[med-svn] r16463 - in trunk/packages/libsbml/trunk/debian: . bin patches
Ivo Maintz
ivomaintz-guest at moszumanska.debian.org
Tue Mar 18 15:30:33 UTC 2014
Author: ivomaintz-guest
Date: 2014-03-18 15:30:33 +0000 (Tue, 18 Mar 2014)
New Revision: 16463
Added:
trunk/packages/libsbml/trunk/debian/bin/python_fix.sh
trunk/packages/libsbml/trunk/debian/patches/doxygen.patch
trunk/packages/libsbml/trunk/debian/patches/spelling.patch
Removed:
trunk/packages/libsbml/trunk/debian/libsbml5-ruby1.8.docs
trunk/packages/libsbml/trunk/debian/libsbml5-ruby1.8.install
Modified:
trunk/packages/libsbml/trunk/debian/README.source
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/hardening.patch
trunk/packages/libsbml/trunk/debian/patches/mexext.patch
trunk/packages/libsbml/trunk/debian/patches/series
trunk/packages/libsbml/trunk/debian/rules
Log:
fixed some build stopper
removed ruby bindings, they actually don't work with ruby1.9
Modified: trunk/packages/libsbml/trunk/debian/README.source
===================================================================
--- trunk/packages/libsbml/trunk/debian/README.source 2014-03-18 15:01:43 UTC (rev 16462)
+++ trunk/packages/libsbml/trunk/debian/README.source 2014-03-18 15:30:33 UTC (rev 16463)
@@ -1,3 +1,14 @@
+libsbml (5.9.2)
+ * render extension is now included in the source distribution, no extra work to do
+
+libsbml (5.9.0)
+ * again, include the render extension
+
+libsbml (5.8.0)
+ * We want to integrate the render extension:
+ download the render extension --> http://sourceforge.net/projects/sbml/files/libsbml/5.8.0/experimental/src/
+ unpack it to the libsbml source directory and repack the stuff
+
libsbml (5.7.0)
* upstream ships two versions: libSBML-core-src.tar.gz and
libSBML-5.7.0-core-plus-packages-src.tar.gz (with the COMP extension)
Added: trunk/packages/libsbml/trunk/debian/bin/python_fix.sh
===================================================================
--- trunk/packages/libsbml/trunk/debian/bin/python_fix.sh (rev 0)
+++ trunk/packages/libsbml/trunk/debian/bin/python_fix.sh 2014-03-18 15:30:33 UTC (rev 16463)
@@ -0,0 +1,5 @@
+#!/bin/sh
+PYTH=$(basename $(python-config --includes | awk '{print $1}' | cut -dI -f2))
+LINE=$(grep -n src/bindings/python/CMakeFiles/binding_python_lib.dir/depend build/CMakeFiles/Makefile2 | cut -d: -f1)
+
+sed -i ""$LINE"i\\\tsed -i \"s#<Python.h>#<"$PYTH"/Python.h>#g\" src/bindings/python/libsbml_wrap.cpp" build/CMakeFiles/Makefile2
Modified: trunk/packages/libsbml/trunk/debian/changelog
===================================================================
--- trunk/packages/libsbml/trunk/debian/changelog 2014-03-18 15:01:43 UTC (rev 16462)
+++ trunk/packages/libsbml/trunk/debian/changelog 2014-03-18 15:30:33 UTC (rev 16463)
@@ -1,11 +1,16 @@
libsbml (5.9.2-1) UNRELEASED; urgency=medium
+ [ Andreas Tille ]
* New upstream version
* debian/upstream -> debian/upstream/metadata
* debian/control: Drop explicite ruby version in Build-Dependencies
- -- Andreas Tille <tille at debian.org> Thu, 27 Feb 2014 08:17:40 +0000
+ [ 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
+ -- Ivo Maintz <ivo at maintz.de> Wed, 05 Mar 2014 10:16:44 +0100
+
libsbml (5.8.0-2) unstable; urgency=medium
* Put *.m files in the Octave path (thanks for the patch to
@@ -20,10 +25,6 @@
* update from upstream
* switched to cmake for configure (following upstream)
* added a patch to use correct matlab extensions in chrooted environments
- * (re)added doc packages for libsbml5, libsbml5-cil, libsbml5-java,
- libsbml5-python and libsbml5-perl
- * debian/*postinst and debian/*postrm:
- fixed to work on upgrade/downgrade too
[ Andreas Tille ]
* debian/control:
Modified: trunk/packages/libsbml/trunk/debian/cmake_opts
===================================================================
--- trunk/packages/libsbml/trunk/debian/cmake_opts 2014-03-18 15:01:43 UTC (rev 16462)
+++ trunk/packages/libsbml/trunk/debian/cmake_opts 2014-03-18 15:30:33 UTC (rev 16463)
@@ -4,6 +4,8 @@
-DENABLE_COMP:BOOL=ON
-DENABLE_FBC:BOOL=ON
-DENABLE_LAYOUT:BOOL=ON
+-DENABLE_GROUPS=ON
+-DENABLE_RENDER=ON
-DWITH_BZIP2:BOOL=ON
-DWITH_CHECK:BOOL=OFF
-DWITH_CPP_NAMESPACE:BOOL=ON
@@ -19,8 +21,9 @@
-DWITH_OCTAVE:BOOL=ON
-DWITH_PERL:BOOL=ON
-DWITH_PYTHON:BOOL=ON
+-DWITH_PYTHON_INCLUDE:PATH=/usr/include/python2.7
-DWITH_R:BOOL=ON
--DWITH_RUBY:BOOL=ON
+-DWITH_RUBY:BOOL=OFF
-DWITH_SWIG:BOOL=ON
-DWITH_WALL:BOOL=ON
-DWITH_XERCES:BOOL=OFF
Modified: trunk/packages/libsbml/trunk/debian/control
===================================================================
--- trunk/packages/libsbml/trunk/debian/control 2014-03-18 15:01:43 UTC (rev 16462)
+++ trunk/packages/libsbml/trunk/debian/control 2014-03-18 15:30:33 UTC (rev 16463)
@@ -5,30 +5,29 @@
Section: science
Priority: optional
Build-Depends: autoconf,
- automake,
- debhelper (>= 9.0.0),
- cmake,
- doxygen (>= 1.8.0),
- swig (>= 2),
- ruby,
- libxml2-dev,
- python-dev,
- ruby-dev,
- perl,
- libperl-dev,
- default-jdk | openjdk-7-jdk,
- octave-pkg-dev,
- r-base-dev,
- r-base-core,
- python-support,
- graphviz,
- zlib1g-dev,
- libbz2-dev,
- mono-devel,
- mono-gmcs,
- cli-common-dev,
- mono-runtime | cli-runtime,
- dpkg-dev (>= 1.16.1~)
+ automake,
+ debhelper (>= 9.0.0),
+ cmake,
+ doxygen (>= 1.8.0),
+ swig (>= 2),
+ libxml2-dev,
+ python-dev,
+ perl,
+ libperl-dev,
+ default-jdk | openjdk-7-jdk | java-gcj-compat-dev | java-sdk,
+ octave-pkg-dev,
+ r-base-dev,
+ r-base-core,
+ python-support,
+ graphviz,
+ zlib1g-dev,
+ libbz2-dev,
+ mono-devel,
+ mono-gmcs,
+ cli-common-dev,
+ cli-runtime,
+ dpkg-dev (>= 1.16.1~),
+ texlive-latex-base
Standards-Version: 3.9.5
Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/libsbml/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/libsbml/trunk/
@@ -97,19 +96,18 @@
but rather a library you can embed in your own applications.
This package contains the Python bindings of LibSBML.
-
-Package: libsbml5-ruby
+Package: libsbml5-matlab
+Section: contrib/math
+Provides: libsbml-matlab
+Conflicts: libsbml4-matlab
Architecture: any
-Section: ruby
-Depends: ${shlibs:Depends},
- ${misc:Depends}
-Provides: libsbml-ruby
-Description: System Biology Markup Language library - Ruby binding
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: System Biology Markup Language library - Matlab bindings
LibSBML is a library designed to help you read, write, manipulate,
translate, and validate SBML files and data streams. It is not an
application itself (though it does come with many example programs),
but rather a library you can embed in your own applications.
- This package contains the Ruby binding of LibSBML.
+ This package contains the Matlab bindings of LibSBML.
Package: libsbml5-java
Architecture: any
Modified: trunk/packages/libsbml/trunk/debian/control.in
===================================================================
--- trunk/packages/libsbml/trunk/debian/control.in 2014-03-18 15:01:43 UTC (rev 16462)
+++ trunk/packages/libsbml/trunk/debian/control.in 2014-03-18 15:30:33 UTC (rev 16463)
@@ -5,30 +5,29 @@
Section: science
Priority: optional
Build-Depends: autoconf,
- automake,
- debhelper (>= 9.0.0),
- cmake,
- doxygen (>= 1.8.0),
- swig (>= 2),
- ruby,
- libxml2-dev,
- python-dev,
- ruby-dev,
- perl,
- libperl-dev,
- default-jdk | openjdk-7-jdk,
- octave-pkg-dev,
- r-base-dev,
- r-base-core,
- python-support,
- graphviz,
- zlib1g-dev,
- libbz2-dev,
- mono-devel,
- mono-gmcs,
- cli-common-dev,
- mono-runtime | cli-runtime,
- dpkg-dev (>= 1.16.1~)
+ automake,
+ debhelper (>= 9.0.0),
+ cmake,
+ doxygen (>= 1.8.0),
+ swig (>= 2),
+ libxml2-dev,
+ python-dev,
+ perl,
+ libperl-dev,
+ default-jdk | openjdk-7-jdk | java-gcj-compat-dev | java-sdk,
+ octave-pkg-dev,
+ r-base-dev,
+ r-base-core,
+ python-support,
+ graphviz,
+ zlib1g-dev,
+ libbz2-dev,
+ mono-devel,
+ mono-gmcs,
+ cli-common-dev,
+ cli-runtime,
+ dpkg-dev (>= 1.16.1~),
+ texlive-latex-base
Standards-Version: 3.9.5
Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/libsbml/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/libsbml/trunk/
@@ -110,19 +109,6 @@
# but rather a library you can embed in your own applications.
# This package contains the Matlab bindings of LibSBML.
-Package: libsbml5-ruby
-Architecture: any
-Section: ruby
-Depends: ${shlibs:Depends},
- ${misc:Depends}
-Provides: libsbml-ruby
-Description: System Biology Markup Language library - Ruby binding
- LibSBML is a library designed to help you read, write, manipulate,
- translate, and validate SBML files and data streams. It is not an
- application itself (though it does come with many example programs),
- but rather a library you can embed in your own applications.
- This package contains the Ruby binding of LibSBML.
-
Package: libsbml5-java
Architecture: any
Section: java
Deleted: trunk/packages/libsbml/trunk/debian/libsbml5-ruby1.8.docs
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-ruby1.8.docs 2014-03-18 15:01:43 UTC (rev 16462)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-ruby1.8.docs 2014-03-18 15:30:33 UTC (rev 16463)
@@ -1 +0,0 @@
-changelog
Deleted: trunk/packages/libsbml/trunk/debian/libsbml5-ruby1.8.install
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-ruby1.8.install 2014-03-18 15:01:43 UTC (rev 16462)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-ruby1.8.install 2014-03-18 15:30:33 UTC (rev 16463)
@@ -1 +0,0 @@
-usr/lib/ruby
Added: trunk/packages/libsbml/trunk/debian/patches/doxygen.patch
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/doxygen.patch (rev 0)
+++ trunk/packages/libsbml/trunk/debian/patches/doxygen.patch 2014-03-18 15:30:33 UTC (rev 16463)
@@ -0,0 +1,30 @@
+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
+ .
+ * New upstream version
+ * debian/upstream -> debian/upstream/metadata
+ * debian/control: Drop explicite ruby version in Build-Dependencies
+Author: Ivo Miantz <ivo at maintz.de>
+
+---
+Last-Update: 2014-02-27
+
+Index: libsbml-5.9.2/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 @@
+ 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)
+- file(TO_NATIVE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/src/doxygen-tabs.css tabs_css)
+- file(TO_NATIVE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/src/search.png search_png)
+- file(TO_NATIVE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/src/search.css search_css)
++ file(TO_NATIVE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/src/css/libsbml-doxygen-tabs.css tabs_css)
++ file(TO_NATIVE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/src/css/search.png search_png)
++ file(TO_NATIVE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/src/css/search.css search_css)
+
+ file(TO_NATIVE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/src/doxygen-config-${lang}.txt api_doc)
+
Modified: trunk/packages/libsbml/trunk/debian/patches/hardening.patch
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/hardening.patch 2014-03-18 15:01:43 UTC (rev 16462)
+++ trunk/packages/libsbml/trunk/debian/patches/hardening.patch 2014-03-18 15:30:33 UTC (rev 16463)
@@ -8,9 +8,11 @@
---
Last-Update: <2013-01-22>
---- a/src/bindings/matlab/Makefile.in
-+++ b/src/bindings/matlab/Makefile.in
-@@ -70,12 +70,7 @@ distfiles = \
+Index: libsbml-5.9.0/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
+@@ -70,12 +70,7 @@
installSBML.m \
isoctave.m \
matlab-tags-regexp.txt \
@@ -24,7 +26,7 @@
test.xml \
test/CMakeLists.txt
-@@ -142,7 +137,7 @@ endif
+@@ -142,7 +137,7 @@
# is really necessary, but it seems prudent.
define matlabrun
@@ -33,9 +35,11 @@
$(LIBTOOL) -dlopen $(TOP_BUILDDIR)/src/libsbml.la --mode=execute $(1)
endef
---- a/src/bindings/matlab/mexopts-R2009-R2010.sh
-+++ b/src/bindings/matlab/mexopts-R2009-R2010.sh
-@@ -324,7 +324,13 @@ echo "Error: Did not imbed 'options.sh'
+Index: libsbml-5.9.0/src/bindings/matlab/mexopts-R2009-R2010.sh
+===================================================================
+--- libsbml-5.9.0.orig/src/bindings/matlab/mexopts-R2009-R2010.sh 2013-11-28 14:51:16.191345434 +0100
++++ libsbml-5.9.0/src/bindings/matlab/mexopts-R2009-R2010.sh 2013-11-28 14:51:16.183345349 +0100
+@@ -324,7 +324,13 @@
#
#----------------------------------------------------------------------------
# CC="$CC"
@@ -50,9 +54,11 @@
# COPTIMFLAGS="$COPTIMFLAGS"
# CDEBUGFLAGS="$CDEBUGFLAGS"
# CLIBS="$CLIBS"
---- a/src/bindings/perl/Makefile.in
-+++ b/src/bindings/perl/Makefile.in
-@@ -177,6 +177,8 @@ ifeq (GCC,$(findstring GCC,$(shell $(CXX
+Index: libsbml-5.9.0/src/bindings/perl/Makefile.in
+===================================================================
+--- libsbml-5.9.0.orig/src/bindings/perl/Makefile.in 2013-11-28 14:51:16.191345434 +0100
++++ libsbml-5.9.0/src/bindings/perl/Makefile.in 2013-11-28 14:51:16.183345349 +0100
+@@ -177,6 +177,8 @@
endif
@@ -61,9 +67,11 @@
# If the last run was made with --enable-layout and this one isn't, or
# vice-versa, the swig wrap files will be wrong for this run. However, you
# can't tell just by looking at file mod times, so you can't use normal
---- a/config/makefile-common-actions.mk
-+++ b/config/makefile-common-actions.mk
-@@ -72,6 +72,15 @@ endif
+Index: libsbml-5.9.0/config/makefile-common-actions.mk
+===================================================================
+--- libsbml-5.9.0.orig/config/makefile-common-actions.mk 2013-11-28 14:51:16.191345434 +0100
++++ libsbml-5.9.0/config/makefile-common-actions.mk 2013-11-28 14:51:16.183345349 +0100
+@@ -72,6 +72,15 @@
# here is only to remove duplicates, which the 'sort' function does as a
# documented side-effect.)
Modified: trunk/packages/libsbml/trunk/debian/patches/mexext.patch
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/mexext.patch 2014-03-18 15:01:43 UTC (rev 16462)
+++ trunk/packages/libsbml/trunk/debian/patches/mexext.patch 2014-03-18 15:30:33 UTC (rev 16463)
@@ -4,11 +4,11 @@
Author: Ivo Maintz <ivo at maintz.de>
---
-Last-Update: <2013-03-14>
+Last-Update: <2014-03-01>
---- a/src/bindings/matlab/FindMatlab.cmake
-+++ b/src/bindings/matlab/FindMatlab.cmake
-@@ -194,7 +194,7 @@ IF(WIN32)
+--- libsbml-5.9.2.orig/src/bindings/matlab/FindMatlab.cmake
++++ libsbml-5.9.2/src/bindings/matlab/FindMatlab.cmake
+@@ -162,7 +162,7 @@ IF(WIN32)
SET(MATLAB_MATLAB_COMMAND "${MATLAB_ROOT_PATH}/bin/matlab.bat")
ELSE (WIN32)
SET(MATLAB_MEX_COMMAND "${MATLAB_ROOT_PATH}/bin/mex")
Modified: trunk/packages/libsbml/trunk/debian/patches/series
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/series 2014-03-18 15:01:43 UTC (rev 16462)
+++ trunk/packages/libsbml/trunk/debian/patches/series 2014-03-18 15:30:33 UTC (rev 16463)
@@ -1,3 +1,5 @@
hardening.patch
mexext.patch
format-security.patch
+doxygen.patch
+spelling.patch
Added: trunk/packages/libsbml/trunk/debian/patches/spelling.patch
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/spelling.patch (rev 0)
+++ trunk/packages/libsbml/trunk/debian/patches/spelling.patch 2014-03-18 15:30:33 UTC (rev 16463)
@@ -0,0 +1,809 @@
+Description: fix spelling errors
+ fixes a lot of spelling errors in the sources
+ .
+ libsbml (5.9.2-1) UNRELEASED; urgency=medium
+ .
+ [ Andreas Tille ]
+ * 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
+
+--- libsbml-5.9.2.orig/OLD_NEWS.txt
++++ libsbml-5.9.2/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
+@@ -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
+ consult your systems administrator or (if you have administrator
+-priviledges) reset the permissions yourself.
++privileges) reset the permissions yourself.
+
+
+ <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 @@
+ * 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
+- * or because the user does not have the necessary access priviledges to
++ * or because the user does not have the necessary access privileges to
+ * 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 @@
+ * 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
+- * or because the user does not have the necessary access priviledges to
++ * or because the user does not have the necessary access privileges to
+ * 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
+ * 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
+- * an other SBMLDocument with different package namespace declarations.
++ * another SBMLDocument with different package namespace 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 to help clarify this:
+@@ -25419,7 +25419,7 @@ 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
+- * than others in a system. Readers are directed to the SBML Level 2
++ * thanothers in a system. Readers are directed to the SBML Level 2
+ * 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:
+ <td class=\'s-na\'>N</td>
+ <td class=\'s-error\'>E</td></tr>
+ <tr><td><code>@link libsbmlcs.libsbml.CompNoMultipleReferences CompNoMultipleReferences @endlink</code></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>
+@@ -51530,7 +51530,7 @@ 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>
+-<td> The performReplacementsAndConversions fuctions is deprecated. </td>
++<td> The performReplacementsAndConversions functions is deprecated. </td>
+ <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
+@@ -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
+ * is used to indicate that a reaction occurs on a vastly faster time scale
+- * than others in a system. Readers are directed to the SBML Level 2
++ * thanothers in a system. Readers are directed to the SBML Level 2
+ * 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
+@@ -4530,7 +4530,7 @@ namespace libsbml {
+ <td class='s-na'>N</td>
+ <td class='s-error'>E</td></tr>
+ <tr><td><code>@link libsbmlcs.libsbml.CompNoMultipleReferences CompNoMultipleReferences @endlink</code></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>
+@@ -4854,7 +4854,7 @@ namespace libsbml {
+ <td class='s-na'>N</td>
+ <td class='s-error'>E</td></tr>
+ <tr><td><code>@link libsbmlcs.libsbml.CompDeprecatedReplaceFunction CompDeprecatedReplaceFunction @endlink</code></td>
+-<td> The performReplacementsAndConversions fuctions is deprecated. </td>
++<td> The performReplacementsAndConversions functions is deprecated. </td>
+ <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
+@@ -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,
+ * a file might be unreadable (either because it does not actually exist
+- * or because the user does not have the necessary access priviledges to
++ * or because the user does not have the necessary access privileges to
+ * 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:
+@@ -340,7 +340,7 @@ 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,
+ * a file might be unreadable (either because it does not actually exist
+- * or because the user does not have the necessary access priviledges to
++ * or because the user does not have the necessary access privileges to
+ * 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
+ * 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
+- * an other SBMLDocument with different package namespace declarations.
++ * another SBMLDocument with different package namespace 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 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
+@@ -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
+ * is used to indicate that a reaction occurs on a vastly faster time scale
+- * than others in a system. Readers are directed to the SBML Level 2
++ * thanothers in a system. Readers are directed to the SBML Level 2
+ * 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
+@@ -4530,7 +4530,7 @@ namespace libsbmlcs {
+ <td class='s-na'>N</td>
+ <td class='s-error'>E</td></tr>
+ <tr><td><code>@link libsbmlcs.libsbml.CompNoMultipleReferences CompNoMultipleReferences @endlink</code></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>
+@@ -4854,7 +4854,7 @@ namespace libsbmlcs {
+ <td class='s-na'>N</td>
+ <td class='s-error'>E</td></tr>
+ <tr><td><code>@link libsbmlcs.libsbml.CompDeprecatedReplaceFunction CompDeprecatedReplaceFunction @endlink</code></td>
+-<td> The performReplacementsAndConversions fuctions is deprecated. </td>
++<td> The performReplacementsAndConversions functions is deprecated. </td>
+ <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
+@@ -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,
+ * a file might be unreadable (either because it does not actually exist
+- * or because the user does not have the necessary access priviledges to
++ * or because the user does not have the necessary access privileges to
+ * 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:
+@@ -341,7 +341,7 @@ 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,
+ * a file might be unreadable (either because it does not actually exist
+- * or because the user does not have the necessary access priviledges to
++ * or because the user does not have the necessary access privileges to
+ * 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
+ * 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
+- * an other SBMLDocument with different package namespace declarations.
++ * another SBMLDocument with different package namespace 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 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
+@@ -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
+ * is used to indicate that a reaction occurs on a vastly faster time scale
+- * than others in a system. Readers are directed to the SBML Level 2
++ * thanothers in a system. Readers are directed to the SBML Level 2
+ * 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
+@@ -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 class='s-na'>N</td>
+ <td class='s-na'>N</td>
+ <td class='s-na'>N</td>
+@@ -4762,7 +4762,7 @@ 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>
+-<td> The performReplacementsAndConversions fuctions is deprecated. </td>
++<td> The performReplacementsAndConversions functions is deprecated. </td>
+ <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
+@@ -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,
+ * a file might be unreadable (either because it does not actually exist
+- * or because the user does not have the necessary access priviledges to
++ * or because the user does not have the necessary access privileges to
+ * 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:
+@@ -288,7 +288,7 @@ 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,
+ * a file might be unreadable (either because it does not actually exist
+- * or because the user does not have the necessary access priviledges to
++ * or because the user does not have the necessary access privileges to
+ * 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.
+ * 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
+- * an other {@link SBMLDocument} with different package namespace declarations.
++ * another {@link SBMLDocument} with different package namespace 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 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.
+ * 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
+- * or because the user does not have the necessary access priviledges to
++ * or because the user does not have the necessary access privileges to
+ * 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.
+ * 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
+- * or because the user does not have the necessary access priviledges to
++ * or because the user does not have the necessary access privileges to
+ * 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.
+ * 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
+- * an other {@link SBMLDocument} with different package namespace declarations.
++ * another {@link SBMLDocument} with different package namespace 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 to help clarify this:
+@@ -24852,7 +24852,7 @@ 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
+- * than others in a system. Readers are directed to the SBML Level 2
++ * thanothers in a system. Readers are directed to the SBML Level 2
+ * 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.
+ <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 class=\'s-na\'>N</td>
+ <td class=\'s-na\'>N</td>
+ <td class=\'s-na\'>N</td>
+@@ -51728,7 +51728,7 @@ 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>
+-<td> The performReplacementsAndConversions fuctions is deprecated. </td>
++<td> The performReplacementsAndConversions functions is deprecated. </td>
+ <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
+ 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
+-or because the user does not have the necessary access priviledges to
++or because the user does not have the necessary access privileges to
+ 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
+ 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
+-or because the user does not have the necessary access priviledges to
++or because the user does not have the necessary access privileges to
+ 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
+ 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
+-an other SBMLDocument with different package namespace declarations.
++another SBMLDocument with different package namespace 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 to help clarify this:
+@@ -16920,7 +16920,7 @@ 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
+-than others in a system. Readers are directed to the SBML Level 2
++thanothers in a system. Readers are directed to the SBML Level 2
+ 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
+ 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
+-or because the user does not have the necessary access priviledges to
++or because the user does not have the necessary access privileges to
+ 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
+ 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
+-or because the user does not have the necessary access priviledges to
++or because the user does not have the necessary access privileges to
+ 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
+ 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
+-an other SBMLDocument with different package namespace declarations.
++another SBMLDocument with different package namespace 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 to help clarify this:
+@@ -16907,7 +16907,7 @@ 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
+-than others in a system. Readers are directed to the SBML Level 2
++thanothers in a system. Readers are directed to the SBML Level 2
+ 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
+@@ -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
+ actually exist or because the user does not have the necessary access
+- priviledges to read it) or some sort of file operation error may have
++ privileges to 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:
+
+@@ -1195,7 +1195,7 @@ 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
+- priviledges to read it) or some sort of file operation error may have
++ privileges to 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:
+
+@@ -1279,7 +1279,7 @@ 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
+- priviledges to read it) or some sort of file operation error may have
++ privileges to 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:
+
+@@ -4650,7 +4650,7 @@ 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
+- an other SBMLDocument with different package namespace declarations.
++ another SBMLDocument with different package namespace 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 to help clarify this:
+@@ -25541,7 +25541,7 @@ 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
+- than others in a system. Readers are directed to the SBML Level 2
++ thanothers in a system. Readers are directed to the SBML Level 2
+ 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):
+ <td class='s-na'>N</td>
+ <td class='s-error'>E</td></tr>
+ <tr><td><code>@link libsbml.CompNoMultipleReferences CompNoMultipleReferences @endlink</code></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>
+@@ -53063,7 +53063,7 @@ 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>
+- <td> The performReplacementsAndConversions fuctions is deprecated. </td>
++ <td> The performReplacementsAndConversions functions is deprecated. </td>
+ <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
+@@ -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
+ actually exist or because the user does not have the necessary access
+- priviledges to read it) or some sort of file operation error may have
++ privileges to 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:
+
+@@ -1184,7 +1184,7 @@ 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
+- priviledges to read it) or some sort of file operation error may have
++ privileges to 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:
+
+@@ -1268,7 +1268,7 @@ 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
+- priviledges to read it) or some sort of file operation error may have
++ privileges to 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:
+
+@@ -4148,7 +4148,7 @@ 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
+- from an other SBMLDocument with different package namespace
++ from another SBMLDocument with different package namespace
+ 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):
+ |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 |
+- |libsbml.CompNoMultipleReferences |Objects may not be referenced by mutiple SBaseRef constructs. |N |N |N |N |N |N |E |
++ |libsbml.CompNoMultipleReferences |Objects may not be referenced by multiple SBaseRef constructs. |N |N |N |N |N |N |E |
+ |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):
+ |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 |
+- |libsbml.CompDeprecatedReplaceFunction |The performReplacementsAndConversions fuctions is deprecated. |N |N |N |N |N |N |E |
++ |libsbml.CompDeprecatedReplaceFunction |The performReplacementsAndConversions functions is deprecated. |N |N |N |N |N |N |E |
+ |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[] = {
+ "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"
+- "priviledges to read it) or some sort of file operation error may have\n"
++ "privileges to read it) or some sort of file operation error may have\n"
+ "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[] = {
+ "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"
+- "priviledges to read it) or some sort of file operation error may have\n"
++ "privileges to read it) or some sort of file operation error may have\n"
+ "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[] = {
+ "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"
+- "from an other SBMLDocument with different package namespace\n"
++ "from another SBMLDocument with different package namespace\n"
+ "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&)
+ 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
+- priviledges to read it) or some sort of file operation error may have
++ privileges to 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:
+
+@@ -674,7 +674,7 @@ 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
+- priviledges to read it) or some sort of file operation error may have
++ privileges to 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:
+
+@@ -772,7 +772,7 @@ 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
+- priviledges to read it) or some sort of file operation error may have
++ privileges to 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/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
+ 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
+-or because the user does not have the necessary access priviledges to
++or because the user does not have the necessary access privileges to
+ 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
+ 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
+-or because the user does not have the necessary access priviledges to
++or because the user does not have the necessary access privileges to
+ 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
+ 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
+-an other SBMLDocument with different package namespace declarations.
++another SBMLDocument with different package namespace 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 to help clarify this:
+@@ -21914,7 +21914,7 @@ 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
+-than others in a system. Readers are directed to the SBML Level 2
++thanothers in a system. Readers are directed to the SBML Level 2
+ 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
+ <td class=\'s-na\'>N</td>
+ <td class=\'s-error\'>E</td></tr>
+ <tr><td><code>@link libsbml.CompNoMultipleReferences CompNoMultipleReferences @endlink</code></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>
+@@ -45418,7 +45418,7 @@ 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>
+-<td> The performReplacementsAndConversions fuctions is deprecated. </td>
++<td> The performReplacementsAndConversions functions is deprecated. </td>
+ <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
+ 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
+-priviledges to read it) or some sort of file operation error may have
++privileges to 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:
+
+@@ -246,7 +246,7 @@ 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
+-priviledges to read it) or some sort of file operation error may have
++privileges to 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:
+
+@@ -2583,7 +2583,7 @@ 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
+-from an other SBMLDocument with different package namespace
++from another SBMLDocument with different package namespace
+ 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
+ |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 |
+- |libsbml.CompNoMultipleReferences |Objects may not be referenced by mutiple SBaseRef constructs. |N |N |N |N |N |N |E |
++ |libsbml.CompNoMultipleReferences |Objects may not be referenced by multiple SBaseRef constructs. |N |N |N |N |N |N |E |
+ |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
+ |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 |
+- |libsbml.CompDeprecatedReplaceFunction |The performReplacementsAndConversions fuctions is deprecated. |N |N |N |N |N |N |E |
++ |libsbml.CompDeprecatedReplaceFunction |The performReplacementsAndConversions functions is deprecated. |N |N |N |N |N |N |E |
+ |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 @@
+ * 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
+- * than others in a system. Readers are directed to the SBML Level 2
++ * thanothers in a system. Readers are directed to the SBML Level 2
+ * 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
+ if (stream.isError())
+ {
+ // If we encountered an error, some parsers will report it sooner
+- // than others. Unfortunately, those that fail sooner do it in an
++ // thanothers. Unfortunately, those that fail sooner do it in an
+ // 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:
+ * 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
+- * or because the user does not have the necessary access priviledges to
++ * or because the user does not have the necessary access privileges to
+ * 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:
+ * 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
+- * or because the user does not have the necessary access priviledges to
++ * or because the user does not have the necessary access privileges to
+ * 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
+ * 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
+- * an other SBMLDocument with different package namespace declarations.
++ * another SBMLDocument with different package namespace 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 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
+ <td class="s-na">N</td>
+ <td class="s-error">E</td></tr>
+ <tr><td><code>@link CompSBMLErrorCode_t#CompNoMultipleReferences CompNoMultipleReferences @endlink</code></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>
+@@ -5717,7 +5717,7 @@ 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>
+-<td> The performReplacementsAndConversions fuctions is deprecated. </td>
++<td> The performReplacementsAndConversions functions is deprecated. </td>
+ <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
+ , 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. */
+-, CompNoMultipleReferences = 1020714 /*!< Objects may not be referenced by mutiple SBaseRef constructs. */
++, CompNoMultipleReferences = 1020714 /*!< Objects may not be referenced by multiple SBaseRef constructs. */
+
+ , CompPortMustReferenceObject = 1020801 /*!< Port must reference an object */
+ , CompPortMustReferenceOnlyOneObject = 1020802 /*!< Port must reference only one other object. */
+@@ -169,7 +169,7 @@ 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. */
+-, CompDeprecatedReplaceFunction = 1090113 /*!< The performReplacementsAndConversions fuctions is deprecated. */
++, CompDeprecatedReplaceFunction = 1090113 /*!< The performReplacementsAndConversions functions is deprecated. */
+ , 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
+
+ // 1020714
+ { CompNoMultipleReferences,
+- "Objects may not be referenced by mutiple SBaseRef constructs.",
++ "Objects may not be referenced by multiple SBaseRef constructs.",
+ 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
+
+ // 1090113
+ { CompDeprecatedReplaceFunction,
+- "The performReplacementsAndConversions fuctions is deprecated.",
++ "The performReplacementsAndConversions functions is deprecated.",
+ LIBSBML_CAT_GENERAL_CONSISTENCY,
+ LIBSBML_SEV_ERROR,
+ "The software used to process this hierarchical model used the deprecated "
Modified: trunk/packages/libsbml/trunk/debian/rules
===================================================================
--- trunk/packages/libsbml/trunk/debian/rules 2014-03-18 15:01:43 UTC (rev 16462)
+++ trunk/packages/libsbml/trunk/debian/rules 2014-03-18 15:30:33 UTC (rev 16463)
@@ -47,6 +47,7 @@
sed -i 's/overriden/overridden/g' $(shell grep -Rl overriden src/) || true
mkdir -p build
cd build ; cmake $(CMAKE_OPTS) ../
+ /bin/sh debian/bin/python_fix.sh
override_dh_auto_build:
cd build ; make
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