[med-svn] r9746 - in trunk/packages/libsbml/trunk/debian: . lintian
Ivo Maintz
ivomaintz-guest at alioth.debian.org
Tue Feb 21 17:49:01 UTC 2012
Author: ivomaintz-guest
Date: 2012-02-21 17:49:01 +0000 (Tue, 21 Feb 2012)
New Revision: 9746
Removed:
trunk/packages/libsbml/trunk/debian/libsbml5-cil-doc.docs
trunk/packages/libsbml/trunk/debian/libsbml5-cil-doc.links
trunk/packages/libsbml/trunk/debian/libsbml5-doc.docs
trunk/packages/libsbml/trunk/debian/libsbml5-doc.links
trunk/packages/libsbml/trunk/debian/libsbml5-examples.docs
trunk/packages/libsbml/trunk/debian/libsbml5-java.docs
trunk/packages/libsbml/trunk/debian/libsbml5-matlab-doc.docs
trunk/packages/libsbml/trunk/debian/libsbml5-matlab-doc.links
trunk/packages/libsbml/trunk/debian/libsbml5-octave-doc.docs
trunk/packages/libsbml/trunk/debian/libsbml5-octave-doc.links
trunk/packages/libsbml/trunk/debian/libsbml5-octave.lintian-overrides
trunk/packages/libsbml/trunk/debian/libsbml5-perl-doc.docs
trunk/packages/libsbml/trunk/debian/libsbml5-perl-doc.links
trunk/packages/libsbml/trunk/debian/libsbml5-perl.lintian-overrides
trunk/packages/libsbml/trunk/debian/libsbml5-python-doc.docs
trunk/packages/libsbml/trunk/debian/libsbml5-python-doc.links
trunk/packages/libsbml/trunk/debian/libsbml5-python.docs
trunk/packages/libsbml/trunk/debian/patches/
Modified:
trunk/packages/libsbml/trunk/debian/changelog
trunk/packages/libsbml/trunk/debian/control
trunk/packages/libsbml/trunk/debian/control.in
trunk/packages/libsbml/trunk/debian/libsbml5-octave.install
trunk/packages/libsbml/trunk/debian/lintian/libsbml5-matlab
trunk/packages/libsbml/trunk/debian/rules
Log:
updated libsbml to version 5.4.0
Modified: trunk/packages/libsbml/trunk/debian/changelog
===================================================================
--- trunk/packages/libsbml/trunk/debian/changelog 2012-02-21 15:46:27 UTC (rev 9745)
+++ trunk/packages/libsbml/trunk/debian/changelog 2012-02-21 17:49:01 UTC (rev 9746)
@@ -1,3 +1,18 @@
+libsbml (5.4.0-1) unstable; urgency=low
+
+ * update from upstream
+ * removed the libsbml5-*-doc packages; the docu don't compile
+ with doxygen > 1.6.3
+ * moved libsbml5-matlab to contrib
+
+ -- Ivo Maintz <ivo at maintz.de> Tue, 21 Feb 2012 10:43:20 +0100
+
+libsbml (5.3.0-1) unstable; urgency=low
+
+ * update from upstream
+
+ -- Ivo Maintz <ivo at maintz.de> Thu, 12 Jan 2012 12:15:56 +0100
+
libsbml (5.2.0-1) unstable; urgency=low
* update from upstream
Modified: trunk/packages/libsbml/trunk/debian/control
===================================================================
--- trunk/packages/libsbml/trunk/debian/control 2012-02-21 15:46:27 UTC (rev 9745)
+++ trunk/packages/libsbml/trunk/debian/control 2012-02-21 17:49:01 UTC (rev 9746)
@@ -5,8 +5,7 @@
Changyan Xie <panchoat at gmail.com>,
Moriyoshi Koizumi <mozo at sfc.keio.ac.jp>,
DM-Upload-Allowed: yes
-Build-Depends: debhelper (>= 7),
- autoconf,
+Build-Depends: autoconf,
automake,
swig (>= 2),
ruby1.8,
@@ -18,11 +17,11 @@
default-jdk | openjdk-6-jdk | java-gcj-compat-dev | java-sdk,
octave-pkg-dev,
python-support,
- doxygen (>= 1.5.8),
graphviz,
zlib1g-dev,
libbz2-dev,
- c-sharp-compiler,
+ mono-devel,
+ mono-gmcs,
cli-common-dev,
cli-runtime
Standards-Version: 3.9.2
@@ -35,8 +34,8 @@
Provides: libsbml-dev
Conflicts: libsbml3-dev
Architecture: any
-Suggests: libsbml5-doc
-Depends: libsbml5 (= ${binary:Version})
+Depends: libsbml5 (= ${binary:Version}),
+ ${misc:Depends}
Description: System Biology Markup Language library - development files
LibSBML is a library designed to help you read, write, manipulate,
translate, and validate SBML files and data streams. It is not an
@@ -50,7 +49,8 @@
Provides: libsbml-dbg
Conflicts: libsbml3-dbg
Architecture: any
-Depends: libsbml5 (= ${binary:Version})
+Depends: libsbml5 (= ${binary:Version}),
+ ${misc:Depends}
Description: System Biology Markup Language library - debug symbols
LibSBML is a library designed to help you read, write, manipulate,
translate, and validate SBML files and data streams. It is not an
@@ -63,7 +63,6 @@
Architecture: any
Provides: libsbml
Conflicts: libsbml1, libsbml2, libsbml3
-Suggests: libsbml5-doc
Depends: ${shlibs:Depends},
${misc:Depends}
Description: System Biology Markup Language library
@@ -81,7 +80,6 @@
libsbml4-python,
libsbml-python
Architecture: any
-Suggests: libsbml5-python-doc
Depends: ${shlibs:Depends},
${misc:Depends},
${python:Depends}
@@ -92,21 +90,20 @@
but rather a library you can embed in your own applications.
This package contains the Python bindings of LibSBML.
-#Package: libsbml5-matlab
-#Section: non-free/math
-#Provides: libsbml-matlab
-#Conflicts: libsbml4-matlab
-#Architecture: amd64
-#Suggests: libsbml5-matlab-doc
-#Depends: ${shlibs:Depends}, ${misc:Depends},
-# libsbml5,
-# libc6 (>= 2.3)
-#Description: System Biology Markup Language library - Matlab bindings
-# LibSBML is a library designed to help you read, write, manipulate,
-# translate, and validate SBML files and data streams. It is not an
-# application itself (though it does come with many example programs),
-# but rather a library you can embed in your own applications.
-# This package contains the Matlab bindings of LibSBML.
+Package: libsbml5-matlab
+Section: contrib/math
+Provides: libsbml-matlab
+Conflicts: libsbml4-matlab
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends},
+ libsbml5,
+ libc6 (>= 2.3)
+Description: System Biology Markup Language library - Matlab bindings
+ LibSBML is a library designed to help you read, write, manipulate,
+ translate, and validate SBML files and data streams. It is not an
+ application itself (though it does come with many example programs),
+ but rather a library you can embed in your own applications.
+ This package contains the Matlab bindings of LibSBML.
Package: libsbml5-ruby1.8
Section: ruby
@@ -127,7 +124,6 @@
Conflicts: libsbml3-java,
libsbml4-java
Architecture: any
-Suggests: libsbml5-java-doc
Depends: ${shlibs:Depends},
${misc:Depends}
Description: System Biology Markup Language library - Java binding
@@ -141,7 +137,6 @@
Section: perl
Provides: libsbml-perl
Conflicts: libsbml3-perl
-Suggests: libsbml5-perl-doc
Depends: ${shlibs:Depends},
${perl:Depends},
${misc:Depends}
@@ -156,7 +151,6 @@
Package: libsbml5-octave
Section: math
Provides: libsbml-octave
-Suggests: libsbml5-octave-doc
Depends: ${shlibs:Depends},
${misc:Depends},
octave3.2,
@@ -172,7 +166,6 @@
Package: libsbml5-cil
Section: cli-mono
Provides: libsbml-cil
-Suggests: libsbml5-cil-doc
Depends: ${shlibs:Depends},
${misc:Depends},
${cli:Depends}
@@ -184,78 +177,6 @@
but rather a library you can embed in your own applications.
This package contains the CLR binding of LibSBML.
-Package: libsbml5-doc
-Section: doc
-Architecture: all
-Depends: ${misc:Depends},
- libjs-jquery
-Description: System Biology Markup Language library - C / C++ API docs
- LibSBML is a library designed to help you read, write, manipulate,
- translate, and validate SBML files and data streams. It is not an
- application itself (though it does come with many example programs),
- but rather a library you can embed in your own applications.
- This package contains C / C++ API documentation of LibSBML.
-
-Package: libsbml5-perl-doc
-Section: doc
-Architecture: all
-Depends: ${misc:Depends},
- libjs-jquery
-Description: System Biology Markup Language library - Perl API docs
- LibSBML is a library designed to help you read, write, manipulate,
- translate, and validate SBML files and data streams. It is not an
- application itself (though it does come with many example programs),
- but rather a library you can embed in your own applications.
- This package contains Perl API documentation of LibSBML.
-
-Package: libsbml5-python-doc
-Section: doc
-Architecture: all
-Depends: ${misc:Depends},
- libjs-jquery
-Description: System Biology Markup Language library - Python API docs
- LibSBML is a library designed to help you read, write, manipulate,
- translate, and validate SBML files and data streams. It is not an
- application itself (though it does come with many example programs),
- but rather a library you can embed in your own applications.
- This package contains Python API documentation of LibSBML.
-
-Package: libsbml5-cil-doc
-Section: doc
-Architecture: all
-Depends: ${misc:Depends},
- libjs-jquery
-Description: System Biology Markup Language library - csharp API docs
- LibSBML is a library designed to help you read, write, manipulate,
- translate, and validate SBML files and data streams. It is not an
- application itself (though it does come with many example programs),
- but rather a library you can embed in your own applications.
- This package contains csharp API documentation of LibSBML.
-
-Package: libsbml5-octave-doc
-Section: doc
-Architecture: all
-Depends: ${misc:Depends},
- libjs-jquery
-Description: System Biology Markup Language library - octave API docs
- LibSBML is a library designed to help you read, write, manipulate,
- translate, and validate SBML files and data streams. It is not an
- application itself (though it does come with many example programs),
- but rather a library you can embed in your own applications.
- This package contains octave API documentation of LibSBML.
-
-#Package: libsbml5-matlab-doc
-#Section: doc
-#Architecture: all
-#Depends: ${misc:Depends},
-# libjs-jquery
-#Description: System Biology Markup Language library - matlab API docs
-# LibSBML is a library designed to help you read, write, manipulate,
-# translate, and validate SBML files and data streams. It is not an
-# application itself (though it does come with many example programs),
-# but rather a library you can embed in your own applications.
-# This package contains matlab API documentation of LibSBML.
-
Package: libsbml5-examples
Section: doc
Architecture: all
Modified: trunk/packages/libsbml/trunk/debian/control.in
===================================================================
--- trunk/packages/libsbml/trunk/debian/control.in 2012-02-21 15:46:27 UTC (rev 9745)
+++ trunk/packages/libsbml/trunk/debian/control.in 2012-02-21 17:49:01 UTC (rev 9746)
@@ -5,9 +5,9 @@
Changyan Xie <panchoat at gmail.com>,
Moriyoshi Koizumi <mozo at sfc.keio.ac.jp>,
DM-Upload-Allowed: yes
-Build-Depends: debhelper (>= 7),
- autoconf,
+Build-Depends: autoconf,
automake,
+ debhelper,
swig (>= 2),
ruby1.8,
libxml2-dev,
@@ -18,11 +18,11 @@
default-jdk | openjdk-6-jdk | java-gcj-compat-dev | java-sdk,
octave-pkg-dev,
python-support,
- doxygen (>= 1.5.8),
graphviz,
zlib1g-dev,
libbz2-dev,
- c-sharp-compiler,
+ mono-devel,
+ mono-gmcs,
cli-common-dev,
cli-runtime
Standards-Version: 3.9.2
@@ -35,8 +35,9 @@
Provides: libsbml-dev
Conflicts: libsbml3-dev
Architecture: any
-Suggests: libsbml5-doc
-Depends: libsbml5 (= ${binary:Version})
+Depends: libsbml5 (= ${binary:Version}),
+ ${shlibs:Depends},
+ ${misc:Depends}
Description: System Biology Markup Language library - development files
LibSBML is a library designed to help you read, write, manipulate,
translate, and validate SBML files and data streams. It is not an
@@ -50,7 +51,9 @@
Provides: libsbml-dbg
Conflicts: libsbml3-dbg
Architecture: any
-Depends: libsbml5 (= ${binary:Version})
+Depends: libsbml5 (= ${binary:Version}),
+ ${shlibs:Depends},
+ ${misc:Depends}
Description: System Biology Markup Language library - debug symbols
LibSBML is a library designed to help you read, write, manipulate,
translate, and validate SBML files and data streams. It is not an
@@ -63,7 +66,6 @@
Architecture: any
Provides: libsbml
Conflicts: libsbml1, libsbml2, libsbml3
-Suggests: libsbml5-doc
Depends: ${shlibs:Depends},
${misc:Depends}
Description: System Biology Markup Language library
@@ -81,7 +83,6 @@
libsbml4-python,
libsbml-python
Architecture: any
-Suggests: libsbml5-python-doc
Depends: ${shlibs:Depends},
${misc:Depends},
${python:Depends}
@@ -93,11 +94,10 @@
This package contains the Python bindings of LibSBML.
#Package: libsbml5-matlab
-#Section: non-free/math
+#Section: contrib/math
#Provides: libsbml-matlab
#Conflicts: libsbml4-matlab
-#Architecture: amd64
-#Suggests: libsbml5-matlab-doc
+#Architecture: any
#Depends: ${shlibs:Depends}, ${misc:Depends},
# libsbml5,
# libc6 (>= 2.3)
@@ -127,7 +127,6 @@
Conflicts: libsbml3-java,
libsbml4-java
Architecture: any
-Suggests: libsbml5-java-doc
Depends: ${shlibs:Depends},
${misc:Depends}
Description: System Biology Markup Language library - Java binding
@@ -141,7 +140,6 @@
Section: perl
Provides: libsbml-perl
Conflicts: libsbml3-perl
-Suggests: libsbml5-perl-doc
Depends: ${shlibs:Depends},
${perl:Depends},
${misc:Depends}
@@ -156,7 +154,6 @@
Package: libsbml5-octave
Section: math
Provides: libsbml-octave
-Suggests: libsbml5-octave-doc
Depends: ${shlibs:Depends},
${misc:Depends},
octave3.2,
@@ -172,7 +169,6 @@
Package: libsbml5-cil
Section: cli-mono
Provides: libsbml-cil
-Suggests: libsbml5-cil-doc
Depends: ${shlibs:Depends},
${misc:Depends},
${cli:Depends}
@@ -184,83 +180,11 @@
but rather a library you can embed in your own applications.
This package contains the CLR binding of LibSBML.
-Package: libsbml5-doc
-Section: doc
-Architecture: all
-Depends: ${misc:Depends},
- libjs-jquery
-Description: System Biology Markup Language library - C / C++ API docs
- LibSBML is a library designed to help you read, write, manipulate,
- translate, and validate SBML files and data streams. It is not an
- application itself (though it does come with many example programs),
- but rather a library you can embed in your own applications.
- This package contains C / C++ API documentation of LibSBML.
-
-Package: libsbml5-perl-doc
-Section: doc
-Architecture: all
-Depends: ${misc:Depends},
- libjs-jquery
-Description: System Biology Markup Language library - Perl API docs
- LibSBML is a library designed to help you read, write, manipulate,
- translate, and validate SBML files and data streams. It is not an
- application itself (though it does come with many example programs),
- but rather a library you can embed in your own applications.
- This package contains Perl API documentation of LibSBML.
-
-Package: libsbml5-python-doc
-Section: doc
-Architecture: all
-Depends: ${misc:Depends},
- libjs-jquery
-Description: System Biology Markup Language library - Python API docs
- LibSBML is a library designed to help you read, write, manipulate,
- translate, and validate SBML files and data streams. It is not an
- application itself (though it does come with many example programs),
- but rather a library you can embed in your own applications.
- This package contains Python API documentation of LibSBML.
-
-Package: libsbml5-cil-doc
-Section: doc
-Architecture: all
-Depends: ${misc:Depends},
- libjs-jquery
-Description: System Biology Markup Language library - csharp API docs
- LibSBML is a library designed to help you read, write, manipulate,
- translate, and validate SBML files and data streams. It is not an
- application itself (though it does come with many example programs),
- but rather a library you can embed in your own applications.
- This package contains csharp API documentation of LibSBML.
-
-Package: libsbml5-octave-doc
-Section: doc
-Architecture: all
-Depends: ${misc:Depends},
- libjs-jquery
-Description: System Biology Markup Language library - octave API docs
- LibSBML is a library designed to help you read, write, manipulate,
- translate, and validate SBML files and data streams. It is not an
- application itself (though it does come with many example programs),
- but rather a library you can embed in your own applications.
- This package contains octave API documentation of LibSBML.
-
-#Package: libsbml5-matlab-doc
-#Section: doc
-#Architecture: all
-#Depends: ${misc:Depends},
-# libjs-jquery
-#Description: System Biology Markup Language library - matlab API docs
-# LibSBML is a library designed to help you read, write, manipulate,
-# translate, and validate SBML files and data streams. It is not an
-# application itself (though it does come with many example programs),
-# but rather a library you can embed in your own applications.
-# This package contains matlab API documentation of LibSBML.
-
Package: libsbml5-examples
Section: doc
Architecture: all
-Depends: libsbml5-dev (= ${binary:Version}),
- ${misc:Depends}
+Depends: ${misc:Depends}
+Suggests: libsbml5-dev (= ${binary:Version})
Description: System Biology Markup Language library -- example files
LibSBML is a library designed to help you read, write, manipulate,
translate, and validate SBML files and data streams. It is not an
Deleted: trunk/packages/libsbml/trunk/debian/libsbml5-cil-doc.docs
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-cil-doc.docs 2012-02-21 15:46:27 UTC (rev 9745)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-cil-doc.docs 2012-02-21 17:49:01 UTC (rev 9746)
@@ -1 +0,0 @@
-debian/tmp/usr/share/doc/libsbml-*/csharp-api
Deleted: trunk/packages/libsbml/trunk/debian/libsbml5-cil-doc.links
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-cil-doc.links 2012-02-21 15:46:27 UTC (rev 9745)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-cil-doc.links 2012-02-21 17:49:01 UTC (rev 9746)
@@ -1 +0,0 @@
-/usr/share/javascript/jquery/jquery.js /usr/share/doc/libsbml5-cil-doc/csharp-api/jquery.js
Deleted: trunk/packages/libsbml/trunk/debian/libsbml5-doc.docs
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-doc.docs 2012-02-21 15:46:27 UTC (rev 9745)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-doc.docs 2012-02-21 17:49:01 UTC (rev 9746)
@@ -1,2 +0,0 @@
-debian/tmp/usr/share/doc/libsbml-*/c-api
-debian/tmp/usr/share/doc/libsbml-*/cpp-api
Deleted: trunk/packages/libsbml/trunk/debian/libsbml5-doc.links
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-doc.links 2012-02-21 15:46:27 UTC (rev 9745)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-doc.links 2012-02-21 17:49:01 UTC (rev 9746)
@@ -1,2 +0,0 @@
-/usr/share/javascript/jquery/jquery.js /usr/share/doc/libsbml5-doc/c-api/jquery.js
-/usr/share/javascript/jquery/jquery.js /usr/share/doc/libsbml5-doc/cpp-api/jquery.js
Deleted: trunk/packages/libsbml/trunk/debian/libsbml5-examples.docs
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-examples.docs 2012-02-21 15:46:27 UTC (rev 9745)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-examples.docs 2012-02-21 17:49:01 UTC (rev 9746)
@@ -1 +0,0 @@
-examples/README.txt
Deleted: trunk/packages/libsbml/trunk/debian/libsbml5-java.docs
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-java.docs 2012-02-21 15:46:27 UTC (rev 9745)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-java.docs 2012-02-21 17:49:01 UTC (rev 9746)
@@ -1 +0,0 @@
-debian/tmp/usr/share/doc/libsbml-*/java.txt
Deleted: trunk/packages/libsbml/trunk/debian/libsbml5-matlab-doc.docs
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-matlab-doc.docs 2012-02-21 15:46:27 UTC (rev 9745)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-matlab-doc.docs 2012-02-21 17:49:01 UTC (rev 9746)
@@ -1 +0,0 @@
-debian/tmp/usr/share/doc/libsbml-*/matlab-api
Deleted: trunk/packages/libsbml/trunk/debian/libsbml5-matlab-doc.links
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-matlab-doc.links 2012-02-21 15:46:27 UTC (rev 9745)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-matlab-doc.links 2012-02-21 17:49:01 UTC (rev 9746)
@@ -1 +0,0 @@
-/usr/share/javascript/jquery/jquery.js /usr/share/doc/libsbml5-matlab-doc/matlab-api/jquery.js
Deleted: trunk/packages/libsbml/trunk/debian/libsbml5-octave-doc.docs
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-octave-doc.docs 2012-02-21 15:46:27 UTC (rev 9745)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-octave-doc.docs 2012-02-21 17:49:01 UTC (rev 9746)
@@ -1 +0,0 @@
-debian/tmp/usr/share/doc/libsbml-*/octave-api
Deleted: trunk/packages/libsbml/trunk/debian/libsbml5-octave-doc.links
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-octave-doc.links 2012-02-21 15:46:27 UTC (rev 9745)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-octave-doc.links 2012-02-21 17:49:01 UTC (rev 9746)
@@ -1 +0,0 @@
-/usr/share/javascript/jquery/jquery.js /usr/share/doc/libsbml5-octave-doc/octave-api/jquery.js
Modified: trunk/packages/libsbml/trunk/debian/libsbml5-octave.install
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-octave.install 2012-02-21 15:46:27 UTC (rev 9745)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-octave.install 2012-02-21 17:49:01 UTC (rev 9746)
@@ -1 +1,2 @@
usr/lib/octave/*
+../lintian/libsbml5-octave usr/share/lintian/overrides
Deleted: trunk/packages/libsbml/trunk/debian/libsbml5-octave.lintian-overrides
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-octave.lintian-overrides 2012-02-21 15:46:27 UTC (rev 9745)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-octave.lintian-overrides 2012-02-21 17:49:01 UTC (rev 9746)
@@ -1,2 +0,0 @@
-libsbml5-octave binary: unstripped-binary-or-object ./usr/lib/octave/site/oct/x86_64-pc-linux-gnu/OutputSBML.mex
-libsbml5-octave binary: unstripped-binary-or-object ./usr/lib/octave/site/oct/x86_64-pc-linux-gnu/TranslateSBML.mex
Deleted: trunk/packages/libsbml/trunk/debian/libsbml5-perl-doc.docs
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-perl-doc.docs 2012-02-21 15:46:27 UTC (rev 9745)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-perl-doc.docs 2012-02-21 17:49:01 UTC (rev 9746)
@@ -1 +0,0 @@
-debian/tmp/usr/share/doc/libsbml-*/perl-api
Deleted: trunk/packages/libsbml/trunk/debian/libsbml5-perl-doc.links
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-perl-doc.links 2012-02-21 15:46:27 UTC (rev 9745)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-perl-doc.links 2012-02-21 17:49:01 UTC (rev 9746)
@@ -1 +0,0 @@
-/usr/share/javascript/jquery/jquery.js /usr/share/doc/libsbml5-perl-doc/perl-api/jquery.js
Deleted: trunk/packages/libsbml/trunk/debian/libsbml5-perl.lintian-overrides
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-perl.lintian-overrides 2012-02-21 15:46:27 UTC (rev 9745)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-perl.lintian-overrides 2012-02-21 17:49:01 UTC (rev 9746)
@@ -1 +0,0 @@
-libsbml5-perl: incorrect-libdir-in-la-file
Deleted: trunk/packages/libsbml/trunk/debian/libsbml5-python-doc.docs
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-python-doc.docs 2012-02-21 15:46:27 UTC (rev 9745)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-python-doc.docs 2012-02-21 17:49:01 UTC (rev 9746)
@@ -1 +0,0 @@
-debian/tmp/usr/share/doc/libsbml-*/python-api
Deleted: trunk/packages/libsbml/trunk/debian/libsbml5-python-doc.links
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-python-doc.links 2012-02-21 15:46:27 UTC (rev 9745)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-python-doc.links 2012-02-21 17:49:01 UTC (rev 9746)
@@ -1 +0,0 @@
-/usr/share/javascript/jquery/jquery.js /usr/share/doc/libsbml5-python-doc/python-api/jquery.js
Deleted: trunk/packages/libsbml/trunk/debian/libsbml5-python.docs
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-python.docs 2012-02-21 15:46:27 UTC (rev 9745)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-python.docs 2012-02-21 17:49:01 UTC (rev 9746)
@@ -1 +0,0 @@
-debian/tmp/usr/share/doc/libsbml-*/python.txt
Modified: trunk/packages/libsbml/trunk/debian/lintian/libsbml5-matlab
===================================================================
--- trunk/packages/libsbml/trunk/debian/lintian/libsbml5-matlab 2012-02-21 15:46:27 UTC (rev 9745)
+++ trunk/packages/libsbml/trunk/debian/lintian/libsbml5-matlab 2012-02-21 17:49:01 UTC (rev 9746)
@@ -1 +1,2 @@
libsbml5-matlab: sharedobject-in-library-directory-missing-soname
+libsbml5-matlab: package-depends-on-hardcoded-libc
Modified: trunk/packages/libsbml/trunk/debian/rules
===================================================================
--- trunk/packages/libsbml/trunk/debian/rules 2012-02-21 15:46:27 UTC (rev 9745)
+++ trunk/packages/libsbml/trunk/debian/rules 2012-02-21 17:49:01 UTC (rev 9746)
@@ -27,7 +27,7 @@
DEB_COMPRESS_EXCLUDE := .xml .pdf .py .c .h .cpp .in .cs .java .pl .rb .xsl
# shared library versions, option 1
-version=5.2.0
+version=5.4.0
major=5
libpack := libsbml
@@ -44,9 +44,9 @@
get-orig-source:
rm -rf $(SRC_TMP) && mkdir $(SRC_TMP)
- [ -f ../libSBML-$(version)-src.zip ] || wget -O ../libsbml-$(version)-src.zip http://qa.debian.org/watch/sf.php/sbml/libSBML-$(version)-src.zip
- cd $(SRC_TMP) && unzip ../../libsbml-$(version)-src.zip
- cd $(SRC_TMP)/libsbml-$(version) && tar cvzf ../../../libsbml_$(version).orig.tar.gz .
+ [ -f ../libsbml-$(version)-src.tar.gz ] || wget -O ../libsbml-$(version)-src.tar.gz http://qa.debian.org/watch/sf.php/sbml/libsbml-$(version)-src.tar.gz
+ cd $(SRC_TMP) && tar -xzf ../../libsbml-$(version)-src.tar.gz
+ cd $(SRC_TMP)/ && tar --owner=root --group=root -czf ../../libsbml_$(version).orig.tar.gz libsbml-$(version)
rm -rf $(SRC_TMP)
config.status: configure
@@ -63,8 +63,10 @@
sed -e 's/^#//' debian/control.in > debian/control ; else \
grep -v ^# debian/control.in > debian/control ; fi
+###-deactivated, because the docu only builds with doxygen-1.6.3-###
+# --with-doxygen \
+
./configure $(CROSS) --prefix=/usr \
- --with-doxygen \
--with-perl \
--with-python \
--with-java \
@@ -79,8 +81,9 @@
CFLAGS="$(CFLAGS)" \
LDFLAGS="-Wl,-z,defs"
-build: build-stamp
-
+build: build-arch build-indep
+build-arch: build-stamp
+build-indep: build-stamp
build-stamp: config.status
dh_testdir
@@ -93,10 +96,60 @@
dh_testdir
dh_testroot
rm -f build-stamp
-
# Add here commands to clean up after the build process.
[ ! -f Makefile ] || $(MAKE) distclean
- rm -f config.sub config.guess
+ ### the clean target of the libsbml makefile is highly b0rken ###
+ ### verx ugly ###
+ find src/bindings -name "*Glyph*" -exec rm -f {} +
+ find * -type d -name .libs -exec rm -rf {} +
+ find * -type f -name "*.o" -exec rm -f {} +
+ find * -type f -name "*.so" -exec rm -f {} +
+ find * -type f -name "*.class" -exec rm -f {} +
+ find * -type f -name "*.exists" -exec rm -f {} +
+ find * -type f -name "*.dll" -exec rm -f {} +
+ find * -type f -name "*.jar" -exec rm -f {} +
+ find * -type f -name "*.lo" -exec rm -f {} +
+ find * -type f -name "Makefile" -exec rm -f {} +
+ find * -type f -name "*.la" -exec rm -f {} +
+ find * -type f -name "*.pyc" -exec rm -f {} +
+ find * -type l -exec rm -f {} +
+ rm -rf config.sub config.guess docs/src/perlmod src/bindings/csharp/libsbmlcs.snk src/bindings/matlab/TranslateSBML.mexa64 \
+ src/bindings/matlab/OutputSBML.mexa64 src/bindings/octave/TranslateSBML.mex src/bindings/octave/OutputSBML.mex \
+ src/bindings/perl/pm_to_blib src/bindings/perl/LibSBML.bs src/bindings/perl/blib/arch/auto/LibSBML/LibSBML.bs \
+ src/bindings/csharp/libsbml_wrap-win.h src/bindings/csharp/csharp-files/BoundingBox.cs \
+ src/bindings/csharp/csharp-files/CubicBezier.cs src/bindings/csharp/csharp-files/Curve.cs \
+ src/bindings/csharp/csharp-files/Dimensions.cs src/bindings/csharp/csharp-files/GraphicalObject.cs \
+ src/bindings/csharp/csharp-files/Layout* src/bindings/csharp/csharp-files/LineSegment.cs \
+ src/bindings/csharp/csharp-files/ListOfGraphicalObjects.cs src/bindings/csharp/csharp-files/ListOfLayouts.cs \
+ src/bindings/csharp/csharp-files/ListOfLineSegments.cs src/bindings/csharp/csharp-files/Point.cs \
+ config/printJavaDataModel.class macosx/build.sh macosx/libsbml-package.pmdoc/*.xml .pc \
+ examples/c++/Makefile examples/c/Makefile examples/csharp/Makefile \
+ examples/java/Makefile examples/layout/Makefile macosx/resources/package-intro.txt macosx/resources/package-readme.txt \
+ src/bindings/csharp/csharp-files-win/BoundingBox.cs src/bindings/csharp/csharp-files-win/CubicBezier.cs \
+ src/bindings/csharp/csharp-files-win/Curve.cs src/bindings/csharp/csharp-files-win/Dimensions.cs \
+ src/bindings/csharp/csharp-files-win/GraphicalObject.cs src/bindings/csharp/csharp-files-win/Layout.cs \
+ src/bindings/csharp/csharp-files-win/LayoutExtension.cs src/bindings/csharp/csharp-files-win/LayoutModelPlugin.cs \
+ src/bindings/csharp/csharp-files-win/LayoutPkgNamespaces.cs src/bindings/csharp/csharp-files-win/LayoutSpeciesReferencePlugin.cs \
+ src/bindings/csharp/csharp-files-win/LineSegment.cs src/bindings/csharp/csharp-files-win/ListOfGraphicalObjects.cs \
+ src/bindings/csharp/csharp-files-win/ListOfLayouts.cs src/bindings/csharp/csharp-files-win/ListOfLineSegments.cs \
+ src/bindings/csharp/csharp-files-win/Point.cs src/bindings/csharp/csharp-files-win/libsbml.cs \
+ src/bindings/csharp/csharp-files-win/libsbmlPINVOKE.cs src/bindings/csharp/csharp-files/libsbml.cs \
+ src/bindings/csharp/csharp-files/libsbmlPINVOKE.cs src/bindings/csharp/libsbml_wrap-win.cpp \
+ src/bindings/csharp/libsbml_wrap.cpp src/bindings/java/Manifest.txt src/bindings/java/java-files/org/sbml/libsbml/BoundingBox.java \
+ src/bindings/java/java-files/org/sbml/libsbml/CubicBezier.java src/bindings/java/java-files/org/sbml/libsbml/Curve.java \
+ src/bindings/java/java-files/org/sbml/libsbml/Dimensions.java src/bindings/java/java-files/org/sbml/libsbml/GraphicalObject.java \
+ src/bindings/java/java-files/org/sbml/libsbml/Layout.java src/bindings/java/java-files/org/sbml/libsbml/LayoutExtension.java \
+ src/bindings/java/java-files/org/sbml/libsbml/LayoutModelPlugin.java src/bindings/java/java-files/org/sbml/libsbml/LayoutPkgNamespaces.java \
+ src/bindings/java/java-files/org/sbml/libsbml/LayoutSpeciesReferencePlugin.java src/bindings/java/java-files/org/sbml/libsbml/LineSegment.java \
+ src/bindings/java/java-files/org/sbml/libsbml/ListOfGraphicalObjects.java src/bindings/java/java-files/org/sbml/libsbml/ListOfLayouts.java \
+ src/bindings/java/java-files/org/sbml/libsbml/ListOfLineSegments.java src/bindings/java/java-files/org/sbml/libsbml/Point.java \
+ src/bindings/java/java-files/org/sbml/libsbml/libsbml.java src/bindings/java/java-files/org/sbml/libsbml/libsbmlConstants.java \
+ src/bindings/java/java-files/org/sbml/libsbml/libsbmlJNI.java src/bindings/java/libsbml_wrap.cpp \
+ src/bindings/matlab/test/Makefile src/bindings/perl/LibSBML.pm src/bindings/perl/LibSBML_wrap.cxx \
+ src/bindings/perl/Makefile.PL src/bindings/python/libsbml-doxygen.py src/bindings/python/libsbml.py \
+ src/bindings/python/libsbml_wrap.cpp src/bindings/ruby/libsbml_wrap.cpp src/sbml/common/libsbml-config-common.h \
+ src/bindings/perl/MYMETA.yml src/bindings/perl/Makefile-perl src/bindings/perl/blib/lib/LibSBML.pod \
+ src/bindings/python/setup.py docs/src/java-files docs/index.html docs/src/common-text/libsbml-version.html docs/src/libsbml-installation.html
dh_clean
@@ -109,7 +162,8 @@
# Add here commands to install the package into debian/libsbml.
mkdir -p $(debtmp)/etc
cp -a debian/etc $(debtmp)
- $(MAKE) install-docs DESTDIR=$(debtmp)
+###-deactivated, because the docu only builds with doxygen-1.6.3-###
+# $(MAKE) install-docs DESTDIR=$(debtmp)
$(MAKE) install DESTDIR=$(debtmp)
# ### not required for python2.7 ###
[ ! -d $(debtmp)/usr/lib/python2.6/ ] || find $(debtmp)/usr/lib/python2.6/ -type d -name site-packages -exec mv {} $(debtmp)/usr/lib/python2.6/dist-packages \; || true
@@ -128,7 +182,7 @@
find $(debtmp)/usr/lib/ -type f -exec chmod 644 {} +
find $(debtmp)/usr/lib/ -type f -name .packlist -exec rm -f {} +
find $(debtmp)/usr/lib/ -type d -iname "*.libs" -exec rm -rf {} +
- find $(debtmp)/usr/share/doc/ -type f -name "jquery.js" -exec rm -f {} +
+# find $(debtmp)/usr/share/doc/ -type f -name "jquery.js" -exec rm -f {} +
sed -i "/dependency_libs/ s/'.*'/''/" `find $(debtmp)/usr/lib/ -name '*.la'`
strip --strip-unneeded $(debtmp)/usr/lib/*.mex* || true
strip --strip-unneeded $(debtmp)/usr/lib/octave/site/oct/*/*.mex || true
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