg-utils_2.2.43-8+b1 gpg_2.2.43-8+b1 gpg-agent_2.2.43-8+b1 gpg-wks-client_2.2.43-8+b1 gpgconf_2.2.43-8+b1 gpgsm_2.2.43-8+b1 gpgv_2.2.43-8+b1 grep_3.11-4 groff-base_1.23.0-5 gzip_1.12-1.1 hostname_3.23+nmu2 init-system-helpers_1.66 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-2 libalgorithm-diff-perl_1.201-1 libapt-pkg6.0t64_2.9.8 libarchive-zip-perl_1.68-1 libasan8_14.2.0-4 libassuan0_2.5.6-1+b1 libassuan9_3.0.1-2 libatomic1_14.2.0-4 libattr1_1:2.5.2-1 libaudit-common_1:4.0.1-1 libaudit1_1:4.0.1-1 libbinutils_2.43.1-4 libbio-perl-perl_1.7.8-1 libblkid1_2.40.2-8 libbsd0_0.12.2-1 libbz2-1.0_1.0.8-6 libc-bin_2.40-2 libc-dev-bin_2.40-2 libc-l10n_2.40-2 libc6_2.40-2 libc6-dev_2.40-2 libcap-ng0_0.8.5-2 libcap2_1:2.66-5 libcapture-tiny-perl_0.48-2 libcc1-0_14.2.0-4 libclass-data-inheritable-perl_0.08-3 libcom-err2_1.47.1-1 libcrypt-dev_1:4.4.36-5 libcrypt1_1:4.4.36-5 libctf-nobfd0_2.43.1-4 libctf0_2.43.1-4 libdata-stag-perl_0.14-3 libdb5.3t64_5.3.28+dfsg2-7 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netbase_6.4 openssl-provider-legacy_3.3.2-1 passwd_1:4.16.0-4 patch_2.7.6-7 perl_5.40.0-5 perl-base_5.40.0-5 perl-modules-5.38_5.38.2-5 perl-modules-5.40_5.40.0-5 pftools_3.2.12-1 pinentry-curses_1.2.1-4+b1 pkgconf_1.8.1-3 pkgconf-bin_1.8.1-3 po-debconf_1.0.21+nmu1 python3_3.12.5-1+b1 python3-minimal_3.12.5-1+b1 python3.12_3.12.6-1 python3.12-minimal_3.12.6-1 readline-common_8.2-5 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.24 sysvinit-utils_3.10-2 tar_1.35+dfsg-3 tzdata_2024a-4 usr-is-merged_39 util-linux_2.40.2-8 xz-utils_5.6.2-2 zlib1g_1:1.3.dfsg+really1.3.1-1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: psortb Binary: psortb Architecture: any Version: 3.0.6+dfsg-4 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Étienne Mollier Homepage: https://www.psort.org/ Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/psortb Vcs-Git: https://salsa.debian.org/med-team/psortb.git Testsuite: autopkgtest-pkg-perl Build-Depends: debhelper-compat (= 13), libsvm-dev, bioperl, ncbi-blast+-legacy, libsquid-dev, libhmmer2-dev, libsvmloc-dev, libmodhmm-dev, pkgconf, pftools Package-List: psortb deb science optional arch=any Checksums-Sha1: c47d0ec328df75f2151dd6d5b5840768006519f8 17036876 psortb_3.0.6+dfsg.orig.tar.xz c10819ffb3b3d31ca99a66f9768493ed46e5a541 7480 psortb_3.0.6+dfsg-4.debian.tar.xz Checksums-Sha256: ed32aa0240bb03daed228b32614a53c146afba6ca66fd087702315d75e23f751 17036876 psortb_3.0.6+dfsg.orig.tar.xz fc09ccbf18a26cefd75e8c6030e192878b94b251a6a3206614931820ef6344d0 7480 psortb_3.0.6+dfsg-4.debian.tar.xz Files: c4feab06d3031fecac1ab90258550209 17036876 psortb_3.0.6+dfsg.orig.tar.xz dbe47096a741a5132191480aa07bb7d4 7480 psortb_3.0.6+dfsg-4.debian.tar.xz Dgit: 4806a2aae47b085aac7d4851a89b803020876c96 debian archive/debian/3.0.6+dfsg-4 https://git.dgit.debian.org/psortb -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmZS6scUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdry2hAAiLUm7A9Zl9L7P13u8spjnNXnKq4o lnUhE1DiKRk798zry3EmPP7q7rynIQJuDoeGNwIRNlNblDxsy7dydcglnUY40uXk qk2rHKooIryioJPSjJdxBElF7+EW70ajIidgWpzR3BNfyVIVF5ivpcIjfrSzmpvf 8GjEO4H9YBnl2AvBWo+wYi+1YYEC1zneDXyOtQ7c1sjEvNXoex0Ud2DEQ2cD+iBq FROVjIN+UUaU0aqxUWd5z+y4mZkM8zW6/VEepv9a4oxb3lIqAZ5Q/1tWxgm0Ww9B I2AMiJNMOd74NsMGKa7eRqYYOXDMVzDUihqBjuPZlAEmQ44ulSvnwNHUs7jRdYM6 lq6hk+w+pTGEeMP3CwkOls77C4QvHTuap/Mk+T5M99cINNWPXMjNmZ1PGvwbIs12 QmeKh+uoQiYRk7RyljqLyVFMrlczC5Pdk9bsLyJm+fQer3ePV32GxQw02ok1ymje OdNvyUFCuBwpHQto53DzRfaTXVkrMGIv1XsHlutIX5CTaXNL74gYAcSiZdCswNhj cZyyVCDmEeuhuIJKsw8rv9X9G/8OMRzRFNrttzz/lWqUQd+aK8/F7eQdYjA8TOaa UrmWZYcKWcmFlq4AD4OCILT4+KB9LY93sj2Ap382mDf+Z+Y2MGVI038u5pokY0cq NULN/MYhxVzrWxE= =bHrm -----END PGP SIGNATURE----- gpgv: Signature made Sun May 26 07:54:47 2024 UTC gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./psortb_3.0.6+dfsg-4.dsc: no acceptable signature found dpkg-source: info: extracting psortb in /<> dpkg-source: info: unpacking psortb_3.0.6+dfsg.orig.tar.xz dpkg-source: info: unpacking psortb_3.0.6+dfsg-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying biosquid_includes.patch dpkg-source: info: applying fix_hmmer_interface.patch dpkg-source: info: applying fix_build_Algorithm-SVM.patch dpkg-source: info: applying remove-bundled-party-libsvm.patch dpkg-source: info: applying path_to_conf.patch dpkg-source: info: applying fix_module_path.patch dpkg-source: info: applying add_missing_header.patch Check disk space ---------------- Sufficient free space for build Hack binNMU version ------------------- Created changelog entry for binNMU version 3.0.6+dfsg-4+b1 +------------------------------------------------------------------------------+ | Starting Timed Build Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network psortb_3.0.6+dfsg-4 perl-5.40 amd64 ---------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network psortb_3.0.6+dfsg-4 perl-5.40 amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANG=en_GB.UTF-8 LANGUAGE=en_GB:en LC_ALL=C.UTF-8 LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so LOGNAME=debomatic PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games PWD=/<> SCHROOT_ALIAS_NAME=perl-5.40-amd64-debomatic SCHROOT_CHROOT_NAME=perl-5.40-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=110 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=perl-5.40-amd64-debomatic-265c8ee1-a5fd-41ef-81d1-84b5afe43ef6 SCHROOT_UID=1002 SCHROOT_USER=debomatic SHELL=/bin/sh USER=debomatic dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -mDebian Perl autobuilder -B -rfakeroot -Zxz dpkg-buildpackage: info: source package psortb dpkg-buildpackage: info: source version 3.0.6+dfsg-4+b1 dpkg-buildpackage: info: source distribution perl-5.40 dpkg-source -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' dh_auto_clean if [ -x psort/bin/psort.debsave ] ; then \ mv psort/bin/psort.debsave psort/bin/psort ; \ fi make[1]: Leaving directory '/<>' dh_clean debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a debian/rules override_dh_auto_configure make[1]: Entering directory '/<>' cp -a psort/bin/psort psort/bin/psort.debsave dh_auto_configure /usr/bin/perl Makefile.PL INSTALLDIRS=vendor "OPTIMIZE=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2" "LD=x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now" External Module XML::RPC, XML Based RPC client, is not installed on this computer. The XML::RPC in PSortb needs it for making calls to remote PSortb servers, if you don't plan to do this, ignore this warning We think we've found blastall, please enter the path if this isn't correct [/usr/bin/] /usr/bin/ We think we've found pfscan, please enter the path if this isn't correct [/usr/bin/] /usr/bin/ Where do you plan to install the psort configuration files? [/usr/local/psortb] /usr/local/psortb Checking if your kit is complete... Looks good hmmer was not found in the dynamic linker path, is there somewhere else we should check? [/usr/local/lib64] /usr/local/lib64 We're still not finding hmmer either in your dynamic linker path (/etc/ld.so.conf) or in /usr/local/lib64. Do you want to continue anyways? [Y/n] [Y] Y squid was not found in the dynamic linker path, is there somewhere else we should check? [/usr/local/lib64] /usr/local/lib64 We're still not finding squid either in your dynamic linker path (/etc/ld.so.conf) or in /usr/local/lib64. Do you want to continue anyways? [Y/n] [Y] Y Checking if your kit is complete... Looks good Writing MYMETA.yml and MYMETA.json svmloc was not found in the dynamic linker path, is there somewhere else we should check? [/usr/local/lib64] /usr/local/lib64 We're still not finding svmloc either in your dynamic linker path (/etc/ld.so.conf) or in /usr/local/lib64. Do you want to continue anyways? [Y/n] [Y] Y Checking if your kit is complete... Looks good Writing MYMETA.yml and MYMETA.json modhmm was not found in the dynamic linker path, is there somewhere else we should check? [/usr/local/lib64] /usr/local/lib64 We're still not finding modhmm either in your dynamic linker path (/etc/ld.so.conf) or in /usr/local/lib64. Do you want to continue anyways? [Y/n] [Y] Y Writing MYMETA.yml and MYMETA.json Generating a Unix-style Makefile Writing Makefile for Bio::Tools::PSort Writing MYMETA.yml and MYMETA.json Updating psort/bin/psort with path hints Making sclblast databases Building a new DB, current time: 09/14/2024 17:24:19 New DB name: /<>/psort/conf/analysis/sclblast/gramneg/sclblast New DB title: sclblast Sequence type: Protein Keep MBits: T Maximum file size: 3000000000B BLAST Database creation error: Error: Duplicate seq_ids are found: LCL|6226665 Program failed, try executing the command manually. Building a new DB, current time: 09/14/2024 17:24:19 New DB name: /<>/psort/conf/analysis/sclblast/grampos/sclblast New DB title: sclblast Sequence type: Protein Keep MBits: T Maximum file size: 3000000000B BLAST Database creation error: Error: Duplicate seq_ids are found: LCL|145559529 Program failed, try executing the command manually. Building a new DB, current time: 09/14/2024 17:24:20 New DB name: /<>/psort/conf/analysis/sclblast/archaea/sclblast New DB title: sclblast Sequence type: Protein Keep MBits: T Maximum file size: 3000000000B FASTA-Reader: Ignoring invalid residues at position(s): On line 46049: 38 FASTA-Reader: Ignoring invalid residues at position(s): On line 87237: 23 FASTA-Reader: Title ends with at least 50 valid amino acid characters. Was the sequence accidentally put in the title line? FASTA-Reader: Ignoring invalid residues at position(s): On line 87252: 4 FASTA-Reader: Ignoring invalid residues at position(s): On line 87263: 8 BLAST Database creation error: Error: Duplicate seq_ids are found: LCL|15596641 Program failed, try executing the command manually. Ready for make, next steps you must run: $ make $ make test $ make install RECOMMENDED: cp -r psort /usr/local/psortb PSortb will then be available at /usr/local/psortb/bin/psort or in your path depending on your configuration make[1]: Leaving directory '/<>' debian/rules override_dh_auto_build make[1]: Entering directory '/<>' # 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 -j2 make[2]: Entering directory '/<>' make[3]: Entering directory '/<>/algorithm-hmm' cp lib/Bio/Tools/PSort/Report/Formatter/long.pm blib/lib/Bio/Tools/PSort/Report/Formatter/long.pm cp lib/Bio/Tools/PSort/Module/SCLBlast.pm blib/lib/Bio/Tools/PSort/Module/SCLBlast.pm cp lib/Bio/Tools/PSort/Module/OutputI.pm blib/lib/Bio/Tools/PSort/Module/OutputI.pm cp lib/Bio/Tools/PSort/Report/Formatter/terse.pm blib/lib/Bio/Tools/PSort/Report/Formatter/terse.pm cp lib/Bio/Tools/PSort/Module/Signal.pm blib/lib/Bio/Tools/PSort/Module/Signal.pm cp lib/Bio/Tools/PSort/Module/SVMLoc.pm blib/lib/Bio/Tools/PSort/Module/SVMLoc.pm cp lib/Bio/Tools/PSort/Module/SVMLocApache.pm blib/lib/Bio/Tools/PSort/Module/SVMLocApache.pm cp lib/Bio/Tools/PSort/Profile/Match.pm blib/lib/Bio/Tools/PSort/Profile/Match.pm cp lib/Bio/Tools/PSort/Constants.pm blib/lib/Bio/Tools/PSort/Constants.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/Motif/Pattern.pm blib/lib/Bio/Tools/Motif/Pattern.pm cp lib/Bio/Tools/PSort/Module/ModHMM.pm blib/lib/Bio/Tools/PSort/Module/ModHMM.pm cp lib/Bio/Tools/PSort/Module/HMMTOP.pm blib/lib/Bio/Tools/PSort/Module/HMMTOP.pm cp lib/Bio/Tools/PSort/Module/Bayesian.pm blib/lib/Bio/Tools/PSort/Module/Bayesian.pm cp lib/Bio/Tools/PSort/Install.pm blib/lib/Bio/Tools/PSort/Install.pm cp lib/Bio/Tools/PSort/Module/Null.pm blib/lib/Bio/Tools/PSort/Module/Null.pm cp lib/Bio/Tools/Motif.pm blib/lib/Bio/Tools/Motif.pm cp lib/Bio/Tools/PSort/Pathway.pm blib/lib/Bio/Tools/PSort/Pathway.pm cp lib/Bio/Tools/PSort/Report/Result.pm blib/lib/Bio/Tools/PSort/Report/Result.pm cp lib/Bio/Tools/PSort/ModuleI.pm blib/lib/Bio/Tools/PSort/ModuleI.pm cp lib/Bio/Tools/PSort/Profile.pm blib/lib/Bio/Tools/PSort/Profile.pm cp lib/Bio/Tools/PSort/Module/Rules.pm blib/lib/Bio/Tools/PSort/Module/Rules.pm cp lib/Bio/Tools/PSort/Module/InputI.pm blib/lib/Bio/Tools/PSort/Module/InputI.pm cp lib/Bio/Tools/PSort/Module/AnalysisI.pm blib/lib/Bio/Tools/PSort/Module/AnalysisI.pm cp lib/Bio/Tools/PSort/Report.pm blib/lib/Bio/Tools/PSort/Report.pm cp lib/Bio/Tools/PSort.pm blib/lib/Bio/Tools/PSort.pm cp lib/Bio/Tools/Motif/Match.pm blib/lib/Bio/Tools/Motif/Match.pm cp lib/Bio/Tools/PSort/Module/Motif.pm blib/lib/Bio/Tools/PSort/Module/Motif.pm cp lib/Bio/Tools/PSort/Module/Profile.pm blib/lib/Bio/Tools/PSort/Module/Profile.pm cp lib/Bio/Tools/PSort/Module/OMPMotif.pm blib/lib/Bio/Tools/PSort/Module/OMPMotif.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/Signal/Report.pm blib/lib/Bio/Tools/Signal/Report.pm cp lib/Bio/Tools/PSort/XMLRPC/Client.pm blib/lib/Bio/Tools/PSort/XMLRPC/Client.pm cp lib/Bio/Tools/Signal.pm blib/lib/Bio/Tools/Signal.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/Run/HMMTOP/Helix.pm blib/lib/Bio/Tools/Run/HMMTOP/Helix.pm cp lib/Bio/Tools/Run/SCLBlastLocal.pm blib/lib/Bio/Tools/Run/SCLBlastLocal.pm cp lib/Bio/Tools/Run/HMMTOP/Report.pm blib/lib/Bio/Tools/Run/HMMTOP/Report.pm cp lib/Bio/Tools/Run/HMMTOP.pm blib/lib/Bio/Tools/Run/HMMTOP.pm Running Mkbootstrap for HMM () chmod 644 "HMM.bs" "/usr/bin/perl" "/usr/share/perl/5.40.0/ExtUtils/xsubpp" -C++ -typemap '/usr/share/perl/5.40/ExtUtils/typemap' -typemap '/<>/algorithm-hmm/typemap' HMM.xs > HMM.xsc cp lib/Algorithm/HMM.pm ../blib/lib/Algorithm/HMM.pm AutoSplitting ../blib/lib/Algorithm/HMM.pm (../blib/lib/auto/Algorithm/HMM) cp lib/Algorithm/HMM/Hit.pm ../blib/lib/Algorithm/HMM/Hit.pm cp lib/Algorithm/HMM/Hit/Domain.pm ../blib/lib/Algorithm/HMM/Hit/Domain.pm cp lib/Algorithm/HMM/Report.pm ../blib/lib/Algorithm/HMM/Report.pm cp lib/Algorithm/HMM/Hit/Global.pm ../blib/lib/Algorithm/HMM/Hit/Global.pm g++ -c -Isrc/include `pkg-config --cflags libsquid` `pkg-config --cflags libhmmer2` -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"0.02\" -DXS_VERSION=\"0.02\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE" hmm-binding.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ Please specify prototyping behavior for HMM.xs (see perlxs manual) mv HMM.xsc HMM.c "/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- HMM.bs ../blib/arch/auto/Algorithm/HMM/HMM.bs 644 g++ -c -Isrc/include `pkg-config --cflags libsquid` `pkg-config --cflags libhmmer2` -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"0.02\" -DXS_VERSION=\"0.02\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE" HMM.c cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ hmm-binding.cpp: In member function ‘HMMReport* HMM::search(char*)’: hmm-binding.cpp:136:71: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 136 | PostprocessSignificantHit(ghit, dhit, trace, model, dseq, seqlen, "SEQ", | ^~~~~ rm -f ../blib/arch/auto/Algorithm/HMM/HMM.so x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -shared -L/usr/local/lib -fstack-protector-strong HMM.o hmm-binding.o -o ../blib/arch/auto/Algorithm/HMM/HMM.so \ -lm -lpthread -lstdc++ -lhmmer -lsquid \ chmod 755 ../blib/arch/auto/Algorithm/HMM/HMM.so Manifying 5 pod documents make[3]: Leaving directory '/<>/algorithm-hmm' make[3]: Entering directory '/<>/bio-tools-psort-svmloc' Running Mkbootstrap for SVMLoc () 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 "/usr/bin/perl" "/usr/share/perl/5.40.0/ExtUtils/xsubpp" -C++ -typemap '/usr/share/perl/5.40/ExtUtils/typemap' -typemap '/<>/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 Please specify prototyping behavior for SVMLoc.xs (see perlxs manual) mv SVMLoc.xsc SVMLoc.c g++ -c -Wall -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"0.01\" -DXS_VERSION=\"0.01\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE" SVMLoc.c cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ rm -f ../blib/arch/auto/Bio/Tools/PSort/SVMLoc/SVMLoc.so x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -shared -L/usr/local/lib -fstack-protector-strong SVMLoc.o -o ../blib/arch/auto/Bio/Tools/PSort/SVMLoc/SVMLoc.so \ -lsvmloc -lm -lsvm -lstdc++ \ chmod 755 ../blib/arch/auto/Bio/Tools/PSort/SVMLoc/SVMLoc.so Manifying 2 pod documents make[3]: Leaving directory '/<>/bio-tools-psort-svmloc' make[3]: Entering directory '/<>/bio-tools-psort-modhmm' Running Mkbootstrap for ModHMM () chmod 644 "ModHMM.bs" "/usr/bin/perl" "/usr/share/perl/5.40.0/ExtUtils/xsubpp" -typemap '/usr/share/perl/5.40/ExtUtils/typemap' -typemap '/<>/bio-tools-psort-modhmm/typemap' modhmm.xs > modhmm.xsc 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) cc -c -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"0.01\" -DXS_VERSION=\"0.01\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE" binding.c mv modhmm.xsc modhmm.c "/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- ModHMM.bs ../blib/arch/auto/Bio/Tools/PSort/ModHMM/ModHMM.bs 644 cc -c -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"0.01\" -DXS_VERSION=\"0.01\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE" modhmm.c rm -f ../blib/arch/auto/Bio/Tools/PSort/ModHMM/ModHMM.so x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -shared -L/usr/local/lib -fstack-protector-strong modhmm.o binding.o -o ../blib/arch/auto/Bio/Tools/PSort/ModHMM/ModHMM.so \ -lm -lstdc++ -lmodhmm \ chmod 755 ../blib/arch/auto/Bio/Tools/PSort/ModHMM/ModHMM.so Manifying 1 pod document make[3]: Leaving directory '/<>/bio-tools-psort-modhmm' Manifying 18 pod documents make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' dh_auto_test -a make -j2 test TEST_VERBOSE=1 make[1]: Entering directory '/<>' make[2]: Entering directory '/<>/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 '/<>/algorithm-hmm' make[2]: Entering directory '/<>/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 '/<>/bio-tools-psort-svmloc' make[2]: Entering directory '/<>/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 '/<>/bio-tools-psort-modhmm' make[2]: Entering directory '/<>/algorithm-hmm' "/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- HMM.bs ../blib/arch/auto/Algorithm/HMM/HMM.bs 644 PERL_DL_NONLAZY=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(1, '../blib/lib', '../blib/arch')" t/*.t t/hmm.t .. 1..5 ok 1 - use Algorithm::HMM; ok 2 Creating new Algorithm::HMM ok 3 - Ensuring we could load a model Saving model... ok 4 - Testing saving a model Loading saved model... ok 5 - Testing reloading a model ok All tests successful. Files=1, Tests=5, 0 wallclock secs ( 0.02 usr 0.00 sys + 0.04 cusr 0.01 csys = 0.07 CPU) Result: PASS make[2]: Leaving directory '/<>/algorithm-hmm' make[2]: Entering directory '/<>/bio-tools-psort-svmloc' "/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- SVMLoc.bs ../blib/arch/auto/Bio/Tools/PSort/SVMLoc/SVMLoc.bs 644 PERL_DL_NONLAZY=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(1, '../blib/lib', '../blib/arch')" t/*.t t/svmloc.t .. 1..15 ok 1 - use Bio::Tools::PSort::SVMLoc; ok 2 - use Bio::Tools::PSort::SVMLoc::DataSet; ok 3 - Loaded SVMLoc Creating new Bio::Tools::PSort::SVMLoc ok 4 - Creating SVMLoc object Checking predictions on loaded model ok 5 - Classify seq 1 ok 6 - Classify seq 2 ok 7 - Classify seq 3 Creating second Bio::Tools::PSort::SVMLoc ok 8 - Creating SVMLoc object 2 Creating new Bio::Tools::PSort::SVMLoc::DataSet objects ok 9 - Dataset 1 created ok 10 - Dataset 2 created ok 11 - Dataset 3 created Adding attributes to Bio::Tools::PSort::SVMLoc::DataSet objects ok 12 Checking predictions on second loaded model ok 13 - Classify seq 1 on model 2 ok 14 - Classify seq 2 on model 2 ok 15 - Classify seq 3 on model 2 Everything looks ok! ok All tests successful. Files=1, Tests=15, 0 wallclock secs ( 0.01 usr 0.01 sys + 0.15 cusr 0.02 csys = 0.19 CPU) Result: PASS make[2]: Leaving directory '/<>/bio-tools-psort-svmloc' make[2]: Entering directory '/<>/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, 1 wallclock secs ( 0.02 usr 0.00 sys + 0.11 cusr 0.01 csys = 0.14 CPU) Result: PASS make[2]: Leaving directory '/<>/bio-tools-psort-modhmm' PERL_DL_NONLAZY=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(1, 'blib/lib', 'blib/arch')" t/*.t t/psort.t .. 1..2 ok 1 - PSort module loaded Creating new Bio::Tools::PSort ok 2 - PSort object made ok All tests successful. Files=1, Tests=2, 0 wallclock secs ( 0.01 usr 0.01 sys + 0.07 cusr 0.01 csys = 0.10 CPU) Result: PASS make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_prep -a dh_auto_install --destdir=debian/psortb/ -a make -j2 install DESTDIR=/<>/psortb-3.0.6\+dfsg/debian/psortb AM_UPDATE_INFO_DIR=no PREFIX=/usr make[1]: Entering directory '/<>' make[2]: Entering directory '/<>/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 '/<>/algorithm-hmm' make[2]: Entering directory '/<>/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 '/<>/bio-tools-psort-svmloc' make[2]: Entering directory '/<>/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 '/<>/bio-tools-psort-modhmm' Manifying 18 pod documents Files found in blib/arch: installing files in blib/lib into architecture dependent library tree Installing /<>/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/auto/Bio/Tools/PSort/ModHMM/ModHMM.so Installing /<>/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/auto/Bio/Tools/PSort/SVMLoc/SVMLoc.so Installing /<>/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/auto/Algorithm/HMM/HMM.so Installing /<>/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/auto/Bio/Tools/PSort/ModHMM/autosplit.ix Installing /<>/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/auto/Bio/Tools/PSort/SVMLoc/autosplit.ix Installing /<>/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/auto/Algorithm/HMM/autosplit.ix Installing /<>/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/SVMLoc.pm Installing /<>/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/Signal.pm Installing /<>/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort.pm Installing /<>/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/Motif.pm Installing /<>/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/Run/SCLBlast.pm Installing /<>/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/Run/HMMTOP.pm Installing /<>/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/Run/SCLBlastLocal.pm Installing /<>/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/Run/SCLBlast/Report.pm Installing /<>/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/Run/SCLBlast/Hit.pm Installing /<>/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/Run/HMMTOP/Report.pm Installing /<>/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/Run/HMMTOP/Helix.pm Installing /<>/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/ModHMM.pm Installing /<>/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/Install.pm Installing /<>/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/Pathway.pm Installing /<>/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/Constants.pm Installing /<>/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/Report.pm Installing /<>/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/SVMLoc.pm Installing /<>/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/Profile.pm Installing /<>/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/ModuleI.pm Installing /<>/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/Profile/Match.pm Installing /<>/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/SVMLoc/DataSet.pm Installing /<>/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/Report/Formatter.pm Installing /<>/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/Report/Result.pm Installing /<>/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/Report/Formatter/normal.pm Installing /<>/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/Report/Formatter/long.pm Installing /<>/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/Report/Formatter/terse.pm Installing /<>/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/Report/Formatter/html.pm Installing /<>/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/XMLRPC/Client.pm Installing /<>/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/Module/Null.pm Installing /<>/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/Module/AnalysisI.pm Installing /<>/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/Module/ModHMM.pm Installing /<>/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/Module/SCLBlast.pm Installing /<>/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/Module/OutputI.pm Installing /<>/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/Module/Bayesian.pm Installing /<>/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/Module/SVMLoc.pm Installing /<>/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/Module/HMMTOP.pm Installing /<>/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/Module/Rules.pm Installing /<>/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/Module/Signal.pm Installing /<>/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/Module/Profile.pm Installing /<>/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/Module/OMPMotif.pm Installing /<>/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/Module/SVMLocApache.pm Installing /<>/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/Module/Motif.pm Installing /<>/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/PSort/Module/InputI.pm Installing /<>/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/Motif/Match.pm Installing /<>/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/Motif/Pattern.pm Installing /<>/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/Tools/Signal/Report.pm Installing /<>/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Algorithm/HMM.pm Installing /<>/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Algorithm/HMM/Report.pm Installing /<>/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Algorithm/HMM/Hit.pm Installing /<>/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Algorithm/HMM/Hit/Domain.pm Installing /<>/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.40/Algorithm/HMM/Hit/Global.pm Installing /<>/debian/psortb/usr/share/man/man3/Bio::Tools::PSort::ModHMM.3pm Installing /<>/debian/psortb/usr/share/man/man3/Bio::Tools::PSort::Module::AnalysisI.3pm Installing /<>/debian/psortb/usr/share/man/man3/Bio::Tools::Run::HMMTOP.3pm Installing /<>/debian/psortb/usr/share/man/man3/Bio::Tools::Signal.3pm Installing /<>/debian/psortb/usr/share/man/man3/Bio::Tools::PSort::SVMLoc.3pm Installing /<>/debian/psortb/usr/share/man/man3/Bio::Tools::PSort::Pathway.3pm Installing /<>/debian/psortb/usr/share/man/man3/Bio::Tools::Motif.3pm Installing /<>/debian/psortb/usr/share/man/man3/Bio::Tools::PSort::SVMLoc::DataSet.3pm Installing /<>/debian/psortb/usr/share/man/man3/Algorithm::HMM::Hit::Domain.3pm Installing /<>/debian/psortb/usr/share/man/man3/Bio::Tools::PSort::Module::OutputI.3pm Installing /<>/debian/psortb/usr/share/man/man3/Bio::Tools::PSort::Module::InputI.3pm Installing /<>/debian/psortb/usr/share/man/man3/Algorithm::HMM::Report.3pm Installing /<>/debian/psortb/usr/share/man/man3/Bio::Tools::PSort::Module::Motif.3pm Installing /<>/debian/psortb/usr/share/man/man3/Bio::Tools::SVMLoc.3pm Installing /<>/debian/psortb/usr/share/man/man3/Bio::Tools::PSort::Module::Null.3pm Installing /<>/debian/psortb/usr/share/man/man3/Bio::Tools::Motif::Pattern.3pm Installing /<>/debian/psortb/usr/share/man/man3/Bio::Tools::PSort.3pm Installing /<>/debian/psortb/usr/share/man/man3/Bio::Tools::PSort::Module::Profile.3pm Installing /<>/debian/psortb/usr/share/man/man3/Bio::Tools::PSort::Module::OMPMotif.3pm Installing /<>/debian/psortb/usr/share/man/man3/Algorithm::HMM::Hit::Global.3pm Installing /<>/debian/psortb/usr/share/man/man3/Bio::Tools::PSort::Profile::Match.3pm Installing /<>/debian/psortb/usr/share/man/man3/Bio::Tools::PSort::Profile.3pm Installing /<>/debian/psortb/usr/share/man/man3/Bio::Tools::PSort::ModuleI.3pm Installing /<>/debian/psortb/usr/share/man/man3/Algorithm::HMM.3pm Installing /<>/debian/psortb/usr/share/man/man3/Bio::Tools::Motif::Match.3pm Installing /<>/debian/psortb/usr/share/man/man3/Algorithm::HMM::Hit.3pm make[1]: Leaving directory '/<>' dh_install -a dh_installdocs -a dh_installchangelogs -a dh_installman -a dh_lintian -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a debian/rules override_dh_fixperms make[1]: Entering directory '/<>' dh_fixperms chmod +x debian/psortb/usr/lib/psort/conf/analysis/signal/archaea/check-sig make[1]: Leaving directory '/<>' dh_missing -a dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib64/ld-linux-x86-64.so.2 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib64/ld-linux-x86-64.so.2.usr-is-merged dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'psortb' in '../psortb_3.0.6+dfsg-4+b1_amd64.deb'. dpkg-deb: building package 'psortb-dbgsym' in '../psortb-dbgsym_3.0.6+dfsg-4+b1_amd64.deb'. dpkg-genbuildinfo --build=any -O../psortb_3.0.6+dfsg-4+b1_amd64.buildinfo dpkg-genchanges --build=any -mDebian Perl autobuilder -O../psortb_3.0.6+dfsg-4+b1_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source -Zxz --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2024-09-14T17:26:08Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ psortb_3.0.6+dfsg-4+b1_amd64.changes: ------------------------------------- Format: 1.8 Date: Sat, 14 Sep 2024 17:24:13 +0000 Source: psortb (3.0.6+dfsg-4) Binary: psortb psortb-dbgsym Binary-Only: yes Architecture: amd64 Version: 3.0.6+dfsg-4+b1 Distribution: perl-5.40 Urgency: low Maintainer: Debian Perl autobuilder Changed-By: Debian Perl autobuilder Description: psortb - bacterial localization prediction tool Changes: psortb (3.0.6+dfsg-4+b1) perl-5.40; urgency=low, binary-only=yes . * Binary-only non-maintainer upload for amd64; no source changes. * Rebuild for Perl 5.40 Checksums-Sha1: fc6033a34790cd33c7036dbbfa441a692f7cfd28 159732 psortb-dbgsym_3.0.6+dfsg-4+b1_amd64.deb 8d3e1ff2f2380a9e2a7f342e809efda27db9c5e5 7349 psortb_3.0.6+dfsg-4+b1_amd64.buildinfo af9b69842b1e33e8e5149523138f576195e94ef1 16374528 psortb_3.0.6+dfsg-4+b1_amd64.deb Checksums-Sha256: c7042c62812efafdb0d7d96cebc42e496d29aa393ef7a283d3935a79908ed47b 159732 psortb-dbgsym_3.0.6+dfsg-4+b1_amd64.deb 9adf79b1b81ad68c8c3b1857eca8d52d775210075f1aca8c6db3998d1f36afa7 7349 psortb_3.0.6+dfsg-4+b1_amd64.buildinfo 6a7d7012d6adc754a6a8f1a9c504f0fa226175d1ab0ed8c86b9a7f7c3d3023d7 16374528 psortb_3.0.6+dfsg-4+b1_amd64.deb Files: b373169b7293bffa7f16c75688e425f8 159732 debug optional psortb-dbgsym_3.0.6+dfsg-4+b1_amd64.deb 26c4b35ab201c15b917f5da38db3fd59 7349 science optional psortb_3.0.6+dfsg-4+b1_amd64.buildinfo 9a4c73dd81dbe098b43a9e82672a50a9 16374528 science optional psortb_3.0.6+dfsg-4+b1_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: psortb (3.0.6+dfsg-4) Binary: psortb psortb-dbgsym Architecture: amd64 Version: 3.0.6+dfsg-4+b1 Binary-Only-Changes: psortb (3.0.6+dfsg-4+b1) perl-5.40; urgency=low, binary-only=yes . * Binary-only non-maintainer upload for amd64; no source changes. * Rebuild for Perl 5.40 . -- Debian Perl autobuilder Sat, 14 Sep 2024 17:24:13 +0000 Checksums-Md5: b373169b7293bffa7f16c75688e425f8 159732 psortb-dbgsym_3.0.6+dfsg-4+b1_amd64.deb 9a4c73dd81dbe098b43a9e82672a50a9 16374528 psortb_3.0.6+dfsg-4+b1_amd64.deb Checksums-Sha1: fc6033a34790cd33c7036dbbfa441a692f7cfd28 159732 psortb-dbgsym_3.0.6+dfsg-4+b1_amd64.deb af9b69842b1e33e8e5149523138f576195e94ef1 16374528 psortb_3.0.6+dfsg-4+b1_amd64.deb Checksums-Sha256: c7042c62812efafdb0d7d96cebc42e496d29aa393ef7a283d3935a79908ed47b 159732 psortb-dbgsym_3.0.6+dfsg-4+b1_amd64.deb 6a7d7012d6adc754a6a8f1a9c504f0fa226175d1ab0ed8c86b9a7f7c3d3023d7 16374528 psortb_3.0.6+dfsg-4+b1_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Sat, 14 Sep 2024 17:26:08 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.72-3), automake (= 1:1.16.5-1.3), autopoint (= 0.22.5-2), autotools-dev (= 20220109.1), base-files (= 13.5), base-passwd (= 3.6.4), bash (= 5.2.32-1+b1), binutils (= 2.43.1-4), binutils-common (= 2.43.1-4), binutils-x86-64-linux-gnu (= 2.43.1-4), bioperl (= 1.7.8-1), bsdextrautils (= 2.40.2-8), bsdutils (= 1:2.40.2-8), build-essential (= 12.10), bzip2 (= 1.0.8-6), coreutils (= 9.4-3.1), cpp (= 4:14.1.0-2), cpp-13 (= 13.3.0-6), cpp-13-x86-64-linux-gnu (= 13.3.0-6), cpp-14 (= 14.2.0-4), cpp-14-x86-64-linux-gnu (= 14.2.0-4), cpp-x86-64-linux-gnu (= 4:14.1.0-2), dash (= 0.5.12-9), debconf (= 1.5.87), debhelper (= 13.20), debianutils (= 5.20), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.14.0-1), diffutils (= 1:3.10-1), dpkg (= 1.22.11), dpkg-dev (= 1.22.11), dwz (= 0.15-1+b1), file (= 1:5.45-3), findutils (= 4.10.0-3), g++ (= 4:14.1.0-2), g++-14 (= 14.2.0-4), g++-14-x86-64-linux-gnu (= 14.2.0-4), g++-x86-64-linux-gnu (= 4:14.1.0-2), gcc (= 4:14.1.0-2), gcc-13 (= 13.3.0-6), gcc-13-base (= 13.3.0-6), gcc-13-x86-64-linux-gnu (= 13.3.0-6), gcc-14 (= 14.2.0-4), gcc-14-base (= 14.2.0-4), gcc-14-x86-64-linux-gnu (= 14.2.0-4), gcc-x86-64-linux-gnu (= 4:14.1.0-2), gettext (= 0.22.5-2), gettext-base (= 0.22.5-2), grep (= 3.11-4), groff-base (= 1.23.0-5), gzip (= 1.12-1.1), hostname (= 3.23+nmu2), init-system-helpers (= 1.66), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-2), libalgorithm-diff-perl (= 1.201-1), libarchive-zip-perl (= 1.68-1), libasan8 (= 14.2.0-4), libatomic1 (= 14.2.0-4), libattr1 (= 1:2.5.2-1), libaudit-common (= 1:4.0.1-1), libaudit1 (= 1:4.0.1-1), libbinutils (= 2.43.1-4), libbio-perl-perl (= 1.7.8-1), libblkid1 (= 2.40.2-8), libbz2-1.0 (= 1.0.8-6), libc-bin (= 2.40-2), libc-dev-bin (= 2.40-2), libc6 (= 2.40-2), libc6-dev (= 2.40-2), libcap-ng0 (= 0.8.5-2), libcap2 (= 1:2.66-5), libcapture-tiny-perl (= 0.48-2), libcc1-0 (= 14.2.0-4), libclass-data-inheritable-perl (= 0.08-3), libcom-err2 (= 1.47.1-1), libcrypt-dev (= 1:4.4.36-5), libcrypt1 (= 1:4.4.36-5), libctf-nobfd0 (= 2.43.1-4), libctf0 (= 2.43.1-4), libdata-stag-perl (= 0.14-3), libdb5.3t64 (= 5.3.28+dfsg2-7), libdebconfclient0 (= 0.272), libdebhelper-perl (= 13.20), libdevel-stacktrace-perl (= 2.0500-1), libdpkg-perl (= 1.22.11), libelf1t64 (= 0.191-2), libexception-class-perl (= 1.45-1), libexpat1 (= 2.6.3-1), libffi8 (= 3.4.6-1), libfile-slurp-perl (= 9999.32-2), libfile-stripnondeterminism-perl (= 1.14.0-1), libgcc-13-dev (= 13.3.0-6), libgcc-14-dev (= 14.2.0-4), libgcc-s1 (= 14.2.0-4), libgdbm-compat4t64 (= 1.24-2), libgdbm6t64 (= 1.24-2), libgfortran5 (= 14.2.0-4), libgmp10 (= 2:6.3.0+dfsg-2+b1), libgomp1 (= 14.2.0-4), libgprofng0 (= 2.43.1-4), libgssapi-krb5-2 (= 1.21.3-3), libhmmer2-dev (= 2.3.2+dfsg-12), libhwasan0 (= 14.2.0-4), libicu72 (= 72.1-5), libio-string-perl (= 1.08-4), libisl23 (= 0.27-1), libitm1 (= 14.2.0-4), libjansson4 (= 2.14-2+b2), libk5crypto3 (= 1.21.3-3), libkeyutils1 (= 1.6.3-3), libkrb5-3 (= 1.21.3-3), libkrb5support0 (= 1.21.3-3), liblmdb0 (= 0.9.31-1+b1), liblsan0 (= 14.2.0-4), liblzma5 (= 5.6.2-2), libmagic-mgc (= 1:5.45-3), libmagic1t64 (= 1:5.45-3), libmbedcrypto7t64 (= 2.28.8-1), libmbedtls14t64 (= 2.28.8-1), libmbedx509-1t64 (= 2.28.8-1), libmd0 (= 1.1.0-2), libmodhmm-dev (= 1.0+dfsg-7), libmodhmm0 (= 1.0+dfsg-7), libmount1 (= 2.40.2-8), libmpc3 (= 1.3.1-1+b2), libmpfr6 (= 4.2.1-1+b1), libncursesw6 (= 6.5-2), libnghttp2-14 (= 1.63.0-1), libnsl2 (= 1.3.0-3+b2), libpam-modules (= 1.5.3-7), libpam-modules-bin (= 1.5.3-7), libpam-runtime (= 1.5.3-7), libpam0g (= 1.5.3-7), libpcre2-8-0 (= 10.42-4+b1), libperl5.40 (= 5.40.0-5), libpipeline1 (= 1.5.8-1), libpkgconf3 (= 1.8.1-3), libpython3-stdlib (= 3.12.5-1+b1), libpython3.12-minimal (= 3.12.6-1), libpython3.12-stdlib (= 3.12.6-1), libquadmath0 (= 14.2.0-4), libreadline8t64 (= 8.2-5), libseccomp2 (= 2.5.5-1+b1), libselinux1 (= 3.7-3), libsframe1 (= 2.43.1-4), libsmartcols1 (= 2.40.2-8), libsqlite3-0 (= 3.46.1-1), libsquid-dev (= 1.9g+cvs20050121-15.1), libsquid1t64 (= 1.9g+cvs20050121-15.1), libssl3t64 (= 3.3.2-1), libstdc++-14-dev (= 14.2.0-4), libstdc++6 (= 14.2.0-4), libsub-uplevel-perl (= 0.2800-3), libsvm-dev (= 3.24+ds-6+b1), libsvm3 (= 3.24+ds-6+b1), libsvmloc-dev (= 1.0+dfsg-7), libsvmloc0 (= 1.0+dfsg-7), libsystemd0 (= 256.6-1), libtest-deep-perl (= 1.204-1), libtest-differences-perl (= 0.71-1), libtest-exception-perl (= 0.43-3), libtest-most-perl (= 0.38-1), libtest-warn-perl (= 0.37-2), libtext-diff-perl (= 1.45-2), libtinfo6 (= 6.5-2), libtirpc-common (= 1.3.4+ds-1.3), libtirpc3t64 (= 1.3.4+ds-1.3), libtool (= 2.4.7-7), libtsan2 (= 14.2.0-4), libubsan1 (= 14.2.0-4), libuchardet0 (= 0.0.8-1+b1), libudev1 (= 256.6-1), libunistring5 (= 1.2-1), libuuid1 (= 2.40.2-8), libuv1t64 (= 1.48.0-6), libxml2 (= 2.12.7+dfsg-3+b1), libzstd1 (= 1.5.6+dfsg-1), linux-libc-dev (= 6.10.9-1), m4 (= 1.4.19-4), make (= 4.3-4.1), man-db (= 2.13.0-1), mawk (= 1.3.4.20240905-1), media-types (= 10.1.0), ncbi-blast+ (= 2.16.0+ds-6), ncbi-blast+-legacy (= 2.16.0+ds-6), ncbi-data (= 6.1.20170106+dfsg2-4), ncurses-base (= 6.5-2), ncurses-bin (= 6.5-2), netbase (= 6.4), openssl-provider-legacy (= 3.3.2-1), patch (= 2.7.6-7), perl (= 5.40.0-5), perl-base (= 5.40.0-5), perl-modules-5.40 (= 5.40.0-5), pftools (= 3.2.12-1), pkgconf (= 1.8.1-3), pkgconf-bin (= 1.8.1-3), po-debconf (= 1.0.21+nmu1), python3 (= 3.12.5-1+b1), python3-minimal (= 3.12.5-1+b1), python3.12 (= 3.12.6-1), python3.12-minimal (= 3.12.6-1), readline-common (= 8.2-5), rpcsvc-proto (= 1.4.3-1), sed (= 4.9-2), sensible-utils (= 0.0.24), sysvinit-utils (= 3.10-2), tar (= 1.35+dfsg-3), tzdata (= 2024a-4), usr-is-merged (= 39), util-linux (= 2.40.2-8), xz-utils (= 5.6.2-2), zlib1g (= 1:1.3.dfsg+really1.3.1-1) Environment: DEB_BUILD_OPTIONS="parallel=2" LANG="C.UTF-8" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" LD_LIBRARY_PATH="/usr/lib/libeatmydata" SOURCE_DATE_EPOCH="1726334653" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ psortb-dbgsym_3.0.6+dfsg-4+b1_amd64.deb --------------------------------------- new Debian package, version 2.0. size 159732 bytes: control archive=696 bytes. 479 bytes, 12 lines control 401 bytes, 4 lines md5sums Package: psortb-dbgsym Source: psortb (3.0.6+dfsg-4) Version: 3.0.6+dfsg-4+b1 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 197 Depends: psortb (= 3.0.6+dfsg-4+b1) Section: debug Priority: optional Description: debug symbols for psortb Build-Ids: 5711f13d4a29d56c95a55862af4dcfed582b5b1d 7c66d43ca9cfe6d8d25abb2554a4d7931d6ef623 9e90db8f34d3966f509ac61048915fc26003201c drwxr-xr-x root/root 0 2024-09-14 17:24 ./ drwxr-xr-x root/root 0 2024-09-14 17:24 ./usr/ drwxr-xr-x root/root 0 2024-09-14 17:24 ./usr/lib/ drwxr-xr-x root/root 0 2024-09-14 17:24 ./usr/lib/debug/ drwxr-xr-x root/root 0 2024-09-14 17:24 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2024-09-14 17:24 ./usr/lib/debug/.build-id/57/ -rw-r--r-- root/root 40872 2024-09-14 17:24 ./usr/lib/debug/.build-id/57/11f13d4a29d56c95a55862af4dcfed582b5b1d.debug drwxr-xr-x root/root 0 2024-09-14 17:24 ./usr/lib/debug/.build-id/7c/ -rw-r--r-- root/root 25968 2024-09-14 17:24 ./usr/lib/debug/.build-id/7c/66d43ca9cfe6d8d25abb2554a4d7931d6ef623.debug drwxr-xr-x root/root 0 2024-09-14 17:24 ./usr/lib/debug/.build-id/9e/ -rw-r--r-- root/root 91496 2024-09-14 17:24 ./usr/lib/debug/.build-id/9e/90db8f34d3966f509ac61048915fc26003201c.debug drwxr-xr-x root/root 0 2024-09-14 17:24 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2024-09-14 17:24 ./usr/lib/debug/.dwz/x86_64-linux-gnu/ -rw-r--r-- root/root 27400 2024-09-14 17:24 ./usr/lib/debug/.dwz/x86_64-linux-gnu/psortb.debug drwxr-xr-x root/root 0 2024-09-14 17:24 ./usr/share/ drwxr-xr-x root/root 0 2024-09-14 17:24 ./usr/share/doc/ lrwxrwxrwx root/root 0 2024-09-14 17:24 ./usr/share/doc/psortb-dbgsym -> psortb psortb_3.0.6+dfsg-4+b1_amd64.deb -------------------------------- new Debian package, version 2.0. size 16374528 bytes: control archive=4892 bytes. 951 bytes, 16 lines control 15647 bytes, 166 lines md5sums Package: psortb Source: psortb (3.0.6+dfsg-4) Version: 3.0.6+dfsg-4+b1 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 116747 Depends: libc6 (>= 2.34), libgcc-s1 (>= 3.0), libmodhmm0 (>= 1.0+dfsg), libsquid1t64 (>= 1.9g+cvs20050121), libstdc++6 (>= 13.1), libsvmloc0 (>= 1.0+dfsg), perl (>= 5.40.0-5), perlapi-5.40.0, libbio-perl-perl, libbio-perl-run-perl, libalgorithm-svm-perl, pftools, librpc-xml-perl Section: science Priority: optional Homepage: https://www.psort.org/ Description: bacterial localization prediction tool PSORTb enables prediction of bacterial protein subcellular localization (SCL) and provides a quick and inexpensive means for gaining insight into protein function, verifying experimental results, annotating newly sequenced bacterial genomes, detecting potential cell surface/secreted drug targets, as well as identifying biomarkers for microbes. drwxr-xr-x root/root 0 2024-09-14 17:24 ./ drwxr-xr-x root/root 0 2024-09-14 17:24 ./usr/ drwxr-xr-x root/root 0 2024-09-14 17:24 ./usr/bin/ -rwxr-xr-x root/root 17095 2024-09-14 17:24 ./usr/bin/psort drwxr-xr-x root/root 0 2024-09-14 17:24 ./usr/lib/ drwxr-xr-x root/root 0 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+------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: any Build-Space: 258980 Build-Time: 114 Distribution: perl-5.40 Host Architecture: amd64 Install-Time: 18 Job: /srv/debomatic/incoming/psortb_3.0.6+dfsg-4.dsc Machine Architecture: amd64 Package: psortb Package-Time: 144 Source-Version: 3.0.6+dfsg-4 Space: 258980 Status: successful Version: 3.0.6+dfsg-4+b1 -------------------------------------------------------------------------------- Finished at 2024-09-14T17:26:08Z Build needed 00:02:24, 258980k disk space