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 <[email protected]> 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 <[email protected]> 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 + <[email protected]> for the original patch) + Closes: #788068 + * forward port patch to build with SWIG 3.x (thanks to Logan Rosen + <[email protected]> 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 <[email protected]> Mon, 22 Sep 2014 10:11:35 +0200 + -- Andreas Tille <[email protected]> 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 <[email protected]> +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 $(CXX CXXFLAGS += -fno-strict-aliasing endif Added: trunk/packages/libsbml/trunk/debian/patches/mips-compile-with-O1.patch =================================================================== --- trunk/packages/libsbml/trunk/debian/patches/mips-compile-with-O1.patch (rev 0) +++ trunk/packages/libsbml/trunk/debian/patches/mips-compile-with-O1.patch 2015-12-14 17:14:56 UTC (rev 20762) @@ -0,0 +1,24 @@ +From: Jurica Stanojkovic <[email protected]> +Date: Mon, 8 Jun 2015 10:05:21 +0000 +Bug-Debian: https://bugs.debian.org/788068 +Subject: package libsbml FTBFS on mipsel + We have successfully built libsbml using -O1 optimization level. + -O1 is used for mips/mipsel, for critical part of package. + . + With this patch we was able to build package on lemote loongson 3a. + +--- a/src/bindings/perl/CMakeLists.txt ++++ b/src/bindings/perl/CMakeLists.txt +@@ -168,6 +168,12 @@ if (LIBSBML_REMOVE_WRAPPERS) + endforeach() + endif(LIBSBML_REMOVE_WRAPPERS) + ++if (WITH_01_COMPILE) ++ set (CMAKE_CXX_FLAGS "${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@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@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@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@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.@endif +@@ -51075,7 +51075,7 @@ from libSBML core.@endif <td class=\'s-error\'></td> </tr> <tr><td class=\'code\'>@link libsbml#CompNoMultipleReferences CompNoMultipleReferences@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.@endif +@@ -51435,7 +51435,7 @@ from libSBML core.@endif <td class=\'s-error\'></td> </tr> <tr><td class=\'code\'>@link libsbml#CompDeprecatedReplaceFunction CompDeprecatedReplaceFunction@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 <[email protected]> +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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
