[Debian-med-packaging] Changes to libsbml

[Andreas Tille]

Hi Ivo,

I have inspected your work on libsbml to sponsor the package.
Unfortunately it has two major issues which need to be fixed first.
One issue is that the source contains a minified JavaScript without
source (prettify.js) which is claimed by lintian as an error.  I
excluded this file from the source via Files-Excluded.

The second issue is that you rebuilded the orig tarball inside the
clean target.  This is definitely a no-go.  Assume we need to build
another Debian package version from this upstream version (to fix
some bug or a security issue).  The md5sum of the new source would
not match any more and there is practically no chance to upload a
new Debian revision since this md5sum is verified against the known
source tarball at the Debian mirror.

The consequence is that we'd rather go with a broken clean target than
doing this dirty trick.  I tried to relax the situation a bit by adding
some autogenerated files to Files-Excluded - but after doing so the
package does not build properly any more.  Ivo, do you have some clue
how to fix the build?  You seem to have more experience with libsbml
than me and perhaps I made things worse.  In any case the JavaScript
without source is not allowed inside the source package and we also
can not repack the source tarball inside the clean target.

Kind regards

       Andreas.

----- Forwarded message from Andreas Tille <tille at moszumanska.debian.org> -----

Date: Sun,  6 Apr 2014 05:53:10 +0000
From: Andreas Tille <tille at moszumanska.debian.org>
To: debian-med-commit at lists.alioth.debian.org
Subject: r16572 - trunk/packages/libsbml/trunk/debian

Author: tille
Date: 2014-04-06 05:53:10 +0000 (Sun, 06 Apr 2014)
New Revision: 16572

Modified:
   trunk/packages/libsbml/trunk/debian/changelog
   trunk/packages/libsbml/trunk/debian/copyright
   trunk/packages/libsbml/trunk/debian/rules
   trunk/packages/libsbml/trunk/debian/watch
Log:
prettify.js must be removed from source and replaced by the code in package libjs-extjs-doc; moreover repackaging the tarball in clean is a no-go


Modified: trunk/packages/libsbml/trunk/debian/changelog
===================================================================
--- trunk/packages/libsbml/trunk/debian/changelog	2014-04-04 19:56:22 UTC (rev 16571)
+++ trunk/packages/libsbml/trunk/debian/changelog	2014-04-06 05:53:10 UTC (rev 16572)
@@ -1,13 +1,16 @@
-libsbml (5.9.2-1) UNRELEASED; urgency=medium
+libsbml (5.9.2+dfsg-1) UNRELEASED; urgency=medium
 
   [ Andreas Tille ]
   * New upstream version
   * debian/upstream -> debian/upstream/metadata
   * debian/control: Drop explicite ruby version in Build-Dependencies
+  * Exclude prettify.js (Javascript without source)
+  * debian/rules: Do not repack source in clean target
 
   [ Ivo Maintz ]
   * added debian/bin/python_fix.sh to bypass a wrong path to the file Python.h
   * drop ruby bindings, can't get it compiled
+    Closes: #735453
 
  -- Ivo Maintz <ivo at maintz.de>  Wed, 05 Mar 2014 10:16:44 +0100
 

Modified: trunk/packages/libsbml/trunk/debian/copyright
===================================================================
--- trunk/packages/libsbml/trunk/debian/copyright	2014-04-04 19:56:22 UTC (rev 16571)
+++ trunk/packages/libsbml/trunk/debian/copyright	2014-04-06 05:53:10 UTC (rev 16572)
@@ -1,6 +1,15 @@
 Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: libsbml
 Source: http://www.sbml.org/software/libsbml/
+Files-Excluded:
+    docs/src/prettify
+    src/sbml/common/libsbml-config-packages.h
+    src/sbml/extension/RegisterExtensions*
+    src/bindings/python/local-downcast*.cpp.in
+    src/bindings/r/local-downcast*.cpp.in
+    src/bindings/swig/libsbml-packages.*
+    src/bindings/ruby/local-downcast*.cpp.in
+    src/bindings/perl/local-downcast*.cpp.in
 
 Files: *
 Copyright: 2005-2012 SBML-TEAM mailto:sbml-team at caltech.edu

Modified: trunk/packages/libsbml/trunk/debian/rules
===================================================================
--- trunk/packages/libsbml/trunk/debian/rules	2014-04-04 19:56:22 UTC (rev 16571)
+++ trunk/packages/libsbml/trunk/debian/rules	2014-04-06 05:53:10 UTC (rev 16572)
@@ -26,17 +26,17 @@
 	dh  $@ --with-python2 --dbg-package=${dbgpack}
 
 get-orig-source:
-	uscan --verbose --force-download --repack
+	uscan --verbose --force-download --repack --repack-compression xz
 
 override_dh_auto_clean:
 	### the clean target of the libsbml makefile is highly b0rken ###
 	### the switch to cmake didn't result in great approvements ###
 	### still inline changes of files ###
 	### very ugly ###
-	rm -rf .pc .debs config docs examples macosx src config.guess config.sub build
-	find -maxdepth 1 -type f -delete
+	#rm -rf .pc .debs config docs examples macosx src config.guess config.sub build
+	#find -maxdepth 1 -type f -delete
 	dh_clean
-	tar --no-same-owner -xzf ../libsbml_$(version).orig.tar.gz --strip-components=1
+	# tar --no-same-owner -xzf ../libsbml_$(version).orig.tar.gz --strip-components=1
 
 override_dh_auto_configure:
 ifdef BIND_MATLAB

Modified: trunk/packages/libsbml/trunk/debian/watch
===================================================================
--- trunk/packages/libsbml/trunk/debian/watch	2014-04-04 19:56:22 UTC (rev 16571)
+++ trunk/packages/libsbml/trunk/debian/watch	2014-04-06 05:53:10 UTC (rev 16572)
@@ -1,3 +1,3 @@
 version=3
-#opts=dversionmangle=s/\-core-plus-packages// \
-http://sf.net/sbml/lib[Ss][Bb][Mm][Ll]-(.*)-core-plus-packages-src\.tar\.gz
+opts=dversionmangle=s/\+dfsg// \
+  http://sf.net/sbml/lib[Ss][Bb][Mm][Ll]-(.*)-core-plus-packages-src\.tar\.gz


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