[med-svn] [Git][med-team/gatb-core][master] 8 commits: Fix autopkgtest with latest hd5 (Thanks to the hint to use /dev/shm to...
Andreas Tille (@tille)
gitlab at salsa.debian.org
Thu Aug 13 15:30:14 BST 2026
Andreas Tille pushed to branch master at Debian Med / gatb-core
Commits:
ce380b55 by Andreas Tille at 2026-08-13T16:07:30+02:00
Fix autopkgtest with latest hd5 (Thanks to the hint to use /dev/shm to https://platform.aim2balance.ai/)
- - - - -
b864c3d8 by Andreas Tille at 2026-08-13T16:09:33+02:00
d/watch: version=5
- - - - -
37bf2893 by Andreas Tille at 2026-08-13T16:09:55+02:00
Standards-Version: 4.7.4 (routine-update)
- - - - -
ff7c4928 by Andreas Tille at 2026-08-13T16:21:49+02:00
Changes made by cme
- - - - -
9d871d28 by Andreas Tille at 2026-08-13T16:21:50+02:00
Drop 'Rules-Requires-Root: no' from d/control (routine-update)
- - - - -
1630ea59 by Andreas Tille at 2026-08-13T15:21:56+01:00
Reformat the Last-Update date as ISO YYYY-MM-DD.
Changes-By: lintian-brush
Fixes: lintian: source: invalid-dep3-format-patch-wrong-last-update [debian/patches/use_debian_packaged_hdf5.patch]
Fixes: lintian: source: invalid-dep3-format-patch-wrong-last-update [debian/patches/fix_hdf5_includes.patch]
Fixes: lintian: source: invalid-dep3-format-patch-wrong-last-update [debian/patches/dynamic_lib.patch]
Fixes: lintian: source: invalid-dep3-format-patch-wrong-last-update [debian/patches/fix_install_location.patch]
Fixes: lintian: source: invalid-dep3-format-patch-wrong-last-update [debian/patches/set_soversion.patch]
Fixes: lintian: source: invalid-dep3-format-patch-wrong-last-update [debian/patches/dynamic_linking_of_tools.patch]
Fixes: lintian: source: invalid-dep3-format-patch-wrong-last-update [debian/patches/multiarch.patch]
Fixes: lintian: source: invalid-dep3-format-patch-wrong-last-update [debian/patches/spelling.patch]
See-also: https://lintian.debian.org/tags/invalid-dep3-format-patch-wrong-last-update.html
- - - - -
92b72372 by Andreas Tille at 2026-08-13T15:21:58+01:00
Set upstream metadata fields: Bug-Database, Repository-Browse.
Changes-By: lintian-brush
Fixes: lintian: source: upstream-metadata-missing-repository [debian/upstream/metadata]
Fixes: lintian: source: upstream-metadata-missing-bug-tracking [debian/upstream/metadata]
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-repository.html
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html
- - - - -
f71d6e09 by Andreas Tille at 2026-08-13T16:28:19+02:00
routine-update: Ready to upload to unstable
- - - - -
14 changed files:
- debian/changelog
- debian/control
- debian/patches/dynamic_lib.patch
- debian/patches/dynamic_linking_of_tools.patch
- debian/patches/fix_hdf5_includes.patch
- debian/patches/fix_install_location.patch
- debian/patches/multiarch.patch
- debian/patches/set_soversion.patch
- debian/patches/spelling.patch
- debian/patches/use_debian_packaged_hdf5.patch
- debian/tests/control
- debian/tests/run-unit-test
- debian/upstream/metadata
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,16 @@
+gatb-core (1.4.2+dfsg-14) unstable; urgency=medium
+
+ * Fix autopkgtest with latest hd5
+ * d/watch: version=5
+ * Standards-Version: 4.7.4 (routine-update)
+ * Reflow Uploaders field (cme)
+ * Remove Priority field (cme)
+ * Drop 'Rules-Requires-Root: no' from d/control (routine-update)
+ * Reformat the Last-Update date as ISO YYYY-MM-DD.
+ * Set upstream metadata fields: Bug-Database, Repository-Browse.
+
+ -- Andreas Tille <tille at debian.org> Thu, 13 Aug 2026 16:22:01 +0200
+
gatb-core (1.4.2+dfsg-13) unstable; urgency=medium
* Add build support for loongarch64
=====================================
debian/control
=====================================
@@ -1,28 +1,29 @@
Source: gatb-core
+Standards-Version: 4.7.4
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Nadiya Sitdykova <rovenskasa at gmail.com>,
- Andreas Tille <tille at debian.org>
+Uploaders:
+ Nadiya Sitdykova <rovenskasa at gmail.com>,
+ Andreas Tille <tille at debian.org>,
Section: science
-Priority: optional
-Build-Depends: debhelper-compat (= 13),
- d-shlibs,
- cmake,
- libcppunit-dev,
- libhdf5-dev,
- libboost-dev,
- libjsoncpp-dev,
- doxygen,
- graphviz
-Standards-Version: 4.6.2
+Build-Depends:
+ debhelper-compat (= 14),
+ d-shlibs,
+ cmake,
+ libcppunit-dev,
+ libhdf5-dev,
+ libboost-dev,
+ libjsoncpp-dev,
+ doxygen,
+ graphviz,
Vcs-Browser: https://salsa.debian.org/med-team/gatb-core
Vcs-Git: https://salsa.debian.org/med-team/gatb-core.git
Homepage: https://github.com/GATB/gatb-core
-Rules-Requires-Root: no
Package: gatb-core
Architecture: any-amd64 arm64 loong64 mips64el ppc64el ia64 ppc64 riscv64 sparc64 alpha
-Depends: ${shlibs:Depends},
- ${misc:Depends},
+Depends:
+ ${shlibs:Depends},
+ ${misc:Depends},
Description: Genome Analysis Toolbox with de-Bruijn graph
The GATB-CORE project provides a set of highly efficient
algorithms to analyse NGS data sets. These methods enable
@@ -40,8 +41,9 @@ Package: libgatbcore3
Architecture: any-amd64 arm64 loong64 mips64el ppc64el ia64 ppc64 riscv64 sparc64 alpha
Multi-Arch: same
Section: libs
-Depends: ${shlibs:Depends},
- ${misc:Depends}
+Depends:
+ ${shlibs:Depends},
+ ${misc:Depends},
Description: dynamic library of the Genome Analysis Toolbox
The GATB-CORE project provides a set of highly efficient
algorithms to analyse NGS data sets. These methods enable
@@ -61,8 +63,9 @@ Package: libgatbcore-dev
Architecture: any-amd64 arm64 loong64 mips64el ppc64el ia64 ppc64 riscv64 sparc64 alpha
Multi-Arch: same
Section: libdevel
-Depends: ${misc:Depends},
- libgatbcore3 (= ${binary:Version})
+Depends:
+ ${misc:Depends},
+ libgatbcore3 (= ${binary:Version}),
Description: development library of the Genome Analysis Toolbox
The GATB-CORE project provides a set of highly efficient
algorithms to analyse NGS data sets. These methods enable
@@ -81,8 +84,9 @@ Description: development library of the Genome Analysis Toolbox
Package: gatb-core-testdata
Architecture: all
-Depends: ${misc:Depends},
- gatb-core
+Depends:
+ ${misc:Depends},
+ gatb-core,
Description: Genome Analysis Toolbox with de-Bruijn graph (test data)
The GATB-CORE project provides a set of highly efficient
algorithms to analyse NGS data sets. These methods enable
=====================================
debian/patches/dynamic_lib.patch
=====================================
@@ -1,5 +1,5 @@
Author: Andreas Tille <tille at debian.org>
-Last-Update: Tue, 28 Nov 2017 10:37:22 +0100
+Last-Update: 2017-11-28
Description: Create additional dynamic library
--- a/gatb-core/src/CMakeLists.txt
=====================================
debian/patches/dynamic_linking_of_tools.patch
=====================================
@@ -1,5 +1,5 @@
Author: Andreas Tille <tille at debian.org>
-Last-Update: Tue, 28 Nov 2017 10:37:22 +0100
+Last-Update: 2017-11-28
Description: Dynamic linking against own library
Does not work unfortunately
=====================================
debian/patches/fix_hdf5_includes.patch
=====================================
@@ -1,5 +1,5 @@
Author: Christian Seiler <christian at iwakd.de>
-Last-Update: Tue, 28 Nov 2017 22:00:48 +0100
+Last-Update: 2017-11-28
Description: Fix hdf5 includes.
--> https://lists.debian.org/debian-mentors/2017/11/msg00227.html
=====================================
debian/patches/fix_install_location.patch
=====================================
@@ -1,5 +1,5 @@
Author: Andreas Tille <tille at debian.org>
-Last-Update: Tue, 28 Nov 2017 10:37:22 +0100
+Last-Update: 2017-11-28
Description: Install examples into correct dir
--- gatb-core.orig/gatb-core/CMakeLists.txt
=====================================
debian/patches/multiarch.patch
=====================================
@@ -1,5 +1,5 @@
Author: Andreas Tille <tille at debian.org>
-Last-Update: Tue, 28 Nov 2017 10:37:22 +0100
+Last-Update: 2017-11-28
Description: Support Multiarch
--- a/gatb-core/src/CMakeLists.txt
=====================================
debian/patches/set_soversion.patch
=====================================
@@ -1,5 +1,5 @@
Author: Andreas Tille <tille at debian.org>
-Last-Update: Tue, 28 Nov 2017 10:37:22 +0100
+Last-Update: 2017-11-28
Description: Invent soversion 0 since upstream does not set soversion
--- a/gatb-core/src/CMakeLists.txt
=====================================
debian/patches/spelling.patch
=====================================
@@ -1,5 +1,5 @@
Author: Andreas Tille <tille at debian.org>
-Last-Update: Tue, 28 Nov 2017 10:37:22 +0100
+Last-Update: 2017-11-28
Description: Fix spelling issues
--- gatb-core.orig/gatb-core/src/gatb/tools/compression/DnaCoder.cpp
=====================================
debian/patches/use_debian_packaged_hdf5.patch
=====================================
@@ -1,5 +1,5 @@
Author: Andreas Tille <tille at debian.org>
-Last-Update: Tue, 28 Nov 2017 10:37:22 +0100
+Last-Update: 2017-11-28
Description: Use Debian packaged hdf5
--- gatb-core.orig/gatb-core/thirdparty/CMakeLists.txt
=====================================
debian/tests/control
=====================================
@@ -1,3 +1,3 @@
Tests: run-unit-test
-Depends: @, @builddeps@, libhdf5-dev ,libopenmpi-dev, pkg-config
-Restrictions: allow-stderr
+Depends: @, @builddeps@, libhdf5-openmpi-dev ,libopenmpi-dev, pkg-config
+Restrictions: allow-stderr
\ No newline at end of file
=====================================
debian/tests/run-unit-test
=====================================
@@ -6,7 +6,8 @@ CUR_DIR=`pwd`
export LC_ALL=C.UTF-8
if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
- AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+ # Using /dev/shm suggested by https://platform.aim2balance.ai/
+ AUTOPKGTEST_TMP=$(mktemp -d /dev/shm/${pkg}-test.XXXXXX)
trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
fi
@@ -22,7 +23,7 @@ for code_snippet in ${code_snippets[*]}
do
prg_name=`echo $code_snippet | cut -d'/' -f4 | cut -d'.' -f1`
# Compiling using installed libs
- g++ $code_snippet -Iinclude -Llib -lgatbcore `pkg-config --libs hdf5` -lhdf5 -lmpi -ldl -lz -lpthread -std=c++0x -O3 -o $prg_name
+ g++ $code_snippet -Iinclude -Llib -lgatbcore `pkg-config --libs hdf5-openmpi` -lmpi -ldl -lz -lpthread -std=c++0x -O3 -o $prg_name
done
echo -e "f6f63f16384efd47a059566413617770 kmer.fa" >> checksums
=====================================
debian/upstream/metadata
=====================================
@@ -1,3 +1,4 @@
+Bug-Database: https://github.com/GATB/gatb-core/issues
Bug-Submit: https://github.com/GATB/gatb-core/issues/new
Cite-As: >
E. Drezen, G. Rizk, R. Chikhi, C. Deltel, C. Lemaitre, P. Peterlongo,
@@ -18,6 +19,7 @@ Reference:
DOI: 10.1093/bioinformatics/btu406
URL: http://dx.doi.org/10.1093/bioinformatics/btu406
Repository: https://github.com/GATB/gatb-core.git
+Repository-Browse: https://github.com/GATB/gatb-core
Registry:
- Name: OMICtools
Entry: OMICS_04834
=====================================
debian/watch
=====================================
@@ -1,9 +1,6 @@
-version=4
+Version: 5
-# Minia does not work with the official release - try HEAD
-#opts="mode=git,pretty=1.4.1+git%cd.%h,repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
-# https://github.com/GATB/gatb-core.git HEAD
-
-# Regular releases
-opts="repacksuffix=+dfsg,dversionmangle=auto,filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE at -$1.tar.gz%" \
- https://github.com/GATB/gatb-core/tags .*/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
+Template: Github
+Dist: https://github.com/GATB/gatb-core
+Dversion-Mangle: auto
+Repack-Suffix: +dfsg
View it on GitLab: https://salsa.debian.org/med-team/gatb-core/-/compare/0d414cbbdb2d3759fcd53f53dcf75271292221b5...f71d6e09b1e9ddd51dbe0861d5213344a8cf2730
--
View it on GitLab: https://salsa.debian.org/med-team/gatb-core/-/compare/0d414cbbdb2d3759fcd53f53dcf75271292221b5...f71d6e09b1e9ddd51dbe0861d5213344a8cf2730
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