[med-svn] [Git][med-team/bamtools][master] 11 commits: Make sure static lib will be installed
Andreas Tille
gitlab at salsa.debian.org
Thu Oct 10 12:31:23 BST 2019
Andreas Tille pushed to branch master at Debian Med / bamtools
Commits:
a6149074 by Andreas Tille at 2019-10-10T10:58:37Z
Make sure static lib will be installed
- - - - -
ef0fab3f by Andreas Tille at 2019-10-10T10:59:03Z
debhelper-compat 12
- - - - -
d1d1fbfe by Andreas Tille at 2019-10-10T10:59:15Z
Standards-Version: 4.4.1
- - - - -
82695878 by Andreas Tille at 2019-10-10T10:59:15Z
Drop useless get-orig-source target
- - - - -
ad8a2cc3 by Andreas Tille at 2019-10-10T10:59:34Z
Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
- - - - -
2990fe94 by Andreas Tille at 2019-10-10T10:59:35Z
Trim trailing whitespace.
Fixes lintian: file-contains-trailing-whitespace
See https://lintian.debian.org/tags/file-contains-trailing-whitespace.html for more details.
- - - - -
0f292788 by Andreas Tille at 2019-10-10T10:59:38Z
Set upstream metadata fields: Repository.
- - - - -
487d1aec by Andreas Tille at 2019-10-10T10:59:38Z
Remove obsolete fields Name from debian/upstream/metadata.
- - - - -
68574ecb by Andreas Tille at 2019-10-10T11:01:03Z
Fix automatic correction
- - - - -
2f90a604 by Andreas Tille at 2019-10-10T11:25:50Z
Revert attempt to install static lib - its not build any more
- - - - -
9f277a61 by Andreas Tille at 2019-10-10T11:26:22Z
Remove unused patch
- - - - -
7 changed files:
- debian/changelog
- − debian/compat
- debian/control
- − debian/patches/fix_soversion.patch
- debian/patches/series
- debian/rules
- debian/upstream/metadata
Changes:
=====================================
debian/changelog
=====================================
@@ -1,8 +1,18 @@
-bamtools (2.5.1+dfsg-4) UNRELEASED; urgency=medium
+bamtools (2.5.1+dfsg-4) unstable; urgency=medium
+ [ Jelmer Vernooij ]
* Trim trailing whitespace.
- -- Jelmer Vernooij <jelmer at debian.org> Sat, 20 Oct 2018 13:08:22 +0000
+ [ Andreas Tille ]
+ * debhelper-compat 12
+ * Standards-Version: 4.4.1
+ * Drop useless get-orig-source target
+ * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
+ * Trim trailing whitespace.
+ * Set upstream metadata fields: Repository.
+ * Remove obsolete fields Name from debian/upstream/metadata.
+
+ -- Andreas Tille <tille at debian.org> Thu, 10 Oct 2019 12:59:38 +0200
bamtools (2.5.1+dfsg-3) unstable; urgency=medium
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-11
=====================================
debian/control
=====================================
@@ -6,14 +6,14 @@ Uploaders: Michael R. Crusoe <michael.crusoe at gmail.com>,
Dominique Belhachemi <domibel at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 11),
- d-shlibs (>= 0.56),
+Build-Depends: debhelper-compat (= 12),
+ d-shlibs,
cmake,
zlib1g-dev,
libjsoncpp-dev,
help2man,
doxygen
-Standards-Version: 4.1.3
+Standards-Version: 4.4.1
Vcs-Browser: https://salsa.debian.org/med-team/bamtools
Vcs-Git: https://salsa.debian.org/med-team/bamtools.git
Homepage: https://github.com/pezmaster31/bamtools/wiki
@@ -57,9 +57,9 @@ Multi-Arch: same
Section: libdevel
Depends: libbamtools2.5.1 (= ${binary:Version}),
${misc:Depends}
+Suggests: libbamtools-doc (= ${binary:Version})
Breaks: libbamtools2.4.0 (<< 2.5.1+dfsg-2~)
Replaces: libbamtools2.4.0 (<< 2.5.1+dfsg-2~)
-Suggests: libbamtools-doc (= ${binary:Version})
Description: C++ API for manipulating BAM (genome alignment) files
BamTools facilitates research analysis and data management using BAM
files. It copes with the enormous amount of data produced by current
=====================================
debian/patches/fix_soversion.patch deleted
=====================================
@@ -1,22 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Fri, 13 Jan 2017 10:09:04 +0100
-Description: Upstream has not fully understood the concept of
- soversion and simply sets it same as upstream version. This
- patch is fixing this.
- .
- FIXME: After the next version bump this should rather be set
- to major.minor number - or just an integer number. However,
- for the moment the binary lib package is has added 2.4.0 and
- we can not revert this to 2.4 since its a lower number.
-
---- a/src/api/CMakeLists.txt
-+++ b/src/api/CMakeLists.txt
-@@ -34,7 +34,7 @@ set( BamToolsAPISources
- # create main BamTools API shared library
- add_library( BamTools SHARED ${BamToolsAPISources} )
- set_target_properties( BamTools PROPERTIES
-- SOVERSION "2.4.1"
-+ SOVERSION "2.4.0"
- OUTPUT_NAME "bamtools" )
-
- # create main BamTools API static library
=====================================
debian/patches/series
=====================================
@@ -4,4 +4,3 @@ doxygen-tweak
0006-Doxygen-reproducibility
0008_Cmake_Test.patch
spelling
-# fix_soversion.patch
=====================================
debian/rules
=====================================
@@ -17,8 +17,10 @@ override_dh_auto_configure-indep:
override_dh_auto_test-indep:
override_dh_auto_test-arch:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
cd obj-* && ln -s src/toolkit/ bin
dh_auto_test --arch
+endif
override_dh_auto_build-indep:
doxygen -u docs/Doxyfile
@@ -35,6 +37,3 @@ override_dh_install-indep:
describe-current-version:
git describe --tags upstream | sed 's,^release-,,;s,-,+,;s,-,~,;'
-
-get-orig-source:
- uscan --verbose --force-download --repack --compression xz
=====================================
debian/upstream/metadata
=====================================
@@ -1,25 +1,25 @@
-Name: BamTools
Reference:
- Author: >
- Derek W. Barnett and Erik K. Garrison and Aaron R. Quinlan and
- Michael P. Stromberg and Gabor T. Marth
- Title: "BamTools: a C++ API and toolkit for analyzing and managing BAM files"
- Journal: Bioinformatics
- Year: 2011
- Volume: 27
- Number: 12
- Pages: 1691-2
- DOI: 10.1093/bioinformatics/btr174
- PMID: 21493652
- URL: http://bioinformatics.oxfordjournals.org/content/27/12/1691
- eprint: >
- http://bioinformatics.oxfordjournals.org/content/27/12/1691.full.pdf+html
+ Author: >
+ Derek W. Barnett and Erik K. Garrison and Aaron R. Quinlan and
+ Michael P. Stromberg and Gabor T. Marth
+ Title: "BamTools: a C++ API and toolkit for analyzing and managing BAM files"
+ Journal: Bioinformatics
+ Year: 2011
+ Volume: 27
+ Number: 12
+ Pages: 1691-2
+ DOI: 10.1093/bioinformatics/btr174
+ PMID: 21493652
+ URL: http://bioinformatics.oxfordjournals.org/content/27/12/1691
+ eprint: >
+ http://bioinformatics.oxfordjournals.org/content/27/12/1691.full.pdf+html
Registry:
- - Name: OMICtools
- Entry: OMICS_11315
- - Name: SciCrunch
- Entry: SCR_015987
- - Name: bio.tools
- Entry: BamTools
- - Name: conda:bioconda
- Entry: bamtools
+- Name: OMICtools
+ Entry: OMICS_11315
+- Name: SciCrunch
+ Entry: SCR_015987
+- Name: bio.tools
+ Entry: BamTools
+- Name: conda:bioconda
+ Entry: bamtools
+Repository: https://github.com/pezmaster31/bamtools
View it on GitLab: https://salsa.debian.org/med-team/bamtools/compare/64169cd6f6ee478cdab208fb1133b3d4612719c3...9f277a61d787afabf3b6377969ecdd6c6492728b
--
View it on GitLab: https://salsa.debian.org/med-team/bamtools/compare/64169cd6f6ee478cdab208fb1133b3d4612719c3...9f277a61d787afabf3b6377969ecdd6c6492728b
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