seqprep →
1.3.2-5 →
armhf → 2020-01-22 05:23:06
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-01
+==============================================================================+
| seqprep 1.3.2-5 (armhf) Wed, 22 Jan 2020 05:16:45 +0000 |
+==============================================================================+
Package: seqprep
Version: 1.3.2-5
Source Version: 1.3.2-5
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bullseye-staging-armhf-sbuild-f9afbd8d-033d-4653-b6be-2b94a998244a' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [11.5 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.8 MB]
Fetched 24.3 MB in 9s (2559 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: 'seqprep' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/seqprep.git
Please use:
git clone https://salsa.debian.org/med-team/seqprep.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 37.2 MB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main seqprep 1.3.2-5 (dsc) [2108 B]
Get:2 http://172.17.0.1/private bullseye-staging/main seqprep 1.3.2-5 (tar) [37.2 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main seqprep 1.3.2-5 (diff) [10.9 kB]
Fetched 37.2 MB in 8s (4728 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/seqprep-qjhRAc/seqprep-1.3.2' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/seqprep-qjhRAc' 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-Tqhdb1/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-Tqhdb1/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-Tqhdb1/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-Tqhdb1/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-Tqhdb1/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-Tqhdb1/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-Tqhdb1/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-Tqhdb1/apt_archive ./ Packages [430 B]
Fetched 2106 B in 0s (9707 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 packages were automatically installed and are no longer required:
libpam-cap netbase
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 2 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-Tqhdb1/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 (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12207 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 (= 12), python3, markdown, zlib1g-dev
Filtered Build-Depends: debhelper-compat (= 12), python3, markdown, zlib1g-dev
dpkg-deb: building package 'sbuild-build-depends-seqprep-dummy' in '/<<BUILDDIR>>/resolver-Tqhdb1/apt_archive/sbuild-build-depends-seqprep-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-seqprep-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-Tqhdb1/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-Tqhdb1/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-Tqhdb1/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-Tqhdb1/apt_archive ./ Sources [516 B]
Get:5 copy:/<<BUILDDIR>>/resolver-Tqhdb1/apt_archive ./ Packages [593 B]
Fetched 2442 B in 0s (11.3 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install seqprep build dependencies (apt-based resolver)
-------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
libpam-cap netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libbsd0 libcroco3
libdebhelper-perl libelf1 libexpat1 libfile-stripnondeterminism-perl
libglib2.0-0 libicu63 libmagic-mgc libmagic1 libmpdec2 libpipeline1
libpython3-stdlib libpython3.7-minimal libpython3.7-stdlib libsigsegv2
libssl1.1 libsub-override-perl libtinfo5 libtool libuchardet0 libxml2 m4
man-db markdown mime-support po-debconf python3 python3-minimal python3.7
python3.7-minimal sensible-utils zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff
libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less
www-browser libmail-box-perl python3-doc python3-tk python3-venv
python3.7-venv python3.7-doc binfmt-support
Recommended packages:
curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libbsd0 libcroco3
libdebhelper-perl libelf1 libexpat1 libfile-stripnondeterminism-perl
libglib2.0-0 libicu63 libmagic-mgc libmagic1 libmpdec2 libpipeline1
libpython3-stdlib libpython3.7-minimal libpython3.7-stdlib libsigsegv2
libssl1.1 libsub-override-perl libtinfo5 libtool libuchardet0 libxml2 m4
man-db markdown mime-support po-debconf python3 python3-minimal python3.7
python3.7-minimal sbuild-build-depends-seqprep-dummy sensible-utils
zlib1g-dev
0 upgraded, 49 newly installed, 0 to remove and 2 not upgraded.
Need to get 24.6 MB of archives.
After this operation, 93.5 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-Tqhdb1/apt_archive ./ sbuild-build-depends-seqprep-dummy 0.invalid.0 [880 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libbsd0 armhf 0.10.0-1 [112 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf libtinfo5 armhf 6.1+20191019-1 [316 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-4 [783 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.2-2 [29.6 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.0-2 [1261 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf libssl1.1 armhf 1.1.1d-2 [1268 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libpython3.7-minimal armhf 3.7.6-1 [585 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf libexpat1 armhf 2.2.9-1 [71.5 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf python3.7-minimal armhf 3.7.6-1 [1527 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf python3-minimal armhf 3.7.5-3 [36.8 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf mime-support all 3.64 [37.8 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf libmpdec2 armhf 2.4.2-2 [67.2 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf libpython3.7-stdlib armhf 3.7.6-1 [1669 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf python3.7 armhf 3.7.6-1 [350 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf libpython3-stdlib armhf 3.7.5-3 [20.2 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf python3 armhf 3.7.5-3 [62.1 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf sensible-utils all 0.0.12+nmu1 [16.0 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.38-3 [262 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.38-3 [112 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.38-3 [66.8 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.1-4 [771 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-11 [547 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 12.7.3 [174 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.67-1 [104 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.6.3-1 [23.6 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.6.3-1 [14.6 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.176-1.1 [158 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-5 [142 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.62.4-1 [1138 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf libicu63 armhf 63.2-2 [7974 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.4+dfsg1-8 [593 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 12.7.3 [1019 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf markdown all 1.0.1-10 [17.4 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Selecting previously unselected package po-debconf.
Preparing to unpack .../27-po-debconf_1.0.21_all.deb ...
Unpacking po-debconf (1.0.21) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../28-debhelper_12.7.3_all.deb ...
Unpacking debhelper (12.7.3) ...
Selecting previously unselected package markdown.
Preparing to unpack .../29-markdown_1.0.1-10_all.deb ...
Unpacking markdown (1.0.1-10) ...
Selecting previously unselected package zlib1g-dev:armhf.
Preparing to unpack .../30-zlib1g-dev_1%3a1.2.11.dfsg-1_armhf.deb ...
Unpacking zlib1g-dev:armhf (1:1.2.11.dfsg-1) ...
Selecting previously unselected package sbuild-build-depends-seqprep-dummy.
Preparing to unpack .../31-sbuild-build-depends-seqprep-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-seqprep-dummy (0.invalid.0) ...
Setting up libpipeline1:armhf (1.5.2-2) ...
Setting up mime-support (3.64) ...
Setting up libmagic-mgc (1:5.38-3) ...
Setting up libarchive-zip-perl (1.67-1) ...
Setting up libglib2.0-0:armhf (2.62.4-1) ...
No schema files found: doing nothing.
Setting up libdebhelper-perl (12.7.3) ...
Setting up libmagic1:armhf (1:5.38-3) ...
Setting up gettext-base (0.19.8.1-10) ...
Setting up file (1:5.38-3) ...
Setting up libicu63:armhf (63.2-2) ...
Setting up autotools-dev (20180224.1) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up autopoint (0.19.8.1-10) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-1) ...
Setting up sensible-utils (0.0.12+nmu1) ...
Setting up libuchardet0:armhf (0.0.6-3) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libmpdec2:armhf (2.4.2-2) ...
Setting up libbsd0:armhf (0.10.0-1) ...
Setting up libtinfo5:armhf (6.1+20191019-1) ...
Setting up libelf1:armhf (0.176-1.1) ...
Setting up libxml2:armhf (2.9.4+dfsg1-8) ...
Setting up markdown (1.0.1-10) ...
Setting up libfile-stripnondeterminism-perl (1.6.3-1) ...
Setting up libpython3.7-stdlib:armhf (3.7.6-1) ...
Setting up libtool (2.4.6-11) ...
Setting up m4 (1.4.18-4) ...
Setting up bsdmainutils (11.1.2) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up libcroco3:armhf (0.6.13-1) ...
Setting up autoconf (2.69-11) ...
Setting up dh-strip-nondeterminism (1.6.3-1) ...
Setting up dwz (0.13-5) ...
Setting up groff-base (1.22.4-4) ...
Setting up libpython3-stdlib:armhf (3.7.5-3) ...
Setting up automake (1:1.16.1-4) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up python3.7 (3.7.6-1) ...
Setting up gettext (0.19.8.1-10) ...
Setting up python3 (3.7.5-3) ...
Setting up man-db (2.9.0-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up po-debconf (1.0.21) ...
Setting up debhelper (12.7.3) ...
Setting up sbuild-build-depends-seqprep-dummy (0.invalid.0) ...
Setting up dh-autoreconf (19) ...
Processing triggers for libc-bin (2.29-7+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.15.0-58-generic armhf (armv8l)
Toolchain package versions: binutils_2.33.1-6+rpi1 dpkg-dev_1.19.7 g++-9_9.2.1-22+rpi1 gcc-9_9.2.1-22+rpi1 libc6-dev_2.29-7+rpi1 libstdc++-9-dev_9.2.1-22+rpi1 libstdc++6_9.2.1-22+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2
Package versions: adduser_3.118 apt_1.8.4 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.47 bash_5.0-5 binutils_2.33.1-6+rpi1 binutils-arm-linux-gnueabihf_2.33.1-6+rpi1 binutils-common_2.33.1-6+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.34-0.1 build-essential_12.8 bzip2_1.0.8-2 coreutils_8.30-3 cpp_4:9.2.1-3.1+rpi1 cpp-9_9.2.1-22+rpi1 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.7.3 debianutils_4.9.1 dh-autoreconf_19 dh-strip-nondeterminism_1.6.3-1 diffutils_1:3.7-3 dirmngr_2.2.19-1 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.5-2 fakeroot_1.24-1 fdisk_2.34-0.1 file_1:5.38-3 findutils_4.7.0-1 g++_4:9.2.1-3.1+rpi1 g++-9_9.2.1-22+rpi1 gcc_4:9.2.1-3.1+rpi1 gcc-9_9.2.1-22+rpi1 gcc-9-base_9.2.1-22+rpi1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gnupg_2.2.19-1 gnupg-l10n_2.2.19-1 gnupg-utils_2.2.19-1 gpg_2.2.19-1 gpg-agent_2.2.19-1 gpg-wks-client_2.2.19-1 gpg-wks-server_2.2.19-1 gpgconf_2.2.19-1 gpgsm_2.2.19-1 gpgv_2.2.19-1 grep_3.3-1 groff-base_1.22.4-4 gzip_1.9-3 hostname_3.23 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20190709-2 libacl1_2.2.53-5 libapt-pkg5.0_1.8.4 libarchive-zip-perl_1.67-1 libasan5_9.2.1-22+rpi1 libassuan0_2.5.3-7 libatomic1_9.2.1-22+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2 libaudit1_1:2.8.5-2+b1 libbinutils_2.33.1-6+rpi1 libblkid1_2.34-0.1 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.29-7+rpi1 libc-dev-bin_2.29-7+rpi1 libc6_2.29-7+rpi1 libc6-dev_2.29-7+rpi1 libcap-ng0_0.7.9-2.1 libcap2_1:2.27-1 libcap2-bin_1:2.27-1 libcc1-0_9.2.1-22+rpi1 libcom-err2_1.45.5-2 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.10-10+b5 libcrypt1_1:4.4.10-10+b5 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.250 libdebhelper-perl_12.7.3 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libexpat1_2.2.9-1 libext2fs2_1.45.5-2 libfakeroot_1.24-1 libfdisk1_2.34-0.1 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.6.3-1 libgcc-9-dev_9.2.1-22+rpi1 libgcc1_1:9.2.1-22+rpi1 libgcrypt20_1.8.5-3 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.62.4-1 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.11.1-2 libgomp1_9.2.1-22+rpi1 libgpg-error0_1.36-7 libhogweed5_3.5.1+really3.5.1-2 libicu63_63.2-2 libidn2-0_2.2.0-2 libisl22_0.22-2 libksba8_1.3.5-2 libldap-2.4-2_2.4.48+dfsg-1+b2 libldap-common_2.4.48+dfsg-1 liblz4-1_1.9.2-2 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-3 libmagic1_1:5.38-3 libmount1_2.34-0.1 libmpc3_1.1.0-1 libmpdec2_2.4.2-2 libmpfr6_4.0.2-1 libncursesw6_6.1+20191019-1 libnettle7_3.5.1+really3.5.1-2 libnpth0_1.6-1 libp11-kit0_0.23.18.1-2 libpam-cap_1:2.27-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.34-7 libpcre3_2:8.39-12 libperl5.30_5.30.0-9 libpipeline1_1.5.2-2 libpython3-stdlib_3.7.5-3 libpython3.7-minimal_3.7.6-1 libpython3.7-stdlib_3.7.6-1 libreadline7_7.0-5 libreadline8_8.0-3 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.2-2+rpi1 libselinux1_3.0-1 libsemanage-common_3.0-1 libsemanage1_3.0-1 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1 libsqlite3-0_3.30.1+fossil191229-1 libss2_1.45.5-2 libssl1.1_1.1.1d-2 libstdc++-9-dev_9.2.1-22+rpi1 libstdc++6_9.2.1-22+rpi1 libsub-override-perl_0.09-2 libsystemd0_244-3+rpi1+b1 libtasn1-6_4.15.0-2 libtinfo5_6.1+20191019-1 libtinfo6_6.1+20191019-1 libtool_2.4.6-11 libubsan1_9.2.1-22+rpi1 libuchardet0_0.0.6-3 libudev1_244-3+rpi1+b1 libunistring2_0.9.10-2 libuuid1_2.34-0.1 libxml2_2.9.4+dfsg1-8 libzstd1_1.4.4+dfsg-1+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2 login_1:4.8-1 logsave_1.45.5-2 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.0-2 markdown_1.0.1-10 mawk_1.3.3-17 mime-support_3.64 mount_2.34-0.1 ncurses-base_6.1+20191019-1 ncurses-bin_6.1+20191019-1 netbase_6.0 passwd_1:4.8-1 patch_2.7.6-6 perl_5.30.0-9 perl-base_5.30.0-9 perl-modules-5.30_5.30.0-9 pinentry-curses_1.1.0-3 po-debconf_1.0.21 python3_3.7.5-3 python3-minimal_3.7.5-3 python3.7_3.7.6-1 python3.7-minimal_3.7.6-1 raspbian-archive-keyring_20120528.2 readline-common_8.0-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-seqprep-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-1 tar_1.30+dfsg-6 tzdata_2019c-3 util-linux_2.34-0.1 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Mon Jan 20 10:45:55 2020 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./seqprep_1.3.2-5.dsc
dpkg-source: info: extracting seqprep in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking seqprep_1.3.2.orig.tar.gz
dpkg-source: info: unpacking seqprep_1.3.2-5.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying fix_unused_variable_errors.patch
dpkg-source: info: applying hardening.patch
dpkg-source: info: applying replace-float-with-double.patch
dpkg-source: info: applying 2to3.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=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-f9afbd8d-033d-4653-b6be-2b94a998244a
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package seqprep
dpkg-buildpackage: info: source version 1.3.2-5
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
dh_auto_clean
make -j4 clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
rm -f SeqPrep.o utils.o stdaln.o SeqPrep
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_clean
rm -f seqprep
rm -f README.html
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules build-arch
dh build-arch
dh_update_autotools_config -a
dh_autoreconf -a
dh_auto_configure -a
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build
make -j4 "INSTALL=install --strip-program=true"
make[2]: Entering directory '/<<PKGBUILDDIR>>'
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu90 -c -Wall -O0 -g -std=c99 SeqPrep.c -o SeqPrep.o
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu90 -c -Wall -O0 -g -std=c99 utils.c -o utils.o
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu90 -c -Wall -O0 -g -std=c99 stdaln.c -o stdaln.o
SeqPrep.c: In function 'main':
SeqPrep.c:166:15: warning: implicit declaration of function 'getopt' [-Wimplicit-function-declaration]
166 | while( (ich=getopt( argc, argv, "f:r:1:2:3:4:q:A:s:y:B:O:E:x:M:N:L:o:m:b:w:W:p:P:X:Q:t:e:Z:n:S6ghz" )) != -1 ) {
| ^~~~~~
cc SeqPrep.o utils.o stdaln.o -Wl,-z,relro -Wl,-z,now -lz -lm -o SeqPrep
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
cp SeqPrep seqprep
markdown README.md > README.html
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
# This checks that the tests run and produce byte-identical results.
cd Test && mkdir -p out info && \
bash -xc 'gzcat(){ zcat "$@" ; } ; . RUNTEST.sh'
+ . RUNTEST.sh
++ ../SeqPrep -6 -f ./data/multiplex_bad_contam_1.fq.gz -r ./data/multiplex_bad_contam_2.fq.gz -A GATCGGAAGAGCACACGTCT -B AGATCGGAAGAGCGTCGT -1 ./out/pe_bad_contam_merged_1.fastq.gz -2 ./out/pe_bad_contam_merged_2.fastq.gz -s ./out/pe_bad_contam_merged_s.fastq.gz -E ./info/alignments_merged.txt.gz
fastq record not beginning with @
fastq record not beginning with @
Pairs Processed: 0
Pairs Merged: 14314
Pairs With Adapters: 4091
Pairs Discarded: 2228
CPU Time Used (Minutes): 0.495980
++ ../SeqPrep -6 -f ./data/multiplex_bad_contam_1.fq.gz -r ./data/multiplex_bad_contam_2.fq.gz -A GATCGGAAGAGCACACGTCT -B AGATCGGAAGAGCGTCGT -1 ./out/pe_bad_contam_trimmed_1.fastq.gz -2 ./out/pe_bad_contam_trimmed_2.fastq.gz -E ./info/alignments_trimmed.txt.gz
fastq record not beginning with @
fastq record not beginning with @
Pairs Processed: 0
Pairs Merged: 0
Pairs With Adapters: 4091
Pairs Discarded: 2228
CPU Time Used (Minutes): 0.465626
++ prog=gzcat
++ gzcat ./out/pe_bad_contam_trimmed_1.fastq.gz
++ zcat ./out/pe_bad_contam_trimmed_1.fastq.gz
++ python3 seqlens.py
++ gzcat ./out/pe_bad_contam_trimmed_2.fastq.gz
++ zcat ./out/pe_bad_contam_trimmed_2.fastq.gz
++ python3 seqlens.py
++ gzcat ./out/pe_bad_contam_merged_1.fastq.gz
++ zcat ./out/pe_bad_contam_merged_1.fastq.gz
++ python3 seqlens.py
++ gzcat ./out/pe_bad_contam_merged_2.fastq.gz
++ zcat ./out/pe_bad_contam_merged_2.fastq.gz
++ python3 seqlens.py
++ gzcat ./out/pe_bad_contam_merged_s.fastq.gz
++ python3 seqlens.py
++ zcat ./out/pe_bad_contam_merged_s.fastq.gz
[ `cat Test/info/pe_*.txt | md5sum | cut -b -10` = 8bc8e0787e ]
# remove output dirs right after testing to make sure the files
# will not be included in the data package
rm -rf Test/info Test/out
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
dh_auto_install -a
make -j4 install DESTDIR=/<<PKGBUILDDIR>>/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true"
make[1]: Entering directory '/<<PKGBUILDDIR>>'
cp SeqPrep /sbuild-nonexistent/bin
cp: cannot create regular file '/sbuild-nonexistent/bin': No such file or directory
make[1]: [Makefile:15: install] Error 1 (ignored)
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_install -a
dh_installdocs -a
dh_installchangelogs -a
dh_installman -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_missing -a
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/seqprep/usr/bin/seqprep was not linked against ld-linux-armhf.so.3 (it uses none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'seqprep' in '../seqprep_1.3.2-5_armhf.deb'.
dpkg-deb: building package 'seqprep-dbgsym' in '../seqprep-dbgsym_1.3.2-5_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../seqprep_1.3.2-5_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 2020-01-22T05:23:03Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
seqprep_1.3.2-5_armhf.changes:
------------------------------
Format: 1.8
Date: Mon, 20 Jan 2020 11:31:59 +0100
Source: seqprep
Binary: seqprep seqprep-dbgsym
Architecture: armhf
Version: 1.3.2-5
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
seqprep - stripping adaptors and/or merging paired reads of DNA sequences w
Closes: 938467
Changes:
seqprep (1.3.2-5) unstable; urgency=medium
.
* Test-Depends: s/python/python3/
Closes: #938467
* Set upstream metadata fields: Bug-Submit.
Checksums-Sha1:
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c4e31a97fe2cb94289c3dea0c31c2d9d6ca3ad60 5012 seqprep_1.3.2-5_armhf.buildinfo
5d5474ca7cfe63631ace806871efc60d25a6bf2d 26988 seqprep_1.3.2-5_armhf.deb
Checksums-Sha256:
619097ea8bfef11409460592f53c76ef52ecc9dffaa70aa3748be1b648f655f9 18656 seqprep-dbgsym_1.3.2-5_armhf.deb
0892f75e5256599bd60bae71f224ee3668fae05e2f21a33d85abe26184f19eb1 5012 seqprep_1.3.2-5_armhf.buildinfo
251af38a9c44d00e5c7a310e5ccf6ba120efd55c4547e5c25b02a810ff17773f 26988 seqprep_1.3.2-5_armhf.deb
Files:
c253f0160113fd9c0656c4b248e68a3a 18656 debug optional seqprep-dbgsym_1.3.2-5_armhf.deb
f32ba9f063b0928540174c706c671636 5012 science optional seqprep_1.3.2-5_armhf.buildinfo
124885f6331a16ad49d170f8ef3a2f29 26988 science optional seqprep_1.3.2-5_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
seqprep-dbgsym_1.3.2-5_armhf.deb
--------------------------------
new Debian package, version 2.0.
size 18656 bytes: control archive=532 bytes.
369 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: seqprep-dbgsym
Source: seqprep
Version: 1.3.2-5
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 34
Depends: seqprep (= 1.3.2-5)
Section: debug
Priority: optional
Description: debug symbols for seqprep
Build-Ids: fb714472b158fe1bfba6e17dfad37fb0d6fbb0c7
drwxr-xr-x root/root 0 2020-01-20 10:31 ./
drwxr-xr-x root/root 0 2020-01-20 10:31 ./usr/
drwxr-xr-x root/root 0 2020-01-20 10:31 ./usr/lib/
drwxr-xr-x root/root 0 2020-01-20 10:31 ./usr/lib/debug/
drwxr-xr-x root/root 0 2020-01-20 10:31 ./usr/lib/debug/.build-id/
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drwxr-xr-x root/root 0 2020-01-20 10:31 ./usr/share/doc/
lrwxrwxrwx root/root 0 2020-01-20 10:31 ./usr/share/doc/seqprep-dbgsym -> seqprep
seqprep_1.3.2-5_armhf.deb
-------------------------
new Debian package, version 2.0.
size 26988 bytes: control archive=1108 bytes.
1172 bytes, 21 lines control
326 bytes, 5 lines md5sums
Package: seqprep
Version: 1.3.2-5
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 103
Depends: libc6 (>= 2.4), zlib1g (>= 1:1.1.4)
Section: science
Priority: optional
Homepage: http://seqanswers.com/wiki/SeqPrep
Description: stripping adaptors and/or merging paired reads of DNA sequences with overlap
SeqPrep is a program to merge paired end Illumina reads that are overlapping
into a single longer read. It may also just be used for its adapter trimming
feature without doing any paired end overlap. When an adapter sequence is
present, that means that the two reads must overlap (in most cases) so they
are forcefully merged. When reads do not have adapter sequence they must be
treated with care when doing the merging, so a much more specific approach is
taken. The default parameters were chosen with specificity in mind, so that
they could be ran on libraries where very few reads are expected to overlap.
It is always safest though to save the overlapping procedure for libraries
where you have some prior knowledge that a significant portion of the reads
will have some overlap.
drwxr-xr-x root/root 0 2020-01-20 10:31 ./
drwxr-xr-x root/root 0 2020-01-20 10:31 ./usr/
drwxr-xr-x root/root 0 2020-01-20 10:31 ./usr/bin/
-rwxr-xr-x root/root 74224 2020-01-20 10:31 ./usr/bin/seqprep
drwxr-xr-x root/root 0 2020-01-20 10:31 ./usr/share/
drwxr-xr-x root/root 0 2020-01-20 10:31 ./usr/share/doc/
drwxr-xr-x root/root 0 2020-01-20 10:31 ./usr/share/doc/seqprep/
-rw-r--r-- root/root 11784 2020-01-20 10:31 ./usr/share/doc/seqprep/README.html
-rw-r--r-- root/root 1316 2020-01-20 10:31 ./usr/share/doc/seqprep/changelog.Debian.gz
-rw-r--r-- root/root 1439 2020-01-20 10:31 ./usr/share/doc/seqprep/copyright
drwxr-xr-x root/root 0 2020-01-20 10:31 ./usr/share/man/
drwxr-xr-x root/root 0 2020-01-20 10:31 ./usr/share/man/man1/
-rw-r--r-- root/root 4566 2020-01-20 10:31 ./usr/share/man/man1/seqprep.1.gz
+------------------------------------------------------------------------------+
| Post Build |
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| Cleanup |
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Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
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| Summary |
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Build Architecture: armhf
Build-Space: 65020
Build-Time: 71
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 281
Job: seqprep_1.3.2-5
Machine Architecture: armhf
Package: seqprep
Package-Time: 378
Source-Version: 1.3.2-5
Space: 65020
Status: successful
Version: 1.3.2-5
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Finished at 2020-01-22T05:23:03Z
Build needed 00:06:18, 65020k disk space