[med-svn] r2248 - trunk/packages/emboss/trunk/debian

plessy at alioth.debian.org plessy at alioth.debian.org
Thu Jul 17 04:28:22 UTC 2008 

Author: plessy
Date: 2008-07-17 04:28:21 +0000 (Thu, 17 Jul 2008)
New Revision: 2248

Added:
   trunk/packages/emboss/trunk/debian/README.source
   trunk/packages/emboss/trunk/debian/emboss-test.dirs
Removed:
   trunk/packages/emboss/trunk/debian/libnucleus7-dev.dirs
Modified:
   trunk/packages/emboss/trunk/debian/changelog
   trunk/packages/emboss/trunk/debian/control
   trunk/packages/emboss/trunk/debian/emboss-doc.doc-base.emboss-apps
   trunk/packages/emboss/trunk/debian/emboss-doc.doc-base.emboss-groups
   trunk/packages/emboss/trunk/debian/rules
Log:
Packaged test data, corrected doc-base file paths, updated to Policy 3.8.0 and debhelper 7.

  * debian/README.source added to document how to patch and unpatch the
    sources.
  * debian/emboss-doc.doc-base.{apps/groups} corrected for new file locations.
  * debian/control:
    - Uses debhelper 7.
    - Incremented the soname of the AJAX and NUCLEUS libraries (conflict and
      replace the previous versions).
    - Incremented Standards-Version to 3.8.0 after adding README.Sources.
    - Added a new package, emboss-test, that contains test data.
    - Build-Depends: tcsh | csh | c-shell to run the tests.
  * debian/rules:
    - Implemented build-time tests.
    - Updated the instructions to build manpages.



Added: trunk/packages/emboss/trunk/debian/README.source
===================================================================
--- trunk/packages/emboss/trunk/debian/README.source	                        (rev 0)
+++ trunk/packages/emboss/trunk/debian/README.source	2008-07-17 04:28:21 UTC (rev 2248)
@@ -0,0 +1,2 @@
+This packages uses a patch system. Please read
+/usr/share/doc/quilt/README.source for more informations.

Modified: trunk/packages/emboss/trunk/debian/changelog
===================================================================
--- trunk/packages/emboss/trunk/debian/changelog	2008-07-17 01:12:33 UTC (rev 2247)
+++ trunk/packages/emboss/trunk/debian/changelog	2008-07-17 04:28:21 UTC (rev 2248)
@@ -1,15 +1,30 @@
-emboss (6.0.0-1) UNRELEASED; urgency=low
+emboss (6.0.1-1) UNRELEASED; urgency=low
 
   * New upstream release:
-    -
-    -
-    -
+    - New applications: aligncopy, aligncopypair, consambig, density,
+      featcopy, featreport, infobase, inforesidue, jaspextract, jaspscan,
+      maskambignuc, maskambigprot, nohtml, nospace, notab, sizeseq,
+      skipredundant, trimspace.
+    - See `/usr/share/doc/emboss/changelog.gz' for more details.
+  * debian/patches:
+    - Removed the patches that are obsoleted by the new release.
+    - Documented the local patch on `tfm' that changes default pager.
+  * debian/README.source added to document how to patch and unpatch the
+    sources.
+  * debian/emboss-doc.doc-base.{apps/groups} corrected for new file locations.
   * debian/control:
-    - Replaced build dependancy on deprecated x-dev by x11proto-core-dev.
+    - Replaced build dependency on deprecated x-dev by x11proto-core-dev.
     - Uses debhelper 7.
-    - Incremented the soname of the AJAX and NUCLEUS libraries.
+    - Incremented the soname of the AJAX and NUCLEUS libraries (conflict and
+      replace the previous versions).
+    - Incremented Standards-Version to 3.8.0 after adding README.Sources.
+    - Added a new package, emboss-test, that contains test data.
+    - Build-Depends: tcsh | csh | c-shell to run the tests.
+  * debian/rules:
+    - Implemented build-time tests.
+    - Updated the instructions to build manpages.
 
- -- Charles Plessy <plessy at debian.org>  Wed, 16 Jul 2008 13:01:53 +0900
+ -- Charles Plessy <plessy at debian.org>  Thu, 17 Jul 2008 12:57:54 +0900
 
 emboss (5.0.0-7) unstable; urgency=low
 

Modified: trunk/packages/emboss/trunk/debian/control
===================================================================
--- trunk/packages/emboss/trunk/debian/control	2008-07-17 01:12:33 UTC (rev 2247)
+++ trunk/packages/emboss/trunk/debian/control	2008-07-17 04:28:21 UTC (rev 2248)
@@ -4,18 +4,18 @@
 Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 DM-Upload-Allowed: yes
 Uploaders: Charles Plessy <plessy at debian.org>, Nelson A. de Oliveira <naoliv at debian.org>
-Build-Depends: debhelper (>= 7), quilt, libx11-dev, x11proto-core-dev, libgdchart-gd2-xpm-dev, zlib1g-dev, libpng12-dev, libpcre3-dev, antiword, sharutils, autotools-dev
+Build-Depends: debhelper (>= 7), quilt, libx11-dev, x11proto-core-dev, libgdchart-gd2-xpm-dev, zlib1g-dev, libpng12-dev, libpcre3-dev, antiword, sharutils, autotools-dev, tcsh | csh | c-shell
 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/emboss/trunk/?rev=0&sc=0trunk
 Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/emboss/trunk/
-Standards-Version: 3.7.3
+Standards-Version: 3.8.0
 Homepage: http://www.emboss.org
 
 Package: emboss
 Architecture: any
 Depends: ${shlibs:Depends}, ${misc:Depends}, emboss-data (= ${source:Version}), csh | c-shell
 Recommends: primer3, dialign
-Suggests: emboss-doc, embassy, clustalw
-Description: The European Molecular Biology Open Software Suite
+Suggests: emboss-doc, emboss-test, embassy, clustalw
+Description: the european molecular biology open software suite
  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
@@ -32,7 +32,7 @@
 
 Package: emboss-data
 Architecture: all
-Description: Data files for the EMBOSS package
+Description: data files for the EMBOSS package
  This package includes data files needed by EMBOSS, the European Molecular
  Biology Open Software Suite.
 
@@ -40,10 +40,22 @@
 Section: doc
 Architecture: all
 Suggests: pdf-viewer | postscript-viewer
-Description: Documentation for EMBOSS
+Description: documentation for EMBOSS
  This package includes non-essential user documentation for EMBOSS, the
  European Molecular Biology Open Software Suite.
 
+Package: emboss-test
+Section: misc
+Architecture: all
+Recommends: tcsh | csh | c-shell
+Suggests: valgrind
+Description: test files for the EMBOSS package
+ This package includes test files for EMBOSS, the European Molecular Biology
+ Open Software Suite.
+ .
+ It is a good idea to use the data from this package for your bug reports when
+ possible.
+
 Package: emboss-lib
 Section: libs
 Architecture: any
@@ -73,7 +85,9 @@
 Section: libdevel
 Architecture: any
 Depends: ${shlibs:Depends}, ${misc:Depends}, libajax6 (= ${binary:Version})
-Description: Development files for libajax
+Conflicts: libajax5-dev
+Replaces: libajax5-dev
+Description: development files for libajax
  This package contains the header and development files needed to build
  programs and packages using libajax.
 
@@ -96,6 +110,8 @@
 Section: libdevel
 Architecture: any
 Depends: ${shlibs:Depends}, ${misc:Depends}, libnucleus6 (= ${binary:Version})
-Description: Development files for libajax
+Conflicts: libnucleus5-dev
+Replaces: libnucleus5-dev
+Description: development files for libajax
  This package contains the header and development files needed to build
  programs and packages using libnucleus.

Modified: trunk/packages/emboss/trunk/debian/emboss-doc.doc-base.emboss-apps
===================================================================
--- trunk/packages/emboss/trunk/debian/emboss-doc.doc-base.emboss-apps	2008-07-17 01:12:33 UTC (rev 2247)
+++ trunk/packages/emboss/trunk/debian/emboss-doc.doc-base.emboss-apps	2008-07-17 04:28:21 UTC (rev 2248)
@@ -3,5 +3,5 @@
 Section: Science/Biology
 
 Format: HTML
-Index: /usr/share/doc/emboss-doc/doc/html/emboss/apps/index.html
-Files: /usr/share/doc/emboss-doc/doc/html/emboss/apps/*.html
+Index: /usr/share/doc/emboss-doc/doc/programs/html/index.html
+Files: /usr/share/doc/emboss-doc/doc/programs/html/*.html

Modified: trunk/packages/emboss/trunk/debian/emboss-doc.doc-base.emboss-groups
===================================================================
--- trunk/packages/emboss/trunk/debian/emboss-doc.doc-base.emboss-groups	2008-07-17 01:12:33 UTC (rev 2247)
+++ trunk/packages/emboss/trunk/debian/emboss-doc.doc-base.emboss-groups	2008-07-17 04:28:21 UTC (rev 2248)
@@ -3,5 +3,5 @@
 Section: Science/Biology
 
 Format: HTML
-Index: /usr/share/doc/emboss-doc/doc/html/emboss/apps/groups.html
-Files: /usr/share/doc/emboss-doc/doc/html/emboss/apps/*.html
+Index: /usr/share/doc/emboss-doc/doc/programs/html/groups.html
+Files: /usr/share/doc/emboss-doc/doc/programs/html/*.html

Added: trunk/packages/emboss/trunk/debian/emboss-test.dirs
===================================================================
--- trunk/packages/emboss/trunk/debian/emboss-test.dirs	                        (rev 0)
+++ trunk/packages/emboss/trunk/debian/emboss-test.dirs	2008-07-17 04:28:21 UTC (rev 2248)
@@ -0,0 +1,2 @@
+usr/share/EMBOSS
+etc/emboss/embossrc.d

Deleted: trunk/packages/emboss/trunk/debian/libnucleus7-dev.dirs
===================================================================
--- trunk/packages/emboss/trunk/debian/libnucleus7-dev.dirs	2008-07-17 01:12:33 UTC (rev 2247)
+++ trunk/packages/emboss/trunk/debian/libnucleus7-dev.dirs	2008-07-17 04:28:21 UTC (rev 2248)
@@ -1,2 +0,0 @@
-usr/lib
-usr/include

Modified: trunk/packages/emboss/trunk/debian/rules
===================================================================
--- trunk/packages/emboss/trunk/debian/rules	2008-07-17 01:12:33 UTC (rev 2247)
+++ trunk/packages/emboss/trunk/debian/rules	2008-07-17 04:28:21 UTC (rev 2248)
@@ -29,13 +29,7 @@
 # In order to use this rule you must install libemboss-acd-perl, xsltproc, docbook-xml and docbook-xsl
 manpages: debian/manpages/success
 debian/manpages/success:
-	if [ -f debian/emboss.manpages ] ; then rm debian/emboss.manpages ; fi
-	rm -f debian/manpages/*.1e debian/manpages/*.xml
-	for acd in $(shell ls ../emboss-6.0.0/emboss/acd/*acd | sed -r 's#.*/.*/(.+).acd#\1#'); \
-		do perl debian/acd2docbook.pl  ../emboss-6.0.0/emboss/acd/$$acd.acd $(VERSION) > debian/manpages/$$acd.xml ;\
-		xsltproc --nonet --param man.charmap.use.subset 0 -o debian/manpages/ debian/manpages/$$acd.xml ;\
-		echo "debian/manpages/$$acd.1e" >> debian/emboss.manpages ;\
-		done
+	debian/build-manpages.sh
 	echo "The manpages have been sucessfully built" > debian/manpages/success
 
 debian/copyright:
@@ -60,10 +54,12 @@
 	rm -rf config.status install-stamp
 	
 	# Temporary fix that may become unecessary in the future.
-	rm -f test/gb/Makefile test/wormpep/Makefile
-	
-	dh_clean debian/copyright config.sub config.guess
+	# rm -f test/gb/Makefile test/wormpep/Makefile
 
+	-cp debian/testembossrcbackup test/.embossrc
+
+	dh_clean debian/copyright config.sub config.guess test-stamp
+
 install: install-stamp
 install-stamp: build-stamp
 	dh_testdir
@@ -114,13 +110,28 @@
 	# dangling LICEN[CS]E FILE
 	#-rm -f $(CURDIR)/debian/emboss-java/usr/share/EMBOSS/jemboss/LICENSE
 
+	### Installation of the test suite
+	cp -a test $(CURDIR)/debian/emboss-test/usr/share/EMBOSS/
+	sed -i "/SET emboss_tempdata/cSET emboss_tempdata /usr/share/EMBOSS/test" $(CURDIR)/debian/emboss-test/usr/share/EMBOSS/test/.embossrc
+	sed -i "/SET emboss_qadata/cSET emboss_qadata /usr/share/EMBOSS/test" $(CURDIR)/debian/emboss-test/usr/share/EMBOSS/test/.embossrc
+	mv $(CURDIR)/debian/emboss-test/usr/share/EMBOSS/test/.embossrc $(CURDIR)/debian/emboss-test/etc/emboss/embossrc.d/
+
 	dh_makeshlibs	# Should it be invoked now ?
 
 	touch install-stamp
 
+test: test-stamp
+test-stamp:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
+	[ ../debian/testembossrcbackup ] || cp test/.embossrc ../debian/testembossrcbackup
+	sed -i "/SET emboss_tempdata/cSET emboss_tempdata $(CURDIR)/test" test/.embossrc
+	sed -i "/SET emboss_qadata/cSET emboss_qadata $(CURDIR)/test" test/.embossrc
+	cd test/qa && PATH=$$PATH:$(CURDIR)/emboss ./qatest.csh
+endif
+
 binary-indep:
 
-binary-arch: build install
+binary-arch: build install test
 	dh_testdir
 	dh_testroot
 	dh_installchangelogs ChangeLog

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