[med-svn] r20762 - in trunk/packages/libsbml/trunk/debian: . patches
Andreas Tille
tille at moszumanska.debian.org
Mon Dec 14 17:14:56 UTC 2015
Author: tille
Date: 2015-12-14 17:14:56 +0000 (Mon, 14 Dec 2015)
New Revision: 20762
Added:
trunk/packages/libsbml/trunk/debian/patches/fix_cmake.patch
trunk/packages/libsbml/trunk/debian/patches/mips-compile-with-O1.patch
trunk/packages/libsbml/trunk/debian/patches/swig-3.x.patch
Modified:
trunk/packages/libsbml/trunk/debian/changelog
trunk/packages/libsbml/trunk/debian/cmake_opts
trunk/packages/libsbml/trunk/debian/control
trunk/packages/libsbml/trunk/debian/control.in
trunk/packages/libsbml/trunk/debian/patches/doxygen.patch
trunk/packages/libsbml/trunk/debian/patches/hardening.patch
trunk/packages/libsbml/trunk/debian/patches/perl-installdirs.patch
trunk/packages/libsbml/trunk/debian/patches/series
trunk/packages/libsbml/trunk/debian/patches/spelling.patch
trunk/packages/libsbml/trunk/debian/rules
Log:
Mass-commit to fix all open bugs and upgrade to latest upstream version - unfortunately build fails with "Cannot generate java documentation, please specify the Java_JAVADOC_JAR"
Modified: trunk/packages/libsbml/trunk/debian/changelog
===================================================================
--- trunk/packages/libsbml/trunk/debian/changelog 2015-12-14 15:46:08 UTC (rev 20761)
+++ trunk/packages/libsbml/trunk/debian/changelog 2015-12-14 17:14:56 UTC (rev 20762)
@@ -1,13 +1,7 @@
-libsbml (5.11.4+dfsg-1) UNRELEASED; urgency=medium
+libsbml (5.12.0+dfsg-1) unstable; urgency=medium
+ [ Ivo Maintz ]
* New upstream version
- * set executable rights on debian/libsbml5-octave.install to let it work also in svn-buildpackage
-
- -- Ivo Maintz <ivo at maintz.de> Mon, 24 Aug 2015 16:27:06 +0200
-
-libsbml (5.11.2+dfsg-2) UNRELEASED; urgency=medium
-
- * New upstream version
* debian/*doc-base: added doc-base integration for the *doc packages
* debian/control.in: fixed some spelling errors
* debian/libsbml5-octave.install: turned into a script to install into the
@@ -16,18 +10,23 @@
debian/libsbml5-octave.links.* are obsolete
install index.html to the proper location
remove wastful *.md5 files
- * new upstrem version
+ * set executable rights on debian/libsbml5-octave.install to let it work also in svn-buildpackage
- -- Ivo Maintz <ivo at maintz.de> Thu, 26 Nov 2015 12:55:51 +0100
-
-libsbml (5.10.0+dfsg-2) UNRELEASED; urgency=medium
-
[ Andreas Tille ]
* According to https://lists.debian.org/debian-bsd/2014/09/msg00133.html
libsbml requires openjdk - so we drop all alternatives from the
dependency list
+ * forward port patch to build on mipsel (thanks to Jurica Stanojkovic
+ <Jurica.Stanojkovic at imgtec.com> for the original patch)
+ Closes: #788068
+ * forward port patch to build with SWIG 3.x (thanks to Logan Rosen
+ <logan at ubuntu.com> for the original patch)
+ Closes: #805584
+ * Rebuild successfully using gcc-5
+ Closes: #793256
+ * Do not Build-Depend from transitional package mono-gmcs but rather mono-mcs
- -- Ivo Maintz <ivo at maintz.de> Mon, 22 Sep 2014 10:11:35 +0200
+ -- Andreas Tille <tille at debian.org> Mon, 14 Dec 2015 15:16:36 +0100
libsbml (5.10.0+dfsg-1) unstable; urgency=medium
Modified: trunk/packages/libsbml/trunk/debian/cmake_opts
===================================================================
--- trunk/packages/libsbml/trunk/debian/cmake_opts 2015-12-14 15:46:08 UTC (rev 20761)
+++ trunk/packages/libsbml/trunk/debian/cmake_opts 2015-12-14 17:14:56 UTC (rev 20762)
@@ -29,3 +29,5 @@
-DWITH_WALL:BOOL=ON
-DWITH_XERCES:BOOL=OFF
-DWITH_ZLIB:BOOL=ON
+-DJDK_PATH:STRING=/usr/lib/jvm/default-java
+-DJAVA_INCLUDE_PATH:STRING=/usr/lib/jvm/default-java/include
Modified: trunk/packages/libsbml/trunk/debian/control
===================================================================
--- trunk/packages/libsbml/trunk/debian/control 2015-12-14 15:46:08 UTC (rev 20761)
+++ trunk/packages/libsbml/trunk/debian/control 2015-12-14 17:14:56 UTC (rev 20762)
@@ -14,7 +14,7 @@
python-dev,
perl,
libperl-dev,
- default-jdk | openjdk-7-jdk,
+ openjdk-7-jdk,
octave-pkg-dev,
r-base-dev,
r-base-core,
@@ -22,7 +22,7 @@
zlib1g-dev,
libbz2-dev,
mono-devel,
- mono-gmcs,
+ mono-mcs,
cli-common-dev,
cli-runtime,
dpkg-dev (>= 1.16.1~),
Modified: trunk/packages/libsbml/trunk/debian/control.in
===================================================================
--- trunk/packages/libsbml/trunk/debian/control.in 2015-12-14 15:46:08 UTC (rev 20761)
+++ trunk/packages/libsbml/trunk/debian/control.in 2015-12-14 17:14:56 UTC (rev 20762)
@@ -22,7 +22,7 @@
zlib1g-dev,
libbz2-dev,
mono-devel,
- mono-gmcs,
+ mono-mcs,
cli-common-dev,
cli-runtime,
dpkg-dev (>= 1.16.1~),
Modified: trunk/packages/libsbml/trunk/debian/patches/doxygen.patch
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/doxygen.patch 2015-12-14 15:46:08 UTC (rev 20761)
+++ trunk/packages/libsbml/trunk/debian/patches/doxygen.patch 2015-12-14 17:14:56 UTC (rev 20762)
@@ -9,8 +9,8 @@
---
Last-Update: <2015-01-12>
---- libsbml-5.11.0+dfsg.orig/docs/CMakeLists.txt
-+++ libsbml-5.11.0+dfsg/docs/CMakeLists.txt
+--- a/docs/CMakeLists.txt
++++ b/docs/CMakeLists.txt
@@ -101,7 +101,7 @@ macro(createManual lang)
file(TO_NATIVE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/formatted/${lang}-api output_path)
file(TO_NATIVE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/formatted/${lang}-api/search search_path)
Added: trunk/packages/libsbml/trunk/debian/patches/fix_cmake.patch
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/fix_cmake.patch (rev 0)
+++ trunk/packages/libsbml/trunk/debian/patches/fix_cmake.patch 2015-12-14 17:14:56 UTC (rev 20762)
@@ -0,0 +1,34 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Mon, 14 Dec 2015 15:16:36 +0100
+Description: Fix cmake errors of type
+ CMake Warning (dev) at src/bindings/octave/CMakeLists.txt:36 (find_package):
+ Syntax Warning in cmake code at
+ .
+ /tmp/buildd/libsbml-5.12.0+dfsg/src/bindings/octave/FindOctave.cmake:83:32
+ .
+ Argument not separated from preceding token by whitespace.
+ This warning is for project developers. Use -Wno-dev to suppress it.
+
+--- a/src/bindings/octave/FindOctave.cmake
++++ b/src/bindings/octave/FindOctave.cmake
+@@ -80,17 +80,17 @@ if(OCTAVE_CONFIG_EXECUTABLE)
+ COMMAND ${OCTAVE_CONFIG_EXECUTABLE} -p CANONICAL_HOST_TYPE
+ OUTPUT_VARIABLE _octave_config_host_type
+ RESULT_VARIABLE _octave_config_failed)
+- string(REGEX REPLACE "[\r\n]""" _octave_config_host_type "${_octave_config_host_type}")
++ string(REGEX REPLACE "[\r\n]" " " _octave_config_host_type "${_octave_config_host_type}")
+ execute_process(
+ COMMAND ${OCTAVE_CONFIG_EXECUTABLE} -p API_VERSION
+ OUTPUT_VARIABLE _octave_config_api_version
+ RESULT_VARIABLE _octave_config_failed)
+- string(REGEX REPLACE "[\r\n]""" _octave_config_api_version "${_octave_config_api_version}")
++ string(REGEX REPLACE "[\r\n]" " " _octave_config_api_version "${_octave_config_api_version}")
+ execute_process(
+ COMMAND ${OCTAVE_CONFIG_EXECUTABLE} -p LOCALVEROCTFILEDIR
+ OUTPUT_VARIABLE _octave_config_localveroctfiledir
+ RESULT_VARIABLE _octave_config_failed)
+- string(REGEX REPLACE "[\r\n]""" _octave_config_localveroctfiledir "${_octave_config_localveroctfiledir}")
++ string(REGEX REPLACE "[\r\n]" " " _octave_config_localveroctfiledir "${_octave_config_localveroctfiledir}")
+
+ set( OCTAVE_HOST_TYPE "${_octave_config_host_type}" )
+ set( OCTAVE_API_VERSION "${_octave_config_api_version}" )
Modified: trunk/packages/libsbml/trunk/debian/patches/hardening.patch
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/hardening.patch 2015-12-14 15:46:08 UTC (rev 20761)
+++ trunk/packages/libsbml/trunk/debian/patches/hardening.patch 2015-12-14 17:14:56 UTC (rev 20762)
@@ -8,8 +8,8 @@
---
Last-Update: <2015-01-09>
---- libsbml-5.11.0+dfsg.orig/config/makefile-common-actions.mk
-+++ libsbml-5.11.0+dfsg/config/makefile-common-actions.mk
+--- a/config/makefile-common-actions.mk
++++ b/config/makefile-common-actions.mk
@@ -77,6 +77,15 @@ endif
# here is only to remove duplicates, which the 'sort' function does as a
# documented side-effect.)
@@ -26,8 +26,8 @@
compile ?= $(LIBTOOL) --mode=compile --tag=CC $(CC) $(sort $(default_includes) $(INCLUDES)) $(CPPFLAGS) \
$(extra_CPPFLAGS) $(CFLAGS) $(extra_CFLAGS)
---- libsbml-5.11.0+dfsg.orig/src/bindings/matlab/Makefile.in
-+++ libsbml-5.11.0+dfsg/src/bindings/matlab/Makefile.in
+--- a/src/bindings/matlab/Makefile.in
++++ b/src/bindings/matlab/Makefile.in
@@ -150,7 +150,7 @@ endif
# is really necessary, but it seems prudent.
@@ -37,8 +37,8 @@
$(LIBTOOL) -dlopen $(TOP_BUILDDIR)/src/libsbml.la --mode=execute $(1)
endef
---- libsbml-5.11.0+dfsg.orig/src/bindings/perl/Makefile.in
-+++ libsbml-5.11.0+dfsg/src/bindings/perl/Makefile.in
+--- a/src/bindings/perl/Makefile.in
++++ b/src/bindings/perl/Makefile.in
@@ -178,6 +178,7 @@ ifeq (GCC,$(findstring GCC,$(shell $(CXX
CXXFLAGS += -fno-strict-aliasing
endif
Added: trunk/packages/libsbml/trunk/debian/patches/mips-compile-with-O1.patch
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/mips-compile-with-O1.patch (rev 0)
+++ trunk/packages/libsbml/trunk/debian/patches/mips-compile-with-O1.patch 2015-12-14 17:14:56 UTC (rev 20762)
@@ -0,0 +1,24 @@
+From: Jurica Stanojkovic <Jurica.Stanojkovic at imgtec.com>
+Date: Mon, 8 Jun 2015 10:05:21 +0000
+Bug-Debian: https://bugs.debian.org/788068
+Subject: package libsbml FTBFS on mipsel
+ We have successfully built libsbml using -O1 optimization level.
+ -O1 is used for mips/mipsel, for critical part of package.
+ .
+ With this patch we was able to build package on lemote loongson 3a.
+
+--- a/src/bindings/perl/CMakeLists.txt
++++ b/src/bindings/perl/CMakeLists.txt
+@@ -168,6 +168,12 @@ if (LIBSBML_REMOVE_WRAPPERS)
+ endforeach()
+ endif(LIBSBML_REMOVE_WRAPPERS)
+
++if (WITH_01_COMPILE)
++ set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O1")
++ set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -O1")
++ set (CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -O1")
++ set (CMAKE_C_FLAGS_RELEASE "${CMAKE_C_FLAGS_RELEASE} -O1")
++endif(WITH_01_COMPILE)
+
+ ADD_CUSTOM_COMMAND(
+ OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/LibSBML_wrap.cpp ${CMAKE_CURRENT_BINARY_DIR}/LibSBML.pod
Modified: trunk/packages/libsbml/trunk/debian/patches/perl-installdirs.patch
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/perl-installdirs.patch 2015-12-14 15:46:08 UTC (rev 20761)
+++ trunk/packages/libsbml/trunk/debian/patches/perl-installdirs.patch 2015-12-14 17:14:56 UTC (rev 20762)
@@ -1,6 +1,6 @@
--- a/src/bindings/perl/Makefile.PL.in
+++ b/src/bindings/perl/Makefile.PL.in
-@@ -58,7 +58,6 @@
+@@ -58,7 +58,6 @@ WriteMakefile(
NAME => "LibSBML",
PREFIX => "@prefix@",
MAKEFILE => 'Makefile-perl',
@@ -10,7 +10,7 @@
CC => "@CXX@",
--- a/src/bindings/perl/CMakeLists.txt
+++ b/src/bindings/perl/CMakeLists.txt
-@@ -168,7 +168,13 @@
+@@ -224,7 +224,13 @@ Could not determine Perl version, please
string(REPLACE "'" "" PERL_PLATFORM ${PERL_PLATFORM})
string(REPLACE ";" "" PERL_PLATFORM ${PERL_PLATFORM})
string(REPLACE "archname=" "" PERL_PLATFORM ${PERL_PLATFORM})
Modified: trunk/packages/libsbml/trunk/debian/patches/series
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/series 2015-12-14 15:46:08 UTC (rev 20761)
+++ trunk/packages/libsbml/trunk/debian/patches/series 2015-12-14 17:14:56 UTC (rev 20762)
@@ -2,3 +2,6 @@
hardening.patch
doxygen.patch
spelling.patch
+swig-3.x.patch
+mips-compile-with-O1.patch
+# fix_cmake.patch # just warnings - ignore
Modified: trunk/packages/libsbml/trunk/debian/patches/spelling.patch
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/spelling.patch 2015-12-14 15:46:08 UTC (rev 20761)
+++ trunk/packages/libsbml/trunk/debian/patches/spelling.patch 2015-12-14 17:14:56 UTC (rev 20762)
@@ -9,8 +9,8 @@
---
Last-Update: <2015-01-12>
---- libsbml-5.11.0+dfsg.orig/docs/src/common-text/libsbml-import-for-python.html
-+++ libsbml-5.11.0+dfsg/docs/src/common-text/libsbml-import-for-python.html
+--- a/docs/src/common-text/libsbml-import-for-python.html
++++ b/docs/src/common-text/libsbml-import-for-python.html
@@ -67,6 +67,6 @@ probably means that <code>PYTHONPATH</co
It may also mean that the read/write permissions of the installed library
files or a directory in the hierarchy containing them are such that you are
@@ -19,9 +19,9 @@
+administrator or (if you have administrator privileges) reset the
permissions yourself.
---- libsbml-5.11.0+dfsg.orig/src/bindings/csharp/csdoc.i
-+++ libsbml-5.11.0+dfsg/src/bindings/csharp/csdoc.i
-@@ -324,7 +324,7 @@
+--- a/src/bindings/csharp/csdoc.i
++++ b/src/bindings/csharp/csdoc.i
+@@ -322,7 +322,7 @@
* enumeration #XMLErrorCode_t)@endif can provide a clue about what
* happened. For example, a file might be unreadable (either because it does
* not actually exist or because the user does not have the necessary access
@@ -30,7 +30,7 @@
* reported by the underlying operating system. Callers can check for these
* situations using a program fragment such as the following:
* @if cpp
-@@ -525,7 +525,7 @@ if (doc.getNumErrors() > 0)
+@@ -523,7 +523,7 @@ if (doc.getNumErrors() > 0)
* enumeration #XMLErrorCode_t)@endif can provide a clue about what
* happened. For example, a file might be unreadable (either because it does
* not actually exist or because the user does not have the necessary access
@@ -39,7 +39,7 @@
* reported by the underlying operating system. Callers can check for these
* situations using a program fragment such as the following:
* @if cpp
-@@ -819,7 +819,7 @@ if (doc.getNumErrors() > 0)
+@@ -817,7 +817,7 @@ if (doc.getNumErrors() > 0)
* enumeration #XMLErrorCode_t)@endif can provide a clue about what
* happened. For example, a file might be unreadable (either because it does
* not actually exist or because the user does not have the necessary access
@@ -48,7 +48,7 @@
* reported by the underlying operating system. Callers can check for these
* situations using a program fragment such as the following:
* @if cpp
-@@ -993,7 +993,7 @@ if (doc.getNumErrors() > 0)
+@@ -991,7 +991,7 @@ if (doc.getNumErrors() > 0)
* enumeration #XMLErrorCode_t)@endif can provide a clue about what
* happened. For example, a file might be unreadable (either because it does
* not actually exist or because the user does not have the necessary access
@@ -57,7 +57,7 @@
* reported by the underlying operating system. Callers can check for these
* situations using a program fragment such as the following:
* @if cpp
-@@ -4869,7 +4869,7 @@ void example (SBase sb)
+@@ -4917,7 +4917,7 @@ void example (SBase sb)
* Hierarchical %Model Composition (“comp”) package, and
* extracted parts of that model in order to construct a new model in
* memory. The new, in-memory model will not accept a component drawn from
@@ -66,7 +66,7 @@
* You could reconstruct the same namespaces in the in-memory model first,
* but as a shortcut, you could also disable the package namespace on the
* object being added. Here is a code example to help clarify this:
-@@ -55313,7 +55313,7 @@ on yyyy-MM-dd HH:mm with libSBML version
+@@ -56612,7 +56612,7 @@ on yyyy-MM-dd HH:mm with libSBML version
<td class=\'s-error\'></td>
</tr>
<tr><td class=\'code\'>@link libsbml#CompNoMultipleReferences CompNoMultipleReferences at endlink</td>
@@ -75,7 +75,7 @@
<td class=\'s-na\'></td>
<td class=\'s-na\'></td>
<td class=\'s-na\'></td>
-@@ -55673,7 +55673,7 @@ on yyyy-MM-dd HH:mm with libSBML version
+@@ -56972,7 +56972,7 @@ on yyyy-MM-dd HH:mm with libSBML version
<td class=\'s-error\'></td>
</tr>
<tr><td class=\'code\'>@link libsbml#CompDeprecatedReplaceFunction CompDeprecatedReplaceFunction at endlink</td>
@@ -84,7 +84,7 @@
<td class=\'s-na\'></td>
<td class=\'s-na\'></td>
<td class=\'s-na\'></td>
-@@ -65167,7 +65167,7 @@ if (doc->getLevel() == 2)
+@@ -66948,7 +66948,7 @@ if (doc->getLevel() == 2)
* <h3><a class=\'anchor\' name=\'math-history\'>Historical notes</a></h3>
*
* Readers may wonder why this part of libSBML uses a seemingly less
@@ -93,8 +93,8 @@
* written in C. All subsequent development was done in C++, but the
* complexity of some of the functionality for converting between infix, AST
* and MathML, coupled with the desire to maintain stability and backward
---- libsbml-5.11.0+dfsg.orig/src/bindings/java/java-files/org/sbml/libsbml/ASTNode.java
-+++ libsbml-5.11.0+dfsg/src/bindings/java/java-files/org/sbml/libsbml/ASTNode.java
+--- a/src/bindings/java/java-files/org/sbml/libsbml/ASTNode.java
++++ b/src/bindings/java/java-files/org/sbml/libsbml/ASTNode.java
@@ -211,7 +211,7 @@ defined in SBML.
* <h3><a class='anchor' name='math-history'>Historical notes</a></h3>
<p>
@@ -104,8 +104,8 @@
* written in C. All subsequent development was done in C++, but the
* complexity of some of the functionality for converting between infix, AST
* and MathML, coupled with the desire to maintain stability and backward
---- libsbml-5.11.0+dfsg.orig/src/bindings/java/java-files/org/sbml/libsbml/SBMLError.java
-+++ libsbml-5.11.0+dfsg/src/bindings/java/java-files/org/sbml/libsbml/SBMLError.java
+--- a/src/bindings/java/java-files/org/sbml/libsbml/SBMLError.java
++++ b/src/bindings/java/java-files/org/sbml/libsbml/SBMLError.java
@@ -5350,7 +5350,7 @@ defined in SBML.
<td class='s-error'></td>
</tr>
@@ -124,8 +124,8 @@
<td class='s-na'></td>
<td class='s-na'></td>
<td class='s-na'></td>
---- libsbml-5.11.0+dfsg.orig/src/bindings/java/java-files/org/sbml/libsbml/SBMLReader.java
-+++ libsbml-5.11.0+dfsg/src/bindings/java/java-files/org/sbml/libsbml/SBMLReader.java
+--- a/src/bindings/java/java-files/org/sbml/libsbml/SBMLReader.java
++++ b/src/bindings/java/java-files/org/sbml/libsbml/SBMLReader.java
@@ -197,7 +197,7 @@ public class SBMLReader {
* appear first. The error code can provide a clue about what
* happened. For example, a file might be unreadable (either because it does
@@ -144,9 +144,9 @@
* reported by the underlying operating system. Callers can check for these
* situations using a program fragment such as the following:
<p>
---- libsbml-5.11.0+dfsg.orig/src/bindings/java/java-files/org/sbml/libsbml/SBase.java
-+++ libsbml-5.11.0+dfsg/src/bindings/java/java-files/org/sbml/libsbml/SBase.java
-@@ -2952,7 +2952,7 @@ void example (SBase sb)
+--- a/src/bindings/java/java-files/org/sbml/libsbml/SBase.java
++++ b/src/bindings/java/java-files/org/sbml/libsbml/SBase.java
+@@ -3015,7 +3015,7 @@ void example (SBase sb)
* Hierarchical Model Composition (“comp”) package, and
* extracted parts of that model in order to construct a new model in
* memory. The new, in-memory model will not accept a component drawn from
@@ -155,9 +155,9 @@
* You could reconstruct the same namespaces in the in-memory model first,
* but as a shortcut, you could also disable the package namespace on the
* object being added. Here is a code example to help clarify this:
---- libsbml-5.11.0+dfsg.orig/src/bindings/java/java-files/org/sbml/libsbml/libsbml.java
-+++ libsbml-5.11.0+dfsg/src/bindings/java/java-files/org/sbml/libsbml/libsbml.java
-@@ -590,7 +590,7 @@ public class libsbml implements libsbmlC
+--- a/src/bindings/java/java-files/org/sbml/libsbml/libsbml.java
++++ b/src/bindings/java/java-files/org/sbml/libsbml/libsbml.java
+@@ -593,7 +593,7 @@ public class libsbml implements libsbmlC
* appear first. The error code can provide a clue about what
* happened. For example, a file might be unreadable (either because it does
* not actually exist or because the user does not have the necessary access
@@ -166,7 +166,7 @@
* reported by the underlying operating system. Callers can check for these
* situations using a program fragment such as the following:
<p>
-@@ -666,7 +666,7 @@ if (doc.getNumErrors() > 0)
+@@ -669,7 +669,7 @@ if (doc.getNumErrors() > 0)
* appear first. The error code can provide a clue about what
* happened. For example, a file might be unreadable (either because it does
* not actually exist or because the user does not have the necessary access
@@ -175,8 +175,8 @@
* reported by the underlying operating system. Callers can check for these
* situations using a program fragment such as the following:
<p>
---- libsbml-5.11.0+dfsg.orig/src/bindings/java/javadoc.i
-+++ libsbml-5.11.0+dfsg/src/bindings/java/javadoc.i
+--- a/src/bindings/java/javadoc.i
++++ b/src/bindings/java/javadoc.i
@@ -311,7 +311,7 @@ defined in SBML.
* appear first. The error code can provide a clue about what
* happened. For example, a file might be unreadable (either because it does
@@ -213,7 +213,7 @@
* reported by the underlying operating system. Callers can check for these
* situations using a program fragment such as the following:
<p>
-@@ -4180,7 +4180,7 @@ void example (SBase sb)
+@@ -4268,7 +4268,7 @@ void example (SBase sb)
* Hierarchical Model Composition (“comp”) package, and
* extracted parts of that model in order to construct a new model in
* memory. The new, in-memory model will not accept a component drawn from
@@ -222,7 +222,7 @@
* You could reconstruct the same namespaces in the in-memory model first,
* but as a shortcut, you could also disable the package namespace on the
* object being added. Here is a code example to help clarify this:
-@@ -51755,7 +51755,7 @@ defined in SBML.
+@@ -53291,7 +53291,7 @@ defined in SBML.
<td class=\'s-error\'></td>
</tr>
<tr><td class=\'code\'>{@link libsbmlConstants#CompNoMultipleReferences CompNoMultipleReferences}</td>
@@ -231,7 +231,7 @@
<td class=\'s-na\'></td>
<td class=\'s-na\'></td>
<td class=\'s-na\'></td>
-@@ -52115,7 +52115,7 @@ defined in SBML.
+@@ -53651,7 +53651,7 @@ defined in SBML.
<td class=\'s-error\'></td>
</tr>
<tr><td class=\'code\'>{@link libsbmlConstants#CompDeprecatedReplaceFunction CompDeprecatedReplaceFunction}</td>
@@ -240,7 +240,7 @@
<td class=\'s-na\'></td>
<td class=\'s-na\'></td>
<td class=\'s-na\'></td>
-@@ -60788,7 +60788,7 @@ defined in SBML.
+@@ -62461,7 +62461,7 @@ defined in SBML.
* <h3><a class=\'anchor\' name=\'math-history\'>Historical notes</a></h3>
<p>
* Readers may wonder why this part of libSBML uses a seemingly less
@@ -249,9 +249,9 @@
* written in C. All subsequent development was done in C++, but the
* complexity of some of the functionality for converting between infix, AST
* and MathML, coupled with the desire to maintain stability and backward
---- libsbml-5.11.0+dfsg.orig/src/bindings/perl/LibSBML.pm
-+++ libsbml-5.11.0+dfsg/src/bindings/perl/LibSBML.pm
-@@ -2565,7 +2565,7 @@ application read an SBML document contai
+--- a/src/bindings/perl/LibSBML.pm
++++ b/src/bindings/perl/LibSBML.pm
+@@ -2591,7 +2591,7 @@ application read an SBML document contai
Hierarchical Model Composition (“comp”) package, and
extracted parts of that model in order to construct a new model in
memory. The new, in-memory model will not accept a component drawn from
@@ -260,7 +260,7 @@
You could reconstruct the same namespaces in the in-memory model first,
but as a shortcut, you could also disable the package namespace on the
object being added. Here is a code example to help clarify this:
-@@ -33142,7 +33142,7 @@ ASTNode} and @sbmlfunction{parseL3Formul
+@@ -33633,7 +33633,7 @@ ASTNode} and @sbmlfunction{parseL3Formul
explanations of the infix syntax they accept.
<h3><a class="anchor" name="math-history">Historical notes</a></h3>
Readers may wonder why this part of libSBML uses a seemingly less
@@ -269,9 +269,9 @@
written in C. All subsequent development was done in C++, but the
complexity of some of the functionality for converting between infix, AST
and MathML, coupled with the desire to maintain stability and backward
---- libsbml-5.11.0+dfsg.orig/src/bindings/perl/LibSBML.pod
-+++ libsbml-5.11.0+dfsg/src/bindings/perl/LibSBML.pod
-@@ -2552,7 +2552,7 @@ application read an SBML document contai
+--- a/src/bindings/perl/LibSBML.pod
++++ b/src/bindings/perl/LibSBML.pod
+@@ -2578,7 +2578,7 @@ application read an SBML document contai
Hierarchical Model Composition (“comp”) package, and
extracted parts of that model in order to construct a new model in
memory. The new, in-memory model will not accept a component drawn from
@@ -280,7 +280,7 @@
You could reconstruct the same namespaces in the in-memory model first,
but as a shortcut, you could also disable the package namespace on the
object being added. Here is a code example to help clarify this:
-@@ -33129,7 +33129,7 @@ ASTNode} and @sbmlfunction{parseL3Formul
+@@ -33620,7 +33620,7 @@ ASTNode} and @sbmlfunction{parseL3Formul
explanations of the infix syntax they accept.
<h3><a class="anchor" name="math-history">Historical notes</a></h3>
Readers may wonder why this part of libSBML uses a seemingly less
@@ -289,9 +289,9 @@
written in C. All subsequent development was done in C++, but the
complexity of some of the functionality for converting between infix, AST
and MathML, coupled with the desire to maintain stability and backward
---- libsbml-5.11.0+dfsg.orig/src/bindings/python/libsbml-doxygen.py
-+++ libsbml-5.11.0+dfsg/src/bindings/python/libsbml-doxygen.py
-@@ -1187,7 +1187,7 @@ class SBMLReader(_object):
+--- a/src/bindings/python/libsbml-doxygen.py
++++ b/src/bindings/python/libsbml-doxygen.py
+@@ -1188,7 +1188,7 @@ class SBMLReader(_object):
enumeration #XMLErrorCode_t)@endif@~ can provide a clue about what
happened. For example, a file might be unreadable (either because it does
not actually exist or because the user does not have the necessary access
@@ -300,7 +300,7 @@
reported by the underlying operating system. Callers can check for these
situations using a program fragment such as the following:
@if cpp
-@@ -1378,7 +1378,7 @@ class SBMLReader(_object):
+@@ -1379,7 +1379,7 @@ class SBMLReader(_object):
enumeration #XMLErrorCode_t)@endif@~ can provide a clue about what
happened. For example, a file might be unreadable (either because it does
not actually exist or because the user does not have the necessary access
@@ -309,7 +309,7 @@
reported by the underlying operating system. Callers can check for these
situations using a program fragment such as the following:
@if cpp
-@@ -1721,7 +1721,7 @@ def readSBML(*args):
+@@ -1722,7 +1722,7 @@ def readSBML(*args):
enumeration #XMLErrorCode_t)@endif@~ can provide a clue about what
happened. For example, a file might be unreadable (either because it does
not actually exist or because the user does not have the necessary access
@@ -318,7 +318,7 @@
reported by the underlying operating system. Callers can check for these
situations using a program fragment such as the following:
@if cpp
-@@ -1888,7 +1888,7 @@ def readSBMLFromFile(*args):
+@@ -1889,7 +1889,7 @@ def readSBMLFromFile(*args):
enumeration #XMLErrorCode_t)@endif@~ can provide a clue about what
happened. For example, a file might be unreadable (either because it does
not actually exist or because the user does not have the necessary access
@@ -327,7 +327,7 @@
reported by the underlying operating system. Callers can check for these
situations using a program fragment such as the following:
@if cpp
-@@ -5524,7 +5524,7 @@ class SBase(_object):
+@@ -5566,7 +5566,7 @@ class SBase(_object):
Hierarchical %Model Composition (“comp”) package, and
extracted parts of that model in order to construct a new model in
memory. The new, in-memory model will not accept a component drawn from
@@ -336,7 +336,7 @@
You could reconstruct the same namespaces in the in-memory model first,
but as a shortcut, you could also disable the package namespace on the
object being added. Here is a code example to help clarify this:
-@@ -56749,7 +56749,7 @@ class SBMLError(XMLError):
+@@ -58581,7 +58581,7 @@ class SBMLError(XMLError):
<td class='s-error'></td>
</tr>
<tr><td class='code'>@link libsbml#CompNoMultipleReferences CompNoMultipleReferences at endlink</td>
@@ -345,7 +345,7 @@
<td class='s-na'></td>
<td class='s-na'></td>
<td class='s-na'></td>
-@@ -57109,7 +57109,7 @@ class SBMLError(XMLError):
+@@ -58941,7 +58941,7 @@ class SBMLError(XMLError):
<td class='s-error'></td>
</tr>
<tr><td class='code'>@link libsbml#CompDeprecatedReplaceFunction CompDeprecatedReplaceFunction at endlink</td>
@@ -354,7 +354,7 @@
<td class='s-na'></td>
<td class='s-na'></td>
<td class='s-na'></td>
-@@ -67516,7 +67516,7 @@ class ASTNode(ASTBase):
+@@ -69613,7 +69613,7 @@ class ASTNode(ASTBase):
<h3><a class='anchor' name='math-history'>Historical notes</a></h3>
Readers may wonder why this part of libSBML uses a seemingly less
@@ -363,8 +363,8 @@
written in C. All subsequent development was done in C++, but the
complexity of some of the functionality for converting between infix, AST
and MathML, coupled with the desire to maintain stability and backward
---- libsbml-5.11.0+dfsg.orig/src/bindings/python/libsbml.py
-+++ libsbml-5.11.0+dfsg/src/bindings/python/libsbml.py
+--- a/src/bindings/python/libsbml.py
++++ b/src/bindings/python/libsbml.py
@@ -812,7 +812,7 @@ def readSBML(*args):
appear first. The error code can provide a clue about what happened.
For example, a file might be unreadable (either because it does not
@@ -374,7 +374,7 @@
been reported by the underlying operating system. Callers can check
for these situations using a program fragment such as the following:
-@@ -1264,7 +1264,7 @@ class SBMLReader(_object):
+@@ -1601,7 +1601,7 @@ class SBMLReader(_object):
appear first. The error code can provide a clue about what happened.
For example, a file might be unreadable (either because it does not
actually exist or because the user does not have the necessary access
@@ -383,7 +383,7 @@
been reported by the underlying operating system. Callers can check
for these situations using a program fragment such as the following:
-@@ -1344,7 +1344,7 @@ class SBMLReader(_object):
+@@ -1681,7 +1681,7 @@ class SBMLReader(_object):
appear first. The error code can provide a clue about what happened.
For example, a file might be unreadable (either because it does not
actually exist or because the user does not have the necessary access
@@ -392,7 +392,7 @@
been reported by the underlying operating system. Callers can check
for these situations using a program fragment such as the following:
-@@ -1569,7 +1569,7 @@ def readSBMLFromFile(*args):
+@@ -1906,7 +1906,7 @@ def readSBMLFromFile(*args):
appear first. The error code can provide a clue about what happened.
For example, a file might be unreadable (either because it does not
actually exist or because the user does not have the necessary access
@@ -401,7 +401,7 @@
been reported by the underlying operating system. Callers can check
for these situations using a program fragment such as the following:
-@@ -48695,7 +48695,7 @@ class SBMLError(XMLError):
+@@ -50754,7 +50754,7 @@ class SBMLError(XMLError):
|CompDeprecatedSBaseRefSpelling |The spelling 'sbaseRef' is deprecated | | | | | | | |
|CompSBaseRefMustReferenceObject |An SBaseRef must reference an object. | | | | | | | |
|CompSBaseRefMustReferenceOnlyOneObject |An SBaseRef must reference only one other object. | | | | | | | |
@@ -410,7 +410,7 @@
|CompPortMustReferenceObject |Port must reference an object | | | | | | | |
|CompPortMustReferenceOnlyOneObject |Port must reference only one other object. | | | | | | | |
|CompPortAllowedAttributes |Allowed attributes on a Port | | | | | | | |
-@@ -48731,7 +48731,7 @@ class SBMLError(XMLError):
+@@ -50790,7 +50790,7 @@ class SBMLError(XMLError):
|CompFlatteningNotImplementedReqd |Flattening not implemented for required package. | | | | | | | |
|CompFlatteningWarning |Flattening reference may come from package. | | | | | | | |
|CompDeprecatedDeleteFunction |The performDeletions functions is deprecated. | | | | | | | |
@@ -419,7 +419,7 @@
|CompDeletedReplacement |Element deleted before a subelement could be replaced. | | | | | | | |
|CompIdRefMayReferenceUnknownPackage |The 'comp:idRef' attribute must be the 'id' of a model element | | | | | | | |
|CompMetaIdRefMayReferenceUnknownPkg |The 'comp:metaIdRef' attribute must be the 'metaid' of a model element | | | | | | | |
-@@ -55596,7 +55596,7 @@ class ASTNode(ASTBase):
+@@ -57539,7 +57539,7 @@ class ASTNode(ASTBase):
......................................................................
Readers may wonder why this part of libSBML uses a seemingly less
@@ -428,9 +428,9 @@
was written in C. All subsequent development was done in C++, but the
complexity of some of the functionality for converting between infix,
AST and MathML, coupled with the desire to maintain stability and
---- libsbml-5.11.0+dfsg.orig/src/bindings/python/libsbml_wrap.cpp
-+++ libsbml-5.11.0+dfsg/src/bindings/python/libsbml_wrap.cpp
-@@ -115177,7 +115177,7 @@ static PyMethodDef SwigMethods[] = {
+--- a/src/bindings/python/libsbml_wrap.cpp
++++ b/src/bindings/python/libsbml_wrap.cpp
+@@ -119949,7 +119949,7 @@ static PyMethodDef SwigMethods[] = {
"appear first. The error code can provide a clue about what happened.\n"
"For example, a file might be unreadable (either because it does not\n"
"actually exist or because the user does not have the necessary access\n"
@@ -439,7 +439,7 @@
"been reported by the underlying operating system. Callers can check\n"
"for these situations using a program fragment such as the following:\n"
"\n"
-@@ -115258,7 +115258,7 @@ static PyMethodDef SwigMethods[] = {
+@@ -120030,7 +120030,7 @@ static PyMethodDef SwigMethods[] = {
"appear first. The error code can provide a clue about what happened.\n"
"For example, a file might be unreadable (either because it does not\n"
"actually exist or because the user does not have the necessary access\n"
@@ -448,7 +448,7 @@
"been reported by the underlying operating system. Callers can check\n"
"for these situations using a program fragment such as the following:\n"
"\n"
-@@ -115419,7 +115419,7 @@ static PyMethodDef SwigMethods[] = {
+@@ -120191,7 +120191,7 @@ static PyMethodDef SwigMethods[] = {
"appear first. The error code can provide a clue about what happened.\n"
"For example, a file might be unreadable (either because it does not\n"
"actually exist or because the user does not have the necessary access\n"
@@ -457,9 +457,9 @@
"been reported by the underlying operating system. Callers can check\n"
"for these situations using a program fragment such as the following:\n"
"\n"
---- libsbml-5.11.0+dfsg.orig/src/bindings/python/local.i
-+++ libsbml-5.11.0+dfsg/src/bindings/python/local.i
-@@ -605,7 +605,7 @@ SBMLReader::readSBML(const std::string&)
+--- a/src/bindings/python/local.i
++++ b/src/bindings/python/local.i
+@@ -560,7 +560,7 @@ SBMLReader::readSBML(const std::string&)
appear first. The error code can provide a clue about what happened.
For example, a file might be unreadable (either because it does not
actually exist or because the user does not have the necessary access
@@ -468,7 +468,7 @@
been reported by the underlying operating system. Callers can check
for these situations using a program fragment such as the following:
-@@ -688,7 +688,7 @@ SBMLReader::readSBMLFromFile(const std::
+@@ -643,7 +643,7 @@ SBMLReader::readSBMLFromFile(const std::
appear first. The error code can provide a clue about what happened.
For example, a file might be unreadable (either because it does not
actually exist or because the user does not have the necessary access
@@ -477,7 +477,7 @@
been reported by the underlying operating system. Callers can check
for these situations using a program fragment such as the following:
-@@ -769,7 +769,7 @@ def readSBML(*args):
+@@ -724,7 +724,7 @@ def readSBML(*args):
appear first. The error code can provide a clue about what happened.
For example, a file might be unreadable (either because it does not
actually exist or because the user does not have the necessary access
@@ -486,8 +486,8 @@
been reported by the underlying operating system. Callers can check
for these situations using a program fragment such as the following:
---- libsbml-5.11.0+dfsg.orig/src/bindings/python/pydoc-doxygen.i
-+++ libsbml-5.11.0+dfsg/src/bindings/python/pydoc-doxygen.i
+--- a/src/bindings/python/pydoc-doxygen.i
++++ b/src/bindings/python/pydoc-doxygen.i
@@ -284,7 +284,7 @@ appear first. The error code @if clike
enumeration #XMLErrorCode_t)@endif@~ can provide a clue about what
happened. For example, a file might be unreadable (either because it does
@@ -524,7 +524,7 @@
reported by the underlying operating system. Callers can check for these
situations using a program fragment such as the following:
@if cpp
-@@ -4030,7 +4030,7 @@ application read an SBML document contai
+@@ -4067,7 +4067,7 @@ application read an SBML document contai
Hierarchical %Model Composition (“comp”) package, and
extracted parts of that model in order to construct a new model in
memory. The new, in-memory model will not accept a component drawn from
@@ -533,7 +533,7 @@
You could reconstruct the same namespaces in the in-memory model first,
but as a shortcut, you could also disable the package namespace on the
object being added. Here is a code example to help clarify this:
-@@ -49596,7 +49596,7 @@ from libSBML core. at endif
+@@ -51075,7 +51075,7 @@ from libSBML core. at endif
<td class=\'s-error\'></td>
</tr>
<tr><td class=\'code\'>@link libsbml#CompNoMultipleReferences CompNoMultipleReferences at endlink</td>
@@ -542,7 +542,7 @@
<td class=\'s-na\'></td>
<td class=\'s-na\'></td>
<td class=\'s-na\'></td>
-@@ -49956,7 +49956,7 @@ from libSBML core. at endif
+@@ -51435,7 +51435,7 @@ from libSBML core. at endif
<td class=\'s-error\'></td>
</tr>
<tr><td class=\'code\'>@link libsbml#CompDeprecatedReplaceFunction CompDeprecatedReplaceFunction at endlink</td>
@@ -551,7 +551,7 @@
<td class=\'s-na\'></td>
<td class=\'s-na\'></td>
<td class=\'s-na\'></td>
-@@ -58742,7 +58742,7 @@ explanations of the infix syntax they ac
+@@ -60481,7 +60481,7 @@ explanations of the infix syntax they ac
<h3><a class=\'anchor\' name=\'math-history\'>Historical notes</a></h3>
Readers may wonder why this part of libSBML uses a seemingly less
@@ -560,8 +560,8 @@
written in C. All subsequent development was done in C++, but the
complexity of some of the functionality for converting between infix, AST
and MathML, coupled with the desire to maintain stability and backward
---- libsbml-5.11.0+dfsg.orig/src/bindings/python/pydoc-normal.i
-+++ libsbml-5.11.0+dfsg/src/bindings/python/pydoc-normal.i
+--- a/src/bindings/python/pydoc-normal.i
++++ b/src/bindings/python/pydoc-normal.i
@@ -265,7 +265,7 @@ If the file 'filename' could not be read
appear first. The error code can provide a clue about what happened.
For example, a file might be unreadable (either because it does not
@@ -598,7 +598,7 @@
been reported by the underlying operating system. Callers can check
for these situations using a program fragment such as the following:
-@@ -40642,7 +40642,7 @@ If the name of a code does not begin wit
+@@ -41952,7 +41952,7 @@ If the name of a code does not begin wit
|CompDeprecatedSBaseRefSpelling |The spelling 'sbaseRef' is deprecated | | | | | | | |
|CompSBaseRefMustReferenceObject |An SBaseRef must reference an object. | | | | | | | |
|CompSBaseRefMustReferenceOnlyOneObject |An SBaseRef must reference only one other object. | | | | | | | |
@@ -607,7 +607,7 @@
|CompPortMustReferenceObject |Port must reference an object | | | | | | | |
|CompPortMustReferenceOnlyOneObject |Port must reference only one other object. | | | | | | | |
|CompPortAllowedAttributes |Allowed attributes on a Port | | | | | | | |
-@@ -40678,7 +40678,7 @@ If the name of a code does not begin wit
+@@ -41988,7 +41988,7 @@ If the name of a code does not begin wit
|CompFlatteningNotImplementedReqd |Flattening not implemented for required package. | | | | | | | |
|CompFlatteningWarning |Flattening reference may come from package. | | | | | | | |
|CompDeprecatedDeleteFunction |The performDeletions functions is deprecated. | | | | | | | |
@@ -616,7 +616,7 @@
|CompDeletedReplacement |Element deleted before a subelement could be replaced. | | | | | | | |
|CompIdRefMayReferenceUnknownPackage |The 'comp:idRef' attribute must be the 'id' of a model element | | | | | | | |
|CompMetaIdRefMayReferenceUnknownPkg |The 'comp:metaIdRef' attribute must be the 'metaid' of a model element | | | | | | | |
-@@ -45871,7 +45871,7 @@ Historical notes
+@@ -46983,7 +46983,7 @@ Historical notes
......................................................................
Readers may wonder why this part of libSBML uses a seemingly less
@@ -625,8 +625,8 @@
was written in C. All subsequent development was done in C++, but the
complexity of some of the functionality for converting between infix,
AST and MathML, coupled with the desire to maintain stability and
---- libsbml-5.11.0+dfsg.orig/src/sbml/SBMLReader.h
-+++ libsbml-5.11.0+dfsg/src/sbml/SBMLReader.h
+--- a/src/sbml/SBMLReader.h
++++ b/src/sbml/SBMLReader.h
@@ -152,7 +152,7 @@
* enumeration #XMLErrorCode_t)@endif@~ can provide a clue about what
* happened. For example, a file might be unreadable (either because it does
@@ -636,9 +636,9 @@
* reported by the underlying operating system. Callers can check for these
* situations using a program fragment such as the following:
* @if cpp
---- libsbml-5.11.0+dfsg.orig/src/sbml/SBase.h
-+++ libsbml-5.11.0+dfsg/src/sbml/SBase.h
-@@ -2748,7 +2748,7 @@ s.setNotes("<body xmlns='http://www.w3.o
+--- a/src/sbml/SBase.h
++++ b/src/sbml/SBase.h
+@@ -2785,7 +2785,7 @@ s.setNotes("<body xmlns='http://www.w3.o
* Hierarchical %Model Composition (“comp”) package, and
* extracted parts of that model in order to construct a new model in
* memory. The new, in-memory model will not accept a component drawn from
@@ -647,8 +647,8 @@
* You could reconstruct the same namespaces in the in-memory model first,
* but as a shortcut, you could also disable the package namespace on the
* object being added. Here is a code example to help clarify this:
---- libsbml-5.11.0+dfsg.orig/src/sbml/common/common-sbmlerror-codes.h
-+++ libsbml-5.11.0+dfsg/src/sbml/common/common-sbmlerror-codes.h
+--- a/src/sbml/common/common-sbmlerror-codes.h
++++ b/src/sbml/common/common-sbmlerror-codes.h
@@ -5197,7 +5197,7 @@
<td class="s-error"></td>
</tr>
@@ -667,8 +667,8 @@
<td class="s-na"></td>
<td class="s-na"></td>
<td class="s-na"></td>
---- libsbml-5.11.0+dfsg.orig/src/sbml/math/ASTNode.h
-+++ libsbml-5.11.0+dfsg/src/sbml/math/ASTNode.h
+--- a/src/sbml/math/ASTNode.h
++++ b/src/sbml/math/ASTNode.h
@@ -71,7 +71,7 @@
* <h3><a class="anchor" name="math-history">Historical notes</a></h3>
*
@@ -678,8 +678,8 @@
* written in C. All subsequent development was done in C++, but the
* complexity of some of the functionality for converting between infix, AST
* and MathML, coupled with the desire to maintain stability and backward
---- libsbml-5.11.0+dfsg.orig/src/sbml/packages/comp/validator/CompSBMLError.h
-+++ libsbml-5.11.0+dfsg/src/sbml/packages/comp/validator/CompSBMLError.h
+--- a/src/sbml/packages/comp/validator/CompSBMLError.h
++++ b/src/sbml/packages/comp/validator/CompSBMLError.h
@@ -124,7 +124,7 @@ typedef enum
, CompDeprecatedSBaseRefSpelling = 1020711 /*!< The spelling 'sbaseRef' is deprecated */
, CompSBaseRefMustReferenceObject = 1020712 /*!< An SBaseRef must reference an object. */
@@ -698,9 +698,9 @@
, CompDeletedReplacement = 1090114 /*!< Element deleted before a subelement could be replaced. */
, CompIdRefMayReferenceUnknownPackage = 1090115 /*!< The 'comp:idRef' attribute must be the 'id' of a model element */
---- libsbml-5.11.0+dfsg.orig/src/sbml/packages/comp/validator/CompSBMLErrorTable.h
-+++ libsbml-5.11.0+dfsg/src/sbml/packages/comp/validator/CompSBMLErrorTable.h
-@@ -949,7 +949,7 @@ static const packageErrorTableEntry comp
+--- a/src/sbml/packages/comp/validator/CompSBMLErrorTable.h
++++ b/src/sbml/packages/comp/validator/CompSBMLErrorTable.h
+@@ -946,7 +946,7 @@ static const packageErrorTableEntry comp
// 1020714
{ CompNoMultipleReferences,
@@ -709,7 +709,7 @@
LIBSBML_CAT_GENERAL_CONSISTENCY,
LIBSBML_SEV_ERROR,
"Any one SBML object may only be referenced in one of the following ways: "
-@@ -1410,7 +1410,7 @@ static const packageErrorTableEntry comp
+@@ -1407,7 +1407,7 @@ static const packageErrorTableEntry comp
// 1090113
{ CompDeprecatedReplaceFunction,
@@ -718,8 +718,8 @@
LIBSBML_CAT_GENERAL_CONSISTENCY,
LIBSBML_SEV_ERROR,
"The software used to process this hierarchical model used the deprecated "
---- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/ColorDefinition.cpp
-+++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/ColorDefinition.cpp
+--- a/src/sbml/packages/render/sbml/ColorDefinition.cpp
++++ b/src/sbml/packages/render/sbml/ColorDefinition.cpp
@@ -117,7 +117,7 @@ ColorDefinition::ColorDefinition (Render
* The XMLNode object has to contain a valid XML representation of a
* ColorDefinition object as defined in the render extension specification.
@@ -738,9 +738,9 @@
*
* @param node the XMLNode object reference that describes the ListOfColorDefinitions
* object to be instantiated.
---- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/ColorDefinition.h
-+++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/ColorDefinition.h
-@@ -112,7 +112,7 @@ public:
+--- a/src/sbml/packages/render/sbml/ColorDefinition.h
++++ b/src/sbml/packages/render/sbml/ColorDefinition.h
+@@ -113,7 +113,7 @@ public:
* The XMLNode object has to contain a valid XML representation of a
* ColorDefinition object as defined in the render extension specification.
* This method is normally called when render information is read from a file and
@@ -749,7 +749,7 @@
*
*
* (FOR BACKWARD COMPATIBILITY)
-@@ -441,7 +441,7 @@ public:
+@@ -442,7 +442,7 @@ public:
* The XMLNode object has to contain a valid XML representation of a
* ListOfColorDefinitions object as defined in the render extension specification.
* This method is normally called when render information is read from a file and
@@ -758,8 +758,8 @@
*
* @param node the XMLNode object reference that describes the ListOfColorDefinitions
* object to be instantiated.
---- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/Ellipse.cpp
-+++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/Ellipse.cpp
+--- a/src/sbml/packages/render/sbml/Ellipse.cpp
++++ b/src/sbml/packages/render/sbml/Ellipse.cpp
@@ -93,7 +93,7 @@ Ellipse::Ellipse (RenderPkgNamespaces* r
* The XMLNode object has to contain a valid XML representation of a
* RadialGradient object as defined in the render extension specification.
@@ -769,8 +769,8 @@
*
* @param node the XMLNode object reference that describes the RadialGradient
* object to be instantiated.
---- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/Ellipse.h
-+++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/Ellipse.h
+--- a/src/sbml/packages/render/sbml/Ellipse.h
++++ b/src/sbml/packages/render/sbml/Ellipse.h
@@ -97,7 +97,7 @@ public:
* The XMLNode object has to contain a valid XML representation of a
* RadialGradient object as defined in the render extension specification.
@@ -780,8 +780,8 @@
*
* @param node the XMLNode object reference that describes the RadialGradient
* object to be instantiated.
---- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/GlobalStyle.cpp
-+++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/GlobalStyle.cpp
+--- a/src/sbml/packages/render/sbml/GlobalStyle.cpp
++++ b/src/sbml/packages/render/sbml/GlobalStyle.cpp
@@ -88,7 +88,7 @@ GlobalStyle::GlobalStyle (RenderPkgNames
* The XMLNode object has to contain a valid XML representation of a
* GlobalStyle object as defined in the render extension specification.
@@ -800,9 +800,9 @@
*
* @param node the XMLNode object reference that describes the ListOfGlobalStyles
* object to be instantiated.
---- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/GlobalStyle.h
-+++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/GlobalStyle.h
-@@ -92,7 +92,7 @@ public:
+--- a/src/sbml/packages/render/sbml/GlobalStyle.h
++++ b/src/sbml/packages/render/sbml/GlobalStyle.h
+@@ -93,7 +93,7 @@ public:
* The XMLNode object has to contain a valid XML representation of a
* GlobalStyle object as defined in the render extension specification.
* This method is normally called when render information is read from a file and
@@ -811,7 +811,7 @@
*
* @param node the XMLNode object reference that describes the GlobalStyle
* object to be instantiated.
-@@ -182,7 +182,7 @@ class LIBSBML_EXTERN ListOfGlobalStyles
+@@ -183,7 +183,7 @@ class LIBSBML_EXTERN ListOfGlobalStyles
* The XMLNode object has to contain a valid XML representation of a
* ListOfGlobalStyles object as defined in the render extension specification.
* This method is normally called when render information is read from a file and
@@ -820,8 +820,8 @@
*
* @param node the XMLNode object reference that describes the ListOfGlobalStyles
* object to be instantiated.
---- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/GradientBase.cpp
-+++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/GradientBase.cpp
+--- a/src/sbml/packages/render/sbml/GradientBase.cpp
++++ b/src/sbml/packages/render/sbml/GradientBase.cpp
@@ -108,7 +108,7 @@ GradientBase::GradientBase (RenderPkgNam
* The XMLNode object has to contain a valid XML representation of a
* GradientBase object as defined in the render extension specification.
@@ -840,8 +840,8 @@
*
* @param node the XMLNode object reference that describes the ListOfGradientDefinitions
* object to be instantiated.
---- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/GradientBase.h
-+++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/GradientBase.h
+--- a/src/sbml/packages/render/sbml/GradientBase.h
++++ b/src/sbml/packages/render/sbml/GradientBase.h
@@ -117,7 +117,7 @@ protected:
* The XMLNode object has to contain a valid XML representation of a
* GradientBase object as defined in the render extension specification.
@@ -860,8 +860,8 @@
*
* @param node the XMLNode object reference that describes the ListOfGradientDefinitions
* object to be instantiated.
---- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/GradientStop.cpp
-+++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/GradientStop.cpp
+--- a/src/sbml/packages/render/sbml/GradientStop.cpp
++++ b/src/sbml/packages/render/sbml/GradientStop.cpp
@@ -134,7 +134,7 @@ ListOfGradientStops::ListOfGradientStops
* The XMLNode object has to contain a valid XML representation of a
* ListOfGradientStops object as defined in the render extension specification.
@@ -880,9 +880,9 @@
*
* @param node the XMLNode object reference that describes the GradientStop
* object to be instantiated.
---- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/GradientStop.h
-+++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/GradientStop.h
-@@ -120,7 +120,7 @@ public:
+--- a/src/sbml/packages/render/sbml/GradientStop.h
++++ b/src/sbml/packages/render/sbml/GradientStop.h
+@@ -118,7 +118,7 @@ public:
* The XMLNode object has to contain a valid XML representation of a
* GradientStop object as defined in the render extension specification.
* This method is normally called when render information is read from a file and
@@ -891,7 +891,7 @@
*
* @param node the XMLNode object reference that describes the GradientStop
* object to be instantiated.
-@@ -326,7 +326,7 @@ public:
+@@ -324,7 +324,7 @@ public:
* The XMLNode object has to contain a valid XML representation of a
* ListOfGradientStops object as defined in the render extension specification.
* This method is normally called when render information is read from a file and
@@ -900,8 +900,8 @@
*
* @param node the XMLNode object reference that describes the ListOfGradientStops
* object to be instantiated.
---- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/GraphicalPrimitive1D.cpp
-+++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/GraphicalPrimitive1D.cpp
+--- a/src/sbml/packages/render/sbml/GraphicalPrimitive1D.cpp
++++ b/src/sbml/packages/render/sbml/GraphicalPrimitive1D.cpp
@@ -113,7 +113,7 @@ GraphicalPrimitive1D::~GraphicalPrimitiv
* The XMLNode object has to contain a valid XML representation of a
* GraphicalPrimitive1D object as defined in the render extension specification.
@@ -911,9 +911,9 @@
*
* @param node the XMLNode object reference that describes the GraphicalPrimitive1D
* object to be instantiated.
---- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/GraphicalPrimitive1D.h
-+++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/GraphicalPrimitive1D.h
-@@ -101,7 +101,7 @@ public:
+--- a/src/sbml/packages/render/sbml/GraphicalPrimitive1D.h
++++ b/src/sbml/packages/render/sbml/GraphicalPrimitive1D.h
+@@ -102,7 +102,7 @@ public:
* The XMLNode object has to contain a valid XML representation of a
* GraphicalPrimitive1D object as defined in the render extension specification.
* This method is normally called when render information is read from a file and
@@ -922,8 +922,8 @@
*
* @param node the XMLNode object reference that describes the GraphicalPrimitive1D
* object to be instantiated.
---- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/GraphicalPrimitive2D.cpp
-+++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/GraphicalPrimitive2D.cpp
+--- a/src/sbml/packages/render/sbml/GraphicalPrimitive2D.cpp
++++ b/src/sbml/packages/render/sbml/GraphicalPrimitive2D.cpp
@@ -83,7 +83,7 @@ GraphicalPrimitive2D::GraphicalPrimitive
* The XMLNode object has to contain a valid XML representation of a
* GraphicalPrimitive2D object as defined in the render extension specification.
@@ -951,9 +951,9 @@
// we have to write it because otherwise
// it is assumed to be inherited.
att.add("fill-rule","nonzero");
---- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/GraphicalPrimitive2D.h
-+++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/GraphicalPrimitive2D.h
-@@ -102,7 +102,7 @@ public:
+--- a/src/sbml/packages/render/sbml/GraphicalPrimitive2D.h
++++ b/src/sbml/packages/render/sbml/GraphicalPrimitive2D.h
+@@ -103,7 +103,7 @@ public:
* The XMLNode object has to contain a valid XML representation of a
* GraphicalPrimitive2D object as defined in the render extension specification.
* This method is normally called when render information is read from a file and
@@ -962,8 +962,8 @@
*
* @param node the XMLNode object reference that describes the GraphicalPrimitive2D
* object to be instantiated.
---- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/Image.cpp
-+++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/Image.cpp
+--- a/src/sbml/packages/render/sbml/Image.cpp
++++ b/src/sbml/packages/render/sbml/Image.cpp
@@ -104,7 +104,7 @@ Image::Image (RenderPkgNamespaces* rende
* The XMLNode object has to contain a valid XML representation of a
* Image object as defined in the render extension specification.
@@ -1009,9 +1009,9 @@
* or a combination of both.
*
* @param z z coordinate of the image position
---- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/Image.h
-+++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/Image.h
-@@ -103,7 +103,7 @@ public:
+--- a/src/sbml/packages/render/sbml/Image.h
++++ b/src/sbml/packages/render/sbml/Image.h
+@@ -104,7 +104,7 @@ public:
* The XMLNode object has to contain a valid XML representation of a
* Image object as defined in the render extension specification.
* This method is normally called when render information is read from a file and
@@ -1020,7 +1020,7 @@
*
* @param node the XMLNode object reference that describes the Image
* object to be instantiated.
-@@ -135,7 +135,7 @@ public:
+@@ -136,7 +136,7 @@ public:
/**
* Sets the position of the image relative to its viewport.
@@ -1029,7 +1029,7 @@
* or a combination of both.
* The z coordinatee can be omitted. In that case it is set to 0.
*
-@@ -147,7 +147,7 @@ public:
+@@ -148,7 +148,7 @@ public:
/**
* Sets the x coordinate of the image position.
@@ -1038,7 +1038,7 @@
* or a combination of both.
*
* @param x x coordinate of the image position
-@@ -156,7 +156,7 @@ public:
+@@ -157,7 +157,7 @@ public:
/**
* Sets the y coordinate of the image position.
@@ -1047,7 +1047,7 @@
* or a combination of both.
*
* @param y y coordinate of the image position
-@@ -165,7 +165,7 @@ public:
+@@ -166,7 +166,7 @@ public:
/**
* Sets the z coordinate of the image position.
@@ -1056,8 +1056,8 @@
* or a combination of both.
*
* @param z z coordinate of the image position
---- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/LineEnding.cpp
-+++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/LineEnding.cpp
+--- a/src/sbml/packages/render/sbml/LineEnding.cpp
++++ b/src/sbml/packages/render/sbml/LineEnding.cpp
@@ -133,7 +133,7 @@ LineEnding::getAllElements(ElementFilter
* The XMLNode object has to contain a valid XML representation of a
* ListOfLineEndings object as defined in the render extension specification.
@@ -1076,9 +1076,9 @@
*
* @param node the XMLNode object reference that describes the LineEnding
* object to be instantiated.
---- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/LineEnding.h
-+++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/LineEnding.h
-@@ -111,7 +111,7 @@ public:
+--- a/src/sbml/packages/render/sbml/LineEnding.h
++++ b/src/sbml/packages/render/sbml/LineEnding.h
+@@ -112,7 +112,7 @@ public:
* The XMLNode object has to contain a valid XML representation of a
* LineEnding object as defined in the render extension specification.
* This method is normally called when render information is read from a file and
@@ -1087,7 +1087,7 @@
*
* @param node the XMLNode object reference that describes the LineEnding
* object to be instantiated.
-@@ -466,7 +466,7 @@ public:
+@@ -467,7 +467,7 @@ public:
* The XMLNode object has to contain a valid XML representation of a
* ListOfLineEndings object as defined in the render extension specification.
* This method is normally called when render information is read from a file and
@@ -1096,8 +1096,8 @@
*
* @param node the XMLNode object reference that describes the ListOfLineEndings
* object to be instantiated.
---- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/LinearGradient.cpp
-+++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/LinearGradient.cpp
+--- a/src/sbml/packages/render/sbml/LinearGradient.cpp
++++ b/src/sbml/packages/render/sbml/LinearGradient.cpp
@@ -102,7 +102,7 @@ LinearGradient::LinearGradient (RenderPk
* The XMLNode object has to contain a valid XML representation of a
* LinearGradient object as defined in the render extension specification.
@@ -1107,9 +1107,9 @@
*
* @param node the XMLNode object reference that describes the LinearGradient
* object to be instantiated.
---- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/LinearGradient.h
-+++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/LinearGradient.h
-@@ -99,7 +99,7 @@ public:
+--- a/src/sbml/packages/render/sbml/LinearGradient.h
++++ b/src/sbml/packages/render/sbml/LinearGradient.h
+@@ -100,7 +100,7 @@ public:
* The XMLNode object has to contain a valid XML representation of a
* LinearGradient object as defined in the render extension specification.
* This method is normally called when render information is read from a file and
@@ -1118,8 +1118,8 @@
*
* @param node the XMLNode object reference that describes the LinearGradient
* object to be instantiated.
---- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/ListOfCurveElements.cpp
-+++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/ListOfCurveElements.cpp
+--- a/src/sbml/packages/render/sbml/ListOfCurveElements.cpp
++++ b/src/sbml/packages/render/sbml/ListOfCurveElements.cpp
@@ -51,7 +51,7 @@ const std::string ListOfCurveElements::E
* The XMLNode object has to contain a valid XML representation of a
* ListOfCurveElements object as defined in the render extension specification.
@@ -1129,9 +1129,9 @@
*
* @param node the XMLNode object reference that describes the ListOfCurveElements
* object to be instantiated.
---- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/ListOfCurveElements.h
-+++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/ListOfCurveElements.h
-@@ -60,7 +60,7 @@ public:
+--- a/src/sbml/packages/render/sbml/ListOfCurveElements.h
++++ b/src/sbml/packages/render/sbml/ListOfCurveElements.h
+@@ -61,7 +61,7 @@ public:
* The XMLNode object has to contain a valid XML representation of a
* ListOfCurveElements object as defined in the render extension specification.
* This method is normally called when render information is read from a file and
@@ -1140,9 +1140,9 @@
*
* @param node the XMLNode object reference that describes the ListOfCurveElements
* object to be instantiated.
---- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/LocalRenderInformation.h
-+++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/LocalRenderInformation.h
-@@ -397,7 +397,7 @@ public:
+--- a/src/sbml/packages/render/sbml/LocalRenderInformation.h
++++ b/src/sbml/packages/render/sbml/LocalRenderInformation.h
+@@ -398,7 +398,7 @@ public:
* The XMLNode object has to contain a valid XML representation of a
* ListOfLocalRenderInformation object as defined in the render extension specification.
* This method is normally called when render information is read from a file and
@@ -1151,8 +1151,8 @@
*
* @param node the XMLNode object reference that describes the ListOfLocalRenderInformation
* object to be instantiated.
---- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/LocalStyle.cpp
-+++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/LocalStyle.cpp
+--- a/src/sbml/packages/render/sbml/LocalStyle.cpp
++++ b/src/sbml/packages/render/sbml/LocalStyle.cpp
@@ -96,7 +96,7 @@ LocalStyle::LocalStyle (RenderPkgNamespa
* The XMLNode object has to contain a valid XML representation of a
* LocalStyle object as defined in the render extension specification.
@@ -1171,8 +1171,8 @@
*
* @param node the XMLNode object reference that describes the ListOfLocalStyles
* object to be instantiated.
---- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/LocalStyle.h
-+++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/LocalStyle.h
+--- a/src/sbml/packages/render/sbml/LocalStyle.h
++++ b/src/sbml/packages/render/sbml/LocalStyle.h
@@ -99,7 +99,7 @@ public:
* The XMLNode object has to contain a valid XML representation of a
* LocalStyle object as defined in the render extension specification.
@@ -1191,8 +1191,8 @@
*
* @param node the XMLNode object reference that describes the ListOfLocalStyles
* object to be instantiated.
---- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/Polygon.cpp
-+++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/Polygon.cpp
+--- a/src/sbml/packages/render/sbml/Polygon.cpp
++++ b/src/sbml/packages/render/sbml/Polygon.cpp
@@ -100,7 +100,7 @@ Polygon::Polygon (RenderPkgNamespaces* r
* The XMLNode object has to contain a valid XML representation of a
* Polygon object as defined in the render extension specification.
@@ -1202,9 +1202,9 @@
*
* @param node the XMLNode object reference that describes the Polygon
* object to be instantiated.
---- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/Polygon.h
-+++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/Polygon.h
-@@ -96,7 +96,7 @@ public:
+--- a/src/sbml/packages/render/sbml/Polygon.h
++++ b/src/sbml/packages/render/sbml/Polygon.h
+@@ -97,7 +97,7 @@ public:
* The XMLNode object has to contain a valid XML representation of a
* Polygon object as defined in the render extension specification.
* This method is normally called when render information is read from a file and
@@ -1213,8 +1213,8 @@
*
* @param node the XMLNode object reference that describes the Polygon
* object to be instantiated.
---- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/RadialGradient.cpp
-+++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/RadialGradient.cpp
+--- a/src/sbml/packages/render/sbml/RadialGradient.cpp
++++ b/src/sbml/packages/render/sbml/RadialGradient.cpp
@@ -108,7 +108,7 @@ RadialGradient::RadialGradient (RenderPk
* The XMLNode object has to contain a valid XML representation of a
* RadialGradient object as defined in the render extension specification.
@@ -1224,9 +1224,9 @@
*
* @param node the XMLNode object reference that describes the RadialGradient
* object to be instantiated.
---- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/RadialGradient.h
-+++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/RadialGradient.h
-@@ -103,7 +103,7 @@ public:
+--- a/src/sbml/packages/render/sbml/RadialGradient.h
++++ b/src/sbml/packages/render/sbml/RadialGradient.h
+@@ -104,7 +104,7 @@ public:
* The XMLNode object has to contain a valid XML representation of a
* RadialGradient object as defined in the render extension specification.
* This method is normally called when render information is read from a file and
@@ -1235,8 +1235,8 @@
*
* @param node the XMLNode object reference that describes the RadialGradient
* object to be instantiated.
---- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/Rectangle.cpp
-+++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/Rectangle.cpp
+--- a/src/sbml/packages/render/sbml/Rectangle.cpp
++++ b/src/sbml/packages/render/sbml/Rectangle.cpp
@@ -106,7 +106,7 @@ Rectangle::Rectangle (RenderPkgNamespace
* The XMLNode object has to contain a valid XML representation of a
* Rectangle object as defined in the render extension specification.
@@ -1246,9 +1246,9 @@
*
* @param node the XMLNode object reference that describes the Rectangle
* object to be instantiated.
---- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/Rectangle.h
-+++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/Rectangle.h
-@@ -84,7 +84,7 @@ public:
+--- a/src/sbml/packages/render/sbml/Rectangle.h
++++ b/src/sbml/packages/render/sbml/Rectangle.h
+@@ -86,7 +86,7 @@ public:
* The XMLNode object has to contain a valid XML representation of a
* Rectangle object as defined in the render extension specification.
* This method is normally called when render information is read from a file and
@@ -1257,8 +1257,8 @@
*
* @param node the XMLNode object reference that describes the Rectangle
* object to be instantiated.
---- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/RenderCubicBezier.cpp
-+++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/RenderCubicBezier.cpp
+--- a/src/sbml/packages/render/sbml/RenderCubicBezier.cpp
++++ b/src/sbml/packages/render/sbml/RenderCubicBezier.cpp
@@ -192,7 +192,7 @@ bool RenderCubicBezier::operator==(const
* The XMLNode object has to contain a valid XML representation of a
* RenderCubicBezier object as defined in the render extension specification.
@@ -1268,8 +1268,8 @@
*
* @param node the XMLNode object reference that describes the RenderCubicBezier
* object to be instantiated.
---- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/RenderCubicBezier.h
-+++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/RenderCubicBezier.h
+--- a/src/sbml/packages/render/sbml/RenderCubicBezier.h
++++ b/src/sbml/packages/render/sbml/RenderCubicBezier.h
@@ -141,7 +141,7 @@ public:
* The XMLNode object has to contain a valid XML representation of a
* RenderCubicBezier object as defined in the render extension specification.
@@ -1279,8 +1279,8 @@
*
* @param node the XMLNode object reference that describes the RenderCubicBezier
* object to be instantiated.
---- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/RenderCurve.cpp
-+++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/RenderCurve.cpp
+--- a/src/sbml/packages/render/sbml/RenderCurve.cpp
++++ b/src/sbml/packages/render/sbml/RenderCurve.cpp
@@ -112,7 +112,7 @@ RenderCurve::RenderCurve (RenderPkgNames
* The XMLNode object has to contain a valid XML representation of a
* RenderCurve object as defined in the render extension specification.
@@ -1290,9 +1290,9 @@
*
* @param node the XMLNode object reference that describes the RenderCurve
* object to be instantiated.
---- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/RenderCurve.h
-+++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/RenderCurve.h
-@@ -100,7 +100,7 @@ public:
+--- a/src/sbml/packages/render/sbml/RenderCurve.h
++++ b/src/sbml/packages/render/sbml/RenderCurve.h
+@@ -101,7 +101,7 @@ public:
* The XMLNode object has to contain a valid XML representation of a
* RenderCurve object as defined in the render extension specification.
* This method is normally called when render information is read from a file and
@@ -1301,8 +1301,8 @@
*
* @param node the XMLNode object reference that describes the RenderCurve
* object to be instantiated.
---- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/RenderGroup.cpp
-+++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/RenderGroup.cpp
+--- a/src/sbml/packages/render/sbml/RenderGroup.cpp
++++ b/src/sbml/packages/render/sbml/RenderGroup.cpp
@@ -258,7 +258,7 @@ void RenderGroup::readAttributes (const
* The XMLNode object has to contain a valid XML representation of a
* RenderGroup object as defined in the render extension specification.
@@ -1312,9 +1312,9 @@
*
* @param node the XMLNode object reference that describes the RenderGroup
* object to be instantiated.
---- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/RenderGroup.h
-+++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/RenderGroup.h
-@@ -294,7 +294,7 @@ public:
+--- a/src/sbml/packages/render/sbml/RenderGroup.h
++++ b/src/sbml/packages/render/sbml/RenderGroup.h
+@@ -295,7 +295,7 @@ public:
* The XMLNode object has to contain a valid XML representation of a
* RenderGroup object as defined in the render extension specification.
* This method is normally called when render information is read from a file and
@@ -1323,8 +1323,8 @@
*
* @param node the XMLNode object reference that describes the RenderGroup
* object to be instantiated.
---- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/RenderInformationBase.cpp
-+++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/RenderInformationBase.cpp
+--- a/src/sbml/packages/render/sbml/RenderInformationBase.cpp
++++ b/src/sbml/packages/render/sbml/RenderInformationBase.cpp
@@ -307,9 +307,9 @@ void RenderInformationBase::setProgramVe
* Global render information objects can only reference other global
* render information objects, local render information objects can reference other local
@@ -1350,8 +1350,8 @@
*/
void RenderInformationBase::setReferenceRenderInformationId(const std::string& id)
{
---- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/RenderInformationBase.h
-+++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/RenderInformationBase.h
+--- a/src/sbml/packages/render/sbml/RenderInformationBase.h
++++ b/src/sbml/packages/render/sbml/RenderInformationBase.h
@@ -195,18 +195,18 @@ public:
* Global render information objects can only reference other global
* render information objects, local render information objects can reference other local
@@ -1375,8 +1375,8 @@
*/
void setReferenceRenderInformationId(const std::string& id);
---- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/RenderPoint.cpp
-+++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/RenderPoint.cpp
+--- a/src/sbml/packages/render/sbml/RenderPoint.cpp
++++ b/src/sbml/packages/render/sbml/RenderPoint.cpp
@@ -185,7 +185,7 @@ void RenderPoint::initDefaults ()
* The XMLNode object has to contain a valid XML representation of a
* RenderPoint object as defined in the render extension specification.
@@ -1386,9 +1386,9 @@
*
* @param node the XMLNode object reference that describes the RenderPoint
* object to be instantiated.
---- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/RenderPoint.h
-+++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/RenderPoint.h
-@@ -109,7 +109,7 @@ public:
+--- a/src/sbml/packages/render/sbml/RenderPoint.h
++++ b/src/sbml/packages/render/sbml/RenderPoint.h
+@@ -110,7 +110,7 @@ public:
* The XMLNode object has to contain a valid XML representation of a
* RenderPoint object as defined in the render extension specification.
* This method is normally called when render information is read from a file and
@@ -1397,8 +1397,8 @@
*
* @param node the XMLNode object reference that describes the RenderPoint
* object to be instantiated.
---- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/Style.cpp
-+++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/Style.cpp
+--- a/src/sbml/packages/render/sbml/Style.cpp
++++ b/src/sbml/packages/render/sbml/Style.cpp
@@ -553,7 +553,7 @@ const std::string& Style::getElementName
* The XMLNode object has to contain a valid XML representation of a
* Style object as defined in the render extension specification.
@@ -1408,9 +1408,9 @@
*
* @param node the XMLNode object reference that describes the Style
* object to be instantiated.
---- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/Style.h
-+++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/Style.h
-@@ -95,7 +95,7 @@ protected:
+--- a/src/sbml/packages/render/sbml/Style.h
++++ b/src/sbml/packages/render/sbml/Style.h
+@@ -96,7 +96,7 @@ protected:
* The XMLNode object has to contain a valid XML representation of a
* Style object as defined in the render extension specification.
* This method is normally called when render information is read from a file and
@@ -1419,8 +1419,8 @@
*
* @param node the XMLNode object reference that describes the Style
* object to be instantiated.
---- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/Text.cpp
-+++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/Text.cpp
+--- a/src/sbml/packages/render/sbml/Text.cpp
++++ b/src/sbml/packages/render/sbml/Text.cpp
@@ -115,7 +115,7 @@ Text::Text (RenderPkgNamespaces* rendern
* The XMLNode object has to contain a valid XML representation of a
* Text object as defined in the render extension specification.
@@ -1430,9 +1430,9 @@
*
* @param node the XMLNode object reference that describes the Text
* object to be instantiated.
---- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/Text.h
-+++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/Text.h
-@@ -128,7 +128,7 @@ public:
+--- a/src/sbml/packages/render/sbml/Text.h
++++ b/src/sbml/packages/render/sbml/Text.h
+@@ -129,7 +129,7 @@ public:
* The XMLNode object has to contain a valid XML representation of a
* Text object as defined in the render extension specification.
* This method is normally called when render information is read from a file and
@@ -1441,8 +1441,8 @@
*
* @param node the XMLNode object reference that describes the Text
* object to be instantiated.
---- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/Transformation.cpp
-+++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/Transformation.cpp
+--- a/src/sbml/packages/render/sbml/Transformation.cpp
++++ b/src/sbml/packages/render/sbml/Transformation.cpp
@@ -113,7 +113,7 @@ Transformation::~Transformation ()
* The XMLNode object has to contain a valid XML representation of a
* Transformation object as defined in the render extension specification.
@@ -1452,9 +1452,9 @@
*
* @param node the XMLNode object reference that describes the Transformation
* object to be instantiated.
---- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/Transformation.h
-+++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/Transformation.h
-@@ -65,7 +65,7 @@ protected:
+--- a/src/sbml/packages/render/sbml/Transformation.h
++++ b/src/sbml/packages/render/sbml/Transformation.h
+@@ -66,7 +66,7 @@ protected:
* The XMLNode object has to contain a valid XML representation of a
* Transformation object as defined in the render extension specification.
* This method is normally called when render information is read from a file and
@@ -1463,8 +1463,8 @@
*
* @param node the XMLNode object reference that describes the Transformation
* object to be instantiated.
---- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/Transformation2D.cpp
-+++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/Transformation2D.cpp
+--- a/src/sbml/packages/render/sbml/Transformation2D.cpp
++++ b/src/sbml/packages/render/sbml/Transformation2D.cpp
@@ -132,7 +132,7 @@ Transformation2D::Transformation2D(Rende
* The XMLNode object has to contain a valid XML representation of a
* Transformation2D object as defined in the render extension specification.
@@ -1474,9 +1474,9 @@
*
* @param node the XMLNode object reference that describes the Transformation2D
* object to be instantiated.
---- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/Transformation2D.h
-+++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/Transformation2D.h
-@@ -99,7 +99,7 @@ public:
+--- a/src/sbml/packages/render/sbml/Transformation2D.h
++++ b/src/sbml/packages/render/sbml/Transformation2D.h
+@@ -100,7 +100,7 @@ public:
* The XMLNode object has to contain a valid XML representation of a
* Transformation2D object as defined in the render extension specification.
* This method is normally called when render information is read from a file and
Added: trunk/packages/libsbml/trunk/debian/patches/swig-3.x.patch
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/swig-3.x.patch (rev 0)
+++ trunk/packages/libsbml/trunk/debian/patches/swig-3.x.patch 2015-12-14 17:14:56 UTC (rev 20762)
@@ -0,0 +1,397 @@
+Author: Logan Rosen <logan at ubuntu.com>
+Date: Thu, 19 Nov 2015 20:12:02 UTC
+Bug-Debian: https://bugs.debian.org/805584
+Description: Build with with SWIG 3.x
+
+--- a/src/bindings/csharp/local.i
++++ b/src/bindings/csharp/local.i
+@@ -115,13 +115,13 @@ static SWIG_CSharpWStringHelperCallback
+ %pragma(csharp) imclasscode=%{
+ protected class SWIGWStringHelper {
+
+- public delegate IntPtr SWIGWStringDelegate(IntPtr message);
++ public delegate global::System.IntPtr SWIGWStringDelegate(global::System.IntPtr message);
+ static SWIGWStringDelegate wstringDelegate = new SWIGWStringDelegate(CreateWString);
+
+- [DllImport("$dllimport", EntryPoint="SWIGRegisterWStringCallback_$module")]
++ [global::System.Runtime.InteropServices.DllImport("$dllimport", EntryPoint="SWIGRegisterWStringCallback_$module")]
+ public static extern void SWIGRegisterWStringCallback_$module(SWIGWStringDelegate wstringDelegate);
+
+- static IntPtr CreateWString([MarshalAs(UnmanagedType.LPWStr)]IntPtr cString) {
++ static global::System.IntPtr CreateWString([MarshalAs(UnmanagedType.LPWStr)]global::System.IntPtr cString) {
+ string ustr = System.Runtime.InteropServices.Marshal.PtrToStringUni(cString);
+ return System.Runtime.InteropServices.Marshal.StringToHGlobalUni(ustr);
+ }
+@@ -201,15 +201,15 @@ SWIGEXPORT void SWIGSTDCALL SWIGRegister
+ */
+ %typemap(cscode) SBMLExtension
+ %{
+- public virtual SBasePlugin DowncastSBasePlugin(IntPtr cPtr, bool owner)
++ public virtual SBasePlugin DowncastSBasePlugin(global::System.IntPtr cPtr, bool owner)
+ {
+- if (cPtr.Equals(IntPtr.Zero)) return null;
++ if (cPtr.Equals(global::System.IntPtr.Zero)) return null;
+ return new SBasePlugin(cPtr, owner);
+ }
+
+- public virtual SBase DowncastSBase(IntPtr cPtr, bool owner)
++ public virtual SBase DowncastSBase(global::System.IntPtr cPtr, bool owner)
+ {
+- if (cPtr.Equals(IntPtr.Zero)) return null;
++ if (cPtr.Equals(global::System.IntPtr.Zero)) return null;
+ return new SBase(cPtr, owner);
+ }
+ %}
+@@ -222,9 +222,9 @@ SWIGEXPORT void SWIGSTDCALL SWIGRegister
+ %pragma(csharp) modulecode =
+ %{
+
+- public static SBMLExtension DowncastExtension(IntPtr cPtr, bool owner)
++ public static SBMLExtension DowncastExtension(global::System.IntPtr cPtr, bool owner)
+ {
+- if (cPtr.Equals(IntPtr.Zero)) return null;
++ if (cPtr.Equals(global::System.IntPtr.Zero)) return null;
+
+ SBMLExtension ext = new SBMLExtension(cPtr, false);
+ string pkgName = ext.getName();
+@@ -235,9 +235,9 @@ SWIGEXPORT void SWIGSTDCALL SWIGRegister
+ return new SBMLExtension(cPtr,owner);
+ }
+
+- public static SBMLNamespaces DowncastSBMLNamespaces(IntPtr cPtr, bool owner)
++ public static SBMLNamespaces DowncastSBMLNamespaces(global::System.IntPtr cPtr, bool owner)
+ {
+- if (cPtr.Equals(IntPtr.Zero)) return null;
++ if (cPtr.Equals(global::System.IntPtr.Zero)) return null;
+
+ SBMLNamespaces sbn = new SBMLNamespaces(cPtr, false);
+ if (sbn != null)
+@@ -287,9 +287,9 @@ SWIGEXPORT void SWIGSTDCALL SWIGRegister
+ return new SBMLConverter(cPtr,owner);
+ }
+
+- public static SBasePlugin DowncastSBasePlugin(IntPtr cPtr, bool owner)
++ public static SBasePlugin DowncastSBasePlugin(global::System.IntPtr cPtr, bool owner)
+ {
+- if (cPtr.Equals(IntPtr.Zero)) return null;
++ if (cPtr.Equals(global::System.IntPtr.Zero)) return null;
+
+ SBasePlugin sbp = new SBasePlugin(cPtr, false);
+ string pkgName = sbp.getPackageName();
+@@ -304,9 +304,9 @@ SWIGEXPORT void SWIGSTDCALL SWIGRegister
+ }
+
+
+- public static SBase DowncastSBase(IntPtr cPtr, bool owner)
++ public static SBase DowncastSBase(global::System.IntPtr cPtr, bool owner)
+ {
+- if (cPtr.Equals(IntPtr.Zero)) return null;
++ if (cPtr.Equals(global::System.IntPtr.Zero)) return null;
+
+ SBase sb = new SBase(cPtr, false);
+ string pkgName = sb.getPackageName();
+@@ -496,9 +496,9 @@ SWIGEXPORT void SWIGSTDCALL SWIGRegister
+
+ %pragma(csharp) modulecode =
+ %{
+- public static ASTBase DowncastASTBase(IntPtr cPtr, bool owner)
++ public static ASTBase DowncastASTBase(global::System.IntPtr cPtr, bool owner)
+ {
+- if (cPtr.Equals(IntPtr.Zero)) return null;
++ if (cPtr.Equals(global::System.IntPtr.Zero)) return null;
+
+ ASTBase ab = new ASTBase(cPtr,false);
+ switch( ab.getTypeCode() )
+@@ -661,23 +661,23 @@ SWIGEXPORT void SWIGSTDCALL SWIGRegister
+
+ %typemap(csbody) TYPENAME
+ %{
+- private HandleRef swigCPtr;
++ private global::System.Runtime.InteropServices.HandleRef swigCPtr;
+ protected bool swigCMemOwn;
+
+- CTOR_ATTRIB $csclassname(IntPtr cPtr, bool cMemoryOwn)
++ CTOR_ATTRIB $csclassname(global::System.IntPtr cPtr, bool cMemoryOwn)
+ {
+ swigCMemOwn = cMemoryOwn;
+- swigCPtr = new HandleRef(this, cPtr);
++ swigCPtr = new global::System.Runtime.InteropServices.HandleRef(this, cPtr);
+ }
+
+- GETCPTR_ATTRIB static HandleRef getCPtr($csclassname obj)
++ GETCPTR_ATTRIB static global::System.Runtime.InteropServices.HandleRef getCPtr($csclassname obj)
+ {
+- return (obj == null) ? new HandleRef(null, IntPtr.Zero) : obj.swigCPtr;
++ return (obj == null) ? new global::System.Runtime.InteropServices.HandleRef(null, global::System.IntPtr.Zero) : obj.swigCPtr;
+ }
+
+- GETCPTR_ATTRIB static HandleRef getCPtrAndDisown ($csclassname obj)
++ GETCPTR_ATTRIB static global::System.Runtime.InteropServices.HandleRef getCPtrAndDisown ($csclassname obj)
+ {
+- HandleRef ptr = new HandleRef(null, IntPtr.Zero);
++ global::System.Runtime.InteropServices.HandleRef ptr = new global::System.Runtime.InteropServices.HandleRef(null, global::System.IntPtr.Zero);
+
+ if (obj != null)
+ {
+@@ -694,22 +694,22 @@ SWIGEXPORT void SWIGSTDCALL SWIGRegister
+
+ %typemap(csbody_derived) TYPENAME
+ %{
+- private HandleRef swigCPtr;
++ private global::System.Runtime.InteropServices.HandleRef swigCPtr;
+
+- CTOR_ATTRIB $csclassname(IntPtr cPtr, bool cMemoryOwn) : base($modulePINVOKE.$csclassname_SWIGUpcast(cPtr), cMemoryOwn)
++ CTOR_ATTRIB $csclassname(global::System.IntPtr cPtr, bool cMemoryOwn) : base($modulePINVOKE.$csclassname_SWIGUpcast(cPtr), cMemoryOwn)
+ {
+ //super($modulePINVOKE.$csclassnameUpcast(cPtr), cMemoryOwn);
+- swigCPtr = new HandleRef(this, cPtr);
++ swigCPtr = new global::System.Runtime.InteropServices.HandleRef(this, cPtr);
+ }
+
+- GETCPTR_ATTRIB static HandleRef getCPtr($csclassname obj)
++ GETCPTR_ATTRIB static global::System.Runtime.InteropServices.HandleRef getCPtr($csclassname obj)
+ {
+- return (obj == null) ? new HandleRef(null, IntPtr.Zero) : obj.swigCPtr;
++ return (obj == null) ? new global::System.Runtime.InteropServices.HandleRef(null, global::System.IntPtr.Zero) : obj.swigCPtr;
+ }
+
+- GETCPTR_ATTRIB static HandleRef getCPtrAndDisown ($csclassname obj)
++ GETCPTR_ATTRIB static global::System.Runtime.InteropServices.HandleRef getCPtrAndDisown ($csclassname obj)
+ {
+- HandleRef ptr = new HandleRef(null, IntPtr.Zero);
++ global::System.Runtime.InteropServices.HandleRef ptr = new global::System.Runtime.InteropServices.HandleRef(null, global::System.IntPtr.Zero);
+
+ if (obj != null)
+ {
+@@ -725,22 +725,22 @@ SWIGEXPORT void SWIGSTDCALL SWIGRegister
+
+ %typemap(csbody_derived) TYPENAME
+ %{
+- private HandleRef swigCPtr;
++ private global::System.Runtime.InteropServices.HandleRef swigCPtr;
+
+- CTOR_ATTRIB $csclassname(IntPtr cPtr, bool cMemoryOwn) : base($modulePINVOKE.$csclassnameUpcast(cPtr), cMemoryOwn)
++ CTOR_ATTRIB $csclassname(global::System.IntPtr cPtr, bool cMemoryOwn) : base($modulePINVOKE.$csclassnameUpcast(cPtr), cMemoryOwn)
+ {
+ //super($modulePINVOKE.$csclassnameUpcast(cPtr), cMemoryOwn);
+- swigCPtr = new HandleRef(this, cPtr);
++ swigCPtr = new global::System.Runtime.InteropServices.HandleRef(this, cPtr);
+ }
+
+- GETCPTR_ATTRIB static HandleRef getCPtr($csclassname obj)
++ GETCPTR_ATTRIB static global::System.Runtime.InteropServices.HandleRef getCPtr($csclassname obj)
+ {
+- return (obj == null) ? new HandleRef(null, IntPtr.Zero) : obj.swigCPtr;
++ return (obj == null) ? new global::System.Runtime.InteropServices.HandleRef(null, global::System.IntPtr.Zero) : obj.swigCPtr;
+ }
+
+- GETCPTR_ATTRIB static HandleRef getCPtrAndDisown ($csclassname obj)
++ GETCPTR_ATTRIB static global::System.Runtime.InteropServices.HandleRef getCPtrAndDisown ($csclassname obj)
+ {
+- HandleRef ptr = new HandleRef(null, IntPtr.Zero);
++ global::System.Runtime.InteropServices.HandleRef ptr = new global::System.Runtime.InteropServices.HandleRef(null, global::System.IntPtr.Zero);
+
+ if (obj != null)
+ {
+@@ -1005,10 +1005,10 @@ COVARIANT_GETID(InitialAssignment)
+ %typemap(csbase) SBMLConstructorException "System.ArgumentException";
+ %typemap(cscode) SBMLConstructorException
+ %{
+- internal SBMLConstructorException(IntPtr cPtr, bool cMemoryOwn, string v) : base(v)
++ internal SBMLConstructorException(global::System.IntPtr cPtr, bool cMemoryOwn, string v) : base(v)
+ {
+ swigCMemOwn = cMemoryOwn;
+- swigCPtr = new HandleRef(this, cPtr);
++ swigCPtr = new global::System.Runtime.InteropServices.HandleRef(this, cPtr);
+ }
+
+ public SBMLConstructorException(string v) :
+@@ -1019,10 +1019,10 @@ COVARIANT_GETID(InitialAssignment)
+ %typemap(csbase) XMLConstructorException "System.ArgumentException";
+ %typemap(cscode) XMLConstructorException
+ %{
+- internal XMLConstructorException(IntPtr cPtr, bool cMemoryOwn, string v) : base(v)
++ internal XMLConstructorException(global::System.IntPtr cPtr, bool cMemoryOwn, string v) : base(v)
+ {
+ swigCMemOwn = cMemoryOwn;
+- swigCPtr = new HandleRef(this, cPtr);
++ swigCPtr = new global::System.Runtime.InteropServices.HandleRef(this, cPtr);
+ }
+
+ public XMLConstructorException(string v) :
+@@ -1061,7 +1061,7 @@ COVARIANT_GETID(InitialAssignment)
+ static CustomExceptionDelegate customDelegate =
+ new CustomExceptionDelegate(SetPendingCustomException);
+
+- [DllImport("$dllimport", EntryPoint="CustomExceptionRegisterCallback")]
++ [global::System.Runtime.InteropServices.DllImport("$dllimport", EntryPoint="CustomExceptionRegisterCallback")]
+ public static extern
+ void CustomExceptionRegisterCallback(CustomExceptionDelegate customCallback);
+
+@@ -1409,8 +1409,8 @@ XMLCONSTRUCTOR_EXCEPTION(XMLTripple)
+ %typemap(cstype) List* _FNAME_ %{ _TYPENAME_ ## List %}
+ %typemap(csout) List* _FNAME_
+ {
+- IntPtr cPtr = $imcall;
+- return (cPtr == IntPtr.Zero) ? null : new _TYPENAME_ ## List(cPtr, true);
++ global::System.IntPtr cPtr = $imcall;
++ return (cPtr == global::System.IntPtr.Zero) ? null : new _TYPENAME_ ## List(cPtr, true);
+ }
+ %typemap(out) List* _FNAME_
+ {
+--- a/src/bindings/csharp/local-packages-arrays.i
++++ b/src/bindings/csharp/local-packages-arrays.i
+@@ -30,9 +30,9 @@
+ */
+ %typemap(cscode) ArraysExtension
+ %{
+- public override SBasePlugin DowncastSBasePlugin(IntPtr cPtr, bool owner)
++ public override SBasePlugin DowncastSBasePlugin(global::System.IntPtr cPtr, bool owner)
+ {
+- if (cPtr.Equals(IntPtr.Zero)) return null;
++ if (cPtr.Equals(global::System.IntPtr.Zero)) return null;
+
+ SBasePlugin sbp = new SBasePlugin(cPtr, false);
+ SBase sb = sbp.getParentSBMLObject();
+@@ -44,9 +44,9 @@
+ }
+ }
+
+- public override SBase DowncastSBase(IntPtr cPtr, bool owner)
++ public override SBase DowncastSBase(global::System.IntPtr cPtr, bool owner)
+ {
+- if (cPtr.Equals(IntPtr.Zero)) return null;
++ if (cPtr.Equals(global::System.IntPtr.Zero)) return null;
+
+ SBase sb = new SBase(cPtr, false);
+ switch( sb.getTypeCode() )
+--- a/src/bindings/csharp/local-packages-groups.i
++++ b/src/bindings/csharp/local-packages-groups.i
+@@ -40,9 +40,9 @@
+ */
+ %typemap(cscode) GroupsExtension
+ %{
+- public override SBasePlugin DowncastSBasePlugin(IntPtr cPtr, bool owner)
++ public override SBasePlugin DowncastSBasePlugin(global::System.IntPtr cPtr, bool owner)
+ {
+- if (cPtr.Equals(IntPtr.Zero)) return null;
++ if (cPtr.Equals(global::System.IntPtr.Zero)) return null;
+
+ SBasePlugin sbp = new SBasePlugin(cPtr, false);
+ SBase sb = sbp.getParentSBMLObject();
+@@ -56,9 +56,9 @@
+ }
+ }
+
+- public override SBase DowncastSBase(IntPtr cPtr, bool owner)
++ public override SBase DowncastSBase(global::System.IntPtr cPtr, bool owner)
+ {
+- if (cPtr.Equals(IntPtr.Zero)) return null;
++ if (cPtr.Equals(global::System.IntPtr.Zero)) return null;
+
+ SBase sb = new SBase(cPtr, false);
+ switch( sb.getTypeCode() )
+--- a/src/bindings/csharp/local-packages-layout.i
++++ b/src/bindings/csharp/local-packages-layout.i
+@@ -33,9 +33,9 @@
+ */
+ %typemap(cscode) LayoutExtension
+ %{
+- public override SBasePlugin DowncastSBasePlugin(IntPtr cPtr, bool owner)
++ public override SBasePlugin DowncastSBasePlugin(global::System.IntPtr cPtr, bool owner)
+ {
+- if (cPtr.Equals(IntPtr.Zero)) return null;
++ if (cPtr.Equals(global::System.IntPtr.Zero)) return null;
+
+ SBasePlugin sbp = new SBasePlugin(cPtr, false);
+ SBase sb = sbp.getParentSBMLObject();
+@@ -52,9 +52,9 @@
+ }
+ }
+
+- public override SBase DowncastSBase(IntPtr cPtr, bool owner)
++ public override SBase DowncastSBase(global::System.IntPtr cPtr, bool owner)
+ {
+- if (cPtr.Equals(IntPtr.Zero)) return null;
++ if (cPtr.Equals(global::System.IntPtr.Zero)) return null;
+
+ SBase sb = new SBase(cPtr, false);
+ switch( sb.getTypeCode() )
+--- a/src/bindings/csharp/local-packages-render.i
++++ b/src/bindings/csharp/local-packages-render.i
+@@ -32,9 +32,9 @@ COVARIANT_RTYPE_FUNCTION(GradientBase, g
+ */
+ %typemap(cscode) RenderExtension
+ %{
+- public override SBasePlugin DowncastSBasePlugin(IntPtr cPtr, bool owner)
++ public override SBasePlugin DowncastSBasePlugin(global::System.IntPtr cPtr, bool owner)
+ {
+- if (cPtr.Equals(IntPtr.Zero)) return null;
++ if (cPtr.Equals(global::System.IntPtr.Zero)) return null;
+
+ SBasePlugin sbp = new SBasePlugin(cPtr, false);
+ SBase sb = sbp.getParentSBMLObject();
+@@ -57,9 +57,9 @@ COVARIANT_RTYPE_FUNCTION(GradientBase, g
+ }
+ }
+
+- public override SBase DowncastSBase(IntPtr cPtr, bool owner)
++ public override SBase DowncastSBase(global::System.IntPtr cPtr, bool owner)
+ {
+- if (cPtr.Equals(IntPtr.Zero)) return null;
++ if (cPtr.Equals(global::System.IntPtr.Zero)) return null;
+
+ SBase sb = new SBase(cPtr, false);
+ switch( sb.getTypeCode() )
+--- a/src/bindings/csharp/local-packages-req.i
++++ b/src/bindings/csharp/local-packages-req.i
+@@ -38,9 +38,9 @@
+ */
+ %typemap(cscode) ReqExtension
+ %{
+- public override SBasePlugin DowncastSBasePlugin(IntPtr cPtr, bool owner)
++ public override SBasePlugin DowncastSBasePlugin(global::System.IntPtr cPtr, bool owner)
+ {
+- if (cPtr.Equals(IntPtr.Zero)) return null;
++ if (cPtr.Equals(global::System.IntPtr.Zero)) return null;
+
+ SBasePlugin sbp = new SBasePlugin(cPtr, false);
+ SBase sb = sbp.getParentSBMLObject();
+@@ -53,9 +53,9 @@
+ }
+ }
+
+- public override SBase DowncastSBase(IntPtr cPtr, bool owner)
++ public override SBase DowncastSBase(global::System.IntPtr cPtr, bool owner)
+ {
+- if (cPtr.Equals(IntPtr.Zero)) return null;
++ if (cPtr.Equals(global::System.IntPtr.Zero)) return null;
+
+ SBase sb = new SBase(cPtr, false);
+ switch( sb.getTypeCode() )
+--- a/src/bindings/csharp/local-packages-spatial.i
++++ b/src/bindings/csharp/local-packages-spatial.i
+@@ -62,9 +62,9 @@ void SampledField::getUncompressed(int *
+ */
+ %typemap(cscode) SpatialExtension
+ %{
+- public override SBasePlugin DowncastSBasePlugin(IntPtr cPtr, bool owner)
++ public override SBasePlugin DowncastSBasePlugin(global::System.IntPtr cPtr, bool owner)
+ {
+- if (cPtr.Equals(IntPtr.Zero)) return null;
++ if (cPtr.Equals(global::System.IntPtr.Zero)) return null;
+
+ SBasePlugin sbp = new SBasePlugin(cPtr, false);
+ SBase sb = sbp.getParentSBMLObject();
+@@ -91,9 +91,9 @@ void SampledField::getUncompressed(int *
+ }
+ }
+
+- public override SBase DowncastSBase(IntPtr cPtr, bool owner)
++ public override SBase DowncastSBase(global::System.IntPtr cPtr, bool owner)
+ {
+- if (cPtr.Equals(IntPtr.Zero)) return null;
++ if (cPtr.Equals(global::System.IntPtr.Zero)) return null;
+
+ SBase sb = new SBase(cPtr, false);
+ switch( sb.getTypeCode() )
Modified: trunk/packages/libsbml/trunk/debian/rules
===================================================================
--- trunk/packages/libsbml/trunk/debian/rules 2015-12-14 15:46:08 UTC (rev 20761)
+++ trunk/packages/libsbml/trunk/debian/rules 2015-12-14 17:14:56 UTC (rev 20762)
@@ -20,6 +20,14 @@
CMAKE_OPTS := $(shell cat debian/cmake_opts)
endif
+ifneq (,$(filter $(DEB_HOST_ARCH), mips mipsel))
+CMAKE_OPTS += -D'WITH_01_COMPILE:BOOL=ON'
+endif
+
+# seems we need to use debian/cmake_opts
+export JDK_PATH=$(readlink -f /usr/bin/javac | sed "s:/bin/javac::")
+export JAVA_INCLUDE_PATH=$(JDK_PATH)/include
+
### let's do it ###
DEB_COMPRESS_EXCLUDE = .pdf
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