pinfish →
0.1.0+ds-3+b1 →
armhf → 2021-10-16 14:52:57
sbuild (Debian sbuild) 0.78.1 (09 February 2019) on test2019
+==============================================================================+
| pinfish 0.1.0+ds-3+b1 (armhf) Sat, 16 Oct 2021 14:43:17 +0000 |
+==============================================================================+
Package: pinfish
Version: 0.1.0+ds-3+b1
Source Version: 0.1.0+ds-3
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
Build Type: any
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/bookworm-staging-armhf-sbuild-2e329ca1-f6ce-4f1a-9bce-a16c794345ec' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/pinfish-MsAivt/resolver-YJAwbS' with '<<RESOLVERDIR>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bookworm-staging/main Sources [12.4 MB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf Packages [13.4 MB]
Fetched 25.9 MB in 10s (2567 kB/s)
Reading package lists...
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'pinfish' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/pinfish.git
Please use:
git clone https://salsa.debian.org/med-team/pinfish.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 73.6 MB of source archives.
Get:1 http://172.17.0.1/private bookworm-staging/main pinfish 0.1.0+ds-3 (dsc) [2533 B]
Get:2 http://172.17.0.1/private bookworm-staging/main pinfish 0.1.0+ds-3 (tar) [68.6 MB]
Get:3 http://172.17.0.1/private bookworm-staging/main pinfish 0.1.0+ds-3 (tar) [5055 kB]
Get:4 http://172.17.0.1/private bookworm-staging/main pinfish 0.1.0+ds-3 (diff) [6372 B]
Fetched 73.6 MB in 9s (7859 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/pinfish-MsAivt/pinfish-0.1.0+ds' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/pinfish-MsAivt' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), dh-golang, golang-any, golang-github-biogo-biogo-dev, golang-github-biogo-hts-dev, golang-github-google-uuid-dev, samtools, build-essential, fakeroot
Filtered Build-Depends: debhelper-compat (= 13), dh-golang, golang-any, golang-github-biogo-biogo-dev, golang-github-biogo-hts-dev, golang-github-google-uuid-dev, samtools, build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [957 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [416 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [500 B]
Fetched 1873 B in 0s (49.3 kB/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 bsdextrautils debhelper
dh-autoreconf dh-golang dh-strip-nondeterminism dwz file gettext
gettext-base golang-1.16-go golang-1.16-src golang-any
golang-github-biogo-biogo-dev golang-github-biogo-hts-dev
golang-github-creack-pty-dev golang-github-google-uuid-dev
golang-github-kr-pretty-dev golang-github-kr-text-dev
golang-github-ulikunitz-xz-dev golang-go golang-gopkg-check.v1-dev
golang-src groff-base intltool-debian libarchive-zip-perl libbrotli1
libcurl3-gnutls libdebhelper-perl libdeflate0 libelf1
libfile-stripnondeterminism-perl libhts3 libhtscodecs2 libicu67 libmagic-mgc
libmagic1 libncurses6 libnghttp2-14 libpipeline1 libpsl5 librtmp1
libsigsegv2 libssh2-1 libsub-override-perl libtool libuchardet0 libxml2 m4
man-db po-debconf samtools sensible-utils
Suggested packages:
autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc
libasprintf-dev libgettextpo-dev bzr | brz ca-certificates git mercurial
subversion groff libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc
apparmor less www-browser libmail-box-perl cwltool
Recommended packages:
curl | wget | lynx pkg-config ca-certificates libarchive-cpio-perl libgpm2
publicsuffix libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils debhelper
dh-autoreconf dh-golang dh-strip-nondeterminism dwz file gettext
gettext-base golang-1.16-go golang-1.16-src golang-any
golang-github-biogo-biogo-dev golang-github-biogo-hts-dev
golang-github-creack-pty-dev golang-github-google-uuid-dev
golang-github-kr-pretty-dev golang-github-kr-text-dev
golang-github-ulikunitz-xz-dev golang-go golang-gopkg-check.v1-dev
golang-src groff-base intltool-debian libarchive-zip-perl libbrotli1
libcurl3-gnutls libdebhelper-perl libdeflate0 libelf1
libfile-stripnondeterminism-perl libhts3 libhtscodecs2 libicu67 libmagic-mgc
libmagic1 libncurses6 libnghttp2-14 libpipeline1 libpsl5 librtmp1
libsigsegv2 libssh2-1 libsub-override-perl libtool libuchardet0 libxml2 m4
man-db po-debconf samtools sbuild-build-depends-main-dummy sensible-utils
0 upgraded, 57 newly installed, 0 to remove and 35 not upgraded.
Need to get 81.0 MB of archives.
After this operation, 425 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [924 B]
Get:2 http://172.17.0.1/private bookworm-staging/main armhf bsdextrautils armhf 2.37.2-3 [135 kB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:4 http://172.17.0.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-7 [793 kB]
Get:5 http://172.17.0.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:6 http://172.17.0.1/private bookworm-staging/main armhf man-db armhf 2.9.4-2 [1307 kB]
Get:7 http://172.17.0.1/private bookworm-staging/main armhf sensible-utils all 0.0.17 [21.5 kB]
Get:8 http://172.17.0.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB]
Get:9 http://172.17.0.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.39-3 [117 kB]
Get:10 http://172.17.0.1/private bookworm-staging/main armhf file armhf 1:5.39-3 [68.0 kB]
Get:11 http://172.17.0.1/private bookworm-staging/main armhf gettext-base armhf 0.21-4 [171 kB]
Get:12 http://172.17.0.1/private bookworm-staging/main armhf libsigsegv2 armhf 2.13-1 [34.3 kB]
Get:13 http://172.17.0.1/private bookworm-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:14 http://172.17.0.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:15 http://172.17.0.1/private bookworm-staging/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get:16 http://172.17.0.1/private bookworm-staging/main armhf automake all 1:1.16.4-2 [819 kB]
Get:17 http://172.17.0.1/private bookworm-staging/main armhf autopoint all 0.21-4 [510 kB]
Get:18 http://172.17.0.1/private bookworm-staging/main armhf libdebhelper-perl all 13.5.2 [192 kB]
Get:19 http://172.17.0.1/private bookworm-staging/main armhf libtool all 2.4.6-15 [513 kB]
Get:20 http://172.17.0.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:21 http://172.17.0.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:22 http://172.17.0.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:23 http://172.17.0.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB]
Get:24 http://172.17.0.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.12.0-1 [15.4 kB]
Get:25 http://172.17.0.1/private bookworm-staging/main armhf libelf1 armhf 0.185-2 [168 kB]
Get:26 http://172.17.0.1/private bookworm-staging/main armhf dwz armhf 0.14-1 [83.0 kB]
Get:27 http://172.17.0.1/private bookworm-staging/main armhf libicu67 armhf 67.1-7 [8291 kB]
Get:28 http://172.17.0.1/private bookworm-staging/main armhf libxml2 armhf 2.9.12+dfsg-5 [584 kB]
Get:29 http://172.17.0.1/private bookworm-staging/main armhf gettext armhf 0.21-4 [1215 kB]
Get:30 http://172.17.0.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:31 http://172.17.0.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:32 http://172.17.0.1/private bookworm-staging/main armhf debhelper all 13.5.2 [1056 kB]
Get:33 http://172.17.0.1/private bookworm-staging/main armhf dh-golang all 1.51 [24.6 kB]
Get:34 http://172.17.0.1/private bookworm-staging/main armhf golang-1.16-src all 1.16.9-2 [14.3 MB]
Get:35 http://172.17.0.1/private bookworm-staging/main armhf golang-1.16-go armhf 1.16.9-2 [46.3 MB]
Get:36 http://172.17.0.1/private bookworm-staging/main armhf golang-src armhf 2:1.16~1 [5220 B]
Get:37 http://172.17.0.1/private bookworm-staging/main armhf golang-go armhf 2:1.16~1 [40.3 kB]
Get:38 http://172.17.0.1/private bookworm-staging/main armhf golang-any armhf 2:1.16~1 [5312 B]
Get:39 http://172.17.0.1/private bookworm-staging/main armhf golang-github-ulikunitz-xz-dev all 0.5.6-2 [352 kB]
Get:40 http://172.17.0.1/private bookworm-staging/main armhf golang-github-biogo-hts-dev all 1.1.0+dfsg1-3 [292 kB]
Get:41 http://172.17.0.1/private bookworm-staging/main armhf golang-github-creack-pty-dev all 1.1.15-1 [9488 B]
Get:42 http://172.17.0.1/private bookworm-staging/main armhf golang-github-kr-text-dev all 0.2.0-1 [11.1 kB]
Get:43 http://172.17.0.1/private bookworm-staging/main armhf golang-github-kr-pretty-dev all 0.2.1+git20200831.59b4212-1 [14.6 kB]
Get:44 http://172.17.0.1/private bookworm-staging/main armhf golang-gopkg-check.v1-dev all 0.0+git20200902.038fdea-1 [32.1 kB]
Get:45 http://172.17.0.1/private bookworm-staging/main armhf golang-github-biogo-biogo-dev all 1.0.3-1 [190 kB]
Get:46 http://172.17.0.1/private bookworm-staging/main armhf golang-github-google-uuid-dev all 1.2.0-1 [15.0 kB]
Get:47 http://172.17.0.1/private bookworm-staging/main armhf libbrotli1 armhf 1.0.9-2+b1 [261 kB]
Get:48 http://172.17.0.1/private bookworm-staging/main armhf libnghttp2-14 armhf 1.43.0-1 [65.3 kB]
Get:49 http://172.17.0.1/private bookworm-staging/main armhf libpsl5 armhf 0.21.0-1.2 [56.2 kB]
Get:50 http://172.17.0.1/private bookworm-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:51 http://172.17.0.1/private bookworm-staging/main armhf libssh2-1 armhf 1.10.0-2 [161 kB]
Get:52 http://172.17.0.1/private bookworm-staging/main armhf libcurl3-gnutls armhf 7.74.0-1.3 [301 kB]
Get:53 http://172.17.0.1/private bookworm-staging/main armhf libdeflate0 armhf 1.8-1 [44.1 kB]
Get:54 http://172.17.0.1/private bookworm-staging/main armhf libhtscodecs2 armhf 1.1.1-3 [49.8 kB]
Get:55 http://172.17.0.1/private bookworm-staging/main armhf libhts3 armhf 1.13+ds-2 [339 kB]
Get:56 http://172.17.0.1/private bookworm-staging/main armhf libncurses6 armhf 6.2+20201114-4 [79.7 kB]
Get:57 http://172.17.0.1/private bookworm-staging/main armhf samtools armhf 1.13-2 [525 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 81.0 MB in 13s (6317 kB/s)
Selecting previously unselected package bsdextrautils.
(Reading database ... 12477 files and directories currently installed.)
Preparing to unpack .../00-bsdextrautils_2.37.2-3_armhf.deb ...
Unpacking bsdextrautils (2.37.2-3) ...
Selecting previously unselected package libuchardet0:armhf.
Preparing to unpack .../01-libuchardet0_0.0.7-1_armhf.deb ...
Unpacking libuchardet0:armhf (0.0.7-1) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../02-groff-base_1.22.4-7_armhf.deb ...
Unpacking groff-base (1.22.4-7) ...
Selecting previously unselected package libpipeline1:armhf.
Preparing to unpack .../03-libpipeline1_1.5.3-1_armhf.deb ...
Unpacking libpipeline1:armhf (1.5.3-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../04-man-db_2.9.4-2_armhf.deb ...
Unpacking man-db (2.9.4-2) ...
Selecting previously unselected package sensible-utils.
Preparing to unpack .../05-sensible-utils_0.0.17_all.deb ...
Unpacking sensible-utils (0.0.17) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../06-libmagic-mgc_1%3a5.39-3_armhf.deb ...
Unpacking libmagic-mgc (1:5.39-3) ...
Selecting previously unselected package libmagic1:armhf.
Preparing to unpack .../07-libmagic1_1%3a5.39-3_armhf.deb ...
Unpacking libmagic1:armhf (1:5.39-3) ...
Selecting previously unselected package file.
Preparing to unpack .../08-file_1%3a5.39-3_armhf.deb ...
Unpacking file (1:5.39-3) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../09-gettext-base_0.21-4_armhf.deb ...
Unpacking gettext-base (0.21-4) ...
Selecting previously unselected package libsigsegv2:armhf.
Preparing to unpack .../10-libsigsegv2_2.13-1_armhf.deb ...
Unpacking libsigsegv2:armhf (2.13-1) ...
Selecting previously unselected package m4.
Preparing to unpack .../11-m4_1.4.18-5_armhf.deb ...
Unpacking m4 (1.4.18-5) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../12-autoconf_2.71-2_all.deb ...
Unpacking autoconf (2.71-2) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../13-autotools-dev_20180224.1+nmu1_all.deb ...
Unpacking autotools-dev (20180224.1+nmu1) ...
Selecting previously unselected package automake.
Preparing to unpack .../14-automake_1%3a1.16.4-2_all.deb ...
Unpacking automake (1:1.16.4-2) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../15-autopoint_0.21-4_all.deb ...
Unpacking autopoint (0.21-4) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../16-libdebhelper-perl_13.5.2_all.deb ...
Unpacking libdebhelper-perl (13.5.2) ...
Selecting previously unselected package libtool.
Preparing to unpack .../17-libtool_2.4.6-15_all.deb ...
Unpacking libtool (2.4.6-15) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../18-dh-autoreconf_20_all.deb ...
Unpacking dh-autoreconf (20) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../19-libarchive-zip-perl_1.68-1_all.deb ...
Unpacking libarchive-zip-perl (1.68-1) ...
Selecting previously unselected package libsub-override-perl.
Preparing to unpack .../20-libsub-override-perl_0.09-2_all.deb ...
Unpacking libsub-override-perl (0.09-2) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../21-libfile-stripnondeterminism-perl_1.12.0-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.12.0-1) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../22-dh-strip-nondeterminism_1.12.0-1_all.deb ...
Unpacking dh-strip-nondeterminism (1.12.0-1) ...
Selecting previously unselected package libelf1:armhf.
Preparing to unpack .../23-libelf1_0.185-2_armhf.deb ...
Unpacking libelf1:armhf (0.185-2) ...
Selecting previously unselected package dwz.
Preparing to unpack .../24-dwz_0.14-1_armhf.deb ...
Unpacking dwz (0.14-1) ...
Selecting previously unselected package libicu67:armhf.
Preparing to unpack .../25-libicu67_67.1-7_armhf.deb ...
Unpacking libicu67:armhf (67.1-7) ...
Selecting previously unselected package libxml2:armhf.
Preparing to unpack .../26-libxml2_2.9.12+dfsg-5_armhf.deb ...
Unpacking libxml2:armhf (2.9.12+dfsg-5) ...
Selecting previously unselected package gettext.
Preparing to unpack .../27-gettext_0.21-4_armhf.deb ...
Unpacking gettext (0.21-4) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../28-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 .../29-po-debconf_1.0.21+nmu1_all.deb ...
Unpacking po-debconf (1.0.21+nmu1) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../30-debhelper_13.5.2_all.deb ...
Unpacking debhelper (13.5.2) ...
Selecting previously unselected package dh-golang.
Preparing to unpack .../31-dh-golang_1.51_all.deb ...
Unpacking dh-golang (1.51) ...
Selecting previously unselected package golang-1.16-src.
Preparing to unpack .../32-golang-1.16-src_1.16.9-2_all.deb ...
Unpacking golang-1.16-src (1.16.9-2) ...
Selecting previously unselected package golang-1.16-go.
Preparing to unpack .../33-golang-1.16-go_1.16.9-2_armhf.deb ...
Unpacking golang-1.16-go (1.16.9-2) ...
Selecting previously unselected package golang-src:armhf.
Preparing to unpack .../34-golang-src_2%3a1.16~1_armhf.deb ...
Unpacking golang-src:armhf (2:1.16~1) ...
Selecting previously unselected package golang-go.
Preparing to unpack .../35-golang-go_2%3a1.16~1_armhf.deb ...
Unpacking golang-go (2:1.16~1) ...
Selecting previously unselected package golang-any:armhf.
Preparing to unpack .../36-golang-any_2%3a1.16~1_armhf.deb ...
Unpacking golang-any:armhf (2:1.16~1) ...
Selecting previously unselected package golang-github-ulikunitz-xz-dev.
Preparing to unpack .../37-golang-github-ulikunitz-xz-dev_0.5.6-2_all.deb ...
Unpacking golang-github-ulikunitz-xz-dev (0.5.6-2) ...
Selecting previously unselected package golang-github-biogo-hts-dev.
Preparing to unpack .../38-golang-github-biogo-hts-dev_1.1.0+dfsg1-3_all.deb ...
Unpacking golang-github-biogo-hts-dev (1.1.0+dfsg1-3) ...
Selecting previously unselected package golang-github-creack-pty-dev.
Preparing to unpack .../39-golang-github-creack-pty-dev_1.1.15-1_all.deb ...
Unpacking golang-github-creack-pty-dev (1.1.15-1) ...
Selecting previously unselected package golang-github-kr-text-dev.
Preparing to unpack .../40-golang-github-kr-text-dev_0.2.0-1_all.deb ...
Unpacking golang-github-kr-text-dev (0.2.0-1) ...
Selecting previously unselected package golang-github-kr-pretty-dev.
Preparing to unpack .../41-golang-github-kr-pretty-dev_0.2.1+git20200831.59b4212-1_all.deb ...
Unpacking golang-github-kr-pretty-dev (0.2.1+git20200831.59b4212-1) ...
Selecting previously unselected package golang-gopkg-check.v1-dev.
Preparing to unpack .../42-golang-gopkg-check.v1-dev_0.0+git20200902.038fdea-1_all.deb ...
Unpacking golang-gopkg-check.v1-dev (0.0+git20200902.038fdea-1) ...
Selecting previously unselected package golang-github-biogo-biogo-dev.
Preparing to unpack .../43-golang-github-biogo-biogo-dev_1.0.3-1_all.deb ...
Unpacking golang-github-biogo-biogo-dev (1.0.3-1) ...
Selecting previously unselected package golang-github-google-uuid-dev.
Preparing to unpack .../44-golang-github-google-uuid-dev_1.2.0-1_all.deb ...
Unpacking golang-github-google-uuid-dev (1.2.0-1) ...
Selecting previously unselected package libbrotli1:armhf.
Preparing to unpack .../45-libbrotli1_1.0.9-2+b1_armhf.deb ...
Unpacking libbrotli1:armhf (1.0.9-2+b1) ...
Selecting previously unselected package libnghttp2-14:armhf.
Preparing to unpack .../46-libnghttp2-14_1.43.0-1_armhf.deb ...
Unpacking libnghttp2-14:armhf (1.43.0-1) ...
Selecting previously unselected package libpsl5:armhf.
Preparing to unpack .../47-libpsl5_0.21.0-1.2_armhf.deb ...
Unpacking libpsl5:armhf (0.21.0-1.2) ...
Selecting previously unselected package librtmp1:armhf.
Preparing to unpack .../48-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_armhf.deb ...
Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Selecting previously unselected package libssh2-1:armhf.
Preparing to unpack .../49-libssh2-1_1.10.0-2_armhf.deb ...
Unpacking libssh2-1:armhf (1.10.0-2) ...
Selecting previously unselected package libcurl3-gnutls:armhf.
Preparing to unpack .../50-libcurl3-gnutls_7.74.0-1.3_armhf.deb ...
Unpacking libcurl3-gnutls:armhf (7.74.0-1.3) ...
Selecting previously unselected package libdeflate0:armhf.
Preparing to unpack .../51-libdeflate0_1.8-1_armhf.deb ...
Unpacking libdeflate0:armhf (1.8-1) ...
Selecting previously unselected package libhtscodecs2:armhf.
Preparing to unpack .../52-libhtscodecs2_1.1.1-3_armhf.deb ...
Unpacking libhtscodecs2:armhf (1.1.1-3) ...
Selecting previously unselected package libhts3:armhf.
Preparing to unpack .../53-libhts3_1.13+ds-2_armhf.deb ...
Unpacking libhts3:armhf (1.13+ds-2) ...
Selecting previously unselected package libncurses6:armhf.
Preparing to unpack .../54-libncurses6_6.2+20201114-4_armhf.deb ...
Unpacking libncurses6:armhf (6.2+20201114-4) ...
Selecting previously unselected package samtools.
Preparing to unpack .../55-samtools_1.13-2_armhf.deb ...
Unpacking samtools (1.13-2) ...
Selecting previously unselected package sbuild-build-depends-main-dummy.
Preparing to unpack .../56-sbuild-build-depends-main-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ...
Setting up libhtscodecs2:armhf (1.1.1-3) ...
Setting up libpipeline1:armhf (1.5.3-1) ...
Setting up libpsl5:armhf (0.21.0-1.2) ...
Setting up bsdextrautils (2.37.2-3) ...
update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode
Setting up golang-github-creack-pty-dev (1.1.15-1) ...
Setting up libicu67:armhf (67.1-7) ...
Setting up libmagic-mgc (1:5.39-3) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libdebhelper-perl (13.5.2) ...
Setting up libbrotli1:armhf (1.0.9-2+b1) ...
Setting up libnghttp2-14:armhf (1.43.0-1) ...
Setting up libmagic1:armhf (1:5.39-3) ...
Setting up libdeflate0:armhf (1.8-1) ...
Setting up gettext-base (0.21-4) ...
Setting up file (1:5.39-3) ...
Setting up autotools-dev (20180224.1+nmu1) ...
Setting up golang-1.16-src (1.16.9-2) ...
Setting up golang-github-kr-text-dev (0.2.0-1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Setting up libncurses6:armhf (6.2+20201114-4) ...
Setting up libsigsegv2:armhf (2.13-1) ...
Setting up autopoint (0.21-4) ...
Setting up sensible-utils (0.0.17) ...
Setting up golang-github-google-uuid-dev (1.2.0-1) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libssh2-1:armhf (1.10.0-2) ...
Setting up golang-src:armhf (2:1.16~1) ...
Setting up libelf1:armhf (0.185-2) ...
Setting up libxml2:armhf (2.9.12+dfsg-5) ...
Setting up golang-github-ulikunitz-xz-dev (0.5.6-2) ...
Setting up golang-github-kr-pretty-dev (0.2.1+git20200831.59b4212-1) ...
Setting up libfile-stripnondeterminism-perl (1.12.0-1) ...
Setting up gettext (0.21-4) ...
Setting up libtool (2.4.6-15) ...
Setting up m4 (1.4.18-5) ...
Setting up golang-1.16-go (1.16.9-2) ...
Setting up libcurl3-gnutls:armhf (7.74.0-1.3) ...
Setting up golang-gopkg-check.v1-dev (0.0+git20200902.038fdea-1) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up golang-github-biogo-hts-dev (1.1.0+dfsg1-3) ...
Setting up autoconf (2.71-2) ...
Setting up dh-strip-nondeterminism (1.12.0-1) ...
Setting up dwz (0.14-1) ...
Setting up groff-base (1.22.4-7) ...
Setting up automake (1:1.16.4-2) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libhts3:armhf (1.13+ds-2) ...
Setting up golang-go (2:1.16~1) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up man-db (2.9.4-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up golang-any:armhf (2:1.16~1) ...
Setting up samtools (1.13-2) ...
Setting up dh-autoreconf (20) ...
Setting up golang-github-biogo-biogo-dev (1.0.3-1) ...
Setting up debhelper (13.5.2) ...
Setting up dh-golang (1.51) ...
Setting up sbuild-build-depends-main-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.32-4+rpi1) ...
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.19.20-v7+ #1 SMP Mon Mar 18 11:37:02 GMT 2019 armhf (armv7l)
Toolchain package versions: binutils_2.37-5+rpi1 dpkg-dev_1.20.9+rpi1 g++-10_10.3.0-9+rpi1 gcc-10_10.3.0-9+rpi1 libc6-dev_2.32-4+rpi1 libstdc++-10-dev_10.3.0-9+rpi1 libstdc++6_11.2.0-4+rpi1 linux-libc-dev_5.10.46-4+rpi1
Package versions: adduser_3.118 apt_2.3.9 autoconf_2.71-2 automake_1:1.16.4-2 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_12+rpi1 base-passwd_3.5.51 bash_5.1-3 binutils_2.37-5+rpi1 binutils-arm-linux-gnueabihf_2.37-5+rpi1 binutils-common_2.37-5+rpi1 bsdextrautils_2.37.2-3 bsdutils_1:2.37.2-1 build-essential_12.9 bzip2_1.0.8-4 coreutils_8.32-4 cpp_4:10.2.1-1+rpi1 cpp-10_10.3.0-9+rpi1 dash_0.5.11+git20210120+802ebd4-1 debconf_1.5.77 debhelper_13.5.2 debianutils_4.11.2 dh-autoreconf_20 dh-golang_1.51 dh-strip-nondeterminism_1.12.0-1 diffutils_1:3.7-5 dirmngr_2.2.27-2 dpkg_1.20.9+rpi1 dpkg-dev_1.20.9+rpi1 dwz_0.14-1 e2fsprogs_1.46.4-1 fakeroot_1.25.3-1.1 file_1:5.39-3 findutils_4.8.0-1 g++_4:10.2.1-1+rpi1 g++-10_10.3.0-9+rpi1 gcc_4:10.2.1-1+rpi1 gcc-10_10.3.0-9+rpi1 gcc-10-base_10.3.0-9+rpi1 gcc-11-base_11.2.0-4+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gettext_0.21-4 gettext-base_0.21-4 gnupg_2.2.27-2 gnupg-l10n_2.2.27-2 gnupg-utils_2.2.27-2 golang-1.16-go_1.16.9-2 golang-1.16-src_1.16.9-2 golang-any_2:1.16~1 golang-github-biogo-biogo-dev_1.0.3-1 golang-github-biogo-hts-dev_1.1.0+dfsg1-3 golang-github-creack-pty-dev_1.1.15-1 golang-github-google-uuid-dev_1.2.0-1 golang-github-kr-pretty-dev_0.2.1+git20200831.59b4212-1 golang-github-kr-text-dev_0.2.0-1 golang-github-ulikunitz-xz-dev_0.5.6-2 golang-go_2:1.16~1 golang-gopkg-check.v1-dev_0.0+git20200902.038fdea-1 golang-src_2:1.16~1 gpg_2.2.27-2 gpg-agent_2.2.27-2 gpg-wks-client_2.2.27-2 gpg-wks-server_2.2.27-2 gpgconf_2.2.27-2 gpgsm_2.2.27-2 gpgv_2.2.27-2 grep_3.7-1 groff-base_1.22.4-7 gzip_1.10-4 hostname_3.23 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 libacl1_2.3.1-1 libapt-pkg6.0_2.3.9 libarchive-zip-perl_1.68-1 libasan6_11.2.0-4+rpi1 libassuan0_2.5.5-1 libatomic1_11.2.0-4+rpi1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.5-1 libaudit1_1:3.0.5-1 libbinutils_2.37-5+rpi1 libblkid1_2.37.2-1 libbrotli1_1.0.9-2+b1 libbz2-1.0_1.0.8-4 libc-bin_2.32-4+rpi1 libc-dev-bin_2.32-4+rpi1 libc6_2.32-4+rpi1 libc6-dev_2.32-4+rpi1 libcap-ng0_0.7.9-2.2+b1 libcc1-0_11.2.0-4+rpi1 libcom-err2_1.46.4-1 libcrypt-dev_1:4.4.25-2 libcrypt1_1:4.4.25-2 libctf-nobfd0_2.37-5+rpi1 libctf0_2.37-5+rpi1 libcurl3-gnutls_7.74.0-1.3 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.260 libdebhelper-perl_13.5.2 libdeflate0_1.8-1 libdpkg-perl_1.20.9+rpi1 libelf1_0.185-2 libext2fs2_1.46.4-1 libfakeroot_1.25.3-1.1 libffi7_3.3-6 libfile-stripnondeterminism-perl_1.12.0-1 libgcc-10-dev_10.3.0-9+rpi1 libgcc-s1_11.2.0-4+rpi1 libgcrypt20_1.9.4-3 libgdbm-compat4_1.21-1 libgdbm6_1.21-1 libgmp10_2:6.2.1+dfsg-2 libgnutls30_3.7.2-2 libgomp1_11.2.0-4+rpi1 libgpg-error0_1.42-3 libgssapi-krb5-2_1.18.3-7 libhogweed6_3.7.3-1 libhts3_1.13+ds-2 libhtscodecs2_1.1.1-3 libicu67_67.1-7 libidn2-0_2.3.2-2 libisl23_0.23-1 libk5crypto3_1.18.3-7 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-7 libkrb5support0_1.18.3-7 libksba8_1.6.0-2 libldap-2.4-2_2.4.59+dfsg-1 liblocale-gettext-perl_1.07-4+b1 liblz4-1_1.9.3-2 liblzma5_5.2.5-2 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmount1_2.37.2-1 libmpc3_1.2.0-1 libmpfr6_4.1.0-3 libncurses6_6.2+20201114-4 libncursesw6_6.2+20201114-4 libnettle8_3.7.3-1 libnghttp2-14_1.43.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.24.0-2 libpam-modules_1.4.0-10 libpam-modules-bin_1.4.0-10 libpam-runtime_1.4.0-10 libpam0g_1.4.0-10 libpcre2-8-0_10.36-2 libpcre3_2:8.39-13 libperl5.32_5.32.1-5 libpipeline1_1.5.3-1 libpsl5_0.21.0-1.2 libreadline8_8.1-2 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.27+dfsg-2.1 libsasl2-modules-db_2.1.27+dfsg-2.1 libseccomp2_2.5.1-1+rpi1 libselinux1_3.1-3 libsemanage-common_3.1-1 libsemanage1_3.1-1+b1 libsepol1_3.1-1 libsigsegv2_2.13-1 libsmartcols1_2.37.2-1 libsqlite3-0_3.36.0-2 libss2_1.46.4-1 libssh2-1_1.10.0-2 libssl1.1_1.1.1l-1 libstdc++-10-dev_10.3.0-9+rpi1 libstdc++6_11.2.0-4+rpi1 libsub-override-perl_0.09-2 libsystemd0_247.9-1+rpi1 libtasn1-6_4.17.0-2 libtext-charwidth-perl_0.04-10+b1 libtext-iconv-perl_1.7-7+b1 libtinfo6_6.2+20201114-4 libtirpc-common_1.3.2-2 libtirpc-dev_1.3.2-2 libtirpc3_1.3.2-2 libtool_2.4.6-15 libubsan1_11.2.0-4+rpi1 libuchardet0_0.0.7-1 libudev1_247.9-1+rpi1 libunistring2_0.9.10-6 libuuid1_2.37.2-1 libxml2_2.9.12+dfsg-5 libxxhash0_0.8.0-2+rpi1 libzstd1_1.4.8+dfsg-2.1+rpi1 linux-libc-dev_5.10.46-4+rpi1 login_1:4.8.1-1 logsave_1.46.4-1 lsb-base_11.1.0+rpi1 m4_1.4.18-5 make_4.3-4.1 man-db_2.9.4-2 mawk_1.3.4.20200120-2 mount_2.37.2-1 ncurses-base_6.2+20201114-4 ncurses-bin_6.2+20201114-4 passwd_1:4.8.1-1 patch_2.7.6-7 perl_5.32.1-5 perl-base_5.32.1-5 perl-modules-5.32_5.32.1-5 pinentry-curses_1.1.0-4 po-debconf_1.0.21+nmu1 raspbian-archive-keyring_20120528.2 readline-common_8.1-2 rpcsvc-proto_1.4.2-4 samtools_1.13-2 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sysvinit-utils_3.00-1 tar_1.34+dfsg-1 tzdata_2021a-1 util-linux_2.37.2-1 xz-utils_5.2.5-2 zlib1g_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: pinfish
Binary: pinfish, pinfish-examples
Architecture: any all
Version: 0.1.0+ds-3
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Nilesh Patra <nilesh@debian.org>
Homepage: https://github.com/nanoporetech/pinfish
Standards-Version: 4.5.1
Vcs-Browser: https://salsa.debian.org/med-team/pinfish
Vcs-Git: https://salsa.debian.org/med-team/pinfish.git
Testsuite: autopkgtest
Build-Depends: debhelper-compat (= 13), dh-golang, golang-any, golang-github-biogo-biogo-dev, golang-github-biogo-hts-dev, golang-github-google-uuid-dev, samtools
Package-List:
pinfish deb science optional arch=any
pinfish-examples deb science optional arch=all
Checksums-Sha1:
72cd9579ffc7d2edd6ad5429c3e934fbe3302746 68559048 pinfish_0.1.0+ds.orig-debian-tests-data.tar.xz
f60646b7255e280e7c3c5487f29707c8de208970 5054956 pinfish_0.1.0+ds.orig.tar.xz
cf52e7e898ca37f3ee60bd7422d7c13d243a0e8b 6372 pinfish_0.1.0+ds-3.debian.tar.xz
Checksums-Sha256:
40957e398ab9bebdc89fe69dbef1c816da544e69a6aeed9c04371430f61f53bb 68559048 pinfish_0.1.0+ds.orig-debian-tests-data.tar.xz
c8213acc3f88d9e1294b9f9014a28b8fd410ebe0aab4793c7bb7263e7e465e4d 5054956 pinfish_0.1.0+ds.orig.tar.xz
ccfbad2121f0a06f90f22604ed06a1f36028ea83e037025de2bbb8e7199ecb48 6372 pinfish_0.1.0+ds-3.debian.tar.xz
Files:
f76133bed3fba383e81cc39b73cccdb1 68559048 pinfish_0.1.0+ds.orig-debian-tests-data.tar.xz
70d87d84ead55e6112f068425ba60c56 5054956 pinfish_0.1.0+ds.orig.tar.xz
f8d0970ad74de5231e6083d4711fe599 6372 pinfish_0.1.0+ds-3.debian.tar.xz
Go-Import-Path: github.com/nanoporetech/pinfish
-----BEGIN PGP SIGNATURE-----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=GthV
-----END PGP SIGNATURE-----
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.N0hPC2xT/trustedkeys.kbx': General error
gpgv: Signature made Tue Aug 17 19:14:28 2021 UTC
gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1
gpgv: issuer "npatra974@gmail.com"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./pinfish_0.1.0+ds-3.dsc
dpkg-source: info: extracting pinfish in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking pinfish_0.1.0+ds.orig.tar.xz
dpkg-source: info: unpacking pinfish_0.1.0+ds.orig-debian-tests-data.tar.xz
dpkg-source: info: unpacking pinfish_0.1.0+ds-3.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying remove-gonum-stat-usage.patch
dpkg-source: info: applying do-not-overflow-int.patch
Check disk space
----------------
Sufficient free space for build
Hack binNMU version
-------------------
Created changelog entry for binNMU version 0.1.0+ds-3+b1
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/112/bus
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
INVOCATION_ID=359bbe4d259442eb9d8f94db1683c24a
JOURNAL_STREAM=8:21869
LANG=en_GB.UTF-8
LC_ALL=C.UTF-8
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PWD=/
SCHROOT_ALIAS_NAME=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=117
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-2e329ca1-f6ce-4f1a-9bce-a16c794345ec
SCHROOT_UID=112
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
XDG_RUNTIME_DIR=/run/user/112
XDG_SESSION_CLASS=background
XDG_SESSION_ID=c9795
XDG_SESSION_TYPE=unspecified
dpkg-buildpackage
-----------------
Command: dpkg-buildpackage -us -uc -mRaspbian pi4 based autobuilder <root@raspbian.org> -B -rfakeroot
dpkg-buildpackage: info: source package pinfish
dpkg-buildpackage: info: source version 0.1.0+ds-3+b1
dpkg-buildpackage: info: source distribution bookworm-staging
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean --builddirectory=_build --buildsystem=golang --with=golang
dh_auto_clean -O--builddirectory=_build -O--buildsystem=golang
dh_autoreconf_clean -O--builddirectory=_build -O--buildsystem=golang
dh_clean -O--builddirectory=_build -O--buildsystem=golang
debian/rules binary-arch
dh binary-arch --builddirectory=_build --buildsystem=golang --with=golang
dh_update_autotools_config -a -O--builddirectory=_build -O--buildsystem=golang
dh_autoreconf -a -O--builddirectory=_build -O--buildsystem=golang
dh_auto_configure -a -O--builddirectory=_build -O--buildsystem=golang
dh_auto_build -a -O--builddirectory=_build -O--buildsystem=golang
cd _build && go install -trimpath -v -p 4 github.com/nanoporetech/pinfish/cluster_gff github.com/nanoporetech/pinfish/collapse_partials github.com/nanoporetech/pinfish/polish_clusters github.com/nanoporetech/pinfish/spliced_bam2gff
internal/unsafeheader
internal/race
runtime/internal/sys
internal/cpu
sync/atomic
unicode
unicode/utf8
runtime/internal/math
math/bits
internal/bytealg
runtime/internal/atomic
math
crypto/internal/subtle
crypto/subtle
runtime
internal/nettrace
runtime/cgo
internal/reflectlite
sync
internal/testlog
math/rand
internal/singleflight
sort
errors
internal/oserror
io
strconv
syscall
path
bytes
strings
hash
crypto
reflect
bufio
github.com/biogo/biogo/feat
github.com/biogo/biogo/feat/gene
github.com/biogo/biogo/io/featio
vendor/golang.org/x/net/dns/dnsmessage
hash/crc32
text/tabwriter
internal/syscall/unix
time
internal/syscall/execenv
container/heap
context
io/fs
internal/poll
internal/fmtsort
encoding/binary
os
crypto/sha1
crypto/md5
crypto/cipher
crypto/aes
path/filepath
fmt
net
io/ioutil
os/exec
encoding/csv
flag
github.com/biogo/biogo/alphabet
math/big
github.com/biogo/biogo/seq
database/sql/driver
github.com/biogo/biogo/feat/genome
github.com/biogo/biogo/io/seqio
github.com/biogo/biogo/seq/linear
github.com/biogo/biogo/io/seqio/fasta
encoding/hex
github.com/biogo/biogo/io/featio/gff
log
compress/flate
github.com/biogo/biogo/io/seqio/fastq
net/url
crypto/rand
compress/gzip
github.com/biogo/hts/bgzf
runtime/pprof
github.com/biogo/hts/bgzf/index
github.com/biogo/hts/internal
github.com/biogo/hts/sam
github.com/biogo/hts/bam
github.com/nanoporetech/pinfish/spliced_bam2gff
github.com/nanoporetech/pinfish/polish_clusters
github.com/google/uuid
github.com/nanoporetech/pinfish/collapse_partials
github.com/nanoporetech/pinfish/cluster_gff
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_test
cd _build && go test -vet=off -v -p 4 github.com/nanoporetech/pinfish/cluster_gff github.com/nanoporetech/pinfish/collapse_partials github.com/nanoporetech/pinfish/polish_clusters github.com/nanoporetech/pinfish/spliced_bam2gff
? github.com/nanoporetech/pinfish/cluster_gff [no test files]
? github.com/nanoporetech/pinfish/collapse_partials [no test files]
? github.com/nanoporetech/pinfish/polish_clusters [no test files]
? github.com/nanoporetech/pinfish/spliced_bam2gff [no test files]
cat debian-tests-data/sirv_e0_sorted.sam| samtools view -Sb - > polish_clusters/test_data/sirv_e0_sorted.bam
cat debian-tests-data/sirv_errors_gmap.sam| samtools view -Sb - > spliced_bam2gff/test_data/sirv_errors_gmap.bam
cat debian-tests-data/sirv_no_errors_gmap.sam| samtools view -Sb - > spliced_bam2gff/test_data/sirv_no_errors_gmap.bam
cat debian-tests-data/sirv_simulated.sam| samtools view -Sb - > spliced_bam2gff/test_data/sirv_simulated.bam
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
create-stamp debian/debhelper-build-stamp
dh_testroot -a -O--builddirectory=_build -O--buildsystem=golang
dh_prep -a -O--builddirectory=_build -O--buildsystem=golang
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_install -- --no-source
cd _build && mkdir -p /<<BUILDDIR>>/pinfish-0.1.0\+ds/debian/tmp/usr
cd _build && cp -r bin /<<BUILDDIR>>/pinfish-0.1.0\+ds/debian/tmp/usr
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_install -a -O--builddirectory=_build -O--buildsystem=golang
dh_installdocs -a -O--builddirectory=_build -O--buildsystem=golang
dh_installchangelogs -a -O--builddirectory=_build -O--buildsystem=golang
dh_installman -a -O--builddirectory=_build -O--buildsystem=golang
dh_installsystemduser -a -O--builddirectory=_build -O--buildsystem=golang
dh_perl -a -O--builddirectory=_build -O--buildsystem=golang
dh_link -a -O--builddirectory=_build -O--buildsystem=golang
dh_strip_nondeterminism -a -O--builddirectory=_build -O--buildsystem=golang
dh_compress -a -O--builddirectory=_build -O--buildsystem=golang
dh_fixperms -a -O--builddirectory=_build -O--buildsystem=golang
dh_missing -a -O--builddirectory=_build -O--buildsystem=golang
dh_dwz -a -O--builddirectory=_build -O--buildsystem=golang
dwz: debian/pinfish/usr/bin/cluster_gff: .debug_info section not present
dwz: debian/pinfish/usr/bin/collapse_partials: .debug_info section not present
dwz: debian/pinfish/usr/bin/polish_clusters: .debug_info section not present
dwz: debian/pinfish/usr/bin/spliced_bam2gff: .debug_info section not present
dwz: Too few files for multifile optimization
dh_dwz: warning: No dwz multifile created, but not explicitly requested either so ignoring it.
dh_dwz: warning: Common issues include no debug information at all (missing -g) and
dh_dwz: warning: compressed debug information (#931891).
dh_strip -a -O--builddirectory=_build -O--buildsystem=golang
dh_strip: warning: Could not find the BuildID in debian/pinfish/usr/bin/spliced_bam2gff
dh_strip: warning: Could not find the BuildID in debian/pinfish/usr/bin/polish_clusters
dh_strip: warning: Could not find the BuildID in debian/pinfish/usr/bin/cluster_gff
dh_strip: warning: Could not find the BuildID in debian/pinfish/usr/bin/collapse_partials
dh_makeshlibs -a -O--builddirectory=_build -O--buildsystem=golang
dh_shlibdeps -a -O--builddirectory=_build -O--buildsystem=golang
dh_installdeb -a -O--builddirectory=_build -O--buildsystem=golang
dh_golang -a -O--builddirectory=_build -O--buildsystem=golang
dh_gencontrol -a -O--builddirectory=_build -O--buildsystem=golang
dpkg-gencontrol: warning: package pinfish: substitution variable ${misc:Built-Using} unused, but is defined
dh_md5sums -a -O--builddirectory=_build -O--buildsystem=golang
dh_builddeb -a -O--builddirectory=_build -O--buildsystem=golang
dpkg-deb: building package 'pinfish' in '../pinfish_0.1.0+ds-3+b1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian pi4 based autobuilder <root@raspbian.org> >../pinfish_0.1.0+ds-3+b1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2021-10-16T14:52:52Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
pinfish_0.1.0+ds-3+b1_armhf.changes:
------------------------------------
Format: 1.8
Date: Sat, 16 Oct 2021 14:51:37 +0000
Source: pinfish (0.1.0+ds-3)
Binary: pinfish
Binary-Only: yes
Architecture: armhf
Version: 0.1.0+ds-3+b1
Distribution: bookworm-staging
Urgency: low
Maintainer: Raspbian pi4 based autobuilder <root@raspbian.org>
Changed-By: Raspbian pi4 based autobuilder <root@raspbian.org>
Description:
pinfish - Collection of tools to annotate genomes using long read transcrip
Changes:
pinfish (0.1.0+ds-3+b1) bookworm-staging; urgency=low, binary-only=yes
.
* Binary-only non-maintainer upload for armhf; no source changes.
* rebuild due to debcheck failure
Checksums-Sha1:
8470b15ff13763b9602452586e275a91296b5c5b 6071 pinfish_0.1.0+ds-3+b1_armhf.buildinfo
327571ee878e9423d4b146d9df4520f2491af01a 1108136 pinfish_0.1.0+ds-3+b1_armhf.deb
Checksums-Sha256:
9ac407e53c48b3acfb188b7471b9afebd553e16d3d900ff501db3ac5f142b341 6071 pinfish_0.1.0+ds-3+b1_armhf.buildinfo
945a75f14053ad3adce276be207ce8aa385c886cdbb358ee3787b759b134f951 1108136 pinfish_0.1.0+ds-3+b1_armhf.deb
Files:
6dcedc2f65525a89a0f6f10053f649a5 6071 science optional pinfish_0.1.0+ds-3+b1_armhf.buildinfo
3bd7098f1ba36403c5b13ed50a0e592c 1108136 science optional pinfish_0.1.0+ds-3+b1_armhf.deb
+------------------------------------------------------------------------------+
| Buildinfo |
+------------------------------------------------------------------------------+
Format: 1.0
Source: pinfish (0.1.0+ds-3)
Binary: pinfish
Architecture: armhf
Version: 0.1.0+ds-3+b1
Binary-Only-Changes:
pinfish (0.1.0+ds-3+b1) bookworm-staging; urgency=low, binary-only=yes
.
* Binary-only non-maintainer upload for armhf; no source changes.
* rebuild due to debcheck failure
.
-- Raspbian pi4 based autobuilder <root@raspbian.org> Sat, 16 Oct 2021 14:51:37 +0000
Checksums-Md5:
3bd7098f1ba36403c5b13ed50a0e592c 1108136 pinfish_0.1.0+ds-3+b1_armhf.deb
Checksums-Sha1:
327571ee878e9423d4b146d9df4520f2491af01a 1108136 pinfish_0.1.0+ds-3+b1_armhf.deb
Checksums-Sha256:
945a75f14053ad3adce276be207ce8aa385c886cdbb358ee3787b759b134f951 1108136 pinfish_0.1.0+ds-3+b1_armhf.deb
Build-Origin: Raspbian
Build-Architecture: armhf
Build-Date: Sat, 16 Oct 2021 14:52:51 +0000
Build-Path: /<<PKGBUILDDIR>>
Installed-Build-Depends:
autoconf (= 2.71-2),
automake (= 1:1.16.4-2),
autopoint (= 0.21-4),
autotools-dev (= 20180224.1+nmu1),
base-files (= 12+rpi1),
base-passwd (= 3.5.51),
bash (= 5.1-3),
binutils (= 2.37-5+rpi1),
binutils-arm-linux-gnueabihf (= 2.37-5+rpi1),
binutils-common (= 2.37-5+rpi1),
bsdextrautils (= 2.37.2-3),
bsdutils (= 1:2.37.2-1),
build-essential (= 12.9),
bzip2 (= 1.0.8-4),
coreutils (= 8.32-4),
cpp (= 4:10.2.1-1+rpi1),
cpp-10 (= 10.3.0-9+rpi1),
dash (= 0.5.11+git20210120+802ebd4-1),
debconf (= 1.5.77),
debhelper (= 13.5.2),
debianutils (= 4.11.2),
dh-autoreconf (= 20),
dh-golang (= 1.51),
dh-strip-nondeterminism (= 1.12.0-1),
diffutils (= 1:3.7-5),
dpkg (= 1.20.9+rpi1),
dpkg-dev (= 1.20.9+rpi1),
dwz (= 0.14-1),
file (= 1:5.39-3),
findutils (= 4.8.0-1),
g++ (= 4:10.2.1-1+rpi1),
g++-10 (= 10.3.0-9+rpi1),
gcc (= 4:10.2.1-1+rpi1),
gcc-10 (= 10.3.0-9+rpi1),
gcc-10-base (= 10.3.0-9+rpi1),
gcc-11-base (= 11.2.0-4+rpi1),
gettext (= 0.21-4),
gettext-base (= 0.21-4),
golang-1.16-go (= 1.16.9-2),
golang-1.16-src (= 1.16.9-2),
golang-any (= 2:1.16~1),
golang-github-biogo-biogo-dev (= 1.0.3-1),
golang-github-biogo-hts-dev (= 1.1.0+dfsg1-3),
golang-github-creack-pty-dev (= 1.1.15-1),
golang-github-google-uuid-dev (= 1.2.0-1),
golang-github-kr-pretty-dev (= 0.2.1+git20200831.59b4212-1),
golang-github-kr-text-dev (= 0.2.0-1),
golang-github-ulikunitz-xz-dev (= 0.5.6-2),
golang-go (= 2:1.16~1),
golang-gopkg-check.v1-dev (= 0.0+git20200902.038fdea-1),
golang-src (= 2:1.16~1),
grep (= 3.7-1),
groff-base (= 1.22.4-7),
gzip (= 1.10-4),
hostname (= 3.23),
init-system-helpers (= 1.60),
intltool-debian (= 0.35.0+20060710.5),
libacl1 (= 2.3.1-1),
libarchive-zip-perl (= 1.68-1),
libasan6 (= 11.2.0-4+rpi1),
libatomic1 (= 11.2.0-4+rpi1),
libattr1 (= 1:2.5.1-1),
libaudit-common (= 1:3.0.5-1),
libaudit1 (= 1:3.0.5-1),
libbinutils (= 2.37-5+rpi1),
libblkid1 (= 2.37.2-1),
libbrotli1 (= 1.0.9-2+b1),
libbz2-1.0 (= 1.0.8-4),
libc-bin (= 2.32-4+rpi1),
libc-dev-bin (= 2.32-4+rpi1),
libc6 (= 2.32-4+rpi1),
libc6-dev (= 2.32-4+rpi1),
libcap-ng0 (= 0.7.9-2.2+b1),
libcc1-0 (= 11.2.0-4+rpi1),
libcom-err2 (= 1.46.4-1),
libcrypt-dev (= 1:4.4.25-2),
libcrypt1 (= 1:4.4.25-2),
libctf-nobfd0 (= 2.37-5+rpi1),
libctf0 (= 2.37-5+rpi1),
libcurl3-gnutls (= 7.74.0-1.3),
libdb5.3 (= 5.3.28+dfsg1-0.8),
libdebconfclient0 (= 0.260),
libdebhelper-perl (= 13.5.2),
libdeflate0 (= 1.8-1),
libdpkg-perl (= 1.20.9+rpi1),
libelf1 (= 0.185-2),
libffi7 (= 3.3-6),
libfile-stripnondeterminism-perl (= 1.12.0-1),
libgcc-10-dev (= 10.3.0-9+rpi1),
libgcc-s1 (= 11.2.0-4+rpi1),
libgcrypt20 (= 1.9.4-3),
libgdbm-compat4 (= 1.21-1),
libgdbm6 (= 1.21-1),
libgmp10 (= 2:6.2.1+dfsg-2),
libgnutls30 (= 3.7.2-2),
libgomp1 (= 11.2.0-4+rpi1),
libgpg-error0 (= 1.42-3),
libgssapi-krb5-2 (= 1.18.3-7),
libhogweed6 (= 3.7.3-1),
libhts3 (= 1.13+ds-2),
libhtscodecs2 (= 1.1.1-3),
libicu67 (= 67.1-7),
libidn2-0 (= 2.3.2-2),
libisl23 (= 0.23-1),
libk5crypto3 (= 1.18.3-7),
libkeyutils1 (= 1.6.1-2),
libkrb5-3 (= 1.18.3-7),
libkrb5support0 (= 1.18.3-7),
libldap-2.4-2 (= 2.4.59+dfsg-1),
liblz4-1 (= 1.9.3-2),
liblzma5 (= 5.2.5-2),
libmagic-mgc (= 1:5.39-3),
libmagic1 (= 1:5.39-3),
libmount1 (= 2.37.2-1),
libmpc3 (= 1.2.0-1),
libmpfr6 (= 4.1.0-3),
libncurses6 (= 6.2+20201114-4),
libnettle8 (= 3.7.3-1),
libnghttp2-14 (= 1.43.0-1),
libnsl-dev (= 1.3.0-2),
libnsl2 (= 1.3.0-2),
libp11-kit0 (= 0.24.0-2),
libpam-modules (= 1.4.0-10),
libpam-modules-bin (= 1.4.0-10),
libpam-runtime (= 1.4.0-10),
libpam0g (= 1.4.0-10),
libpcre2-8-0 (= 10.36-2),
libpcre3 (= 2:8.39-13),
libperl5.32 (= 5.32.1-5),
libpipeline1 (= 1.5.3-1),
libpsl5 (= 0.21.0-1.2),
librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b2),
libsasl2-2 (= 2.1.27+dfsg-2.1),
libsasl2-modules-db (= 2.1.27+dfsg-2.1),
libseccomp2 (= 2.5.1-1+rpi1),
libselinux1 (= 3.1-3),
libsigsegv2 (= 2.13-1),
libsmartcols1 (= 2.37.2-1),
libssh2-1 (= 1.10.0-2),
libssl1.1 (= 1.1.1l-1),
libstdc++-10-dev (= 10.3.0-9+rpi1),
libstdc++6 (= 11.2.0-4+rpi1),
libsub-override-perl (= 0.09-2),
libsystemd0 (= 247.9-1+rpi1),
libtasn1-6 (= 4.17.0-2),
libtinfo6 (= 6.2+20201114-4),
libtirpc-common (= 1.3.2-2),
libtirpc-dev (= 1.3.2-2),
libtirpc3 (= 1.3.2-2),
libtool (= 2.4.6-15),
libubsan1 (= 11.2.0-4+rpi1),
libuchardet0 (= 0.0.7-1),
libudev1 (= 247.9-1+rpi1),
libunistring2 (= 0.9.10-6),
libuuid1 (= 2.37.2-1),
libxml2 (= 2.9.12+dfsg-5),
libzstd1 (= 1.4.8+dfsg-2.1+rpi1),
linux-libc-dev (= 5.10.46-4+rpi1),
login (= 1:4.8.1-1),
lsb-base (= 11.1.0+rpi1),
m4 (= 1.4.18-5),
make (= 4.3-4.1),
man-db (= 2.9.4-2),
mawk (= 1.3.4.20200120-2),
ncurses-base (= 6.2+20201114-4),
ncurses-bin (= 6.2+20201114-4),
patch (= 2.7.6-7),
perl (= 5.32.1-5),
perl-base (= 5.32.1-5),
perl-modules-5.32 (= 5.32.1-5),
po-debconf (= 1.0.21+nmu1),
rpcsvc-proto (= 1.4.2-4),
samtools (= 1.13-2),
sed (= 4.8-1),
sensible-utils (= 0.0.17),
sysvinit-utils (= 3.00-1),
tar (= 1.34+dfsg-1),
util-linux (= 2.37.2-1),
xz-utils (= 5.2.5-2),
zlib1g (= 1:1.2.11.dfsg-2)
Environment:
DEB_BUILD_OPTIONS="parallel=4"
LANG="en_GB.UTF-8"
LC_ALL="C.UTF-8"
SOURCE_DATE_EPOCH="1634395897"
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
pinfish_0.1.0+ds-3+b1_armhf.deb
-------------------------------
new Debian package, version 2.0.
size 1108136 bytes: control archive=1456 bytes.
1683 bytes, 39 lines control
748 bytes, 11 lines md5sums
Package: pinfish
Source: pinfish (0.1.0+ds-3)
Version: 0.1.0+ds-3+b1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 7429
Depends: libc6 (>= 2.32), minimap2, racon
Section: science
Priority: optional
Homepage: https://github.com/nanoporetech/pinfish
Description: Collection of tools to annotate genomes using long read transcriptomics data
The toolchain is composed of the following tools:
1. spliced_bam2gff - a tool for converting sorted BAM
files containing spliced alignments
into GFF2 format. Each read will be represented as a distinct
transcript. This tool comes handy when visualizing spliced
reads at particular loci and to provide input to the rest
of the toolchain.
.
2. cluster_gff - this tool takes a sorted GFF2 file as
input and clusters together reads having similar
exon/intron structure and creates a rough consensus
of the clusters by taking the median of exon
boundaries from all transcripts in the cluster.
.
3. polish_clusters - this tool takes the cluster
definitions generated by cluster_gff and for each
cluster creates an error corrected read by mapping
all reads on the read with the median length
and polishing it using racon. The polished reads
can be mapped to the genome using minimap2 or GMAP.
.
4. collapse_partials - this tool takes GFFs generated
by either cluster_gff or polish_clusters and filters
out transcripts which are likely to be based on RNA
degradation products from the 5' end. The tool clusters
the input transcripts into "loci" by the 3' ends and
discards transcripts which have a compatible transcripts
in the loci with more exons.
drwxr-xr-x root/root 0 2021-10-16 14:51 ./
drwxr-xr-x root/root 0 2021-10-16 14:51 ./usr/
drwxr-xr-x root/root 0 2021-10-16 14:51 ./usr/bin/
-rwxr-xr-x root/root 1933752 2021-10-16 14:51 ./usr/bin/cluster_gff
-rwxr-xr-x root/root 1933752 2021-10-16 14:51 ./usr/bin/collapse_partials
-rwxr-xr-x root/root 1926116 2021-10-16 14:51 ./usr/bin/polish_clusters
-rwxr-xr-x root/root 1794484 2021-10-16 14:51 ./usr/bin/spliced_bam2gff
drwxr-xr-x root/root 0 2021-10-16 14:51 ./usr/share/
drwxr-xr-x root/root 0 2021-10-16 14:51 ./usr/share/doc/
drwxr-xr-x root/root 0 2021-10-16 14:51 ./usr/share/doc/pinfish/
-rw-r--r-- root/root 221 2021-10-16 14:51 ./usr/share/doc/pinfish/changelog.Debian.armhf.gz
-rw-r--r-- root/root 400 2021-10-16 14:51 ./usr/share/doc/pinfish/changelog.Debian.gz
-rw-r--r-- root/root 1213 2021-08-17 15:56 ./usr/share/doc/pinfish/copyright
drwxr-xr-x root/root 0 2021-10-16 14:51 ./usr/share/man/
drwxr-xr-x root/root 0 2021-10-16 14:51 ./usr/share/man/man1/
-rw-r--r-- root/root 532 2021-10-16 14:51 ./usr/share/man/man1/cluster_gff.1.gz
-rw-r--r-- root/root 536 2021-10-16 14:51 ./usr/share/man/man1/collapse_partials.1.gz
-rw-r--r-- root/root 548 2021-10-16 14:51 ./usr/share/man/man1/polish_clusters.1.gz
-rw-r--r-- root/root 482 2021-10-16 14:51 ./usr/share/man/man1/spliced_bam2gff.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build Type: any
Build-Space: 475036
Build-Time: 75
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 447
Job: pinfish_0.1.0+ds-3
Machine Architecture: armhf
Package: pinfish
Package-Time: 575
Source-Version: 0.1.0+ds-3
Space: 475036
Status: successful
Version: 0.1.0+ds-3+b1
--------------------------------------------------------------------------------
Finished at 2021-10-16T14:52:52Z
Build needed 00:09:35, 475036k disk space