[med-svn] r12909 - in trunk/packages/libsbml/trunk/debian: . lintian patches
Ivo Maintz
ivomaintz-guest at alioth.debian.org
Mon Feb 4 15:32:40 UTC 2013
Author: ivomaintz-guest
Date: 2013-02-04 15:32:40 +0000 (Mon, 04 Feb 2013)
New Revision: 12909
Added:
trunk/packages/libsbml/trunk/debian/patches/comp.patch
Modified:
trunk/packages/libsbml/trunk/debian/README.source
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-java.docs
trunk/packages/libsbml/trunk/debian/libsbml5-python.docs
trunk/packages/libsbml/trunk/debian/lintian/libsbml5-matlab
trunk/packages/libsbml/trunk/debian/patches/hardening.patch
trunk/packages/libsbml/trunk/debian/patches/series
trunk/packages/libsbml/trunk/debian/patches/spelling.patch
trunk/packages/libsbml/trunk/debian/rules
trunk/packages/libsbml/trunk/debian/watch
Log:
updated package
added some options to the build process
still some trouble with hardening
Modified: trunk/packages/libsbml/trunk/debian/README.source
===================================================================
--- trunk/packages/libsbml/trunk/debian/README.source 2013-02-03 23:34:37 UTC (rev 12908)
+++ trunk/packages/libsbml/trunk/debian/README.source 2013-02-04 15:32:40 UTC (rev 12909)
@@ -1,3 +1,11 @@
+libsbml (5.7.0)
+ * upstream ships two versions: libSBML-core-src.tar.gz and
+ libSBML-5.7.0-core-plus-packages-src.tar.gz (with the COMP extension)
+ we use libSBML-5.7.0-core-plus-packages-src.tar.gz, uscan with the option "rename"
+ instead of "symlink" can handle this.
+
+ -- Ivo Maintz <ivo at maintz.de> 04 Feb 2013 16:30:19 +0100
+
libsbml (5.5.0)
* a lot of spelling errors, remove with
find docs -type f -exec sed -i -e 's/overriden/overridden/' -e 's/pacakge/package/' {} +
Modified: trunk/packages/libsbml/trunk/debian/changelog
===================================================================
--- trunk/packages/libsbml/trunk/debian/changelog 2013-02-03 23:34:37 UTC (rev 12908)
+++ trunk/packages/libsbml/trunk/debian/changelog 2013-02-04 15:32:40 UTC (rev 12909)
@@ -1,5 +1,11 @@
-libsbml (5.6.0-1) UNSTABLE; urgency=low
+libsbml (5.7.0-1) UNRELEASED; urgency=low
+ * update from upstream
+
+ -- Ivo Maintz <ivo at maintz.de> Wed, 23 Jan 2013 12:39:29 +0100
+
+libsbml (5.6.0-1) unstable; urgency=low
+
[ Ivo Maintz ]
* update from upstream
* configured now with --enable-cpp-namespace
Modified: trunk/packages/libsbml/trunk/debian/control
===================================================================
--- trunk/packages/libsbml/trunk/debian/control 2013-02-03 23:34:37 UTC (rev 12908)
+++ trunk/packages/libsbml/trunk/debian/control 2013-02-04 15:32:40 UTC (rev 12909)
@@ -5,7 +5,8 @@
DM-Upload-Allowed: yes
Build-Depends: autoconf,
automake,
- debhelper (>= 9.2012~),
+ debhelper (>= 9.20120101),
+ doxygen,
swig (>= 2),
ruby1.8,
libxml2-dev,
@@ -33,7 +34,8 @@
Package: libsbml5-dev
Section: libdevel
Provides: libsbml-dev
-Conflicts: libsbml3-dev
+Conflicts: libsbml3-dev,
+ libsbml4-dev
Architecture: any
Depends: libsbml5 (= ${binary:Version}),
${misc:Depends}
@@ -48,7 +50,8 @@
Section: debug
Priority: extra
Provides: libsbml-dbg
-Conflicts: libsbml3-dbg
+Conflicts: libsbml3-dbg,
+ libsbml4-dbg
Architecture: any
Depends: libsbml5 (= ${binary:Version}), ${misc:Depends}
Description: System Biology Markup Language library - debug symbols
Modified: trunk/packages/libsbml/trunk/debian/control.in
===================================================================
--- trunk/packages/libsbml/trunk/debian/control.in 2013-02-03 23:34:37 UTC (rev 12908)
+++ trunk/packages/libsbml/trunk/debian/control.in 2013-02-04 15:32:40 UTC (rev 12909)
@@ -5,7 +5,8 @@
DM-Upload-Allowed: yes
Build-Depends: autoconf,
automake,
- debhelper (>= 9.20120608),
+ debhelper (>= 9.20120101),
+ doxygen,
swig (>= 2),
ruby1.8,
libxml2-dev,
@@ -33,7 +34,8 @@
Package: libsbml5-dev
Section: libdevel
Provides: libsbml-dev
-Conflicts: libsbml3-dev
+Conflicts: libsbml3-dev,
+ libsbml4-dev
Architecture: any
Depends: libsbml5 (= ${binary:Version}),
${misc:Depends}
@@ -48,7 +50,8 @@
Section: debug
Priority: extra
Provides: libsbml-dbg
-Conflicts: libsbml3-dbg
+Conflicts: libsbml3-dbg,
+ libsbml4-dbg
Architecture: any
Depends: libsbml5 (= ${binary:Version}), ${misc:Depends}
Description: System Biology Markup Language library - debug symbols
Modified: trunk/packages/libsbml/trunk/debian/libsbml5-java.docs
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-java.docs 2013-02-03 23:34:37 UTC (rev 12908)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-java.docs 2013-02-04 15:32:40 UTC (rev 12909)
@@ -1 +1,2 @@
changelog
+debian/tmp/usr/share/doc/libsbml-*/java.txt
Modified: trunk/packages/libsbml/trunk/debian/libsbml5-python.docs
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-python.docs 2013-02-03 23:34:37 UTC (rev 12908)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-python.docs 2013-02-04 15:32:40 UTC (rev 12909)
@@ -1 +1,2 @@
changelog
+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 2013-02-03 23:34:37 UTC (rev 12908)
+++ trunk/packages/libsbml/trunk/debian/lintian/libsbml5-matlab 2013-02-04 15:32:40 UTC (rev 12909)
@@ -1 +1,3 @@
libsbml5-matlab: sharedobject-in-library-directory-missing-soname
+libsbml5-matlab: hardening-no-relro
+libsbml5-matlab: hardening-no-fortify-functions
Added: trunk/packages/libsbml/trunk/debian/patches/comp.patch
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/comp.patch (rev 0)
+++ trunk/packages/libsbml/trunk/debian/patches/comp.patch 2013-02-04 15:32:40 UTC (rev 12909)
@@ -0,0 +1,26 @@
+Description: enable comp
+ enable hierarchical model composition package
+ .
+ libsbml (5.7.0-1) UNRELEASED; urgency=low
+ .
+ * update from upstream
+Author: Ivo Maintz <ivo at maintz.de>
+
+---
+The information above should follow the Patch Tagging Guidelines, please
+checkout http://dep.debian.net/deps/dep3/ to learn about the format. Here
+are templates for supplementary fields that you might want to add:
+
+Last-Update: <2012-01-25>
+
+--- libsbml-5.7.0.orig/comp-package.cmake
++++ libsbml-5.7.0/comp-package.cmake
+@@ -7,7 +7,7 @@
+ # $HeadURL$
+ #
+
+-option(ENABLE_COMP "Enable hierarchical model composition package" OFF )
++option(ENABLE_COMP "Enable hierarchical model composition package" ON )
+
+ if(ENABLE_COMP)
+ add_definitions(-DUSE_COMP)
Modified: trunk/packages/libsbml/trunk/debian/patches/hardening.patch
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/hardening.patch 2013-02-03 23:34:37 UTC (rev 12908)
+++ trunk/packages/libsbml/trunk/debian/patches/hardening.patch 2013-02-04 15:32:40 UTC (rev 12909)
@@ -1,43 +1,17 @@
Description: hardening
-
.
- libsbml (5.6.0-1) UNRELEASED; urgency=low
+ libsbml (5.7.0-1) UNRELEASED; urgency=low
.
- * [ Ivo Maintz ]
- update from upstream
+ * update from upstream
Author: Ivo Maintz <ivo at maintz.de>
---
-The information above should follow the Patch Tagging Guidelines, please
-checkout http://dep.debian.net/deps/dep3/ to learn about the format. Here
-are templates for supplementary fields that you might want to add:
+Last-Update: <2013-01-22>
-Last-Update: <2012-08-17>
-
-Index: libsbml-5.6.0/config/makefile-common-actions.mk
+Index: libsbml-5.7.0/src/bindings/matlab/Makefile.in
===================================================================
---- libsbml-5.6.0.orig/config/makefile-common-actions.mk 2012-01-13 02:25:36.000000000 +0100
-+++ libsbml-5.6.0/config/makefile-common-actions.mk 2012-08-20 12:11:30.473569165 +0200
-@@ -72,6 +72,15 @@
- # here is only to remove duplicates, which the 'sort' function does as a
- # documented side-effect.)
-
-+# hardening
-+CFLAGS = $(shell dpkg-buildflags --get CFLAGS)
-+CFLAGS += -Wall
-+CXXFLAGS = $(shell dpkg-buildflags --get CXXFLAGS)
-+CXXFLAGS += -Wall
-+LDFLAGS = $(shell dpkg-buildflags --get LDFLAGS)
-+CPPFLAGS = $(shell dpkg-buildflags --get CPPFLAGS)
-+CCFLAGS = $(shell dpkg-buildflags --get CFLAGS)
-+
- compile ?= $(LIBTOOL) --mode=compile --tag=CC $(CC) $(sort $(default_includes) $(INCLUDES)) $(CPPFLAGS) \
- $(extra_CPPFLAGS) $(CFLAGS) $(extra_CFLAGS)
-
-Index: libsbml-5.6.0/src/bindings/matlab/Makefile.in
-===================================================================
---- libsbml-5.6.0.orig/src/bindings/matlab/Makefile.in 2012-08-01 13:43:49.000000000 +0200
-+++ libsbml-5.6.0/src/bindings/matlab/Makefile.in 2012-08-20 12:21:12.429587787 +0200
+--- libsbml-5.7.0.orig/src/bindings/matlab/Makefile.in 2013-01-13 09:33:06.000000000 +0100
++++ libsbml-5.7.0/src/bindings/matlab/Makefile.in 2013-01-22 19:23:43.984536958 +0100
@@ -70,12 +70,7 @@
installSBML.m \
isoctave.m \
@@ -48,11 +22,11 @@
- mexopts-xcode43.sh \
- mexopts-xcode45.sh \
- mexopts-lion.sh \
-+ mexopts .sh \
++ mexopts-R2009-2010.sh \
test.xml \
test/CMakeLists.txt
-@@ -134,7 +129,7 @@
+@@ -142,7 +137,7 @@
# is really necessary, but it seems prudent.
define matlabrun
@@ -61,23 +35,10 @@
$(LIBTOOL) -dlopen $(TOP_BUILDDIR)/src/libsbml.la --mode=execute $(1)
endef
-Index: libsbml-5.6.0/src/bindings/perl/Makefile.in
+Index: libsbml-5.7.0/src/bindings/matlab/mexopts-R2009-R2010.sh
===================================================================
---- libsbml-5.6.0.orig/src/bindings/perl/Makefile.in 2012-08-01 13:43:52.000000000 +0200
-+++ libsbml-5.6.0/src/bindings/perl/Makefile.in 2012-08-20 12:11:30.473569165 +0200
-@@ -180,6 +180,8 @@
- CXXFLAGS += -DUSE_LAYOUT
- endif
-
-+CXXFLAGS = $(shell dpkg-buildflags --get CXXFLAGS)
-+
- # If the last run was made with --enable-layout and this one isn't, or
- # vice-versa, the swig wrap files will be wrong for this run. However, you
- # can't tell just by looking at file mod times, so you can't use normal
-Index: libsbml-5.6.0/src/bindings/matlab/mexopts-R2009-R2010.sh
-===================================================================
---- libsbml-5.6.0.orig/src/bindings/matlab/mexopts-R2009-R2010.sh 2012-08-01 13:43:49.000000000 +0200
-+++ libsbml-5.6.0/src/bindings/matlab/mexopts-R2009-R2010.sh 2012-08-20 12:11:30.477569165 +0200
+--- libsbml-5.7.0.orig/src/bindings/matlab/mexopts-R2009-R2010.sh 2013-01-13 09:33:06.000000000 +0100
++++ libsbml-5.7.0/src/bindings/matlab/mexopts-R2009-R2010.sh 2013-01-22 19:22:22.000000000 +0100
@@ -324,7 +324,13 @@
#
#----------------------------------------------------------------------------
@@ -93,3 +54,36 @@
# COPTIMFLAGS="$COPTIMFLAGS"
# CDEBUGFLAGS="$CDEBUGFLAGS"
# CLIBS="$CLIBS"
+Index: libsbml-5.7.0/src/bindings/perl/Makefile.in
+===================================================================
+--- libsbml-5.7.0.orig/src/bindings/perl/Makefile.in 2013-01-13 09:33:11.000000000 +0100
++++ libsbml-5.7.0/src/bindings/perl/Makefile.in 2013-01-22 19:22:22.000000000 +0100
+@@ -180,6 +180,8 @@
+ CXXFLAGS += -DUSE_LAYOUT
+ endif
+
++CXXFLAGS = $(shell dpkg-buildflags --get CXXFLAGS)
++
+ # If the last run was made with --enable-layout and this one isn't, or
+ # vice-versa, the swig wrap files will be wrong for this run. However, you
+ # can't tell just by looking at file mod times, so you can't use normal
+Index: libsbml-5.7.0/config/makefile-common-actions.mk
+===================================================================
+--- libsbml-5.7.0.orig/config/makefile-common-actions.mk 2012-01-13 02:25:36.000000000 +0100
++++ libsbml-5.7.0/config/makefile-common-actions.mk 2013-01-22 19:22:22.000000000 +0100
+@@ -72,6 +72,15 @@
+ # here is only to remove duplicates, which the 'sort' function does as a
+ # documented side-effect.)
+
++# hardening
++CFLAGS = $(shell dpkg-buildflags --get CFLAGS)
++CFLAGS += -Wall
++CXXFLAGS = $(shell dpkg-buildflags --get CXXFLAGS)
++CXXFLAGS += -Wall
++LDFLAGS = $(shell dpkg-buildflags --get LDFLAGS)
++CPPFLAGS = $(shell dpkg-buildflags --get CPPFLAGS)
++CCFLAGS = $(shell dpkg-buildflags --get CFLAGS)
++
+ compile ?= $(LIBTOOL) --mode=compile --tag=CC $(CC) $(sort $(default_includes) $(INCLUDES)) $(CPPFLAGS) \
+ $(extra_CPPFLAGS) $(CFLAGS) $(extra_CFLAGS)
+
Modified: trunk/packages/libsbml/trunk/debian/patches/series
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/series 2013-02-03 23:34:37 UTC (rev 12908)
+++ trunk/packages/libsbml/trunk/debian/patches/series 2013-02-04 15:32:40 UTC (rev 12909)
@@ -1,2 +1,3 @@
spelling.patch
hardening.patch
+comp.patch
Modified: trunk/packages/libsbml/trunk/debian/patches/spelling.patch
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/spelling.patch 2013-02-03 23:34:37 UTC (rev 12908)
+++ trunk/packages/libsbml/trunk/debian/patches/spelling.patch 2013-02-04 15:32:40 UTC (rev 12909)
@@ -1,13 +1,10 @@
Description: Spelling errors
There are still a lot of similar spellling errors, so I did simply
"grep -Rl overriden * | xargs sed -i 's/overriden/overridden/'"
- "grep -Rl pacakge * | xargs sed -i 's/pacakge/package/'"
-
.
- libsbml (5.6.0-1) UNRELEASED; urgency=low
+ libsbml (5.7.0-1) UNRELEASED; urgency=low
.
- * [ Ivo Maintz ]
- update from upstream
+ * update from upstream
Author: Ivo Maintz <ivo at maintz.de>
---
@@ -15,186 +12,11 @@
checkout http://dep.debian.net/deps/dep3/ to learn about the format. Here
are templates for supplementary fields that you might want to add:
-Last-Update: <2012-08-16>
+Last-Update: <2013-01-22>
---- libsbml-5.6.0.orig/docs/00README-ChangesInSBase.txt
-+++ libsbml-5.6.0/docs/00README-ChangesInSBase.txt
-@@ -68,12 +68,12 @@ developers.
-
- 3) XMLAttributes mAttributesOfUnknownPkg
-
-- An XMLAttributes object containing attributes of unknown pacakges.
-+ An XMLAttributes object containing attributes of unknown packages.
-
-
- 4) XMLNode mElementsOfUnknownPkg
-
-- An XMLNode object containing elements of unknown pacakges.
-+ An XMLNode object containing elements of unknown packages.
-
- ---------------------------------------------------------------------------
- 2. Added member functions in SBase class
-@@ -319,7 +319,7 @@ developers.
- (NOTE)
-
- In summary, each SBase derived class that represents a top-level
-- element of its pacakge extension must override this function.
-+ element of its package extension must override this function.
- ------------------------------------------------------------
-
-
---- libsbml-5.6.0.orig/docs/00README-ExtensionSupportClasses.txt
-+++ libsbml-5.6.0/docs/00README-ExtensionSupportClasses.txt
-@@ -316,7 +316,7 @@ package extensions.
- 8) SBMLExtensionException class
-
- SBMLExtensionException class is a exception class which can be thrown
-- when an exception about pacakge extension occurs (e.g. required package
-+ when an exception about package extension occurs (e.g. required package
- is not registered).
-
- Currently, the exception can be thrown in the following functions if
---- libsbml-5.6.0.orig/docs/00README-HowToImplementPackageExtension.txt
-+++ libsbml-5.6.0/docs/00README-HowToImplementPackageExtension.txt
-@@ -34,8 +34,8 @@ Table of contents:
- ----------------------------------------------------------------------
- (NOTE)
-
-- "src/pacakges/groups/extension/GroupsExtension.{h,cpp}" and
-- "src/pacakges/layout/extension/LayoutExtension.{h,cpp}" are
-+ "src/packages/groups/extension/GroupsExtension.{h,cpp}" and
-+ "src/packages/layout/extension/LayoutExtension.{h,cpp}" are
- example files in which SBMLExtension derived classes are implemented.
- ----------------------------------------------------------------------
-
-@@ -484,7 +484,7 @@ based on the following steps:
- ----------------------------------------------------------------------
- (NOTE)
-
-- - default level, default version, and default pacakge version
-+ - default level, default version, and default package version
- should be given as default arguments.
- (This may change in the future release).
-
-@@ -527,7 +527,7 @@ based on the following steps:
- // connect child elements to this element
- connectToChild();
-
-- // load pacakge extensions bound with this object (if any)
-+ // load package extensions bound with this object (if any)
- loadPlugins(groupsns);
- }
-
-@@ -794,7 +794,7 @@ based on the following steps:
- 3. Implement one or more SBasePlugin derived classes
- --------------------------------------------------------------------------------
-
--Thirdly, SBasePlugin derived classes for the pacakge needs to be implemented.
-+Thirdly, SBasePlugin derived classes for the package needs to be implemented.
-
- ------------------------------------------------------------------------------
- 3-1) Identify which core SBML elements (e.g. Model, Reaction,..) to be extended
---- libsbml-5.6.0.orig/docs/00README-HowToUsePackageExtension.txt
-+++ libsbml-5.6.0/docs/00README-HowToUsePackageExtension.txt
-@@ -37,7 +37,7 @@ Table of contents:
- (e.g. Group, ListOfGroups, Member, and ListOfMembers are the SBase
- derived classes of the groups package.)
-
-- Each pacakge extension provides a single header file which serves to include
-+ Each package extension provides a single header file which serves to include
- most of the above header files in a similar fashion to the SBMLTypes.h file
- in libSBML core.
- For example, GroupsExtensionTypes.h is provided by the groups package.
-@@ -94,7 +94,7 @@ Table of contents:
- For example, two SBasePlugin derived classes, SBMLDocumentPlugin and
- GroupsModelPlugin, are used by the groups extension.
- SBMLDocumentPlugin, which is plugged in the sbml element, is a common plugin
-- class for pacakge extensions which use only 'required' attribute in the
-+ class for package extensions which use only 'required' attribute in the
- SBMLDocument class, and thus the class is basically not used in user's
- code (**).
- On the other hand, GroupsModelPlugin, which is plugged into the model element,
---- libsbml-5.6.0.orig/docs/src/libsbml-extension-support-classes.txt
-+++ libsbml-5.6.0/docs/src/libsbml-extension-support-classes.txt
-@@ -90,7 +90,7 @@ when each library is loaded.
- </li>
-
- <li> <a href="#SBMLExtensionException"> SBMLExtensionException</a> class is a exception class
--which can be thrown when an exception about pacakge extension occurs.
-+which can be thrown when an exception about package extension occurs.
- </li>
- </ul>
-
-@@ -574,7 +574,7 @@ extensions which are not registered in t
-
- <p>
- SBMLExtensionException class is an exception class which can be thrown
-- when an exception about pacakge extension occurs (e.g., required package
-+ when an exception about package extension occurs (e.g., required package
- is not registered).
- </p>
-
---- libsbml-5.6.0.orig/docs/src/libsbml-howto-implement-extension.txt
-+++ libsbml-5.6.0/docs/src/libsbml-howto-implement-extension.txt
-@@ -141,7 +141,7 @@ based on the steps described in SBMLExte
- <p><em>NOTE</em></p>
- <ul>
- <li>
-- default level, default version, and default pacakge version
-+ default level, default version, and default package version
- should be given as default arguments.
- (This may change in the future release).
-
-@@ -187,7 +187,7 @@ based on the steps described in SBMLExte
- // connect child elements to this element
- connectToChild();
-
-- // load pacakge extensions bound with this object (if any)
-+ // load package extensions bound with this object (if any)
- loadPlugins(groupsns);
- }
- @endverbatim
-@@ -479,7 +479,7 @@ based on the steps described in SBMLExte
- <h3><a class="anchor" name="i3">3. Implement SBasePlugin derived classes</a></h3>
-
- <p>
--Thirdly, SBasePlugin derived classes for the pacakge needs to be implemented.
-+Thirdly, SBasePlugin derived classes for the package needs to be implemented.
-
- <h4><a class="anchor" name="i3-1">3-1. Identify which core SBML elements (e.g. Model, Reaction,..) to be extended (i.e. adding attributes and/or elements) for your package extensions.</a></h4>
- <p>
---- libsbml-5.6.0.orig/src/bindings/csharp/csdoc.i
-+++ libsbml-5.6.0/src/bindings/csharp/csdoc.i
-@@ -47999,8 +47999,8 @@ success = sbmlObject.setAnnotation(annot
- * The extended class is implemented based on the following steps:
- *
- * (NOTE:
-- * \'src/pacakges/groups/extension/GroupsExtension.{h,cpp}\' and
-- * \'src/pacakges/layout/extension/LayoutExtension.{h,cpp}\' are
-+ * \'src/packages/groups/extension/GroupsExtension.{h,cpp}\' and
-+ * \'src/packages/layout/extension/LayoutExtension.{h,cpp}\' are
- * example files in which SBMLExtension derived classes are implemented)
- *
- * <ol>
-@@ -48346,7 +48346,7 @@ GroupsExtension::init()
- {
- //-------------------------------------------------------------------------
- //
-- // 1. Checks if the groups pacakge has already been registered.
-+ // 1. Checks if the groups package has already been registered.
- //
- //-------------------------------------------------------------------------
-
-@@ -48494,7 +48494,7 @@ GroupsExtension::init()
- *
- * Returns the ith URI (the supported package version)
- *
-- * @param i the index of the list of URI (the list of supporeted pacakge versions)
-+ * @param i the index of the list of URI (the list of supporeted package versions)
- * @return the URI of supported package version with the given index.
- */ public
- ";
-@@ -48745,7 +48745,7 @@ GroupsExtension::init()
+--- libsbml-5.7.0.orig/src/bindings/csharp/csdoc.i
++++ libsbml-5.7.0/src/bindings/csharp/csdoc.i
+@@ -49197,7 +49197,7 @@ GroupsExtension::init()
%csmethodmodifiers SBMLExtensionRegistry::removeL2Namespaces(XMLNamespaces *xmlns) const "
/**
* Remove all L2 Extension namespaces from the namespace list. This will call all
@@ -203,7 +25,7 @@
*/ public
";
-@@ -48753,7 +48753,7 @@ GroupsExtension::init()
+@@ -49205,7 +49205,7 @@ GroupsExtension::init()
%csmethodmodifiers SBMLExtensionRegistry::addL2Namespaces(XMLNamespaces *xmlns) const "
/**
* adds all L2 Extension namespaces to the namespace list. This will call all
@@ -212,39 +34,8 @@
*/ public
";
---- libsbml-5.6.0.orig/src/bindings/csharp/csharp-files/SBMLExtension.cs
-+++ libsbml-5.6.0/src/bindings/csharp/csharp-files/SBMLExtension.cs
-@@ -29,8 +29,8 @@ namespace libsbmlcs {
- * The extended class is implemented based on the following steps:
- *
- * (NOTE:
-- * 'src/pacakges/groups/extension/GroupsExtension.{h,cpp}' and
-- * 'src/pacakges/layout/extension/LayoutExtension.{h,cpp}' are
-+ * 'src/packages/groups/extension/GroupsExtension.{h,cpp}' and
-+ * 'src/packages/layout/extension/LayoutExtension.{h,cpp}' are
- * example files in which SBMLExtension derived classes are implemented)
- *
- * <ol>
-@@ -376,7 +376,7 @@ GroupsExtension::init()
- {
- //-------------------------------------------------------------------------
- //
-- // 1. Checks if the groups pacakge has already been registered.
-+ // 1. Checks if the groups package has already been registered.
- //
- //-------------------------------------------------------------------------
-
-@@ -569,7 +569,7 @@ public class SBMLExtension : IDisposable
- *
- * Returns the ith URI (the supported package version)
- *
-- * @param i the index of the list of URI (the list of supporeted pacakge versions)
-+ * @param i the index of the list of URI (the list of supporeted package versions)
- * @return the URI of supported package version with the given index.
- */ public
- string getSupportedPackageURI(long i) {
---- libsbml-5.6.0.orig/src/bindings/csharp/csharp-files/SBMLExtensionRegistry.cs
-+++ libsbml-5.6.0/src/bindings/csharp/csharp-files/SBMLExtensionRegistry.cs
+--- libsbml-5.7.0.orig/src/bindings/csharp/csharp-files/SBMLExtensionRegistry.cs
++++ libsbml-5.7.0/src/bindings/csharp/csharp-files/SBMLExtensionRegistry.cs
@@ -105,7 +105,7 @@ public class SBMLExtensionRegistry : IDi
/**
@@ -263,39 +54,8 @@
*/ public
void addL2Namespaces(XMLNamespaces xmlns) {
libsbmlPINVOKE.SBMLExtensionRegistry_addL2Namespaces(swigCPtr, XMLNamespaces.getCPtr(xmlns));
---- libsbml-5.6.0.orig/src/bindings/csharp/csharp-files-win/SBMLExtension.cs
-+++ libsbml-5.6.0/src/bindings/csharp/csharp-files-win/SBMLExtension.cs
-@@ -29,8 +29,8 @@ namespace libsbml {
- * The extended class is implemented based on the following steps:
- *
- * (NOTE:
-- * 'src/pacakges/groups/extension/GroupsExtension.{h,cpp}' and
-- * 'src/pacakges/layout/extension/LayoutExtension.{h,cpp}' are
-+ * 'src/packages/groups/extension/GroupsExtension.{h,cpp}' and
-+ * 'src/packages/layout/extension/LayoutExtension.{h,cpp}' are
- * example files in which SBMLExtension derived classes are implemented)
- *
- * <ol>
-@@ -376,7 +376,7 @@ GroupsExtension::init()
- {
- //-------------------------------------------------------------------------
- //
-- // 1. Checks if the groups pacakge has already been registered.
-+ // 1. Checks if the groups package has already been registered.
- //
- //-------------------------------------------------------------------------
-
-@@ -568,7 +568,7 @@ public class SBMLExtension : IDisposable
- *
- * Returns the ith URI (the supported package version)
- *
-- * @param i the index of the list of URI (the list of supporeted pacakge versions)
-+ * @param i the index of the list of URI (the list of supporeted package versions)
- * @return the URI of supported package version with the given index.
- */ public
- string getSupportedPackageURI(long i) {
---- libsbml-5.6.0.orig/src/bindings/csharp/csharp-files-win/SBMLExtensionRegistry.cs
-+++ libsbml-5.6.0/src/bindings/csharp/csharp-files-win/SBMLExtensionRegistry.cs
+--- libsbml-5.7.0.orig/src/bindings/csharp/csharp-files-win/SBMLExtensionRegistry.cs
++++ libsbml-5.7.0/src/bindings/csharp/csharp-files-win/SBMLExtensionRegistry.cs
@@ -104,7 +104,7 @@ public class SBMLExtensionRegistry : IDi
/**
@@ -314,38 +74,9 @@
*/ public
void addL2Namespaces(XMLNamespaces xmlns) {
libsbmlPINVOKE.SBMLExtensionRegistry_addL2Namespaces(swigCPtr, XMLNamespaces.getCPtr(xmlns));
---- libsbml-5.6.0.orig/src/bindings/java/javadoc.i
-+++ libsbml-5.6.0/src/bindings/java/javadoc.i
-@@ -50570,8 +50570,8 @@ success = sbmlObject.setAnnotation(
- * The extended class is implemented based on the following steps:
- * <p>
- * (NOTE:
-- * \'src/pacakges/groups/extension/GroupsExtension.{h,cpp}\' and
-- * \'src/pacakges/layout/extension/LayoutExtension.{h,cpp}\' are
-+ * \'src/packages/groups/extension/GroupsExtension.{h,cpp}\' and
-+ * \'src/packages/layout/extension/LayoutExtension.{h,cpp}\' are
- * example files in which {@link SBMLExtension} derived classes are implemented)
- * <p>
- * <ol>
-@@ -50917,7 +50917,7 @@ void
- {
- //-------------------------------------------------------------------------
- //
-- // 1. Checks if the groups pacakge has already been registered.
-+ // 1. Checks if the groups package has already been registered.
- //
- //-------------------------------------------------------------------------
-
-@@ -51065,7 +51065,7 @@ void
- * <p>
- * Returns the ith URI (the supported package version)
- * <p>
-- * @param i the index of the list of URI (the list of supporeted pacakge versions)
-+ * @param i the index of the list of URI (the list of supporeted package versions)
- * @return the URI of supported package version with the given index.
- */ public
- ";
-@@ -51315,7 +51315,7 @@ void
+--- libsbml-5.7.0.orig/src/bindings/java/javadoc.i
++++ libsbml-5.7.0/src/bindings/java/javadoc.i
+@@ -51801,7 +51801,7 @@ void
%javamethodmodifiers SBMLExtensionRegistry::removeL2Namespaces(XMLNamespaces *xmlns) const "
/**
* Remove all L2 Extension namespaces from the namespace list. This will call all
@@ -354,7 +85,7 @@
*/ public
";
-@@ -51323,7 +51323,7 @@ void
+@@ -51809,7 +51809,7 @@ void
%javamethodmodifiers SBMLExtensionRegistry::addL2Namespaces(XMLNamespaces *xmlns) const "
/**
* adds all L2 Extension namespaces to the namespace list. This will call all
@@ -363,39 +94,8 @@
*/ public
";
---- libsbml-5.6.0.orig/src/bindings/java/java-files/org/sbml/libsbml/SBMLExtension.java
-+++ libsbml-5.6.0/src/bindings/java/java-files/org/sbml/libsbml/SBMLExtension.java
-@@ -26,8 +26,8 @@ package org.sbml.libsbml;
- * The extended class is implemented based on the following steps:
- * <p>
- * (NOTE:
-- * 'src/pacakges/groups/extension/GroupsExtension.{h,cpp}' and
-- * 'src/pacakges/layout/extension/LayoutExtension.{h,cpp}' are
-+ * 'src/packages/groups/extension/GroupsExtension.{h,cpp}' and
-+ * 'src/packages/layout/extension/LayoutExtension.{h,cpp}' are
- * example files in which {@link SBMLExtension} derived classes are implemented)
- * <p>
- * <ol>
-@@ -373,7 +373,7 @@ void
- {
- //-------------------------------------------------------------------------
- //
-- // 1. Checks if the groups pacakge has already been registered.
-+ // 1. Checks if the groups package has already been registered.
- //
- //-------------------------------------------------------------------------
-
-@@ -571,7 +571,7 @@ public class SBMLExtension {
- * <p>
- * Returns the ith URI (the supported package version)
- * <p>
-- * @param i the index of the list of URI (the list of supporeted pacakge versions)
-+ * @param i the index of the list of URI (the list of supporeted package versions)
- * @return the URI of supported package version with the given index.
- */ public
- String getSupportedPackageURI(long i) {
---- libsbml-5.6.0.orig/src/bindings/java/java-files/org/sbml/libsbml/SBMLExtensionRegistry.java
-+++ libsbml-5.6.0/src/bindings/java/java-files/org/sbml/libsbml/SBMLExtensionRegistry.java
+--- libsbml-5.7.0.orig/src/bindings/java/java-files/org/sbml/libsbml/SBMLExtensionRegistry.java
++++ libsbml-5.7.0/src/bindings/java/java-files/org/sbml/libsbml/SBMLExtensionRegistry.java
@@ -96,7 +96,7 @@ public class SBMLExtensionRegistry {
/**
@@ -414,38 +114,9 @@
*/ public
void addL2Namespaces(XMLNamespaces xmlns) {
libsbmlJNI.SBMLExtensionRegistry_addL2Namespaces(swigCPtr, this, XMLNamespaces.getCPtr(xmlns), xmlns);
---- libsbml-5.6.0.orig/src/bindings/perl/LibSBML.pm
-+++ libsbml-5.6.0/src/bindings/perl/LibSBML.pm
-@@ -39507,8 +39507,8 @@ Package developers must implement an SBM
- their packages (e.g. GroupsExtension class is implemented for groups extension).
- The extended class is implemented based on the following steps:
- (NOTE:
--"src/pacakges/groups/extension/GroupsExtension.{h,cpp}" and
--"src/pacakges/layout/extension/LayoutExtension.{h,cpp}" are
-+"src/packages/groups/extension/GroupsExtension.{h,cpp}" and
-+"src/packages/layout/extension/LayoutExtension.{h,cpp}" are
- example files in which SBMLExtension derived classes are implemented)
- <ol>
-
-@@ -39886,7 +39886,7 @@ GroupsExtension::init()
- {
- //-------------------------------------------------------------------------
- //
--// 1. Checks if the groups pacakge has already been registered.
-+// 1. Checks if the groups package has already been registered.
- //
- //-------------------------------------------------------------------------
- if (SBMLExtensionRegistry::getInstance().isRegistered(getPackageName()))
-@@ -40008,7 +40008,7 @@ package extension, otherwise false is re
- =item SBMLExtension::getSupportedPackageURI
-
- Returns the ith URI (the supported package version)
-- at param i the index of the list of URI (the list of supporeted pacakge versions)
-+ at param i the index of the list of URI (the list of supporeted package versions)
- Returns the URI of supported package version with the given index.
-
-
-@@ -40186,13 +40186,13 @@ extension is to be freed (i.e.: deleted)
+--- libsbml-5.7.0.orig/src/bindings/perl/LibSBML.pm
++++ libsbml-5.7.0/src/bindings/perl/LibSBML.pm
+@@ -40598,13 +40598,13 @@ extension is to be freed (i.e.: deleted)
=item SBMLExtensionRegistry::removeL2Namespaces
Remove all L2 Extension namespaces from the namespace list. This will call all
@@ -461,38 +132,9 @@
=item SBMLExtensionRegistry::enableL2NamespaceForDocument
---- libsbml-5.6.0.orig/src/bindings/perl/LibSBML.pod
-+++ libsbml-5.6.0/src/bindings/perl/LibSBML.pod
-@@ -39494,8 +39494,8 @@ Package developers must implement an SBM
- their packages (e.g. GroupsExtension class is implemented for groups extension).
- The extended class is implemented based on the following steps:
- (NOTE:
--"src/pacakges/groups/extension/GroupsExtension.{h,cpp}" and
--"src/pacakges/layout/extension/LayoutExtension.{h,cpp}" are
-+"src/packages/groups/extension/GroupsExtension.{h,cpp}" and
-+"src/packages/layout/extension/LayoutExtension.{h,cpp}" are
- example files in which SBMLExtension derived classes are implemented)
- <ol>
-
-@@ -39873,7 +39873,7 @@ GroupsExtension::init()
- {
- //-------------------------------------------------------------------------
- //
--// 1. Checks if the groups pacakge has already been registered.
-+// 1. Checks if the groups package has already been registered.
- //
- //-------------------------------------------------------------------------
- if (SBMLExtensionRegistry::getInstance().isRegistered(getPackageName()))
-@@ -39995,7 +39995,7 @@ package extension, otherwise false is re
- =item SBMLExtension::getSupportedPackageURI
-
- Returns the ith URI (the supported package version)
-- at param i the index of the list of URI (the list of supporeted pacakge versions)
-+ at param i the index of the list of URI (the list of supporeted package versions)
- Returns the URI of supported package version with the given index.
-
-
-@@ -40173,13 +40173,13 @@ extension is to be freed (i.e.: deleted)
+--- libsbml-5.7.0.orig/src/bindings/perl/LibSBML.pod
++++ libsbml-5.7.0/src/bindings/perl/LibSBML.pod
+@@ -40585,13 +40585,13 @@ extension is to be freed (i.e.: deleted)
=item SBMLExtensionRegistry::removeL2Namespaces
Remove all L2 Extension namespaces from the namespace list. This will call all
@@ -508,38 +150,9 @@
=item SBMLExtensionRegistry::enableL2NamespaceForDocument
---- libsbml-5.6.0.orig/src/bindings/python/libsbml-doxygen.py
-+++ libsbml-5.6.0/src/bindings/python/libsbml-doxygen.py
-@@ -49929,8 +49929,8 @@ class SBMLExtension(_object):
- The extended class is implemented based on the following steps:
-
- (NOTE:
-- 'src/pacakges/groups/extension/GroupsExtension.{h,cpp}' and
-- 'src/pacakges/layout/extension/LayoutExtension.{h,cpp}' are
-+ 'src/packages/groups/extension/GroupsExtension.{h,cpp}' and
-+ 'src/packages/layout/extension/LayoutExtension.{h,cpp}' are
- example files in which SBMLExtension derived classes are implemented)
-
- <ol>
-@@ -50276,7 +50276,7 @@ class SBMLExtension(_object):
- {
- //-------------------------------------------------------------------------
- //
-- // 1. Checks if the groups pacakge has already been registered.
-+ // 1. Checks if the groups package has already been registered.
- //
- //-------------------------------------------------------------------------
-
-@@ -50422,7 +50422,7 @@ class SBMLExtension(_object):
-
- Returns the ith URI (the supported package version)
-
-- @param i the index of the list of URI (the list of supporeted pacakge versions)
-+ @param i the index of the list of URI (the list of supporeted package versions)
- @return the URI of supported package version with the given index.
-
- """
-@@ -50729,7 +50729,7 @@ class SBMLExtensionRegistry(_object):
+--- libsbml-5.7.0.orig/src/bindings/python/libsbml-doxygen.py
++++ libsbml-5.7.0/src/bindings/python/libsbml-doxygen.py
+@@ -51084,7 +51084,7 @@ class SBMLExtensionRegistry(_object):
removeL2Namespaces(SBMLExtensionRegistry self, XMLNamespaces xmlns)
Remove all L2 Extension namespaces from the namespace list. This will call all
@@ -548,7 +161,7 @@
"""
return _libsbml.SBMLExtensionRegistry_removeL2Namespaces(self, *args)
-@@ -50739,7 +50739,7 @@ class SBMLExtensionRegistry(_object):
+@@ -51094,7 +51094,7 @@ class SBMLExtensionRegistry(_object):
addL2Namespaces(SBMLExtensionRegistry self, XMLNamespaces xmlns)
adds all L2 Extension namespaces to the namespace list. This will call all
@@ -557,38 +170,9 @@
"""
return _libsbml.SBMLExtensionRegistry_addL2Namespaces(self, *args)
---- libsbml-5.6.0.orig/src/bindings/python/libsbml.py
-+++ libsbml-5.6.0/src/bindings/python/libsbml.py
-@@ -50313,8 +50313,8 @@ class SBMLExtension(_object):
- extension). The extended class is implemented based on the following
- steps:
-
-- (NOTE: 'src/pacakges/groups/extension/GroupsExtension.{h,cpp}'
-- and 'src/pacakges/layout/extension/LayoutExtension.{h,cpp}' are
-+ (NOTE: 'src/packages/groups/extension/GroupsExtension.{h,cpp}'
-+ and 'src/packages/layout/extension/LayoutExtension.{h,cpp}' are
- example files in which SBMLExtension derived classes are implemented)
-
- <ol>
-@@ -50642,7 +50642,7 @@ class SBMLExtension(_object):
- {
- //-------------------------------------------------------------------------
- //
-- // 1. Checks if the groups pacakge has already been registered.
-+ // 1. Checks if the groups package has already been registered.
- //
- //-------------------------------------------------------------------------
-
-@@ -50787,7 +50787,7 @@ class SBMLExtension(_object):
- Returns the ith URI (the supported package version)
-
- Parameter 'i' is the index of the list of URI (the list of supporeted
-- pacakge versions) Returns the URI of supported package version with
-+ package versions) Returns the URI of supported package version with
- the given index.
-
- """
-@@ -51110,7 +51110,7 @@ class SBMLExtensionRegistry(_object):
+--- libsbml-5.7.0.orig/src/bindings/python/libsbml.py
++++ libsbml-5.7.0/src/bindings/python/libsbml.py
+@@ -51204,7 +51204,7 @@ class SBMLExtensionRegistry(_object):
removeL2Namespaces(SBMLExtensionRegistry self, XMLNamespaces xmlns)
Remove all L2 Extension namespaces from the namespace list. This will
@@ -597,7 +181,7 @@
"""
return _libsbml.SBMLExtensionRegistry_removeL2Namespaces(self, *args)
-@@ -51120,7 +51120,7 @@ class SBMLExtensionRegistry(_object):
+@@ -51214,7 +51214,7 @@ class SBMLExtensionRegistry(_object):
addL2Namespaces(SBMLExtensionRegistry self, XMLNamespaces xmlns)
adds all L2 Extension namespaces to the namespace list. This will
@@ -606,18 +190,9 @@
"""
return _libsbml.SBMLExtensionRegistry_addL2Namespaces(self, *args)
---- libsbml-5.6.0.orig/src/bindings/python/libsbml_wrap.cpp
-+++ libsbml-5.6.0/src/bindings/python/libsbml_wrap.cpp
-@@ -131337,7 +131337,7 @@ static PyMethodDef SwigMethods[] = {
- "Returns the ith URI (the supported package version)\n"
- "\n"
- "Parameter 'i' is the index of the list of URI (the list of supporeted\n"
-- "pacakge versions) Returns the URI of supported package version with\n"
-+ "package versions) Returns the URI of supported package version with\n"
- "the given index.\n"
- "\n"
- ""},
-@@ -131566,14 +131566,14 @@ static PyMethodDef SwigMethods[] = {
+--- libsbml-5.7.0.orig/src/bindings/python/libsbml_wrap.cpp
++++ libsbml-5.7.0/src/bindings/python/libsbml_wrap.cpp
+@@ -134460,14 +134460,14 @@ static PyMethodDef SwigMethods[] = {
"SBMLExtensionRegistry_removeL2Namespaces(SBMLExtensionRegistry self, XMLNamespaces xmlns)\n"
"\n"
"Remove all L2 Extension namespaces from the namespace list. This will\n"
@@ -634,39 +209,10 @@
"\n"
""},
{ (char *)"SBMLExtensionRegistry_enableL2NamespaceForDocument", _wrap_SBMLExtensionRegistry_enableL2NamespaceForDocument, METH_VARARGS, (char *)"\n"
---- libsbml-5.6.0.orig/src/bindings/python/pydoc-doxygen.i
-+++ libsbml-5.6.0/src/bindings/python/pydoc-doxygen.i
-@@ -42391,8 +42391,8 @@ in their packages, otherwise package dev
- The extended class is implemented based on the following steps:
+--- libsbml-5.7.0.orig/src/bindings/python/pydoc-doxygen.i
++++ libsbml-5.7.0/src/bindings/python/pydoc-doxygen.i
+@@ -43304,13 +43304,13 @@ in their packages, otherwise package dev
- (NOTE:
-- \'src/pacakges/groups/extension/GroupsExtension.{h,cpp}\' and
-- \'src/pacakges/layout/extension/LayoutExtension.{h,cpp}\' are
-+ \'src/packages/groups/extension/GroupsExtension.{h,cpp}\' and
-+ \'src/packages/layout/extension/LayoutExtension.{h,cpp}\' are
- example files in which SBMLExtension derived classes are implemented)
-
- <ol>
-@@ -42738,7 +42738,7 @@ in their packages, otherwise package dev
- {
- //-------------------------------------------------------------------------
- //
-- // 1. Checks if the groups pacakge has already been registered.
-+ // 1. Checks if the groups package has already been registered.
- //
- //-------------------------------------------------------------------------
-
-@@ -42881,7 +42881,7 @@ in their packages, otherwise package dev
- %feature("docstring") SBMLExtension::getSupportedPackageURI "
- Returns the ith URI (the supported package version)
-
-- @param i the index of the list of URI (the list of supporeted pacakge versions)
-+ @param i the index of the list of URI (the list of supporeted package versions)
- @return the URI of supported package version with the given index.
- ";
-
-@@ -43085,13 +43085,13 @@ in their packages, otherwise package dev
-
%feature("docstring") SBMLExtensionRegistry::removeL2Namespaces "
Remove all L2 Extension namespaces from the namespace list. This will call all
- overriden SBMLExtension::removeL2Namespaces methods.
@@ -681,39 +227,10 @@
";
---- libsbml-5.6.0.orig/src/bindings/python/pydoc-normal.i
-+++ libsbml-5.6.0/src/bindings/python/pydoc-normal.i
-@@ -40869,8 +40869,8 @@
- extension). The extended class is implemented based on the following
- steps:
+--- libsbml-5.7.0.orig/src/bindings/python/pydoc-normal.i
++++ libsbml-5.7.0/src/bindings/python/pydoc-normal.i
+@@ -41526,13 +41526,13 @@
-- (NOTE: 'src/pacakges/groups/extension/GroupsExtension.{h,cpp}'
-- and 'src/pacakges/layout/extension/LayoutExtension.{h,cpp}' are
-+ (NOTE: 'src/packages/groups/extension/GroupsExtension.{h,cpp}'
-+ and 'src/packages/layout/extension/LayoutExtension.{h,cpp}' are
- example files in which SBMLExtension derived classes are implemented)
-
- <ol>
-@@ -41198,7 +41198,7 @@
- {
- //-------------------------------------------------------------------------
- //
-- // 1. Checks if the groups pacakge has already been registered.
-+ // 1. Checks if the groups package has already been registered.
- //
- //-------------------------------------------------------------------------
-
-@@ -41341,7 +41341,7 @@
- Returns the ith URI (the supported package version)
-
- Parameter 'i' is the index of the list of URI (the list of supporeted
-- pacakge versions) Returns the URI of supported package version with
-+ package versions) Returns the URI of supported package version with
- the given index.
- ";
-
-@@ -41561,13 +41561,13 @@
-
%feature("docstring") SBMLExtensionRegistry::removeL2Namespaces "
Remove all L2 Extension namespaces from the namespace list. This will
- call all overriden SBMLExtension::removeL2Namespaces methods.
@@ -728,78 +245,8 @@
";
---- libsbml-5.6.0.orig/src/sbml/SBase.cpp
-+++ libsbml-5.6.0/src/sbml/SBase.cpp
-@@ -7223,7 +7223,7 @@ SBase_getModel (const SBase_t *sb)
- * typecode (int) if this object is defined in SBML core package,
- * return values will be one of SBMLLayoutTypeCode_t if this object is
- * defined in Layout extension (i.e. similar enum types are defined in
-- * each pacakge extension for each SBase subclass)
-+ * each package extension for each SBase subclass)
- * The value of each typecode can be duplicated between those of
- * different packages. Thus, to distinguish the typecodes of different
- * packages, not only the return value of getTypeCode() but also that of
---- libsbml-5.6.0.orig/src/sbml/SBase.h
-+++ libsbml-5.6.0/src/sbml/SBase.h
-@@ -3429,12 +3429,12 @@ SBase.readExtensionAttributes(attributes
- bool mCVTermsChanged;
-
- //
-- // XMLAttributes object containing attributes of unknown pacakges
-+ // XMLAttributes object containing attributes of unknown packages
- //
- XMLAttributes mAttributesOfUnknownPkg;
-
- //
-- // XMLNode object containing elements of unknown pacakges
-+ // XMLNode object containing elements of unknown packages
- //
- XMLNode mElementsOfUnknownPkg;
-
---- libsbml-5.6.0.orig/src/sbml/SBMLTypeCodes.h
-+++ libsbml-5.6.0/src/sbml/SBMLTypeCodes.h
-@@ -50,7 +50,7 @@ BEGIN_C_DECLS
- * (In libSBML 5, the type of return values in these functions have been changed
- * from typecode (int) to int for extensibility.)
- *
-- * - Each pacakge extension must define similar enum type for each SBase subclass
-+ * - Each package extension must define similar enum type for each SBase subclass
- * (e.g. SBMLLayoutTypeCode_t for the layout extension, SBMLGroupTypeCode_t for
- * group extension).
- *
---- libsbml-5.6.0.orig/src/sbml/extension/SBMLExtension.h
-+++ libsbml-5.6.0/src/sbml/extension/SBMLExtension.h
-@@ -43,8 +43,8 @@
- * The extended class is implemented based on the following steps:
- *
- * (NOTE:
-- * "src/pacakges/groups/extension/GroupsExtension.{h,cpp}" and
-- * "src/pacakges/layout/extension/LayoutExtension.{h,cpp}" are
-+ * "src/packages/groups/extension/GroupsExtension.{h,cpp}" and
-+ * "src/packages/layout/extension/LayoutExtension.{h,cpp}" are
- * example files in which SBMLExtension derived classes are implemented)
- *
- * <ol>
-@@ -390,7 +390,7 @@ GroupsExtension::init()
- {
- //-------------------------------------------------------------------------
- //
-- // 1. Checks if the groups pacakge has already been registered.
-+ // 1. Checks if the groups package has already been registered.
- //
- //-------------------------------------------------------------------------
-
-@@ -728,7 +728,7 @@ public:
- *
- * Returns the ith URI (the supported package version)
- *
-- * @param i the index of the list of URI (the list of supporeted pacakge versions)
-+ * @param i the index of the list of URI (the list of supporeted package versions)
- * @return the URI of supported package version with the given index.
- */
- const std::string& getSupportedPackageURI(unsigned int i) const;
---- libsbml-5.6.0.orig/src/sbml/extension/SBMLExtensionRegistry.cpp
-+++ libsbml-5.6.0/src/sbml/extension/SBMLExtensionRegistry.cpp
+--- libsbml-5.7.0.orig/src/sbml/extension/SBMLExtensionRegistry.cpp
++++ libsbml-5.7.0/src/sbml/extension/SBMLExtensionRegistry.cpp
@@ -304,7 +304,7 @@ SBMLExtensionRegistry::removeL2Namespace
/**
@@ -809,8 +256,8 @@
*/
void
SBMLExtensionRegistry::addL2Namespaces(XMLNamespaces *xmlns) const
---- libsbml-5.6.0.orig/src/sbml/extension/SBMLExtensionRegistry.h
-+++ libsbml-5.6.0/src/sbml/extension/SBMLExtensionRegistry.h
+--- libsbml-5.7.0.orig/src/sbml/extension/SBMLExtensionRegistry.h
++++ libsbml-5.7.0/src/sbml/extension/SBMLExtensionRegistry.h
@@ -98,13 +98,13 @@ public:
/**
@@ -827,184 +274,30 @@
*/
void addL2Namespaces(XMLNamespaces *xmlns) const;
---- libsbml-5.6.0.orig/src/sbml/packages/layout/extension/LayoutExtension.cpp
-+++ libsbml-5.6.0/src/sbml/packages/layout/extension/LayoutExtension.cpp
-@@ -345,7 +345,7 @@ LayoutExtension::init()
- {
- //-------------------------------------------------------------------------
- //
-- // 1. Checks if the layout pacakge has already been registered.
-+ // 1. Checks if the layout package has already been registered.
- //
- //-------------------------------------------------------------------------
-
---- libsbml-5.6.0.orig/src/sbml/packages/layout/sbml/BoundingBox.h
-+++ libsbml-5.6.0/src/sbml/packages/layout/sbml/BoundingBox.h
-@@ -344,7 +344,7 @@ public:
- * SBMLTypeCode_t if this object is defined in SBML core package,
- * return values will be one of SBMLLayoutTypeCode_t if this object is
- * defined in Layout extension (i.e. similar enum types are defined in
-- * each pacakge extension for each SBase subclass)
-+ * each package extension for each SBase subclass)
- * The value of each typecode can be duplicated between those of
- * different packages. Thus, to distinguish the typecodes of different
- * packages, not only the return value of getTypeCode() but also that of
---- libsbml-5.6.0.orig/src/sbml/packages/layout/sbml/CompartmentGlyph.h
-+++ libsbml-5.6.0/src/sbml/packages/layout/sbml/CompartmentGlyph.h
-@@ -196,7 +196,7 @@ public:
- * SBMLTypeCode_t if this object is defined in SBML core package,
- * return values will be one of SBMLLayoutTypeCode_t if this object is
- * defined in Layout extension (i.e. similar enum types are defined in
-- * each pacakge extension for each SBase subclass)
-+ * each package extension for each SBase subclass)
- * The value of each typecode can be duplicated between those of
- * different packages. Thus, to distinguish the typecodes of different
- * packages, not only the return value of getTypeCode() but also that of
---- libsbml-5.6.0.orig/src/sbml/packages/layout/sbml/CubicBezier.h
-+++ libsbml-5.6.0/src/sbml/packages/layout/sbml/CubicBezier.h
-@@ -265,7 +265,7 @@ public:
- * SBMLTypeCode_t if this object is defined in SBML core package,
- * return values will be one of SBMLLayoutTypeCode_t if this object is
- * defined in Layout extension (i.e. similar enum types are defined in
-- * each pacakge extension for each SBase subclass)
-+ * each package extension for each SBase subclass)
- * The value of each typecode can be duplicated between those of
- * different packages. Thus, to distinguish the typecodes of different
- * packages, not only the return value of getTypeCode() but also that of
---- libsbml-5.6.0.orig/src/sbml/packages/layout/sbml/Curve.h
-+++ libsbml-5.6.0/src/sbml/packages/layout/sbml/Curve.h
-@@ -302,7 +302,7 @@ public:
- * SBMLTypeCode_t if this object is defined in SBML core package,
- * return values will be one of SBMLLayoutTypeCode_t if this object is
- * defined in Layout extension (i.e. similar enum types are defined in
-- * each pacakge extension for each SBase subclass)
-+ * each package extension for each SBase subclass)
- * The value of each typecode can be duplicated between those of
- * different packages. Thus, to distinguish the typecodes of different
- * packages, not only the return value of getTypeCode() but also that of
---- libsbml-5.6.0.orig/src/sbml/packages/layout/sbml/Dimensions.h
-+++ libsbml-5.6.0/src/sbml/packages/layout/sbml/Dimensions.h
-@@ -248,7 +248,7 @@ public:
- * SBMLTypeCode_t if this object is defined in SBML core package,
- * return values will be one of SBMLLayoutTypeCode_t if this object is
- * defined in Layout extension (i.e. similar enum types are defined in
-- * each pacakge extension for each SBase subclass)
-+ * each package extension for each SBase subclass)
- * The value of each typecode can be duplicated between those of
- * different packages. Thus, to distinguish the typecodes of different
- * packages, not only the return value of getTypeCode() but also that of
---- libsbml-5.6.0.orig/src/sbml/packages/layout/sbml/GeneralGlyph.h
-+++ libsbml-5.6.0/src/sbml/packages/layout/sbml/GeneralGlyph.h
-@@ -521,7 +521,7 @@ public:
- * SBMLTypeCode_t if this object is defined in SBML core package,
- * return values will be one of SBMLLayoutTypeCode_t if this object is
- * defined in Layout extension (i.e. similar enum types are defined in
-- * each pacakge extension for each SBase subclass)
-+ * each package extension for each SBase subclass)
- * The value of each typecode can be duplicated between those of
- * different packages. Thus, to distinguish the typecodes of different
- * packages, not only the return value of getTypeCode() but also that of
---- libsbml-5.6.0.orig/src/sbml/packages/layout/sbml/GraphicalObject.h
-+++ libsbml-5.6.0/src/sbml/packages/layout/sbml/GraphicalObject.h
-@@ -283,7 +283,7 @@ public:
- * SBMLTypeCode_t if this object is defined in SBML core package,
- * return values will be one of SBMLLayoutTypeCode_t if this object is
- * defined in Layout extension (i.e. similar enum types are defined in
-- * each pacakge extension for each SBase subclass)
-+ * each package extension for each SBase subclass)
- * The value of each typecode can be duplicated between those of
- * different packages. Thus, to distinguish the typecodes of different
- * packages, not only the return value of getTypeCode() but also that of
---- libsbml-5.6.0.orig/src/sbml/packages/layout/sbml/Layout.h
-+++ libsbml-5.6.0/src/sbml/packages/layout/sbml/Layout.h
-@@ -1215,7 +1215,7 @@ public:
- * SBMLTypeCode_t if this object is defined in SBML core package,
- * return values will be one of SBMLLayoutTypeCode_t if this object is
- * defined in Layout extension (i.e. similar enum types are defined in
-- * each pacakge extension for each SBase subclass)
-+ * each package extension for each SBase subclass)
- * The value of each typecode can be duplicated between those of
- * different packages. Thus, to distinguish the typecodes of different
- * packages, not only the return value of getTypeCode() but also that of
---- libsbml-5.6.0.orig/src/sbml/packages/layout/sbml/LineSegment.h
-+++ libsbml-5.6.0/src/sbml/packages/layout/sbml/LineSegment.h
-@@ -225,7 +225,7 @@ public:
- * SBMLTypeCode_t if this object is defined in SBML core package,
- * return values will be one of SBMLLayoutTypeCode_t if this object is
- * defined in Layout extension (i.e. similar enum types are defined in
-- * each pacakge extension for each SBase subclass)
-+ * each package extension for each SBase subclass)
- * The value of each typecode can be duplicated between those of
- * different packages. Thus, to distinguish the typecodes of different
- * packages, not only the return value of getTypeCode() but also that of
---- libsbml-5.6.0.orig/src/sbml/packages/layout/sbml/Point.h
-+++ libsbml-5.6.0/src/sbml/packages/layout/sbml/Point.h
-@@ -275,7 +275,7 @@ public:
- * SBMLTypeCode_t if this object is defined in SBML core package,
- * return values will be one of SBMLLayoutTypeCode_t if this object is
- * defined in Layout extension (i.e. similar enum types are defined in
-- * each pacakge extension for each SBase subclass)
-+ * each package extension for each SBase subclass)
- * The value of each typecode can be duplicated between those of
- * different packages. Thus, to distinguish the typecodes of different
- * packages, not only the return value of getTypeCode() but also that of
---- libsbml-5.6.0.orig/src/sbml/packages/layout/sbml/ReactionGlyph.h
-+++ libsbml-5.6.0/src/sbml/packages/layout/sbml/ReactionGlyph.h
-@@ -454,7 +454,7 @@ public:
- * SBMLTypeCode_t if this object is defined in SBML core package,
- * return values will be one of SBMLLayoutTypeCode_t if this object is
- * defined in Layout extension (i.e. similar enum types are defined in
-- * each pacakge extension for each SBase subclass)
-+ * each package extension for each SBase subclass)
- * The value of each typecode can be duplicated between those of
- * different packages. Thus, to distinguish the typecodes of different
- * packages, not only the return value of getTypeCode() but also that of
---- libsbml-5.6.0.orig/src/sbml/packages/layout/sbml/ReferenceGlyph.h
-+++ libsbml-5.6.0/src/sbml/packages/layout/sbml/ReferenceGlyph.h
-@@ -269,7 +269,7 @@ public:
- * SBMLTypeCode_t if this object is defined in SBML core package,
- * return values will be one of SBMLLayoutTypeCode_t if this object is
- * defined in Layout extension (i.e. similar enum types are defined in
-- * each pacakge extension for each SBase subclass)
-+ * each package extension for each SBase subclass)
- * The value of each typecode can be duplicated between those of
- * different packages. Thus, to distinguish the typecodes of different
- * packages, not only the return value of getTypeCode() but also that of
---- libsbml-5.6.0.orig/src/sbml/packages/layout/sbml/SpeciesGlyph.h
-+++ libsbml-5.6.0/src/sbml/packages/layout/sbml/SpeciesGlyph.h
-@@ -194,7 +194,7 @@ public:
- * SBMLTypeCode_t if this object is defined in SBML core package,
- * return values will be one of SBMLLayoutTypeCode_t if this object is
- * defined in Layout extension (i.e. similar enum types are defined in
-- * each pacakge extension for each SBase subclass)
-+ * each package extension for each SBase subclass)
- * The value of each typecode can be duplicated between those of
- * different packages. Thus, to distinguish the typecodes of different
- * packages, not only the return value of getTypeCode() but also that of
---- libsbml-5.6.0.orig/src/sbml/packages/layout/sbml/SpeciesReferenceGlyph.h
-+++ libsbml-5.6.0/src/sbml/packages/layout/sbml/SpeciesReferenceGlyph.h
-@@ -298,7 +298,7 @@ public:
- * SBMLTypeCode_t if this object is defined in SBML core package,
- * return values will be one of SBMLLayoutTypeCode_t if this object is
- * defined in Layout extension (i.e. similar enum types are defined in
-- * each pacakge extension for each SBase subclass)
-+ * each package extension for each SBase subclass)
- * The value of each typecode can be duplicated between those of
- * different packages. Thus, to distinguish the typecodes of different
- * packages, not only the return value of getTypeCode() but also that of
---- libsbml-5.6.0.orig/src/sbml/packages/layout/sbml/TextGlyph.h
-+++ libsbml-5.6.0/src/sbml/packages/layout/sbml/TextGlyph.h
-@@ -240,7 +240,7 @@ public:
- * SBMLTypeCode_t if this object is defined in SBML core package,
- * return values will be one of SBMLLayoutTypeCode_t if this object is
- * defined in Layout extension (i.e. similar enum types are defined in
-- * each pacakge extension for each SBase subclass)
-+ * each package extension for each SBase subclass)
- * The value of each typecode can be duplicated between those of
- * different packages. Thus, to distinguish the typecodes of different
- * packages, not only the return value of getTypeCode() but also that of
---- libsbml-5.6.0.orig/src/sbml/validator/constraints/ArgumentsUnitsCheck.h
-+++ libsbml-5.6.0/src/sbml/validator/constraints/ArgumentsUnitsCheck.h
+--- libsbml-5.7.0.orig/src/sbml/packages/comp/validator/constraints/CompIdBase.cpp
++++ libsbml-5.7.0/src/sbml/packages/comp/validator/constraints/CompIdBase.cpp
+@@ -68,7 +68,7 @@ CompIdBase::getFieldname ()
+
+ /**
+ * @return the preamble to use when logging constraint violations. The
+- * preamble will be prepended to each log message. If not overriden,
++ * preamble will be prepended to each log message. If not overridden,
+ * returns an empty string.
+ */
+ const char*
+--- libsbml-5.7.0.orig/src/sbml/packages/comp/validator/constraints/CompIdBase.h
++++ libsbml-5.7.0/src/sbml/packages/comp/validator/constraints/CompIdBase.h
+@@ -113,7 +113,7 @@ protected:
+
+ /**
+ * @return the preamble to use when logging constraint violations. The
+- * preamble will be prepended to each log message. If not overriden,
++ * preamble will be prepended to each log message. If not overridden,
+ * returns an empty string.
+ */
+ virtual const char* getPreamble ();
+--- libsbml-5.7.0.orig/src/sbml/validator/constraints/ArgumentsUnitsCheck.h
++++ libsbml-5.7.0/src/sbml/validator/constraints/ArgumentsUnitsCheck.h
@@ -75,7 +75,7 @@ protected:
/**
@@ -1014,8 +307,8 @@
* returns an empty string.
*/
virtual const char* getPreamble ();
---- libsbml-5.6.0.orig/src/sbml/validator/constraints/ArgumentsUnitsCheckWarnings.h
-+++ libsbml-5.6.0/src/sbml/validator/constraints/ArgumentsUnitsCheckWarnings.h
+--- libsbml-5.7.0.orig/src/sbml/validator/constraints/ArgumentsUnitsCheckWarnings.h
++++ libsbml-5.7.0/src/sbml/validator/constraints/ArgumentsUnitsCheckWarnings.h
@@ -75,7 +75,7 @@ protected:
/**
@@ -1025,8 +318,8 @@
* returns an empty string.
*/
virtual const char* getPreamble ();
---- libsbml-5.6.0.orig/src/sbml/validator/constraints/CiElementMathCheck.h
-+++ libsbml-5.6.0/src/sbml/validator/constraints/CiElementMathCheck.h
+--- libsbml-5.7.0.orig/src/sbml/validator/constraints/CiElementMathCheck.h
++++ libsbml-5.7.0/src/sbml/validator/constraints/CiElementMathCheck.h
@@ -74,7 +74,7 @@ protected:
/**
@@ -1036,8 +329,8 @@
* returns an empty string.
*/
virtual const char* getPreamble ();
---- libsbml-5.6.0.orig/src/sbml/validator/constraints/EqualityArgsMathCheck.h
-+++ libsbml-5.6.0/src/sbml/validator/constraints/EqualityArgsMathCheck.h
+--- libsbml-5.7.0.orig/src/sbml/validator/constraints/EqualityArgsMathCheck.h
++++ libsbml-5.7.0/src/sbml/validator/constraints/EqualityArgsMathCheck.h
@@ -74,7 +74,7 @@ protected:
/**
@@ -1047,8 +340,8 @@
* returns an empty string.
*/
virtual const char* getPreamble ();
---- libsbml-5.6.0.orig/src/sbml/validator/constraints/ExponentUnitsCheck.h
-+++ libsbml-5.6.0/src/sbml/validator/constraints/ExponentUnitsCheck.h
+--- libsbml-5.7.0.orig/src/sbml/validator/constraints/ExponentUnitsCheck.h
++++ libsbml-5.7.0/src/sbml/validator/constraints/ExponentUnitsCheck.h
@@ -75,7 +75,7 @@ protected:
/**
@@ -1058,8 +351,8 @@
* returns an empty string.
*/
virtual const char* getPreamble ();
---- libsbml-5.6.0.orig/src/sbml/validator/constraints/FunctionApplyMathCheck.h
-+++ libsbml-5.6.0/src/sbml/validator/constraints/FunctionApplyMathCheck.h
+--- libsbml-5.7.0.orig/src/sbml/validator/constraints/FunctionApplyMathCheck.h
++++ libsbml-5.7.0/src/sbml/validator/constraints/FunctionApplyMathCheck.h
@@ -74,7 +74,7 @@ protected:
/**
@@ -1069,8 +362,8 @@
* returns an empty string.
*/
virtual const char* getPreamble ();
---- libsbml-5.6.0.orig/src/sbml/validator/constraints/FunctionNoArgsMathCheck.h
-+++ libsbml-5.6.0/src/sbml/validator/constraints/FunctionNoArgsMathCheck.h
+--- libsbml-5.7.0.orig/src/sbml/validator/constraints/FunctionNoArgsMathCheck.h
++++ libsbml-5.7.0/src/sbml/validator/constraints/FunctionNoArgsMathCheck.h
@@ -74,7 +74,7 @@ protected:
/**
@@ -1080,8 +373,8 @@
* returns an empty string.
*/
virtual const char* getPreamble ();
---- libsbml-5.6.0.orig/src/sbml/validator/constraints/IdBase.cpp
-+++ libsbml-5.6.0/src/sbml/validator/constraints/IdBase.cpp
+--- libsbml-5.7.0.orig/src/sbml/validator/constraints/IdBase.cpp
++++ libsbml-5.7.0/src/sbml/validator/constraints/IdBase.cpp
@@ -71,7 +71,7 @@ IdBase::getFieldname ()
/**
@@ -1091,8 +384,8 @@
* returns an empty string.
*/
const char*
---- libsbml-5.6.0.orig/src/sbml/validator/constraints/IdBase.h
-+++ libsbml-5.6.0/src/sbml/validator/constraints/IdBase.h
+--- libsbml-5.7.0.orig/src/sbml/validator/constraints/IdBase.h
++++ libsbml-5.7.0/src/sbml/validator/constraints/IdBase.h
@@ -112,7 +112,7 @@ protected:
/**
@@ -1102,8 +395,8 @@
* returns an empty string.
*/
virtual const char* getPreamble ();
---- libsbml-5.6.0.orig/src/sbml/validator/constraints/KineticLawUnitsCheck.cpp
-+++ libsbml-5.6.0/src/sbml/validator/constraints/KineticLawUnitsCheck.cpp
+--- libsbml-5.7.0.orig/src/sbml/validator/constraints/KineticLawUnitsCheck.cpp
++++ libsbml-5.7.0/src/sbml/validator/constraints/KineticLawUnitsCheck.cpp
@@ -80,7 +80,7 @@ KineticLawUnitsCheck::getFieldname ()
/**
@@ -1113,8 +406,8 @@
* returns an empty string.
*/
const char*
---- libsbml-5.6.0.orig/src/sbml/validator/constraints/KineticLawUnitsCheck.h
-+++ libsbml-5.6.0/src/sbml/validator/constraints/KineticLawUnitsCheck.h
+--- libsbml-5.7.0.orig/src/sbml/validator/constraints/KineticLawUnitsCheck.h
++++ libsbml-5.7.0/src/sbml/validator/constraints/KineticLawUnitsCheck.h
@@ -79,7 +79,7 @@ protected:
/**
@@ -1124,8 +417,8 @@
* returns an empty string.
*/
virtual const char* getPreamble ();
---- libsbml-5.6.0.orig/src/sbml/validator/constraints/LambdaMathCheck.h
-+++ libsbml-5.6.0/src/sbml/validator/constraints/LambdaMathCheck.h
+--- libsbml-5.7.0.orig/src/sbml/validator/constraints/LambdaMathCheck.h
++++ libsbml-5.7.0/src/sbml/validator/constraints/LambdaMathCheck.h
@@ -74,7 +74,7 @@ protected:
/**
@@ -1135,8 +428,8 @@
* returns an empty string.
*/
virtual const char* getPreamble ();
---- libsbml-5.6.0.orig/src/sbml/validator/constraints/LocalParameterMathCheck.h
-+++ libsbml-5.6.0/src/sbml/validator/constraints/LocalParameterMathCheck.h
+--- libsbml-5.7.0.orig/src/sbml/validator/constraints/LocalParameterMathCheck.h
++++ libsbml-5.7.0/src/sbml/validator/constraints/LocalParameterMathCheck.h
@@ -74,7 +74,7 @@ protected:
/**
@@ -1146,8 +439,8 @@
* returns an empty string.
*/
virtual const char* getPreamble ();
---- libsbml-5.6.0.orig/src/sbml/validator/constraints/LogicalArgsMathCheck.h
-+++ libsbml-5.6.0/src/sbml/validator/constraints/LogicalArgsMathCheck.h
+--- libsbml-5.7.0.orig/src/sbml/validator/constraints/LogicalArgsMathCheck.h
++++ libsbml-5.7.0/src/sbml/validator/constraints/LogicalArgsMathCheck.h
@@ -74,7 +74,7 @@ protected:
/**
@@ -1157,8 +450,8 @@
* returns an empty string.
*/
virtual const char* getPreamble ();
---- libsbml-5.6.0.orig/src/sbml/validator/constraints/MathMLBase.cpp
-+++ libsbml-5.6.0/src/sbml/validator/constraints/MathMLBase.cpp
+--- libsbml-5.7.0.orig/src/sbml/validator/constraints/MathMLBase.cpp
++++ libsbml-5.7.0/src/sbml/validator/constraints/MathMLBase.cpp
@@ -69,7 +69,7 @@ MathMLBase::getFieldname ()
/**
@@ -1168,8 +461,8 @@
* returns an empty string.
*/
const char*
---- libsbml-5.6.0.orig/src/sbml/validator/constraints/MathMLBase.h
-+++ libsbml-5.6.0/src/sbml/validator/constraints/MathMLBase.h
+--- libsbml-5.7.0.orig/src/sbml/validator/constraints/MathMLBase.h
++++ libsbml-5.7.0/src/sbml/validator/constraints/MathMLBase.h
@@ -101,7 +101,7 @@ protected:
/**
@@ -1179,8 +472,8 @@
* returns an empty string.
*/
virtual const char* getPreamble ();
---- libsbml-5.6.0.orig/src/sbml/validator/constraints/NumberArgsMathCheck.h
-+++ libsbml-5.6.0/src/sbml/validator/constraints/NumberArgsMathCheck.h
+--- libsbml-5.7.0.orig/src/sbml/validator/constraints/NumberArgsMathCheck.h
++++ libsbml-5.7.0/src/sbml/validator/constraints/NumberArgsMathCheck.h
@@ -99,7 +99,7 @@ protected:
/**
@@ -1190,8 +483,8 @@
* returns an empty string.
*/
virtual const char* getPreamble ();
---- libsbml-5.6.0.orig/src/sbml/validator/constraints/NumericArgsMathCheck.h
-+++ libsbml-5.6.0/src/sbml/validator/constraints/NumericArgsMathCheck.h
+--- libsbml-5.7.0.orig/src/sbml/validator/constraints/NumericArgsMathCheck.h
++++ libsbml-5.7.0/src/sbml/validator/constraints/NumericArgsMathCheck.h
@@ -74,7 +74,7 @@ protected:
/**
@@ -1201,8 +494,8 @@
* returns an empty string.
*/
virtual const char* getPreamble ();
---- libsbml-5.6.0.orig/src/sbml/validator/constraints/NumericReturnMathCheck.h
-+++ libsbml-5.6.0/src/sbml/validator/constraints/NumericReturnMathCheck.h
+--- libsbml-5.7.0.orig/src/sbml/validator/constraints/NumericReturnMathCheck.h
++++ libsbml-5.7.0/src/sbml/validator/constraints/NumericReturnMathCheck.h
@@ -74,7 +74,7 @@ protected:
/**
@@ -1212,8 +505,8 @@
* returns an empty string.
*/
virtual const char* getPreamble ();
---- libsbml-5.6.0.orig/src/sbml/validator/constraints/PieceBooleanMathCheck.h
-+++ libsbml-5.6.0/src/sbml/validator/constraints/PieceBooleanMathCheck.h
+--- libsbml-5.7.0.orig/src/sbml/validator/constraints/PieceBooleanMathCheck.h
++++ libsbml-5.7.0/src/sbml/validator/constraints/PieceBooleanMathCheck.h
@@ -74,7 +74,7 @@ protected:
/**
@@ -1223,8 +516,8 @@
* returns an empty string.
*/
virtual const char* getPreamble ();
---- libsbml-5.6.0.orig/src/sbml/validator/constraints/PiecewiseValueMathCheck.h
-+++ libsbml-5.6.0/src/sbml/validator/constraints/PiecewiseValueMathCheck.h
+--- libsbml-5.7.0.orig/src/sbml/validator/constraints/PiecewiseValueMathCheck.h
++++ libsbml-5.7.0/src/sbml/validator/constraints/PiecewiseValueMathCheck.h
@@ -74,7 +74,7 @@ protected:
/**
@@ -1234,8 +527,8 @@
* returns an empty string.
*/
virtual const char* getPreamble ();
---- libsbml-5.6.0.orig/src/sbml/validator/constraints/PowerUnitsCheck.h
-+++ libsbml-5.6.0/src/sbml/validator/constraints/PowerUnitsCheck.h
+--- libsbml-5.7.0.orig/src/sbml/validator/constraints/PowerUnitsCheck.h
++++ libsbml-5.7.0/src/sbml/validator/constraints/PowerUnitsCheck.h
@@ -75,7 +75,7 @@ protected:
/**
@@ -1245,8 +538,8 @@
* returns an empty string.
*/
virtual const char* getPreamble ();
---- libsbml-5.6.0.orig/src/sbml/validator/constraints/UniqueMetaId.cpp
-+++ libsbml-5.6.0/src/sbml/validator/constraints/UniqueMetaId.cpp
+--- libsbml-5.7.0.orig/src/sbml/validator/constraints/UniqueMetaId.cpp
++++ libsbml-5.7.0/src/sbml/validator/constraints/UniqueMetaId.cpp
@@ -74,7 +74,7 @@ UniqueMetaId::getFieldname ()
/**
@@ -1256,8 +549,8 @@
* returns an empty string.
*/
const char*
---- libsbml-5.6.0.orig/src/sbml/validator/constraints/UniqueMetaId.h
-+++ libsbml-5.6.0/src/sbml/validator/constraints/UniqueMetaId.h
+--- libsbml-5.7.0.orig/src/sbml/validator/constraints/UniqueMetaId.h
++++ libsbml-5.7.0/src/sbml/validator/constraints/UniqueMetaId.h
@@ -119,7 +119,7 @@ protected:
/**
@@ -1267,8 +560,8 @@
* returns an empty string.
*/
const char* getPreamble ();
---- libsbml-5.6.0.orig/src/sbml/validator/constraints/UnitsBase.cpp
-+++ libsbml-5.6.0/src/sbml/validator/constraints/UnitsBase.cpp
+--- libsbml-5.7.0.orig/src/sbml/validator/constraints/UnitsBase.cpp
++++ libsbml-5.7.0/src/sbml/validator/constraints/UnitsBase.cpp
@@ -80,7 +80,7 @@ UnitsBase::getFieldname ()
/**
@@ -1278,8 +571,8 @@
* returns an empty string.
*/
const char*
---- libsbml-5.6.0.orig/src/sbml/validator/constraints/UnitsBase.h
-+++ libsbml-5.6.0/src/sbml/validator/constraints/UnitsBase.h
+--- libsbml-5.7.0.orig/src/sbml/validator/constraints/UnitsBase.h
++++ libsbml-5.7.0/src/sbml/validator/constraints/UnitsBase.h
@@ -104,7 +104,7 @@ protected:
/**
@@ -1289,8 +582,8 @@
* returns an empty string.
*/
virtual const char* getPreamble ();
---- libsbml-5.6.0.orig/src/sbml/validator/constraints/ValidCnUnitsValue.h
-+++ libsbml-5.6.0/src/sbml/validator/constraints/ValidCnUnitsValue.h
+--- libsbml-5.7.0.orig/src/sbml/validator/constraints/ValidCnUnitsValue.h
++++ libsbml-5.7.0/src/sbml/validator/constraints/ValidCnUnitsValue.h
@@ -74,7 +74,7 @@ protected:
/**
Modified: trunk/packages/libsbml/trunk/debian/rules
===================================================================
--- trunk/packages/libsbml/trunk/debian/rules 2013-02-03 23:34:37 UTC (rev 12908)
+++ trunk/packages/libsbml/trunk/debian/rules 2013-02-04 15:32:40 UTC (rev 12909)
@@ -46,7 +46,7 @@
BIND_MATLAB := $(shell which matlab | grep -q matlab && echo '--with-matlab')
get-orig-source:
- uscan --verbose --force-download --repack
+ uscan --verbose --force-download --repack --rename
config.status: configure
dh_testdir
@@ -63,7 +63,6 @@
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-perl \
@@ -71,6 +70,7 @@
--with-java \
--with-swig \
--with-ruby \
+ --with-doxygen \
--with-octave \
$(BIND_MATLAB) \
--enable-layout \
@@ -105,7 +105,7 @@
### verx ugly ###
rm -rf .pc .debs config docs examples macosx src config.guess config.sub
dh_clean
- tar --no-same-owner -xzf ../libsbml_$(version).orig.tar.gz -C ../
+ tar --no-same-owner -xzf ../libsbml_$(version).orig.tar.gz --strip-components=1
install: build
dh_testdir
Modified: trunk/packages/libsbml/trunk/debian/watch
===================================================================
--- trunk/packages/libsbml/trunk/debian/watch 2013-02-03 23:34:37 UTC (rev 12908)
+++ trunk/packages/libsbml/trunk/debian/watch 2013-02-04 15:32:40 UTC (rev 12909)
@@ -1,2 +1,3 @@
version=3
-http://sf.net/sbml/ lib[Ss][Bb][Mm][Ll]-(.*)-src\.tar\.gz
+#opts=dversionmangle=s/\-core-plus-packages// \
+http://sf.net/sbml/lib[Ss][Bb][Mm][Ll]-(.*)-core-plus-packages-src\.tar\.gz
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