pinfish →
0.1.0+ds-3 →
armhf → 2021-08-23 23:30:54
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-01
+==============================================================================+
| pinfish 0.1.0+ds-3 (armhf) Mon, 23 Aug 2021 23:25:49 +0000 |
+==============================================================================+
Package: pinfish
Version: 0.1.0+ds-3
Source Version: 0.1.0+ds-3
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bookworm-staging-armhf-sbuild-2ba48a6c-f108-460f-a7ce-9d7de1d05b4c' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| 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 [12.3 MB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf Packages [13.3 MB]
Fetched 25.6 MB in 9s (2786 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| 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 21s (3490 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/pinfish-ebYJoJ/pinfish-0.1.0+ds' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/pinfish-ebYJoJ' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-pxe4tG/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-pxe4tG/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-pxe4tG/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-pxe4tG/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-pxe4tG/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-pxe4tG/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-pxe4tG/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-pxe4tG/apt_archive ./ Packages [433 B]
Fetched 2109 B in 0s (9859 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 18 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-pxe4tG/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (66.6 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12488 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| 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
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
dpkg-deb: building package 'sbuild-build-depends-pinfish-dummy' in '/<<BUILDDIR>>/resolver-pxe4tG/apt_archive/sbuild-build-depends-pinfish-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-pinfish-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-pxe4tG/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-pxe4tG/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-pxe4tG/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-pxe4tG/apt_archive ./ Sources [538 B]
Get:5 copy:/<<BUILDDIR>>/resolver-pxe4tG/apt_archive ./ Packages [626 B]
Fetched 2497 B in 0s (11.7 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install pinfish build dependencies (apt-based resolver)
-------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
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-1.15-go golang-1.15-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 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-1.15-go golang-1.15-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 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-pinfish-dummy sensible-utils
0 upgraded, 56 newly installed, 0 to remove and 18 not upgraded.
Need to get 77.2 MB of archives.
After this operation, 406 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-pxe4tG/apt_archive ./ sbuild-build-depends-pinfish-dummy 0.invalid.0 [908 B]
Get:2 http://172.17.0.1/private bookworm-staging/main armhf bsdextrautils armhf 2.36.1-8 [137 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 1.22.4-6 [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 0.0.14 [14.8 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 2.69-14 [313 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 1:1.16.3-2 [814 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 13.4.1 [191 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 2.9.10+dfsg-6.7 [580 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 13.4.1 [1039 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-1.15-src armhf 1.15.9-6+rpi1 [13.8 MB]
Get:35 http://172.17.0.1/private bookworm-staging/main armhf golang-1.15-go armhf 1.15.9-6+rpi1 [43.1 MB]
Get:36 http://172.17.0.1/private bookworm-staging/main armhf golang-src armhf 2:1.15~1 [4856 B]
Get:37 http://172.17.0.1/private bookworm-staging/main armhf golang-go armhf 2:1.15~1 [23.9 kB]
Get:38 http://172.17.0.1/private bookworm-staging/main armhf golang-any armhf 2:1.15~1 [4976 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+dfsg1-2 [292 kB]
Get:41 http://172.17.0.1/private bookworm-staging/main armhf golang-github-creack-pty-dev all 1.1.11-1 [8380 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 1.9.0-3 [151 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 1.7-1 [44.0 kB]
Get:54 http://172.17.0.1/private bookworm-staging/main armhf libhts3 armhf 1.11-4 [324 kB]
Get:55 http://172.17.0.1/private bookworm-staging/main armhf libncurses6 armhf 6.2+20201114-2 [79.9 kB]
Get:56 http://172.17.0.1/private bookworm-staging/main armhf samtools armhf 1.11-1 [502 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Unpacking golang-github-google-uuid-dev (1.2.0-1) ...
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Unpacking libnghttp2-14:armhf (1.43.0-1) ...
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Unpacking sbuild-build-depends-pinfish-dummy (0.invalid.0) ...
Setting up libpipeline1:armhf (1.5.3-1) ...
Setting up libpsl5:armhf (0.21.0-1.2) ...
Setting up bsdextrautils (2.36.1-8) ...
update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode
Setting up golang-github-creack-pty-dev (1.1.11-1) ...
Setting up libicu67:armhf (67.1-7) ...
Setting up libmagic-mgc (1:5.39-3) ...
Setting up golang-1.15-src (1.15.9-6+rpi1) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libdebhelper-perl (13.4.1) ...
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 (1.7-1) ...
Setting up gettext-base (0.21-4) ...
Setting up file (1:5.39-3) ...
Setting up autotools-dev (20180224.1+nmu1) ...
Setting up golang-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+20201114-2) ...
Setting up libsigsegv2:armhf (2.13-1) ...
Setting up autopoint (0.21-4) ...
Setting up sensible-utils (0.0.14) ...
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 (1.9.0-3) ...
Setting up golang-src:armhf (2:1.15~1) ...
Setting up golang-1.15-go (1.15.9-6+rpi1) ...
Setting up libelf1:armhf (0.185-2) ...
Setting up libxml2:armhf (2.9.10+dfsg-6.7) ...
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 golang-go (2:1.15~1) ...
Setting up m4 (1.4.18-5) ...
Setting up libcurl3-gnutls:armhf (7.74.0-1.3) ...
Setting up golang-gopkg-check.v1-dev (0.0+git20200902.038fdea-1) ...
Setting up golang-any:armhf (2:1.15~1) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up golang-github-biogo-hts-dev (1.1.0+dfsg1-2) ...
Setting up autoconf (2.69-14) ...
Setting up dh-strip-nondeterminism (1.12.0-1) ...
Setting up dwz (0.14-1) ...
Setting up groff-base (1.22.4-6) ...
Setting up automake (1:1.16.3-2) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libhts3:armhf (1.11-4) ...
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 samtools (1.11-1) ...
Setting up dh-autoreconf (20) ...
Setting up golang-github-biogo-biogo-dev (1.0.3-1) ...
Setting up debhelper (13.4.1) ...
Setting up dh-golang (1.51) ...
Setting up sbuild-build-depends-pinfish-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.31-13+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.15.0-76-generic armhf (armv8l)
Toolchain package versions: binutils_2.35.2-2+rpi1 dpkg-dev_1.20.9+rpi1 g++-10_10.2.1-6+rpi1 gcc-10_10.2.1-6+rpi1 libc6-dev_2.31-13+rpi1 libstdc++-10-dev_10.2.1-6+rpi1 libstdc++6_10.2.1-6+rpi1 linux-libc-dev_5.10.46-4+rpi1
Package versions: adduser_3.118 apt_2.2.4 autoconf_2.69-14 automake_1:1.16.3-2 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_11.1+rpi1 base-passwd_3.5.51 bash_5.1-2 binutils_2.35.2-2+rpi1 binutils-arm-linux-gnueabihf_2.35.2-2+rpi1 binutils-common_2.35.2-2+rpi1 bsdextrautils_2.36.1-8 bsdutils_1:2.36.1-8 build-essential_12.9 bzip2_1.0.8-4 coreutils_8.32-4 cpp_4:10.2.1-1+rpi1 cpp-10_10.2.1-6+rpi1 dash_0.5.11+git20200708+dd9ef66-5 debconf_1.5.77 debhelper_13.4.1 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_1.46.2-2 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_10.2.1-6+rpi1 gcc_4:10.2.1-1+rpi1 gcc-10_10.2.1-6+rpi1 gcc-10-base_10.2.1-6+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.3.0-22+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-1.15-go_1.15.9-6+rpi1 golang-1.15-src_1.15.9-6+rpi1 golang-any_2:1.15~1 golang-github-biogo-biogo-dev_1.0.3-1 golang-github-biogo-hts-dev_1.1.0+dfsg1-2 golang-github-creack-pty-dev_1.1.11-1 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_2:1.15~1 golang-gopkg-check.v1-dev_0.0+git20200902.038fdea-1 golang-src_2:1.15~1 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_3.6-1 groff-base_1.22.4-6 gzip_1.10-4 hostname_3.23 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-10 libapt-pkg6.0_2.2.4 libarchive-zip-perl_1.68-1 libasan6_10.2.1-6+rpi1 libassuan0_2.5.3-7.1 libatomic1_10.2.1-6+rpi1 libattr1_1:2.4.48-6 libaudit-common_1:3.0-2 libaudit1_1:3.0-2 libbinutils_2.35.2-2+rpi1 libblkid1_2.36.1-8 libbrotli1_1.0.9-2+b1 libbz2-1.0_1.0.8-4 libc-bin_2.31-13+rpi1 libc-dev-bin_2.31-13+rpi1 libc6_2.31-13+rpi1 libc6-dev_2.31-13+rpi1 libcap-ng0_0.7.9-2.2+b1 libcc1-0_10.2.1-6+rpi1 libcom-err2_1.46.2-2 libcrypt-dev_1:4.4.18-4 libcrypt1_1:4.4.18-4 libctf-nobfd0_2.35.2-2+rpi1 libctf0_2.35.2-2+rpi1 libcurl3-gnutls_7.74.0-1.3 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.260 libdebhelper-perl_13.4.1 libdeflate0_1.7-1 libdpkg-perl_1.20.9+rpi1 libelf1_0.185-2 libext2fs2_1.46.2-2 libfakeroot_1.25.3-1.1 libffi7_3.3-6 libfile-stripnondeterminism-perl_1.12.0-1 libgcc-10-dev_10.2.1-6+rpi1 libgcc-s1_10.2.1-6+rpi1 libgcrypt20_1.8.7-6 libgdbm-compat4_1.19-2 libgdbm6_1.19-2 libgmp10_2:6.2.1+dfsg-1 libgnutls30_3.7.1-5 libgomp1_10.2.1-6+rpi1 libgpg-error0_1.38-2 libgssapi-krb5-2_1.18.3-6 libhogweed6_3.7.3-1 libhts3_1.11-4 libicu67_67.1-7 libidn2-0_2.3.0-5 libisl23_0.23-1 libk5crypto3_1.18.3-6 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-6 libkrb5support0_1.18.3-6 libksba8_1.5.0-3 libldap-2.4-2_2.4.57+dfsg-3 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_2.36.1-8 libmpc3_1.2.0-1 libmpfr6_4.1.0-3 libncurses6_6.2+20201114-2 libncursesw6_6.2+20201114-2 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_0.23.22-1 libpam-modules_1.4.0-9 libpam-modules-bin_1.4.0-9 libpam-runtime_1.4.0-9 libpam0g_1.4.0-9 libpcre2-8-0_10.36-2 libpcre3_2:8.39-13 libperl5.32_5.32.1-4+deb11u1 libpipeline1_1.5.3-1 libpsl5_0.21.0-1.2 libreadline8_8.1-1 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_2.36.1-8 libsqlite3-0_3.34.1-3 libss2_1.46.2-2 libssh2-1_1.9.0-3 libssl1.1_1.1.1k-1 libstdc++-10-dev_10.2.1-6+rpi1 libstdc++6_10.2.1-6+rpi1 libsub-override-perl_0.09-2 libsystemd0_247.3-6+rpi1 libtasn1-6_4.16.0-2 libtext-charwidth-perl_0.04-10+b1 libtext-iconv-perl_1.7-7+b1 libtinfo6_6.2+20201114-2 libtirpc-common_1.3.1-1 libtirpc-dev_1.3.1-1 libtirpc3_1.3.1-1 libtool_2.4.6-15 libubsan1_10.2.1-6+rpi1 libuchardet0_0.0.7-1 libudev1_247.3-6+rpi1 libunistring2_0.9.10-4 libuuid1_2.36.1-8 libxml2_2.9.10+dfsg-6.7 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_1.46.2-2 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_2.36.1-8 ncurses-base_6.2+20201114-2 ncurses-bin_6.2+20201114-2 netbase_6.3 passwd_1:4.8.1-1 patch_2.7.6-7 perl_5.32.1-4+deb11u1 perl-base_5.32.1-4+deb11u1 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 samtools_1.11-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-pinfish-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.14 sysvinit-utils_2.96-7 tar_1.34+dfsg-1 tzdata_2021a-1 util-linux_2.36.1-8 xz-utils_5.2.5-2 zlib1g_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.jhAwcStz/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 /<<BUILDDIR>>/pinfish-0.1.0+ds
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
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-2ba48a6c-f108-460f-a7ce-9d7de1d05b4c
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package pinfish
dpkg-buildpackage: info: source version 0.1.0+ds-3
dpkg-buildpackage: info: source distribution unstable
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
runtime/internal/sys
internal/race
internal/cpu
sync/atomic
unicode
runtime/internal/math
unicode/utf8
runtime/internal/atomic
internal/bytealg
math/bits
internal/testlog
crypto/internal/subtle
math
runtime
crypto/subtle
internal/nettrace
runtime/cgo
internal/reflectlite
sync
internal/singleflight
math/rand
errors
sort
strconv
internal/oserror
io
syscall
vendor/golang.org/x/net/dns/dnsmessage
bytes
strings
reflect
hash
crypto
bufio
github.com/biogo/biogo/feat
github.com/biogo/biogo/feat/gene
internal/syscall/unix
time
internal/syscall/execenv
github.com/biogo/biogo/io/featio
hash/crc32
text/tabwriter
container/heap
context
internal/poll
internal/fmtsort
encoding/binary
os
crypto/sha1
crypto/cipher
crypto/md5
path/filepath
fmt
crypto/aes
net
io/ioutil
os/exec
encoding/csv
flag
github.com/biogo/biogo/alphabet
math/big
database/sql/driver
github.com/biogo/biogo/seq
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 '/<<BUILDDIR>>/pinfish-0.1.0+ds'
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 '/<<BUILDDIR>>/pinfish-0.1.0+ds'
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 '/<<BUILDDIR>>/pinfish-0.1.0+ds'
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 '/<<BUILDDIR>>/pinfish-0.1.0+ds'
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 -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 -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/collapse_partials
dh_strip: warning: Could not find the BuildID in debian/pinfish/usr/bin/cluster_gff
dh_makeshlibs -a -a -O--builddirectory=_build -O--buildsystem=golang
dh_shlibdeps -a -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_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../pinfish_0.1.0+ds-3_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 2021-08-23T23:30:49Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
pinfish_0.1.0+ds-3_armhf.changes:
---------------------------------
Format: 1.8
Date: Tue, 17 Aug 2021 21:33:10 +0530
Source: pinfish
Binary: pinfish
Architecture: armhf
Version: 0.1.0+ds-3
Distribution: bookworm-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Nilesh Patra <nilesh@debian.org>
Description:
pinfish - Collection of tools to annotate genomes using long read transcrip
Changes:
pinfish (0.1.0+ds-3) unstable; urgency=medium
.
* Declare compliance with policy 4.5.1
* Remove d/gitlab-ci.yml, add d/salsa-ci.yml
* d/p/do-not-overflow-int.patch: Declare minlen as
per arch that we are building on to avoid
integer overflow
Checksums-Sha1:
7cf503737b6b0afdd8a828d008d0149b0610288d 5690 pinfish_0.1.0+ds-3_armhf.buildinfo
169edb3c77ae3977c71f401a82fa4deefa5455a2 1188376 pinfish_0.1.0+ds-3_armhf.deb
Checksums-Sha256:
d0f6268b7556697e80a2e6abe6ef903e062056100072ae81983502c33e6e370f 5690 pinfish_0.1.0+ds-3_armhf.buildinfo
681150ce935e27977b38dcadb3f47f2a4abc0014aaaf5f1c1a289acc56304fda 1188376 pinfish_0.1.0+ds-3_armhf.deb
Files:
78dd4bb2b52ec492a188f4c69f0cc15d 5690 science optional pinfish_0.1.0+ds-3_armhf.buildinfo
f2625b31fffbbaf4132ead79fcf0abe8 1188376 science optional pinfish_0.1.0+ds-3_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
pinfish_0.1.0+ds-3_armhf.deb
----------------------------
new Debian package, version 2.0.
size 1188376 bytes: control archive=1424 bytes.
1650 bytes, 38 lines control
666 bytes, 10 lines md5sums
Package: pinfish
Version: 0.1.0+ds-3
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 7512
Depends: libc6 (>= 2.4), 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 2021-08-17 16:03 ./
drwxr-xr-x root/root 0 2021-08-17 16:03 ./usr/
drwxr-xr-x root/root 0 2021-08-17 16:03 ./usr/bin/
-rwxr-xr-x root/root 1922096 2021-08-17 16:03 ./usr/bin/cluster_gff
-rwxr-xr-x root/root 1922096 2021-08-17 16:03 ./usr/bin/collapse_partials
-rwxr-xr-x root/root 2045884 2021-08-17 16:03 ./usr/bin/polish_clusters
-rwxr-xr-x root/root 1783132 2021-08-17 16:03 ./usr/bin/spliced_bam2gff
drwxr-xr-x root/root 0 2021-08-17 16:03 ./usr/share/
drwxr-xr-x root/root 0 2021-08-17 16:03 ./usr/share/doc/
drwxr-xr-x root/root 0 2021-08-17 16:03 ./usr/share/doc/pinfish/
-rw-r--r-- root/root 400 2021-08-17 16:03 ./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 2021-08-17 16:03 ./usr/share/man/
drwxr-xr-x root/root 0 2021-08-17 16:03 ./usr/share/man/man1/
-rw-r--r-- root/root 532 2021-08-17 16:03 ./usr/share/man/man1/cluster_gff.1.gz
-rw-r--r-- root/root 536 2021-08-17 16:03 ./usr/share/man/man1/collapse_partials.1.gz
-rw-r--r-- root/root 548 2021-08-17 16:03 ./usr/share/man/man1/polish_clusters.1.gz
-rw-r--r-- root/root 482 2021-08-17 16:03 ./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-Space: 469128
Build-Time: 53
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 195
Job: pinfish_0.1.0+ds-3
Machine Architecture: armhf
Package: pinfish
Package-Time: 300
Source-Version: 0.1.0+ds-3
Space: 469128
Status: successful
Version: 0.1.0+ds-3
--------------------------------------------------------------------------------
Finished at 2021-08-23T23:30:49Z
Build needed 00:05:00, 469128k disk space