seqprep →
1.3.2-7 →
armhf → 2021-10-05 06:40:47
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-03
+==============================================================================+
| seqprep 1.3.2-7 (armhf) Tue, 05 Oct 2021 06:31:18 +0000 |
+==============================================================================+
Package: seqprep
Version: 1.3.2-7
Source Version: 1.3.2-7
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-2aed6063-7a26-4e5c-87a1-4282efc74e6b' 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 [12.4 MB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf Packages [13.4 MB]
Fetched 25.8 MB in 26s (1000 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 bookworm-staging/main seqprep 1.3.2-7 (dsc) [2143 B]
Get:2 http://172.17.0.1/private bookworm-staging/main seqprep 1.3.2-7 (tar) [37.2 MB]
Get:3 http://172.17.0.1/private bookworm-staging/main seqprep 1.3.2-7 (diff) [12.0 kB]
Fetched 37.2 MB in 4s (10.3 MB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/seqprep-DBJve9/seqprep-1.3.2' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/seqprep-DBJve9' 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-cVqIy4/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-cVqIy4/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-cVqIy4/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: 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 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: 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-cVqIy4/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-cVqIy4/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-cVqIy4/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-cVqIy4/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-cVqIy4/apt_archive ./ Packages [433 B]
Fetched 2109 B in 1s (2539 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 22 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-cVqIy4/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (22.4 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12484 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), python3, zlib1g-dev
Filtered Build-Depends: debhelper-compat (= 13), python3, zlib1g-dev
dpkg-deb: building package 'sbuild-build-depends-seqprep-dummy' in '/<<BUILDDIR>>/resolver-cVqIy4/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-cVqIy4/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-cVqIy4/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-cVqIy4/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-cVqIy4/apt_archive ./ Sources [515 B]
Get:5 copy:/<<BUILDDIR>>/resolver-cVqIy4/apt_archive ./ Packages [586 B]
Fetched 2434 B in 1s (3280 B/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 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-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libdebhelper-perl libelf1
libexpat1 libffi8 libfile-stripnondeterminism-perl libicu67 libmagic-mgc
libmagic1 libmpdec3 libpipeline1 libpython3-stdlib libpython3.9-minimal
libpython3.9-stdlib libsigsegv2 libsub-override-perl libtool libuchardet0
libxml2 m4 man-db media-types po-debconf python3 python3-minimal python3.9
python3.9-minimal sensible-utils zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc 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 python3.9-venv
python3.9-doc binfmt-support
Recommended packages:
curl | wget | lynx libarchive-cpio-perl ca-certificates libltdl-dev
libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libdebhelper-perl libelf1
libexpat1 libffi8 libfile-stripnondeterminism-perl libicu67 libmagic-mgc
libmagic1 libmpdec3 libpipeline1 libpython3-stdlib libpython3.9-minimal
libpython3.9-stdlib libsigsegv2 libsub-override-perl libtool libuchardet0
libxml2 m4 man-db media-types po-debconf python3 python3-minimal python3.9
python3.9-minimal sbuild-build-depends-seqprep-dummy sensible-utils
zlib1g-dev
0 upgraded, 44 newly installed, 0 to remove and 22 not upgraded.
Need to get 22.5 MB of archives.
After this operation, 84.2 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-cVqIy4/apt_archive ./ sbuild-build-depends-seqprep-dummy 0.invalid.0 [876 B]
Get:2 http://172.17.0.1/private bookworm-staging/main armhf bsdextrautils armhf 2.37.2-1 [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 libpython3.9-minimal armhf 3.9.7-4+rpi1 [794 kB]
Get:8 http://172.17.0.1/private bookworm-staging/main armhf libexpat1 armhf 2.4.1-2 [80.3 kB]
Get:9 http://172.17.0.1/private bookworm-staging/main armhf python3.9-minimal armhf 3.9.7-4+rpi1 [1632 kB]
Get:10 http://172.17.0.1/private bookworm-staging/main armhf python3-minimal armhf 3.9.2-3 [38.2 kB]
Get:11 http://172.17.0.1/private bookworm-staging/main armhf media-types all 4.0.0 [30.3 kB]
Get:12 http://172.17.0.1/private bookworm-staging/main armhf libffi8 armhf 3.4.2-2 [21.2 kB]
Get:13 http://172.17.0.1/private bookworm-staging/main armhf libmpdec3 armhf 2.5.1-2+rpi1 [73.5 kB]
Get:14 http://172.17.0.1/private bookworm-staging/main armhf libpython3.9-stdlib armhf 3.9.7-4+rpi1 [1618 kB]
Get:15 http://172.17.0.1/private bookworm-staging/main armhf python3.9 armhf 3.9.7-4+rpi1 [480 kB]
Get:16 http://172.17.0.1/private bookworm-staging/main armhf libpython3-stdlib armhf 3.9.2-3 [21.4 kB]
Get:17 http://172.17.0.1/private bookworm-staging/main armhf python3 armhf 3.9.2-3 [37.9 kB]
Get:18 http://172.17.0.1/private bookworm-staging/main armhf sensible-utils all 0.0.17 [21.5 kB]
Get:19 http://172.17.0.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB]
Get:20 http://172.17.0.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.39-3 [117 kB]
Get:21 http://172.17.0.1/private bookworm-staging/main armhf file armhf 1:5.39-3 [68.0 kB]
Get:22 http://172.17.0.1/private bookworm-staging/main armhf gettext-base armhf 0.21-4 [171 kB]
Get:23 http://172.17.0.1/private bookworm-staging/main armhf libsigsegv2 armhf 2.13-1 [34.3 kB]
Get:24 http://172.17.0.1/private bookworm-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:25 http://172.17.0.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:26 http://172.17.0.1/private bookworm-staging/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get:27 http://172.17.0.1/private bookworm-staging/main armhf automake all 1:1.16.4-2 [819 kB]
Get:28 http://172.17.0.1/private bookworm-staging/main armhf autopoint all 0.21-4 [510 kB]
Get:29 http://172.17.0.1/private bookworm-staging/main armhf libdebhelper-perl all 13.5.2 [192 kB]
Get:30 http://172.17.0.1/private bookworm-staging/main armhf libtool all 2.4.6-15 [513 kB]
Get:31 http://172.17.0.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:32 http://172.17.0.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:33 http://172.17.0.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:34 http://172.17.0.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB]
Get:35 http://172.17.0.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.12.0-1 [15.4 kB]
Get:36 http://172.17.0.1/private bookworm-staging/main armhf libelf1 armhf 0.185-2 [168 kB]
Get:37 http://172.17.0.1/private bookworm-staging/main armhf dwz armhf 0.14-1 [83.0 kB]
Get:38 http://172.17.0.1/private bookworm-staging/main armhf libicu67 armhf 67.1-7 [8291 kB]
Get:39 http://172.17.0.1/private bookworm-staging/main armhf libxml2 armhf 2.9.12+dfsg-5 [584 kB]
Get:40 http://172.17.0.1/private bookworm-staging/main armhf gettext armhf 0.21-4 [1215 kB]
Get:41 http://172.17.0.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:42 http://172.17.0.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:43 http://172.17.0.1/private bookworm-staging/main armhf debhelper all 13.5.2 [1056 kB]
Get:44 http://172.17.0.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
debconf: delaying package configuration, since apt-utils is not installed
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update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode
Setting up libicu67:armhf (67.1-7) ...
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Setting up gettext-base (0.21-4) ...
Setting up file (1:5.39-3) ...
Setting up autotools-dev (20180224.1+nmu1) ...
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Setting up libffi8:armhf (3.4.2-2) ...
Setting up sensible-utils (0.0.17) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libmpdec3:armhf (2.5.1-2+rpi1) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libelf1:armhf (0.185-2) ...
Setting up libxml2:armhf (2.9.12+dfsg-5) ...
Setting up libpython3.9-stdlib:armhf (3.9.7-4+rpi1) ...
Setting up libpython3-stdlib:armhf (3.9.2-3) ...
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 intltool-debian (0.35.0+20060710.5) ...
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 python3.9 (3.9.7-4+rpi1) ...
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 po-debconf (1.0.21+nmu1) ...
Setting up python3 (3.9.2-3) ...
Setting up man-db (2.9.4-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up dh-autoreconf (20) ...
Setting up debhelper (13.5.2) ...
Setting up sbuild-build-depends-seqprep-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.32-4+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.2-armmp 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_2.37.2-1 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-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 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 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 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.260 libdebhelper-perl_13.5.2 libdpkg-perl_1.20.9+rpi1 libelf1_0.185-2 libexpat1_2.4.1-2 libext2fs2_1.46.4-1 libfakeroot_1.25.3-1.1 libffi7_3.3-6 libffi8_3.4.2-2 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 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 libmpdec3_2.5.1-2+rpi1 libmpfr6_4.1.0-3 libncursesw6_6.2+20201114-4 libnettle8_3.7.3-1 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 libpython3-stdlib_3.9.2-3 libpython3.9-minimal_3.9.7-4+rpi1 libpython3.9-stdlib_3.9.7-4+rpi1 libreadline8_8.1-2 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 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 media-types_4.0.0 mount_2.37.2-1 ncurses-base_6.2+20201114-4 ncurses-bin_6.2+20201114-4 netbase_6.3 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 python3_3.9.2-3 python3-minimal_3.9.2-3 python3.9_3.9.7-4+rpi1 python3.9-minimal_3.9.7-4+rpi1 raspbian-archive-keyring_20120528.2 readline-common_8.1-2 rpcsvc-proto_1.4.2-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-seqprep-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 zlib1g-dev_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.LxzFqss7/trustedkeys.kbx': General error
gpgv: Signature made Fri Oct 1 14:17:09 2021 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_1.3.2-7.dsc
dpkg-source: info: extracting seqprep in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking seqprep_1.3.2.orig.tar.gz
dpkg-source: info: unpacking seqprep_1.3.2-7.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 disc 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=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-2aed6063-7a26-4e5c-87a1-4282efc74e6b
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package seqprep
dpkg-buildpackage: info: source version 1.3.2-7
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
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 binary-arch
dh binary-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 -ffile-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 -ffile-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 -ffile-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
mv /<<PKGBUILDDIR>>/debian/README.html /<<PKGBUILDDIR>>
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): 1.805215
++ ../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): 1.707274
++ 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
++ python3 seqlens.py
++ zcat ./out/pe_bad_contam_merged_2.fastq.gz
++ 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
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 /<<PKGBUILDDIR>>/debian/.debhelper/generated/_source/home/bin
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_1.3.2-7_armhf.deb'.
dpkg-deb: building package 'seqprep-dbgsym' in '../seqprep-dbgsym_1.3.2-7_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../seqprep_1.3.2-7_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 2021-10-05T06:40:42Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
seqprep_1.3.2-7_armhf.changes:
------------------------------
Format: 1.8
Date: Fri, 01 Oct 2021 16:09:25 +0200
Source: seqprep
Binary: seqprep seqprep-dbgsym
Architecture: armhf
Version: 1.3.2-7
Distribution: bookworm-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
seqprep - stripping adaptors and/or merging paired reads of DNA sequences w
Changes:
seqprep (1.3.2-7) unstable; urgency=medium
.
* Fix watchfile to detect new versions on github
* Standards-Version: 4.6.0 (routine-update)
* debhelper-compat 13 (routine-update)
* Add salsa-ci file (routine-update)
* Rules-Requires-Root: no (routine-update)
* watch file standard 4 (routine-update)
Checksums-Sha1:
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ab662551e99ea3d5e9fd50bacb544503c780e637 5336 seqprep_1.3.2-7_armhf.buildinfo
9daebce3215bd5ecb297ee4afcecda34d266bc5a 27328 seqprep_1.3.2-7_armhf.deb
Checksums-Sha256:
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b880294747017b6cfc37d79e83cb62f79a9a1f1a220dc777bb794ac6c8928729 5336 seqprep_1.3.2-7_armhf.buildinfo
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Files:
df07fdc72147ed9cc0e79a4fd8055b84 18552 debug optional seqprep-dbgsym_1.3.2-7_armhf.deb
b62f61a687acd7f9651c15290fc9fa35 5336 science optional seqprep_1.3.2-7_armhf.buildinfo
3e789fa82fb7b21f5df2dbc1d62deae6 27328 science optional seqprep_1.3.2-7_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
seqprep-dbgsym_1.3.2-7_armhf.deb
--------------------------------
new Debian package, version 2.0.
size 18552 bytes: control archive=532 bytes.
369 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: seqprep-dbgsym
Source: seqprep
Version: 1.3.2-7
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 33
Depends: seqprep (= 1.3.2-7)
Section: debug
Priority: optional
Description: debug symbols for seqprep
Build-Ids: 9734e784a91b04dd95c02af380090ec3c23181d8
drwxr-xr-x root/root 0 2021-10-01 14:09 ./
drwxr-xr-x root/root 0 2021-10-01 14:09 ./usr/
drwxr-xr-x root/root 0 2021-10-01 14:09 ./usr/lib/
drwxr-xr-x root/root 0 2021-10-01 14:09 ./usr/lib/debug/
drwxr-xr-x root/root 0 2021-10-01 14:09 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2021-10-01 14:09 ./usr/lib/debug/.build-id/97/
-rw-r--r-- root/root 23512 2021-10-01 14:09 ./usr/lib/debug/.build-id/97/34e784a91b04dd95c02af380090ec3c23181d8.debug
drwxr-xr-x root/root 0 2021-10-01 14:09 ./usr/share/
drwxr-xr-x root/root 0 2021-10-01 14:09 ./usr/share/doc/
lrwxrwxrwx root/root 0 2021-10-01 14:09 ./usr/share/doc/seqprep-dbgsym -> seqprep
seqprep_1.3.2-7_armhf.deb
-------------------------
new Debian package, version 2.0.
size 27328 bytes: control archive=1104 bytes.
1172 bytes, 21 lines control
326 bytes, 5 lines md5sums
Package: seqprep
Version: 1.3.2-7
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 2021-10-01 14:09 ./
drwxr-xr-x root/root 0 2021-10-01 14:09 ./usr/
drwxr-xr-x root/root 0 2021-10-01 14:09 ./usr/bin/
-rwxr-xr-x root/root 74224 2021-10-01 14:09 ./usr/bin/seqprep
drwxr-xr-x root/root 0 2021-10-01 14:09 ./usr/share/
drwxr-xr-x root/root 0 2021-10-01 14:09 ./usr/share/doc/
drwxr-xr-x root/root 0 2021-10-01 14:09 ./usr/share/doc/seqprep/
-rw-r--r-- root/root 11784 2021-10-01 14:09 ./usr/share/doc/seqprep/README.html
-rw-r--r-- root/root 1546 2021-10-01 14:09 ./usr/share/doc/seqprep/changelog.Debian.gz
-rw-r--r-- root/root 1439 2021-10-01 14:09 ./usr/share/doc/seqprep/copyright
drwxr-xr-x root/root 0 2021-10-01 14:09 ./usr/share/man/
drwxr-xr-x root/root 0 2021-10-01 14:09 ./usr/share/man/man1/
-rw-r--r-- root/root 4566 2021-10-01 14:09 ./usr/share/man/man1/seqprep.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 65140
Build-Time: 255
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 251
Job: seqprep_1.3.2-7
Machine Architecture: armhf
Package: seqprep
Package-Time: 564
Source-Version: 1.3.2-7
Space: 65140
Status: successful
Version: 1.3.2-7
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Finished at 2021-10-05T06:40:42Z
Build needed 00:09:24, 65140k disc space