[med-svn] r16722 - in trunk/packages/libsbml/trunk/debian: . patches
Ivo Maintz
ivomaintz-guest at moszumanska.debian.org
Thu Apr 17 15:03:09 UTC 2014
Author: ivomaintz-guest
Date: 2014-04-17 15:03:09 +0000 (Thu, 17 Apr 2014)
New Revision: 16722
Modified:
trunk/packages/libsbml/trunk/debian/changelog
trunk/packages/libsbml/trunk/debian/cmake_opts
trunk/packages/libsbml/trunk/debian/patches/doxygen.patch
trunk/packages/libsbml/trunk/debian/patches/hardening.patch
trunk/packages/libsbml/trunk/debian/patches/mexext.patch
trunk/packages/libsbml/trunk/debian/patches/series
trunk/packages/libsbml/trunk/debian/patches/spelling.patch
trunk/packages/libsbml/trunk/debian/rules
Log:
some minor changes to compile the newest source
one problem: at least for me the command "debian/rules get-orig-source"
don't exclude the in "debian/copyright" under Files-Excluded:
mentioned directory
Modified: trunk/packages/libsbml/trunk/debian/changelog
===================================================================
--- trunk/packages/libsbml/trunk/debian/changelog 2014-04-17 13:54:42 UTC (rev 16721)
+++ trunk/packages/libsbml/trunk/debian/changelog 2014-04-17 15:03:09 UTC (rev 16722)
@@ -1,3 +1,12 @@
+libsbml (5.10.0-1) UNRELEASED; urgency=medium
+
+ [Ivo Maintz]
+ * New upstream version
+ * debian/cmake_opts: enabled the qual extension
+ * debian/rules: added "--download-current-version" to the get-orig-source target
+
+ -- Ivo Maintz <ivo at maintz.de> Mon, 14 Apr 2014 15:26:28 +0200
+
libsbml (5.9.2+dfsg-1) UNRELEASED; urgency=medium
[ Andreas Tille ]
Modified: trunk/packages/libsbml/trunk/debian/cmake_opts
===================================================================
--- trunk/packages/libsbml/trunk/debian/cmake_opts 2014-04-17 13:54:42 UTC (rev 16721)
+++ trunk/packages/libsbml/trunk/debian/cmake_opts 2014-04-17 15:03:09 UTC (rev 16722)
@@ -4,8 +4,8 @@
-DENABLE_COMP:BOOL=ON
-DENABLE_FBC:BOOL=ON
-DENABLE_LAYOUT:BOOL=ON
--DENABLE_GROUPS=ON
--DENABLE_RENDER=ON
+-DENABLE_GROUPS:BOOL=ON
+-DENABLE_QUAL:BOOL=ON
-DWITH_BZIP2:BOOL=ON
-DWITH_CHECK:BOOL=OFF
-DWITH_CPP_NAMESPACE:BOOL=ON
@@ -28,3 +28,4 @@
-DWITH_WALL:BOOL=ON
-DWITH_XERCES:BOOL=OFF
-DWITH_ZLIB:BOOL=ON
+-DWITH_RENDER:BOOL=ON
Modified: trunk/packages/libsbml/trunk/debian/patches/doxygen.patch
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/doxygen.patch 2014-04-17 13:54:42 UTC (rev 16721)
+++ trunk/packages/libsbml/trunk/debian/patches/doxygen.patch 2014-04-17 15:03:09 UTC (rev 16722)
@@ -1,21 +1,19 @@
Description: fix a wrong file name
docs/CMakeLists.txt contains a wrong file name: doxygen-tabs.css instead of libsbml-doxygen-tabs.css
.
- libsbml (5.9.2-1) UNRELEASED; urgency=medium
+ libsbml (5.10.0-1) UNRELEASED; urgency=medium
.
* New upstream version
- * debian/upstream -> debian/upstream/metadata
- * debian/control: Drop explicite ruby version in Build-Dependencies
-Author: Ivo Miantz <ivo at maintz.de>
+Author: Ivo Maintz <ivo at maintz.de>
---
Last-Update: 2014-02-27
-Index: libsbml-5.9.2/docs/CMakeLists.txt
+Index: libsbml-5.10.0/docs/CMakeLists.txt
===================================================================
---- libsbml-5.9.2.orig/docs/CMakeLists.txt 2014-02-27 17:13:31.272841048 +0100
-+++ libsbml-5.9.2/docs/CMakeLists.txt 2014-02-27 17:15:58.322470772 +0100
-@@ -99,9 +99,9 @@
+--- libsbml-5.10.0.orig/docs/CMakeLists.txt 2014-04-16 09:50:09.860337829 +0200
++++ libsbml-5.10.0/docs/CMakeLists.txt 2014-04-16 09:51:51.893469161 +0200
+@@ -104,9 +104,9 @@
file(TO_NATIVE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/src/common-graphics/official-sbml-supported-40.jpg logo_file)
file(TO_NATIVE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/src/common-graphics/right-arrow.gif right_arrow)
file(TO_NATIVE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/src/sbml.js sbml_js)
@@ -28,3 +26,12 @@
file(TO_NATIVE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/src/doxygen-config-${lang}.txt api_doc)
+@@ -168,7 +168,7 @@
+ ADD_CUSTOM_COMMAND(
+ OUTPUT ${CMAKE_CURRENT_SOURCE_DIR}/src/libsbml.py
+ COMMAND ${PYTHON_EXECUTABLE}
+- ARGS pythondocpreprocessor.py
++ ARGS utilities/pythondocpreprocessor.py
+ ${CMAKE_CURRENT_BINARY_DIR}/../src/bindings/python/libsbml-doxygen.py
+ libsbml.py
+ ${PYTHON_SUBSTITUTIONS}
Modified: trunk/packages/libsbml/trunk/debian/patches/hardening.patch
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/hardening.patch 2014-04-17 13:54:42 UTC (rev 16721)
+++ trunk/packages/libsbml/trunk/debian/patches/hardening.patch 2014-04-17 15:03:09 UTC (rev 16722)
@@ -1,6 +1,6 @@
Description: hardening
.
- libsbml (5.7.0-1) UNRELEASED; urgency=low
+ libsbml (5.10.0-1) UNRELEASED; urgency=low
.
* update from upstream
Author: Ivo Maintz <ivo at maintz.de>
@@ -8,10 +8,10 @@
---
Last-Update: <2013-01-22>
-Index: libsbml-5.9.0/src/bindings/matlab/Makefile.in
+Index: libsbml-5.10.0/src/bindings/matlab/Makefile.in
===================================================================
---- libsbml-5.9.0.orig/src/bindings/matlab/Makefile.in 2013-11-28 14:51:16.191345434 +0100
-+++ libsbml-5.9.0/src/bindings/matlab/Makefile.in 2013-11-28 14:51:16.183345349 +0100
+--- libsbml-5.10.0.orig/src/bindings/matlab/Makefile.in 2013-11-28 14:51:16.191345434 +0100
++++ libsbml-5.10.0/src/bindings/matlab/Makefile.in 2013-11-28 14:51:16.183345349 +0100
@@ -70,12 +70,7 @@
installSBML.m \
isoctave.m \
@@ -35,10 +35,10 @@
$(LIBTOOL) -dlopen $(TOP_BUILDDIR)/src/libsbml.la --mode=execute $(1)
endef
-Index: libsbml-5.9.0/src/bindings/matlab/mexopts-R2009-R2010.sh
+Index: libsbml-5.10.0/src/bindings/matlab/mexopts-R2009-R2010.sh
===================================================================
---- libsbml-5.9.0.orig/src/bindings/matlab/mexopts-R2009-R2010.sh 2013-11-28 14:51:16.191345434 +0100
-+++ libsbml-5.9.0/src/bindings/matlab/mexopts-R2009-R2010.sh 2013-11-28 14:51:16.183345349 +0100
+--- libsbml-5.10.0.orig/src/bindings/matlab/mexopts-R2009-R2010.sh 2013-11-28 14:51:16.191345434 +0100
++++ libsbml-5.10.0/src/bindings/matlab/mexopts-R2009-R2010.sh 2013-11-28 14:51:16.183345349 +0100
@@ -324,7 +324,13 @@
#
#----------------------------------------------------------------------------
@@ -54,10 +54,10 @@
# COPTIMFLAGS="$COPTIMFLAGS"
# CDEBUGFLAGS="$CDEBUGFLAGS"
# CLIBS="$CLIBS"
-Index: libsbml-5.9.0/src/bindings/perl/Makefile.in
+Index: libsbml-5.10.0/src/bindings/perl/Makefile.in
===================================================================
---- libsbml-5.9.0.orig/src/bindings/perl/Makefile.in 2013-11-28 14:51:16.191345434 +0100
-+++ libsbml-5.9.0/src/bindings/perl/Makefile.in 2013-11-28 14:51:16.183345349 +0100
+--- libsbml-5.10.0.orig/src/bindings/perl/Makefile.in 2013-11-28 14:51:16.191345434 +0100
++++ libsbml-5.10.0/src/bindings/perl/Makefile.in 2013-11-28 14:51:16.183345349 +0100
@@ -177,6 +177,8 @@
endif
@@ -67,10 +67,10 @@
# If the last run was made with --enable-layout and this one isn't, or
# vice-versa, the swig wrap files will be wrong for this run. However, you
# can't tell just by looking at file mod times, so you can't use normal
-Index: libsbml-5.9.0/config/makefile-common-actions.mk
+Index: libsbml-5.10.0/config/makefile-common-actions.mk
===================================================================
---- libsbml-5.9.0.orig/config/makefile-common-actions.mk 2013-11-28 14:51:16.191345434 +0100
-+++ libsbml-5.9.0/config/makefile-common-actions.mk 2013-11-28 14:51:16.183345349 +0100
+--- libsbml-5.10.0.orig/config/makefile-common-actions.mk 2013-11-28 14:51:16.191345434 +0100
++++ libsbml-5.10.0/config/makefile-common-actions.mk 2013-11-28 14:51:16.183345349 +0100
@@ -72,6 +72,15 @@
# here is only to remove duplicates, which the 'sort' function does as a
# documented side-effect.)
Modified: trunk/packages/libsbml/trunk/debian/patches/mexext.patch
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/mexext.patch 2014-04-17 13:54:42 UTC (rev 16721)
+++ trunk/packages/libsbml/trunk/debian/patches/mexext.patch 2014-04-17 15:03:09 UTC (rev 16722)
@@ -6,8 +6,8 @@
---
Last-Update: <2014-03-01>
---- libsbml-5.9.2.orig/src/bindings/matlab/FindMatlab.cmake
-+++ libsbml-5.9.2/src/bindings/matlab/FindMatlab.cmake
+--- libsbml-5.10.0.orig/src/bindings/matlab/FindMatlab.cmake
++++ libsbml-5.10.0/src/bindings/matlab/FindMatlab.cmake
@@ -162,7 +162,7 @@ IF(WIN32)
SET(MATLAB_MATLAB_COMMAND "${MATLAB_ROOT_PATH}/bin/matlab.bat")
ELSE (WIN32)
Modified: trunk/packages/libsbml/trunk/debian/patches/series
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/series 2014-04-17 13:54:42 UTC (rev 16721)
+++ trunk/packages/libsbml/trunk/debian/patches/series 2014-04-17 15:03:09 UTC (rev 16722)
@@ -1,5 +1,4 @@
hardening.patch
mexext.patch
-format-security.patch
doxygen.patch
spelling.patch
Modified: trunk/packages/libsbml/trunk/debian/patches/spelling.patch
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/spelling.patch 2014-04-17 13:54:42 UTC (rev 16721)
+++ trunk/packages/libsbml/trunk/debian/patches/spelling.patch 2014-04-17 15:03:09 UTC (rev 16722)
@@ -1,34 +1,28 @@
-Description: fix spelling errors
- fixes a lot of spelling errors in the sources
+Description: fixes spelling errors
+ This patch fixes spelling errors; lintian informed about "spelling-error-in-binary"
.
- libsbml (5.9.2-1) UNRELEASED; urgency=medium
+ libsbml (5.10.0-1) UNRELEASED; urgency=medium
.
- [ Andreas Tille ]
+ [Ivo Maintz]
* New upstream version
- * debian/upstream -> debian/upstream/metadata
- * debian/control: Drop explicite ruby version in Build-Dependencies
- .
- [ Ivo Maintz ]
- * added debian/bin/python_fix.sh to bypass a wrong path to the file Python.h
- * drop ruby bindings, can't get it compiled
Author: Ivo Maintz <ivo at maintz.de>
---
-Last-Update: 2014-03-13
+Last-Update: 2014-04-16
---- libsbml-5.9.2.orig/OLD_NEWS.txt
-+++ libsbml-5.9.2/OLD_NEWS.txt
+--- libsbml-5.10.0.orig/OLD_NEWS.txt
++++ libsbml-5.10.0/OLD_NEWS.txt
@@ -1102,7 +1102,7 @@ Version 3.1.1 (released 2008-02-25)
- Thanks to Chris Meyers for reporting this.
-
- - Tracker issue #1880570.
-- The previous fix for a piecewise without an otherwise statement
-+ The previous fix for a piecewise without anotherwise statement
- did not propagate for the use of piecewise within a lambda
- function. This is now fixed and multiple tests included to catch
- this and similar potential failures.
---- libsbml-5.9.2.orig/docs/src/libsbml-accessing.html
-+++ libsbml-5.9.2/docs/src/libsbml-accessing.html
+ Thanks to Chris Meyers for reporting this.
+
+ - Tracker issue #1880570.
+- The previous fix for a piecewise without an otherwise statement
++ The previous fix for a piecewise without anotherwise statement
+ did not propagate for the use of piecewise within a lambda
+ function. This is now fixed and multiple tests included to catch
+ this and similar potential failures.
+--- libsbml-5.10.0.orig/docs/src/libsbml-accessing.html
++++ libsbml-5.10.0/docs/src/libsbml-accessing.html
@@ -366,7 +366,7 @@ correctly. It may also mean that the re
installed library files or a directory in the hierarchy containing them are
such that you are not allowed to access the files. In that case, please
@@ -38,9 +32,9 @@
<h3><a class="anchor" name="accessing-matlab">MATLAB</a></h3>
---- libsbml-5.9.2.orig/src/bindings/csharp/csdoc.i
-+++ libsbml-5.9.2/src/bindings/csharp/csdoc.i
-@@ -205,7 +205,7 @@
+--- libsbml-5.10.0.orig/src/bindings/csharp/csdoc.i
++++ libsbml-5.10.0/src/bindings/csharp/csdoc.i
+@@ -246,7 +246,7 @@
* appear first. The error code @if clike (a value drawn from the 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
@@ -49,7 +43,7 @@
* read it) or some sort of file operation error may have been reported
* by the underlying operating system. Callers can check for these
* situations using a program fragment such as the following:
-@@ -363,7 +363,7 @@
+@@ -404,7 +404,7 @@
* appear first. The error code @if clike (a value drawn from the 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
@@ -58,7 +52,7 @@
* read it) or some sort of file operation error may have been reported
* by the underlying operating system. Callers can check for these
* situations using a program fragment such as the following:
-@@ -3912,7 +3912,7 @@ s.setNotes(\'<body xmlns=\'http://www.w3
+@@ -4074,7 +4074,7 @@ s.setNotes(\'<body xmlns=\'http://www.w3
* 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
@@ -67,7 +61,7 @@
* 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:
-@@ -25419,7 +25419,7 @@ sp.setId(\'MySpecies\');
+@@ -25953,7 +25953,7 @@ sp.setId(\'MySpecies\');
* This attribute is optional in SBML Level 2, with a default of @c
* false; it is mandatory in SBML Level 3 (with no default value). It
* is used to indicate that a reaction occurs on a vastly faster time scale
@@ -76,7 +70,7 @@
* Version 4 specification, which provides more detail about the
* conditions under which a reaction can be considered to be fast in this
* sense. The attribute\'s default value is @c false. SBML Level 1
-@@ -51206,7 +51206,7 @@ else:
+@@ -49145,7 +49145,7 @@ else:
<td class=\'s-na\'>N</td>
<td class=\'s-error\'>E</td></tr>
<tr><td><code>@link libsbmlcs.libsbml.CompNoMultipleReferences CompNoMultipleReferences @endlink</code></td>
@@ -85,7 +79,7 @@
<td class=\'s-na\'>N</td>
<td class=\'s-na\'>N</td>
<td class=\'s-na\'>N</td>
-@@ -51530,7 +51530,7 @@ else:
+@@ -49469,7 +49469,7 @@ else:
<td class=\'s-na\'>N</td>
<td class=\'s-error\'>E</td></tr>
<tr><td><code>@link libsbmlcs.libsbml.CompDeprecatedReplaceFunction CompDeprecatedReplaceFunction @endlink</code></td>
@@ -94,8 +88,8 @@
<td class=\'s-na\'>N</td>
<td class=\'s-na\'>N</td>
<td class=\'s-na\'>N</td>
---- libsbml-5.9.2.orig/src/bindings/csharp/csharp-files-win/Reaction.cs
-+++ libsbml-5.9.2/src/bindings/csharp/csharp-files-win/Reaction.cs
+--- libsbml-5.10.0.orig/src/bindings/csharp/csharp-files-win/Reaction.cs
++++ libsbml-5.10.0/src/bindings/csharp/csharp-files-win/Reaction.cs
@@ -96,7 +96,7 @@ namespace libsbml {
* This attribute is optional in SBML Level 2, with a default of @c
* false; it is mandatory in SBML Level 3 (with no default value). It
@@ -105,8 +99,8 @@
* Version 4 specification, which provides more detail about the
* conditions under which a reaction can be considered to be fast in this
* sense. The attribute's default value is @c false. SBML Level 1
---- libsbml-5.9.2.orig/src/bindings/csharp/csharp-files-win/SBMLError.cs
-+++ libsbml-5.9.2/src/bindings/csharp/csharp-files-win/SBMLError.cs
+--- libsbml-5.10.0.orig/src/bindings/csharp/csharp-files-win/SBMLError.cs
++++ libsbml-5.10.0/src/bindings/csharp/csharp-files-win/SBMLError.cs
@@ -4530,7 +4530,7 @@ namespace libsbml {
<td class='s-na'>N</td>
<td class='s-error'>E</td></tr>
@@ -125,8 +119,8 @@
<td class='s-na'>N</td>
<td class='s-na'>N</td>
<td class='s-na'>N</td>
---- libsbml-5.9.2.orig/src/bindings/csharp/csharp-files-win/SBMLReader.cs
-+++ libsbml-5.9.2/src/bindings/csharp/csharp-files-win/SBMLReader.cs
+--- libsbml-5.10.0.orig/src/bindings/csharp/csharp-files-win/SBMLReader.cs
++++ libsbml-5.10.0/src/bindings/csharp/csharp-files-win/SBMLReader.cs
@@ -179,7 +179,7 @@ public class SBMLReader : IDisposable {
* appear first. The error code @if clike (a value drawn from the enumeration
* #XMLErrorCode_t) @endif can provide a clue about what happened. For example,
@@ -145,9 +139,9 @@
* read it) or some sort of file operation error may have been reported
* by the underlying operating system. Callers can check for these
* situations using a program fragment such as the following:
---- libsbml-5.9.2.orig/src/bindings/csharp/csharp-files-win/SBase.cs
-+++ libsbml-5.9.2/src/bindings/csharp/csharp-files-win/SBase.cs
-@@ -2900,7 +2900,7 @@ s.setNotes('<body xmlns='http://www.w3.o
+--- libsbml-5.10.0.orig/src/bindings/csharp/csharp-files-win/SBase.cs
++++ libsbml-5.10.0/src/bindings/csharp/csharp-files-win/SBase.cs
+@@ -2901,7 +2901,7 @@ 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
@@ -156,8 +150,8 @@
* 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-5.9.2.orig/src/bindings/csharp/csharp-files/Reaction.cs
-+++ libsbml-5.9.2/src/bindings/csharp/csharp-files/Reaction.cs
+--- libsbml-5.10.0.orig/src/bindings/csharp/csharp-files/Reaction.cs
++++ libsbml-5.10.0/src/bindings/csharp/csharp-files/Reaction.cs
@@ -96,7 +96,7 @@ namespace libsbmlcs {
* This attribute is optional in SBML Level 2, with a default of @c
* false; it is mandatory in SBML Level 3 (with no default value). It
@@ -167,8 +161,8 @@
* Version 4 specification, which provides more detail about the
* conditions under which a reaction can be considered to be fast in this
* sense. The attribute's default value is @c false. SBML Level 1
---- libsbml-5.9.2.orig/src/bindings/csharp/csharp-files/SBMLError.cs
-+++ libsbml-5.9.2/src/bindings/csharp/csharp-files/SBMLError.cs
+--- libsbml-5.10.0.orig/src/bindings/csharp/csharp-files/SBMLError.cs
++++ libsbml-5.10.0/src/bindings/csharp/csharp-files/SBMLError.cs
@@ -4530,7 +4530,7 @@ namespace libsbmlcs {
<td class='s-na'>N</td>
<td class='s-error'>E</td></tr>
@@ -187,8 +181,8 @@
<td class='s-na'>N</td>
<td class='s-na'>N</td>
<td class='s-na'>N</td>
---- libsbml-5.9.2.orig/src/bindings/csharp/csharp-files/SBMLReader.cs
-+++ libsbml-5.9.2/src/bindings/csharp/csharp-files/SBMLReader.cs
+--- libsbml-5.10.0.orig/src/bindings/csharp/csharp-files/SBMLReader.cs
++++ libsbml-5.10.0/src/bindings/csharp/csharp-files/SBMLReader.cs
@@ -179,7 +179,7 @@ public class SBMLReader : IDisposable {
* appear first. The error code @if clike (a value drawn from the enumeration
* #XMLErrorCode_t) @endif can provide a clue about what happened. For example,
@@ -207,9 +201,9 @@
* read it) or some sort of file operation error may have been reported
* by the underlying operating system. Callers can check for these
* situations using a program fragment such as the following:
---- libsbml-5.9.2.orig/src/bindings/csharp/csharp-files/SBase.cs
-+++ libsbml-5.9.2/src/bindings/csharp/csharp-files/SBase.cs
-@@ -2930,7 +2930,7 @@ s.setNotes('<body xmlns='http://www.w3.o
+--- libsbml-5.10.0.orig/src/bindings/csharp/csharp-files/SBase.cs
++++ libsbml-5.10.0/src/bindings/csharp/csharp-files/SBase.cs
+@@ -2931,7 +2931,7 @@ 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
@@ -218,8 +212,8 @@
* 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-5.9.2.orig/src/bindings/java/java-files/org/sbml/libsbml/Reaction.java
-+++ libsbml-5.9.2/src/bindings/java/java-files/org/sbml/libsbml/Reaction.java
+--- libsbml-5.10.0.orig/src/bindings/java/java-files/org/sbml/libsbml/Reaction.java
++++ libsbml-5.10.0/src/bindings/java/java-files/org/sbml/libsbml/Reaction.java
@@ -91,7 +91,7 @@ package org.sbml.libsbml;
* This attribute is optional in SBML Level 2, with a default of
* <code>false</code>; it is mandatory in SBML Level 3 (with no default value). It
@@ -229,14 +223,14 @@
* Version 4 specification, which provides more detail about the
* conditions under which a reaction can be considered to be fast in this
* sense. The attribute's default value is <code>false.</code> SBML Level 1
---- libsbml-5.9.2.orig/src/bindings/java/java-files/org/sbml/libsbml/SBMLError.java
-+++ libsbml-5.9.2/src/bindings/java/java-files/org/sbml/libsbml/SBMLError.java
+--- libsbml-5.10.0.orig/src/bindings/java/java-files/org/sbml/libsbml/SBMLError.java
++++ libsbml-5.10.0/src/bindings/java/java-files/org/sbml/libsbml/SBMLError.java
@@ -4438,7 +4438,7 @@ defined in SBML.
<td class='s-na'>N</td>
<td class='s-error'>E</td></tr>
<tr><td><code>{@link libsbmlConstants#CompNoMultipleReferences CompNoMultipleReferences }</code></td>
--<td> Objects may not be referenced by mutiple {@link SBaseRef} constructs. </td>
-+<td> Objects may not be referenced by multiple {@link SBaseRef} constructs. </td>
+-<td> Objects may not be referenced by mutiple SBaseRef constructs. </td>
++<td> Objects may not be referenced by multiple SBaseRef constructs. </td>
<td class='s-na'>N</td>
<td class='s-na'>N</td>
<td class='s-na'>N</td>
@@ -249,8 +243,8 @@
<td class='s-na'>N</td>
<td class='s-na'>N</td>
<td class='s-na'>N</td>
---- libsbml-5.9.2.orig/src/bindings/java/java-files/org/sbml/libsbml/SBMLReader.java
-+++ libsbml-5.9.2/src/bindings/java/java-files/org/sbml/libsbml/SBMLReader.java
+--- libsbml-5.10.0.orig/src/bindings/java/java-files/org/sbml/libsbml/SBMLReader.java
++++ libsbml-5.10.0/src/bindings/java/java-files/org/sbml/libsbml/SBMLReader.java
@@ -193,7 +193,7 @@ public class SBMLReader {
* If the file <code>filename</code> could not be read, the file-reading error will
* appear first. The error code can provide a clue about what happened. For example,
@@ -269,9 +263,9 @@
* read it) or some sort of file operation error may have been reported
* by the underlying operating system. Callers can check for these
* situations using a program fragment such as the following:
---- libsbml-5.9.2.orig/src/bindings/java/java-files/org/sbml/libsbml/SBase.java
-+++ libsbml-5.9.2/src/bindings/java/java-files/org/sbml/libsbml/SBase.java
-@@ -2789,7 +2789,7 @@ appears in the documentation.
+--- libsbml-5.10.0.orig/src/bindings/java/java-files/org/sbml/libsbml/SBase.java
++++ libsbml-5.10.0/src/bindings/java/java-files/org/sbml/libsbml/SBase.java
+@@ -2790,7 +2790,7 @@ appears in the documentation.
* Hierarchical {@link 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
@@ -280,9 +274,9 @@
* 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-5.9.2.orig/src/bindings/java/javadoc.i
-+++ libsbml-5.9.2/src/bindings/java/javadoc.i
-@@ -209,7 +209,7 @@ defined in SBML.
+--- libsbml-5.10.0.orig/src/bindings/java/javadoc.i
++++ libsbml-5.10.0/src/bindings/java/javadoc.i
+@@ -235,7 +235,7 @@ defined in SBML.
* If the file <code>filename</code> could not be read, the file-reading error will
* 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
@@ -291,7 +285,7 @@
* read it) or some sort of file operation error may have been reported
* by the underlying operating system. Callers can check for these
* situations using a program fragment such as the following:
-@@ -302,7 +302,7 @@ defined in SBML.
+@@ -328,7 +328,7 @@ defined in SBML.
* If the file <code>filename</code> could not be read, the file-reading error will
* 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
@@ -300,7 +294,7 @@
* read it) or some sort of file operation error may have been reported
* by the underlying operating system. Callers can check for these
* situations using a program fragment such as the following:
-@@ -3785,7 +3785,7 @@ appears in the documentation.
+@@ -3882,7 +3882,7 @@ appears in the documentation.
* Hierarchical {@link 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
@@ -309,7 +303,7 @@
* 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:
-@@ -24852,7 +24852,7 @@ attributes.</caption>
+@@ -25033,7 +25033,7 @@ attributes.</caption>
* This attribute is optional in SBML Level 2, with a default of
* <code>false</code>; it is mandatory in SBML Level 3 (with no default value). It
* is used to indicate that a reaction occurs on a vastly faster time scale
@@ -318,16 +312,16 @@
* Version 4 specification, which provides more detail about the
* conditions under which a reaction can be considered to be fast in this
* sense. The attribute\'s default value is <code>false.</code> SBML Level 1
-@@ -51404,7 +51404,7 @@ defined in SBML.
+@@ -48043,7 +48043,7 @@ defined in SBML.
<td class=\'s-na\'>N</td>
<td class=\'s-error\'>E</td></tr>
<tr><td><code>{@link libsbmlConstants#CompNoMultipleReferences CompNoMultipleReferences }</code></td>
--<td> Objects may not be referenced by mutiple {@link SBaseRef} constructs. </td>
-+<td> Objects may not be referenced by multiple {@link SBaseRef} constructs. </td>
+-<td> Objects may not be referenced by mutiple SBaseRef constructs. </td>
++<td> Objects may not be referenced by multiple SBaseRef constructs. </td>
<td class=\'s-na\'>N</td>
<td class=\'s-na\'>N</td>
<td class=\'s-na\'>N</td>
-@@ -51728,7 +51728,7 @@ defined in SBML.
+@@ -48367,7 +48367,7 @@ defined in SBML.
<td class=\'s-na\'>N</td>
<td class=\'s-error\'>E</td></tr>
<tr><td><code>{@link libsbmlConstants#CompDeprecatedReplaceFunction CompDeprecatedReplaceFunction }</code></td>
@@ -336,9 +330,9 @@
<td class=\'s-na\'>N</td>
<td class=\'s-na\'>N</td>
<td class=\'s-na\'>N</td>
---- libsbml-5.9.2.orig/src/bindings/perl/LibSBML.pm
-+++ libsbml-5.9.2/src/bindings/perl/LibSBML.pm
-@@ -224,7 +224,7 @@ If the file C<filename> could not be rea
+--- libsbml-5.10.0.orig/src/bindings/perl/LibSBML.pm
++++ libsbml-5.10.0/src/bindings/perl/LibSBML.pm
+@@ -261,7 +261,7 @@ If the file C<filename> could not be rea
appear first. The error code @if clike (a value drawn from the 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
@@ -347,7 +341,7 @@
read it) or some sort of file operation error may have been reported
by the underlying operating system. Callers can check for these
situations using a program fragment such as the following:
-@@ -330,7 +330,7 @@ If the file C<filename> could not be rea
+@@ -367,7 +367,7 @@ If the file C<filename> could not be rea
appear first. The error code @if clike (a value drawn from the 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
@@ -356,7 +350,7 @@
read it) or some sort of file operation error may have been reported
by the underlying operating system. Callers can check for these
situations using a program fragment such as the following:
-@@ -2730,7 +2730,7 @@ application read an SBML document contai
+@@ -2835,7 +2835,7 @@ 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
@@ -365,7 +359,7 @@
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:
-@@ -16920,7 +16920,7 @@ The Reaction object class has another bo
+@@ -17001,7 +17001,7 @@ The Reaction object class has another bo
This attribute is optional in SBML Level 2, with a default of @c
false; it is mandatory in SBML Level 3 (with no default value). It
is used to indicate that a reaction occurs on a vastly faster time scale
@@ -374,9 +368,9 @@
Version 4 specification, which provides more detail about the
conditions under which a reaction can be considered to be fast in this
sense. The attribute's default value is C<false>. SBML Level 1
---- libsbml-5.9.2.orig/src/bindings/perl/LibSBML.pod
-+++ libsbml-5.9.2/src/bindings/perl/LibSBML.pod
-@@ -211,7 +211,7 @@ If the file C<filename> could not be rea
+--- libsbml-5.10.0.orig/src/bindings/perl/LibSBML.pod
++++ libsbml-5.10.0/src/bindings/perl/LibSBML.pod
+@@ -248,7 +248,7 @@ If the file C<filename> could not be rea
appear first. The error code @if clike (a value drawn from the 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
@@ -385,7 +379,7 @@
read it) or some sort of file operation error may have been reported
by the underlying operating system. Callers can check for these
situations using a program fragment such as the following:
-@@ -317,7 +317,7 @@ If the file C<filename> could not be rea
+@@ -354,7 +354,7 @@ If the file C<filename> could not be rea
appear first. The error code @if clike (a value drawn from the 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
@@ -394,7 +388,7 @@
read it) or some sort of file operation error may have been reported
by the underlying operating system. Callers can check for these
situations using a program fragment such as the following:
-@@ -2717,7 +2717,7 @@ application read an SBML document contai
+@@ -2822,7 +2822,7 @@ 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
@@ -403,7 +397,7 @@
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:
-@@ -16907,7 +16907,7 @@ The Reaction object class has another bo
+@@ -16988,7 +16988,7 @@ The Reaction object class has another bo
This attribute is optional in SBML Level 2, with a default of @c
false; it is mandatory in SBML Level 3 (with no default value). It
is used to indicate that a reaction occurs on a vastly faster time scale
@@ -412,8 +406,8 @@
Version 4 specification, which provides more detail about the
conditions under which a reaction can be considered to be fast in this
sense. The attribute's default value is C<false>. SBML Level 1
---- libsbml-5.9.2.orig/src/bindings/python/libsbml-doxygen.py
-+++ libsbml-5.9.2/src/bindings/python/libsbml-doxygen.py
+--- libsbml-5.10.0.orig/src/bindings/python/libsbml-doxygen.py
++++ libsbml-5.10.0/src/bindings/python/libsbml-doxygen.py
@@ -781,7 +781,7 @@ 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
@@ -423,7 +417,7 @@
been reported by the underlying operating system. Callers can check
for these situations using a program fragment such as the following:
-@@ -1195,7 +1195,7 @@ class SBMLReader(_object):
+@@ -1245,7 +1245,7 @@ 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
@@ -432,7 +426,7 @@
been reported by the underlying operating system. Callers can check
for these situations using a program fragment such as the following:
-@@ -1279,7 +1279,7 @@ class SBMLReader(_object):
+@@ -1329,7 +1329,7 @@ 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
@@ -441,7 +435,7 @@
been reported by the underlying operating system. Callers can check
for these situations using a program fragment such as the following:
-@@ -4650,7 +4650,7 @@ class SBase(_object):
+@@ -4831,7 +4831,7 @@ 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
@@ -450,7 +444,7 @@
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:
-@@ -25541,7 +25541,7 @@ class Reaction(SBase):
+@@ -26201,7 +26201,7 @@ class Reaction(SBase):
This attribute is optional in SBML Level 2, with a default of @c
false; it is mandatory in SBML Level 3 (with no default value). It
is used to indicate that a reaction occurs on a vastly faster time scale
@@ -459,7 +453,7 @@
Version 4 specification, which provides more detail about the
conditions under which a reaction can be considered to be fast in this
sense. The attribute's default value is @c False. SBML Level 1
-@@ -52739,7 +52739,7 @@ class SBMLError(XMLError):
+@@ -50681,7 +50681,7 @@ class SBMLError(XMLError):
<td class='s-na'>N</td>
<td class='s-error'>E</td></tr>
<tr><td><code>@link libsbml.CompNoMultipleReferences CompNoMultipleReferences @endlink</code></td>
@@ -468,7 +462,7 @@
<td class='s-na'>N</td>
<td class='s-na'>N</td>
<td class='s-na'>N</td>
-@@ -53063,7 +53063,7 @@ class SBMLError(XMLError):
+@@ -51005,7 +51005,7 @@ class SBMLError(XMLError):
<td class='s-na'>N</td>
<td class='s-error'>E</td></tr>
<tr><td><code>@link libsbml.CompDeprecatedReplaceFunction CompDeprecatedReplaceFunction @endlink</code></td>
@@ -477,8 +471,8 @@
<td class='s-na'>N</td>
<td class='s-na'>N</td>
<td class='s-na'>N</td>
---- libsbml-5.9.2.orig/src/bindings/python/libsbml.py
-+++ libsbml-5.9.2/src/bindings/python/libsbml.py
+--- libsbml-5.10.0.orig/src/bindings/python/libsbml.py
++++ libsbml-5.10.0/src/bindings/python/libsbml.py
@@ -782,7 +782,7 @@ 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
@@ -488,7 +482,7 @@
been reported by the underlying operating system. Callers can check
for these situations using a program fragment such as the following:
-@@ -1184,7 +1184,7 @@ class SBMLReader(_object):
+@@ -1209,7 +1209,7 @@ 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
@@ -497,7 +491,7 @@
been reported by the underlying operating system. Callers can check
for these situations using a program fragment such as the following:
-@@ -1268,7 +1268,7 @@ class SBMLReader(_object):
+@@ -1293,7 +1293,7 @@ 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
@@ -506,7 +500,7 @@
been reported by the underlying operating system. Callers can check
for these situations using a program fragment such as the following:
-@@ -4148,7 +4148,7 @@ class SBase(_object):
+@@ -4255,7 +4255,7 @@ class SBase(_object):
SBML 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
@@ -515,7 +509,7 @@
declarations. 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
-@@ -47095,7 +47095,7 @@ class SBMLError(XMLError):
+@@ -44795,7 +44795,7 @@ class SBMLError(XMLError):
|libsbml.CompDeprecatedSBaseRefSpelling |The spelling 'sbaseRef' is deprecated |N |N |N |N |N |N |W |
|libsbml.CompSBaseRefMustReferenceObject |An SBaseRef must reference an object. |N |N |N |N |N |N |E |
|libsbml.CompSBaseRefMustReferenceOnlyOneObject |An SBaseRef must reference only one other object. |N |N |N |N |N |N |E |
@@ -524,7 +518,7 @@
|libsbml.CompPortMustReferenceObject |Port must reference an object |N |N |N |N |N |N |E |
|libsbml.CompPortMustReferenceOnlyOneObject |Port must reference only one other object. |N |N |N |N |N |N |E |
|libsbml.CompPortAllowedAttributes |Allowed attributes on a Port |N |N |N |N |N |N |E |
-@@ -47131,7 +47131,7 @@ class SBMLError(XMLError):
+@@ -44831,7 +44831,7 @@ class SBMLError(XMLError):
|libsbml.CompFlatteningNotImplementedReqd |Flattening not implemented for required package. |N |N |N |N |N |N |W |
|libsbml.CompFlatteningWarning |Flattening reference may come from package. |N |N |N |N |N |N |W |
|libsbml.CompDeprecatedDeleteFunction |The performDeletions functions is deprecated. |N |N |N |N |N |N |E |
@@ -533,9 +527,9 @@
|libsbml.CompDeletedReplacement |Element deleted before a subelement could be replaced. |N |N |N |N |N |N |E |
|libsbml.CompIdRefMayReferenceUnknownPackage |The 'comp:idRef' attribute must be the 'id' of a model element |N |N |N |N |N |N |W |
|libsbml.CompMetaIdRefMayReferenceUnknownPkg |The 'comp:metaIdRef' attribute must be the 'metaid' of a model element |N |N |N |N |N |N |W |
---- libsbml-5.9.2.orig/src/bindings/python/libsbml_wrap.cpp
-+++ libsbml-5.9.2/src/bindings/python/libsbml_wrap.cpp
-@@ -104172,7 +104172,7 @@ static PyMethodDef SwigMethods[] = {
+--- libsbml-5.10.0.orig/src/bindings/python/libsbml_wrap.cpp
++++ libsbml-5.10.0/src/bindings/python/libsbml_wrap.cpp
+@@ -111129,7 +111129,7 @@ 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"
@@ -544,7 +538,7 @@
"been reported by the underlying operating system. Callers can check\n"
"for these situations using a program fragment such as the following:\n"
"\n"
-@@ -104250,7 +104250,7 @@ static PyMethodDef SwigMethods[] = {
+@@ -111207,7 +111207,7 @@ 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"
@@ -553,7 +547,7 @@
"been reported by the underlying operating system. Callers can check\n"
"for these situations using a program fragment such as the following:\n"
"\n"
-@@ -106514,7 +106514,7 @@ static PyMethodDef SwigMethods[] = {
+@@ -113545,7 +113545,7 @@ static PyMethodDef SwigMethods[] = {
"SBML Hierarchical Model Composition (“comp”) package, and\n"
"extracted parts of that model in order to construct a new model in\n"
"memory. The new, in-memory model will not accept a component drawn\n"
@@ -562,9 +556,9 @@
"declarations. You could reconstruct the same namespaces in the in-\n"
"memory model first, but as a shortcut, you could also disable the\n"
"package namespace on the object being added. Here is a code example\n"
---- libsbml-5.9.2.orig/src/bindings/python/local.i
-+++ libsbml-5.9.2/src/bindings/python/local.i
-@@ -587,7 +587,7 @@ SBMLReader::readSBML(const std::string&)
+--- libsbml-5.10.0.orig/src/bindings/python/local.i
++++ libsbml-5.10.0/src/bindings/python/local.i
+@@ -592,7 +592,7 @@ 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
@@ -573,7 +567,7 @@
been reported by the underlying operating system. Callers can check
for these situations using a program fragment such as the following:
-@@ -674,7 +674,7 @@ SBMLReader::readSBMLFromFile(const std::
+@@ -679,7 +679,7 @@ 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
@@ -582,7 +576,7 @@
been reported by the underlying operating system. Callers can check
for these situations using a program fragment such as the following:
-@@ -772,7 +772,7 @@ def readSBML(*args):
+@@ -777,7 +777,7 @@ 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
@@ -591,9 +585,9 @@
been reported by the underlying operating system. Callers can check
for these situations using a program fragment such as the following:
---- libsbml-5.9.2.orig/src/bindings/python/pydoc-doxygen.i
-+++ libsbml-5.9.2/src/bindings/python/pydoc-doxygen.i
-@@ -181,7 +181,7 @@ If the file @p filename could not be rea
+--- libsbml-5.10.0.orig/src/bindings/python/pydoc-doxygen.i
++++ libsbml-5.10.0/src/bindings/python/pydoc-doxygen.i
+@@ -215,7 +215,7 @@ If the file @p filename could not be rea
appear first. The error code @if clike (a value drawn from the 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
@@ -602,7 +596,7 @@
read it) or some sort of file operation error may have been reported
by the underlying operating system. Callers can check for these
situations using a program fragment such as the following:
-@@ -331,7 +331,7 @@ If the file @p filename could not be rea
+@@ -365,7 +365,7 @@ If the file @p filename could not be rea
appear first. The error code @if clike (a value drawn from the 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
@@ -611,7 +605,7 @@
read it) or some sort of file operation error may have been reported
by the underlying operating system. Callers can check for these
situations using a program fragment such as the following:
-@@ -3240,7 +3240,7 @@ application read an SBML document contai
+@@ -3427,7 +3427,7 @@ 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
@@ -620,7 +614,7 @@
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:
-@@ -21914,7 +21914,7 @@ The Reaction object class has another bo
+@@ -22938,7 +22938,7 @@ The Reaction object class has another bo
This attribute is optional in SBML Level 2, with a default of @c
false; it is mandatory in SBML Level 3 (with no default value). It
is used to indicate that a reaction occurs on a vastly faster time scale
@@ -629,7 +623,7 @@
Version 4 specification, which provides more detail about the
conditions under which a reaction can be considered to be fast in this
sense. The attribute\'s default value is @c False. SBML Level 1
-@@ -45094,7 +45094,7 @@ from libSBML core. at endif
+@@ -44129,7 +44129,7 @@ from libSBML core. at endif
<td class=\'s-na\'>N</td>
<td class=\'s-error\'>E</td></tr>
<tr><td><code>@link libsbml.CompNoMultipleReferences CompNoMultipleReferences @endlink</code></td>
@@ -638,7 +632,7 @@
<td class=\'s-na\'>N</td>
<td class=\'s-na\'>N</td>
<td class=\'s-na\'>N</td>
-@@ -45418,7 +45418,7 @@ from libSBML core. at endif
+@@ -44453,7 +44453,7 @@ from libSBML core. at endif
<td class=\'s-na\'>N</td>
<td class=\'s-error\'>E</td></tr>
<tr><td><code>@link libsbml.CompDeprecatedReplaceFunction CompDeprecatedReplaceFunction @endlink</code></td>
@@ -647,9 +641,9 @@
<td class=\'s-na\'>N</td>
<td class=\'s-na\'>N</td>
<td class=\'s-na\'>N</td>
---- libsbml-5.9.2.orig/src/bindings/python/pydoc-normal.i
-+++ libsbml-5.9.2/src/bindings/python/pydoc-normal.i
-@@ -169,7 +169,7 @@ If the file 'filename' could not be read
+--- libsbml-5.10.0.orig/src/bindings/python/pydoc-normal.i
++++ libsbml-5.10.0/src/bindings/python/pydoc-normal.i
+@@ -187,7 +187,7 @@ 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
actually exist or because the user does not have the necessary access
@@ -658,7 +652,7 @@
been reported by the underlying operating system. Callers can check
for these situations using a program fragment such as the following:
-@@ -246,7 +246,7 @@ If the file 'filename' could not be read
+@@ -264,7 +264,7 @@ 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
actually exist or because the user does not have the necessary access
@@ -667,7 +661,7 @@
been reported by the underlying operating system. Callers can check
for these situations using a program fragment such as the following:
-@@ -2583,7 +2583,7 @@ application read an SBML document contai
+@@ -2693,7 +2693,7 @@ application read an SBML document contai
SBML 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
@@ -676,7 +670,7 @@
declarations. 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
-@@ -38215,7 +38215,7 @@ If the name of a code does not begin wit
+@@ -36352,7 +36352,7 @@ If the name of a code does not begin wit
|libsbml.CompDeprecatedSBaseRefSpelling |The spelling 'sbaseRef' is deprecated |N |N |N |N |N |N |W |
|libsbml.CompSBaseRefMustReferenceObject |An SBaseRef must reference an object. |N |N |N |N |N |N |E |
|libsbml.CompSBaseRefMustReferenceOnlyOneObject |An SBaseRef must reference only one other object. |N |N |N |N |N |N |E |
@@ -685,7 +679,7 @@
|libsbml.CompPortMustReferenceObject |Port must reference an object |N |N |N |N |N |N |E |
|libsbml.CompPortMustReferenceOnlyOneObject |Port must reference only one other object. |N |N |N |N |N |N |E |
|libsbml.CompPortAllowedAttributes |Allowed attributes on a Port |N |N |N |N |N |N |E |
-@@ -38251,7 +38251,7 @@ If the name of a code does not begin wit
+@@ -36388,7 +36388,7 @@ If the name of a code does not begin wit
|libsbml.CompFlatteningNotImplementedReqd |Flattening not implemented for required package. |N |N |N |N |N |N |W |
|libsbml.CompFlatteningWarning |Flattening reference may come from package. |N |N |N |N |N |N |W |
|libsbml.CompDeprecatedDeleteFunction |The performDeletions functions is deprecated. |N |N |N |N |N |N |E |
@@ -694,9 +688,9 @@
|libsbml.CompDeletedReplacement |Element deleted before a subelement could be replaced. |N |N |N |N |N |N |E |
|libsbml.CompIdRefMayReferenceUnknownPackage |The 'comp:idRef' attribute must be the 'id' of a model element |N |N |N |N |N |N |W |
|libsbml.CompMetaIdRefMayReferenceUnknownPkg |The 'comp:metaIdRef' attribute must be the 'metaid' of a model element |N |N |N |N |N |N |W |
---- libsbml-5.9.2.orig/src/sbml/Reaction.h
-+++ libsbml-5.9.2/src/sbml/Reaction.h
-@@ -108,7 +108,7 @@
+--- libsbml-5.10.0.orig/src/sbml/Reaction.h
++++ libsbml-5.10.0/src/sbml/Reaction.h
+@@ -113,7 +113,7 @@
* This attribute is optional in SBML Level 2, with a default of @c
* false; it is mandatory in SBML Level 3 (with no default value). It
* is used to indicate that a reaction occurs on a vastly faster time scale
@@ -705,9 +699,9 @@
* Version 4 specification, which provides more detail about the
* conditions under which a reaction can be considered to be fast in this
* sense. The attribute's default value is @c false. SBML Level 1
---- libsbml-5.9.2.orig/src/sbml/SBMLReader.cpp
-+++ libsbml-5.9.2/src/sbml/SBMLReader.cpp
-@@ -233,7 +233,7 @@ SBMLReader::readInternal (const char* co
+--- libsbml-5.10.0.orig/src/sbml/SBMLReader.cpp
++++ libsbml-5.10.0/src/sbml/SBMLReader.cpp
+@@ -238,7 +238,7 @@ SBMLReader::readInternal (const char* co
if (stream.isError())
{
// If we encountered an error, some parsers will report it sooner
@@ -716,9 +710,9 @@
// opaque call, so we can't change the behavior. Since we don't want
// different parsers to report different validation errors, we bring
// all parsers back to the same point.
---- libsbml-5.9.2.orig/src/sbml/SBMLReader.h
-+++ libsbml-5.9.2/src/sbml/SBMLReader.h
-@@ -180,7 +180,7 @@ public:
+--- libsbml-5.10.0.orig/src/sbml/SBMLReader.h
++++ libsbml-5.10.0/src/sbml/SBMLReader.h
+@@ -185,7 +185,7 @@ public:
* appear first. The error code @if clike (a value drawn from the 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
@@ -727,7 +721,7 @@
* read it) or some sort of file operation error may have been reported
* by the underlying operating system. Callers can check for these
* situations using a program fragment such as the following:
-@@ -301,7 +301,7 @@ public:
+@@ -306,7 +306,7 @@ public:
* appear first. The error code @if clike (a value drawn from the 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
@@ -736,9 +730,9 @@
* read it) or some sort of file operation error may have been reported
* by the underlying operating system. Callers can check for these
* situations using a program fragment such as the following:
---- libsbml-5.9.2.orig/src/sbml/SBase.h
-+++ libsbml-5.9.2/src/sbml/SBase.h
-@@ -2718,7 +2718,7 @@ s.setNotes("<body xmlns='http://www.w3.o
+--- libsbml-5.10.0.orig/src/sbml/SBase.h
++++ libsbml-5.10.0/src/sbml/SBase.h
+@@ -2724,7 +2724,7 @@ 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
@@ -747,9 +741,9 @@
* 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-5.9.2.orig/src/sbml/common/common-documentation.h
-+++ libsbml-5.9.2/src/sbml/common/common-documentation.h
-@@ -5393,7 +5393,7 @@ e><a href="libsbml.html#parseL3Formula(j
+--- libsbml-5.10.0.orig/src/sbml/common/common-documentation.h
++++ libsbml-5.10.0/src/sbml/common/common-documentation.h
+@@ -5414,7 +5414,7 @@ e><a href="libsbml.html#parseL3Formula(j
<td class="s-na">N</td>
<td class="s-error">E</td></tr>
<tr><td><code>@link CompSBMLErrorCode_t#CompNoMultipleReferences CompNoMultipleReferences @endlink</code></td>
@@ -758,7 +752,7 @@
<td class="s-na">N</td>
<td class="s-na">N</td>
<td class="s-na">N</td>
-@@ -5717,7 +5717,7 @@ e><a href="libsbml.html#parseL3Formula(j
+@@ -5738,7 +5738,7 @@ e><a href="libsbml.html#parseL3Formula(j
<td class="s-na">N</td>
<td class="s-error">E</td></tr>
<tr><td><code>@link CompSBMLErrorCode_t#CompDeprecatedReplaceFunction CompDeprecatedReplaceFunction @endlink</code></td>
@@ -767,9 +761,9 @@
<td class="s-na">N</td>
<td class="s-na">N</td>
<td class="s-na">N</td>
---- libsbml-5.9.2.orig/src/sbml/packages/comp/validator/CompSBMLError.h
-+++ libsbml-5.9.2/src/sbml/packages/comp/validator/CompSBMLError.h
-@@ -126,7 +126,7 @@ typedef enum
+--- libsbml-5.10.0.orig/src/sbml/packages/comp/validator/CompSBMLError.h
++++ libsbml-5.10.0/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. */
, CompSBaseRefMustReferenceOnlyOneObject= 1020713 /*!< An SBaseRef must reference only one other object. */
@@ -778,7 +772,7 @@
, CompPortMustReferenceObject = 1020801 /*!< Port must reference an object */
, CompPortMustReferenceOnlyOneObject = 1020802 /*!< Port must reference only one other object. */
-@@ -169,7 +169,7 @@ typedef enum
+@@ -167,7 +167,7 @@ typedef enum
, CompFlatteningNotImplementedReqd = 1090110 /*!< Flattening not implemented for required package. */
, CompFlatteningWarning = 1090111 /*!< Flattening reference may come from package. */
, CompDeprecatedDeleteFunction = 1090112 /*!< The performDeletions functions is deprecated. */
@@ -787,9 +781,9 @@
, 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-5.9.2.orig/src/sbml/packages/comp/validator/CompSBMLErrorTable.h
-+++ libsbml-5.9.2/src/sbml/packages/comp/validator/CompSBMLErrorTable.h
-@@ -951,7 +951,7 @@ static const packageErrorTableEntry comp
+--- libsbml-5.10.0.orig/src/sbml/packages/comp/validator/CompSBMLErrorTable.h
++++ libsbml-5.10.0/src/sbml/packages/comp/validator/CompSBMLErrorTable.h
+@@ -949,7 +949,7 @@ static const packageErrorTableEntry comp
// 1020714
{ CompNoMultipleReferences,
@@ -798,7 +792,7 @@
LIBSBML_CAT_GENERAL_CONSISTENCY,
LIBSBML_SEV_ERROR,
"Any one SBML object may only be referenced in one of the following ways: "
-@@ -1412,7 +1412,7 @@ static const packageErrorTableEntry comp
+@@ -1410,7 +1410,7 @@ static const packageErrorTableEntry comp
// 1090113
{ CompDeprecatedReplaceFunction,
Modified: trunk/packages/libsbml/trunk/debian/rules
===================================================================
--- trunk/packages/libsbml/trunk/debian/rules 2014-04-17 13:54:42 UTC (rev 16721)
+++ trunk/packages/libsbml/trunk/debian/rules 2014-04-17 15:03:09 UTC (rev 16722)
@@ -26,7 +26,7 @@
dh $@ --with-python2 --dbg-package=${dbgpack}
get-orig-source:
- uscan --verbose --force-download --repack --repack-compression xz
+ uscan --verbose --download-current-version --force-download --repack
override_dh_auto_clean:
### the clean target of the libsbml makefile is highly b0rken ###
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