[med-svn] [Git][med-team/emboss][master] 9 commits: debhelper 11
Andreas Tille
gitlab at salsa.debian.org
Fri Aug 3 05:22:47 BST 2018
Andreas Tille pushed to branch master at Debian Med / emboss
Commits:
014d12b9 by Andreas Tille at 2018-08-03T02:18:37Z
debhelper 11
- - - - -
7ab9c026 by Andreas Tille at 2018-08-03T02:24:09Z
Point Vcs fields to salsa.debian.org
- - - - -
c4a48e10 by Andreas Tille at 2018-08-03T02:24:09Z
Standards-Version: 4.1.5
- - - - -
b30d4be9 by Andreas Tille at 2018-08-03T03:00:18Z
Drop unused lintian-overrides
- - - - -
72975f86 by Andreas Tille at 2018-08-03T03:02:30Z
Respect DEB_BUILD_OPTIONS in override_dh_auto_test
- - - - -
a12accad by Andreas Tille at 2018-08-03T03:18:28Z
Drop autotools from d/rules
- - - - -
6e58879d by Andreas Tille at 2018-08-03T03:52:42Z
Really drop autoreconf commands
- - - - -
c4a47c67 by Andreas Tille at 2018-08-03T03:59:04Z
Lintian override for script-with-language-extension
More verbose package descriptions for all packages
- - - - -
1f6d29eb by Andreas Tille at 2018-08-03T04:19:36Z
Upload to unstable
- - - - -
6 changed files:
- debian/changelog
- debian/compat
- debian/control
- − debian/emboss-doc.lintian-overrides
- + debian/jemboss.lintian-overrides
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,15 @@
+emboss (6.6.0+dfsg-7) unstable; urgency=medium
+
+ * debhelper 11
+ * Point Vcs fields to salsa.debian.org
+ * Standards-Version: 4.1.5
+ * Drop unused lintian-overrides
+ * Respect DEB_BUILD_OPTIONS in override_dh_auto_test
+ * Lintian override for script-with-language-extension
+ * More verbose package descriptions for all packages
+
+ -- Andreas Tille <tille at debian.org> Fri, 03 Aug 2018 05:59:14 +0200
+
emboss (6.6.0+dfsg-6) unstable; urgency=medium
* debhelper 10
=====================================
debian/compat
=====================================
--- a/debian/compat
+++ b/debian/compat
@@ -1 +1 @@
-10
+11
=====================================
debian/control
=====================================
--- a/debian/control
+++ b/debian/control
@@ -5,7 +5,7 @@ Uploaders: Charles Plessy <plessy at debian.org>,
Andreas Tille <tille at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 10),
+Build-Depends: debhelper (>= 11~),
# javahelper,
libx11-dev,
x11proto-core-dev,
@@ -18,16 +18,14 @@ Build-Depends: debhelper (>= 10),
libpq-dev,
antiword,
sharutils,
- autotools-dev,
tcsh | csh | c-shell,
- dh-autoreconf,
# Needed until the following is solved: https://sourceforge.net/tracker/?func=detail&aid=3033326&group_id=93650&atid=605031
default-jdk,
ant
-#Build-Depends-Indep: default-jdk
-Standards-Version: 3.9.8
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/emboss.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/emboss.git
+# #Build-Depends-Indep: default-jdk
+Standards-Version: 4.1.5
+Vcs-Browser: https://salsa.debian.org/med-team/emboss
+Vcs-Git: https://salsa.debian.org/med-team/emboss.git
Homepage: http://emboss.sourceforge.net
Package: emboss
@@ -57,6 +55,16 @@ Package: emboss-data
Architecture: all
Depends: ${misc:Depends}
Description: data files for the EMBOSS package
+ EMBOSS is a free Open Source software analysis package specially developed for
+ the needs of the molecular biology (e.g. EMBnet) user community. The software
+ automatically copes with data in a variety of formats and even allows
+ transparent retrieval of sequence data from the web. Also, as extensive
+ libraries are provided with the package, it is a platform to allow other
+ scientists to develop and release software in true open source spirit. EMBOSS
+ also integrates a range of currently available packages and tools for sequence
+ analysis into a seamless whole. EMBOSS breaks the historical trend towards
+ commercial software packages.
+ .
This package includes data files needed by EMBOSS, the European Molecular
Biology Open Software Suite.
@@ -66,6 +74,16 @@ Section: doc
Depends: ${misc:Depends}
Suggests: evince | pdf-viewer | postscript-viewer
Description: documentation for EMBOSS
+ EMBOSS is a free Open Source software analysis package specially developed for
+ the needs of the molecular biology (e.g. EMBnet) user community. The software
+ automatically copes with data in a variety of formats and even allows
+ transparent retrieval of sequence data from the web. Also, as extensive
+ libraries are provided with the package, it is a platform to allow other
+ scientists to develop and release software in true open source spirit. EMBOSS
+ also integrates a range of currently available packages and tools for sequence
+ analysis into a seamless whole. EMBOSS breaks the historical trend towards
+ commercial software packages.
+ .
This package includes non-essential user documentation for EMBOSS, the
European Molecular Biology Open Software Suite.
@@ -76,6 +94,16 @@ Depends: ${misc:Depends}
Recommends: tcsh | csh | c-shell
Suggests: valgrind
Description: test files for the EMBOSS package
+ EMBOSS is a free Open Source software analysis package specially developed for
+ the needs of the molecular biology (e.g. EMBnet) user community. The software
+ automatically copes with data in a variety of formats and even allows
+ transparent retrieval of sequence data from the web. Also, as extensive
+ libraries are provided with the package, it is a platform to allow other
+ scientists to develop and release software in true open source spirit. EMBOSS
+ also integrates a range of currently available packages and tools for sequence
+ analysis into a seamless whole. EMBOSS breaks the historical trend towards
+ commercial software packages.
+ .
This package includes test files for EMBOSS, the European Molecular Biology
Open Software Suite.
.
@@ -121,5 +149,15 @@ Depends: ${shlibs:Depends},
default-jre
# libgnujaf-java
Description: graphical user interface to EMBOSS
+ EMBOSS is a free Open Source software analysis package specially developed for
+ the needs of the molecular biology (e.g. EMBnet) user community. The software
+ automatically copes with data in a variety of formats and even allows
+ transparent retrieval of sequence data from the web. Also, as extensive
+ libraries are provided with the package, it is a platform to allow other
+ scientists to develop and release software in true open source spirit. EMBOSS
+ also integrates a range of currently available packages and tools for sequence
+ analysis into a seamless whole. EMBOSS breaks the historical trend towards
+ commercial software packages.
+ .
Jemboss is a Graphical User Interface (GUI) to EMBOSS, the European Molecular
Biology Open Software Suite. It is part of the EMBOSS distribution.
=====================================
debian/emboss-doc.lintian-overrides deleted
=====================================
--- a/debian/emboss-doc.lintian-overrides
+++ /dev/null
@@ -1,5 +0,0 @@
-# false positives: These files are just carbon copies of the files in upstream tarball
-emboss-doc: package-contains-timestamped-gzip usr/share/EMBOSS/doc/manuals/adminguide.tar.gz
-emboss-doc: package-contains-timestamped-gzip usr/share/EMBOSS/doc/manuals/program.ps.gz
-emboss-doc: package-contains-timestamped-gzip usr/share/EMBOSS/doc/tutorials/emboss_tut.tar.gz
-
=====================================
debian/jemboss.lintian-overrides
=====================================
--- /dev/null
+++ b/debian/jemboss.lintian-overrides
@@ -0,0 +1,2 @@
+# see https://lists.debian.org/debian-med/2018/06/msg00043.html
+jemboss: script-with-language-extension usr/bin/runJemboss.sh
=====================================
debian/rules
=====================================
--- a/debian/rules
+++ b/debian/rules
@@ -10,7 +10,7 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all
#export CLASSPATH=/usr/share/java/activation.jar:
%:
- dh $@ --with autotools-dev,autoreconf
+ dh $@
VERSION := $(shell dpkg-parsechangelog | grep Ver | cut -d' ' -f2 | cut -d- -f1)
RENAMED := cons pscan
@@ -37,7 +37,6 @@ DEB_LDFLAGS += $(shell dpkg-buildflags --get LDFLAGS)
#DEB_LDFLAGS += $(shell pg_config | grep LIBS | cut -f2 -d=)
override_dh_auto_configure:
- dh_autotools-dev_updateconfig
dh_auto_configure -- $(CONFFLAGS)
override_dh_auto_build:
@@ -47,7 +46,6 @@ override_dh_auto_build:
cd jemboss && jar uf lib/jemboss.jar resources/version resources/*.properties
override_dh_clean:
- dh_autotools-dev_restoreconfig
rm -rf debian/emboss_tmp
find jemboss/ -type f -name "*.class" -delete
[ ! -d debian/testbackup ] || ( $(RM) --recursive test ; mv debian/testbackup test )
@@ -107,6 +105,7 @@ override_dh_auto_install-indep:
find debian/emboss-test/usr/share/EMBOSS/test -type f -name .cvsignore -delete
override_dh_auto_test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
$(RM) test-stamp
[ -d debian/testbackup ] || cp -a test debian/testbackup
sed -i "/SET emboss_tempdata/cSET emboss_tempdata $(CURDIR)/test" test/.embossrc
@@ -115,6 +114,7 @@ override_dh_auto_test:
echo "SET emboss_data $(CURDIR)/emboss/data" >> test/.embossrc
echo "SET emboss_docroot $(CURDIR)/doc" >> test/.embossrc
cd test/qa && LS_COLORS='' EMBOSSRC=$(CURDIR)/test PATH=$(CURDIR)/emboss:$$PATH EMBOSS_ROOT=../../../ ./qatest.csh
+endif
override_dh_installchangelogs:
dh_installchangelogs -k ChangeLog
View it on GitLab: https://salsa.debian.org/med-team/emboss/compare/d6089bb1746430f9f8b71a25e21e6fb6a5976264...1f6d29ebeaa4feb00772ffdb299402083e1c9c5b
--
View it on GitLab: https://salsa.debian.org/med-team/emboss/compare/d6089bb1746430f9f8b71a25e21e6fb6a5976264...1f6d29ebeaa4feb00772ffdb299402083e1c9c5b
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