[med-svn] r10189 - in trunk/packages/libsbml/trunk/debian: . patches
Ivo Maintz
ivomaintz-guest at alioth.debian.org
Fri Mar 30 12:16:21 UTC 2012
Author: ivomaintz-guest
Date: 2012-03-30 12:16:20 +0000 (Fri, 30 Mar 2012)
New Revision: 10189
Added:
trunk/packages/libsbml/trunk/debian/libsbml5-cil.docs
trunk/packages/libsbml/trunk/debian/libsbml5-dev.docs
trunk/packages/libsbml/trunk/debian/libsbml5-example.docs
trunk/packages/libsbml/trunk/debian/libsbml5-java.docs
trunk/packages/libsbml/trunk/debian/libsbml5-matlab.docs
trunk/packages/libsbml/trunk/debian/libsbml5-octave.docs
trunk/packages/libsbml/trunk/debian/libsbml5-perl.docs
trunk/packages/libsbml/trunk/debian/libsbml5-python.docs
trunk/packages/libsbml/trunk/debian/libsbml5-ruby1.8.docs
trunk/packages/libsbml/trunk/debian/libsbml5.docs
trunk/packages/libsbml/trunk/debian/patches/
trunk/packages/libsbml/trunk/debian/patches/series
trunk/packages/libsbml/trunk/debian/patches/spelling.patch
Modified:
trunk/packages/libsbml/trunk/debian/rules
Log:
some tweaks regarding lintian remarks
Added: trunk/packages/libsbml/trunk/debian/libsbml5-cil.docs
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-cil.docs (rev 0)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-cil.docs 2012-03-30 12:16:20 UTC (rev 10189)
@@ -0,0 +1 @@
+changelog
Added: trunk/packages/libsbml/trunk/debian/libsbml5-dev.docs
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-dev.docs (rev 0)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-dev.docs 2012-03-30 12:16:20 UTC (rev 10189)
@@ -0,0 +1 @@
+changelog
Added: trunk/packages/libsbml/trunk/debian/libsbml5-example.docs
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-example.docs (rev 0)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-example.docs 2012-03-30 12:16:20 UTC (rev 10189)
@@ -0,0 +1 @@
+changelog
Added: trunk/packages/libsbml/trunk/debian/libsbml5-java.docs
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-java.docs (rev 0)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-java.docs 2012-03-30 12:16:20 UTC (rev 10189)
@@ -0,0 +1 @@
+changelog
Added: trunk/packages/libsbml/trunk/debian/libsbml5-matlab.docs
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-matlab.docs (rev 0)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-matlab.docs 2012-03-30 12:16:20 UTC (rev 10189)
@@ -0,0 +1 @@
+changelog
Added: trunk/packages/libsbml/trunk/debian/libsbml5-octave.docs
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-octave.docs (rev 0)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-octave.docs 2012-03-30 12:16:20 UTC (rev 10189)
@@ -0,0 +1 @@
+changelog
Added: trunk/packages/libsbml/trunk/debian/libsbml5-perl.docs
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-perl.docs (rev 0)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-perl.docs 2012-03-30 12:16:20 UTC (rev 10189)
@@ -0,0 +1 @@
+changelog
Added: trunk/packages/libsbml/trunk/debian/libsbml5-python.docs
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-python.docs (rev 0)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-python.docs 2012-03-30 12:16:20 UTC (rev 10189)
@@ -0,0 +1 @@
+changelog
Added: trunk/packages/libsbml/trunk/debian/libsbml5-ruby1.8.docs
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-ruby1.8.docs (rev 0)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-ruby1.8.docs 2012-03-30 12:16:20 UTC (rev 10189)
@@ -0,0 +1 @@
+changelog
Added: trunk/packages/libsbml/trunk/debian/libsbml5.docs
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5.docs (rev 0)
+++ trunk/packages/libsbml/trunk/debian/libsbml5.docs 2012-03-30 12:16:20 UTC (rev 10189)
@@ -0,0 +1,6 @@
+changelog
+AUTHORS.txt
+FUNDING.txt
+README.txt
+README.txt
+VERSION.txt
Added: trunk/packages/libsbml/trunk/debian/patches/series
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/series (rev 0)
+++ trunk/packages/libsbml/trunk/debian/patches/series 2012-03-30 12:16:20 UTC (rev 10189)
@@ -0,0 +1 @@
+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 2012-03-30 12:16:20 UTC (rev 10189)
@@ -0,0 +1,1441 @@
+Description: Spelling errors
+ There are a lot of similar spellling errors, so I did simply
+ "grep -Rl overriden * | xargs sed -i 's/overriden/overridden/'"
+ "grep -Rl pacakge * | xargs sed -i 's/pacakge/package/'"
+ .
+ libsbml (5.4.1-1) UNRELEASED; urgency=low
+ .
+ [ Ivo Maintz ]
+ * update from upstream (Closes: #665837)
+ * debian/control.in: added swig to libsbml5-python dependencies
+ * debian/README.source:
+ added some information
+ .
+ [ Andreas Tille ]
+ * debian/control:
+ - Added Homepage field
+ - Versioned debhelper dependency
+ * debian/compat: 8
+ * debian/rules:
+ - remove useless dh_make boilerplate
+ - adapt get-orig-source target to what is written
+ in README.source and removed older repackaging
+ code
+ * mv debian/README.Debian-source debian/README.source
+ * debian/docs: No point in installing debian/README.source
+ * delete advise about how to get the source tarball in favour
+ of the code written in debian/rules:get-orig-source target
+ * debian/upstream: citation information
+Author: Andreas Tille <tille at debian.org>
+Bug-Debian: http://bugs.debian.org/665837
+
+---
+The information above should follow the Patch Tagging Guidelines, please
+checkout http://dep.debian.net/deps/dep3/ to learn about the format. Here
+are templates for supplementary fields that you might want to add:
+
+Origin: <vendor|upstream|other>, <url of original patch>
+Bug: <url in upstream bugtracker>
+Bug-Debian: http://bugs.debian.org/<bugnumber>
+Bug-Ubuntu: https://launchpad.net/bugs/<bugnumber>
+Forwarded: <no|not-needed|url proving that it has been forwarded>
+Reviewed-By: <name and email of someone who approved the patch>
+Last-Update: <YYYY-MM-DD>
+
+Index: libsbml-5.4.1/src/sbml/SBMLTypeCodes.h
+===================================================================
+--- libsbml-5.4.1.orig/src/sbml/SBMLTypeCodes.h 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/sbml/SBMLTypeCodes.h 2012-03-30 13:03:03.000000000 +0200
+@@ -50,7 +50,7 @@
+ * (In libSBML 5, the type of return values in these functions have been changed
+ * from typecode (int) to int for extensibility.)
+ *
+- * - Each pacakge extension must define similar enum type for each SBase subclass
++ * - Each package extension must define similar enum type for each SBase subclass
+ * (e.g. SBMLLayoutTypeCode_t for the layout extension, SBMLGroupTypeCode_t for
+ * group extension).
+ *
+Index: libsbml-5.4.1/src/sbml/SBase.h
+===================================================================
+--- libsbml-5.4.1.orig/src/sbml/SBase.h 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/sbml/SBase.h 2012-03-30 13:03:03.000000000 +0200
+@@ -3282,12 +3282,12 @@
+ std::string mURI;
+
+ //
+- // XMLAttributes object containing attributes of unknown pacakges
++ // XMLAttributes object containing attributes of unknown packages
+ //
+ XMLAttributes mAttributesOfUnknownPkg;
+
+ //
+- // XMLNode object containing elements of unknown pacakges
++ // XMLNode object containing elements of unknown packages
+ //
+ XMLNode mElementsOfUnknownPkg;
+
+Index: libsbml-5.4.1/src/sbml/SBase.cpp
+===================================================================
+--- libsbml-5.4.1.orig/src/sbml/SBase.cpp 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/sbml/SBase.cpp 2012-03-30 13:03:03.000000000 +0200
+@@ -6473,7 +6473,7 @@
+ * typecode (int) if this object is defined in SBML core package,
+ * return values will be one of SBMLLayoutTypeCode_t if this object is
+ * defined in Layout extension (i.e. similar enum types are defined in
+- * each pacakge extension for each SBase subclass)
++ * each package extension for each SBase subclass)
+ * The value of each typecode can be duplicated between those of
+ * different packages. Thus, to distinguish the typecodes of different
+ * packages, not only the return value of getTypeCode() but also that of
+Index: libsbml-5.4.1/src/sbml/validator/constraints/ValidCnUnitsValue.h
+===================================================================
+--- libsbml-5.4.1.orig/src/sbml/validator/constraints/ValidCnUnitsValue.h 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/sbml/validator/constraints/ValidCnUnitsValue.h 2012-03-30 13:03:03.000000000 +0200
+@@ -74,7 +74,7 @@
+
+ /**
+ * @return the preamble to use when logging constraint violations. The
+- * preamble will be prepended to each log message. If not overriden,
++ * preamble will be prepended to each log message. If not overridden,
+ * returns an empty string.
+ */
+ virtual const char* getPreamble ();
+Index: libsbml-5.4.1/src/sbml/validator/constraints/UnitsBase.h
+===================================================================
+--- libsbml-5.4.1.orig/src/sbml/validator/constraints/UnitsBase.h 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/sbml/validator/constraints/UnitsBase.h 2012-03-30 13:03:03.000000000 +0200
+@@ -104,7 +104,7 @@
+
+ /**
+ * @return the preamble to use when logging constraint violations. The
+- * preamble will be prepended to each log message. If not overriden,
++ * preamble will be prepended to each log message. If not overridden,
+ * returns an empty string.
+ */
+ virtual const char* getPreamble ();
+Index: libsbml-5.4.1/src/sbml/validator/constraints/UnitsBase.cpp
+===================================================================
+--- libsbml-5.4.1.orig/src/sbml/validator/constraints/UnitsBase.cpp 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/sbml/validator/constraints/UnitsBase.cpp 2012-03-30 13:03:03.000000000 +0200
+@@ -80,7 +80,7 @@
+
+ /**
+ * @return the preamble to use when logging constraint violations. The
+- * preamble will be prepended to each log message. If not overriden,
++ * preamble will be prepended to each log message. If not overridden,
+ * returns an empty string.
+ */
+ const char*
+Index: libsbml-5.4.1/src/sbml/validator/constraints/UniqueMetaId.h
+===================================================================
+--- libsbml-5.4.1.orig/src/sbml/validator/constraints/UniqueMetaId.h 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/sbml/validator/constraints/UniqueMetaId.h 2012-03-30 13:03:03.000000000 +0200
+@@ -119,7 +119,7 @@
+
+ /**
+ * @return the preamble to use when logging constraint violations. The
+- * preamble will be prepended to each log message. If not overriden,
++ * preamble will be prepended to each log message. If not overridden,
+ * returns an empty string.
+ */
+ const char* getPreamble ();
+Index: libsbml-5.4.1/src/sbml/validator/constraints/UniqueMetaId.cpp
+===================================================================
+--- libsbml-5.4.1.orig/src/sbml/validator/constraints/UniqueMetaId.cpp 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/sbml/validator/constraints/UniqueMetaId.cpp 2012-03-30 13:03:03.000000000 +0200
+@@ -73,7 +73,7 @@
+
+ /**
+ * @return the preamble to use when logging constraint violations. The
+- * preamble will be prepended to each log message. If not overriden,
++ * preamble will be prepended to each log message. If not overridden,
+ * returns an empty string.
+ */
+ const char*
+Index: libsbml-5.4.1/src/sbml/validator/constraints/PowerUnitsCheck.h
+===================================================================
+--- libsbml-5.4.1.orig/src/sbml/validator/constraints/PowerUnitsCheck.h 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/sbml/validator/constraints/PowerUnitsCheck.h 2012-03-30 13:03:03.000000000 +0200
+@@ -75,7 +75,7 @@
+
+ /**
+ * @return the preamble to use when logging constraint violations. The
+- * preamble will be prepended to each log message. If not overriden,
++ * preamble will be prepended to each log message. If not overridden,
+ * returns an empty string.
+ */
+ virtual const char* getPreamble ();
+Index: libsbml-5.4.1/src/sbml/validator/constraints/PiecewiseValueMathCheck.h
+===================================================================
+--- libsbml-5.4.1.orig/src/sbml/validator/constraints/PiecewiseValueMathCheck.h 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/sbml/validator/constraints/PiecewiseValueMathCheck.h 2012-03-30 13:03:03.000000000 +0200
+@@ -74,7 +74,7 @@
+
+ /**
+ * @return the preamble to use when logging constraint violations. The
+- * preamble will be prepended to each log message. If not overriden,
++ * preamble will be prepended to each log message. If not overridden,
+ * returns an empty string.
+ */
+ virtual const char* getPreamble ();
+Index: libsbml-5.4.1/src/sbml/validator/constraints/PieceBooleanMathCheck.h
+===================================================================
+--- libsbml-5.4.1.orig/src/sbml/validator/constraints/PieceBooleanMathCheck.h 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/sbml/validator/constraints/PieceBooleanMathCheck.h 2012-03-30 13:03:03.000000000 +0200
+@@ -74,7 +74,7 @@
+
+ /**
+ * @return the preamble to use when logging constraint violations. The
+- * preamble will be prepended to each log message. If not overriden,
++ * preamble will be prepended to each log message. If not overridden,
+ * returns an empty string.
+ */
+ virtual const char* getPreamble ();
+Index: libsbml-5.4.1/src/sbml/validator/constraints/NumericReturnMathCheck.h
+===================================================================
+--- libsbml-5.4.1.orig/src/sbml/validator/constraints/NumericReturnMathCheck.h 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/sbml/validator/constraints/NumericReturnMathCheck.h 2012-03-30 13:03:03.000000000 +0200
+@@ -74,7 +74,7 @@
+
+ /**
+ * @return the preamble to use when logging constraint violations. The
+- * preamble will be prepended to each log message. If not overriden,
++ * preamble will be prepended to each log message. If not overridden,
+ * returns an empty string.
+ */
+ virtual const char* getPreamble ();
+Index: libsbml-5.4.1/src/sbml/validator/constraints/NumericArgsMathCheck.h
+===================================================================
+--- libsbml-5.4.1.orig/src/sbml/validator/constraints/NumericArgsMathCheck.h 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/sbml/validator/constraints/NumericArgsMathCheck.h 2012-03-30 13:03:03.000000000 +0200
+@@ -74,7 +74,7 @@
+
+ /**
+ * @return the preamble to use when logging constraint violations. The
+- * preamble will be prepended to each log message. If not overriden,
++ * preamble will be prepended to each log message. If not overridden,
+ * returns an empty string.
+ */
+ virtual const char* getPreamble ();
+Index: libsbml-5.4.1/src/sbml/validator/constraints/NumberArgsMathCheck.h
+===================================================================
+--- libsbml-5.4.1.orig/src/sbml/validator/constraints/NumberArgsMathCheck.h 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/sbml/validator/constraints/NumberArgsMathCheck.h 2012-03-30 13:03:03.000000000 +0200
+@@ -99,7 +99,7 @@
+
+ /**
+ * @return the preamble to use when logging constraint violations. The
+- * preamble will be prepended to each log message. If not overriden,
++ * preamble will be prepended to each log message. If not overridden,
+ * returns an empty string.
+ */
+ virtual const char* getPreamble ();
+Index: libsbml-5.4.1/src/sbml/validator/constraints/MathMLBase.h
+===================================================================
+--- libsbml-5.4.1.orig/src/sbml/validator/constraints/MathMLBase.h 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/sbml/validator/constraints/MathMLBase.h 2012-03-30 13:03:03.000000000 +0200
+@@ -101,7 +101,7 @@
+
+ /**
+ * @return the preamble to use when logging constraint violations. The
+- * preamble will be prepended to each log message. If not overriden,
++ * preamble will be prepended to each log message. If not overridden,
+ * returns an empty string.
+ */
+ virtual const char* getPreamble ();
+Index: libsbml-5.4.1/src/sbml/validator/constraints/MathMLBase.cpp
+===================================================================
+--- libsbml-5.4.1.orig/src/sbml/validator/constraints/MathMLBase.cpp 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/sbml/validator/constraints/MathMLBase.cpp 2012-03-30 13:03:03.000000000 +0200
+@@ -69,7 +69,7 @@
+
+ /**
+ * @return the preamble to use when logging constraint violations. The
+- * preamble will be prepended to each log message. If not overriden,
++ * preamble will be prepended to each log message. If not overridden,
+ * returns an empty string.
+ */
+ const char*
+Index: libsbml-5.4.1/src/sbml/validator/constraints/LogicalArgsMathCheck.h
+===================================================================
+--- libsbml-5.4.1.orig/src/sbml/validator/constraints/LogicalArgsMathCheck.h 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/sbml/validator/constraints/LogicalArgsMathCheck.h 2012-03-30 13:03:03.000000000 +0200
+@@ -74,7 +74,7 @@
+
+ /**
+ * @return the preamble to use when logging constraint violations. The
+- * preamble will be prepended to each log message. If not overriden,
++ * preamble will be prepended to each log message. If not overridden,
+ * returns an empty string.
+ */
+ virtual const char* getPreamble ();
+Index: libsbml-5.4.1/src/sbml/validator/constraints/LocalParameterMathCheck.h
+===================================================================
+--- libsbml-5.4.1.orig/src/sbml/validator/constraints/LocalParameterMathCheck.h 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/sbml/validator/constraints/LocalParameterMathCheck.h 2012-03-30 13:03:03.000000000 +0200
+@@ -74,7 +74,7 @@
+
+ /**
+ * @return the preamble to use when logging constraint violations. The
+- * preamble will be prepended to each log message. If not overriden,
++ * preamble will be prepended to each log message. If not overridden,
+ * returns an empty string.
+ */
+ virtual const char* getPreamble ();
+Index: libsbml-5.4.1/src/sbml/validator/constraints/LambdaMathCheck.h
+===================================================================
+--- libsbml-5.4.1.orig/src/sbml/validator/constraints/LambdaMathCheck.h 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/sbml/validator/constraints/LambdaMathCheck.h 2012-03-30 13:03:03.000000000 +0200
+@@ -74,7 +74,7 @@
+
+ /**
+ * @return the preamble to use when logging constraint violations. The
+- * preamble will be prepended to each log message. If not overriden,
++ * preamble will be prepended to each log message. If not overridden,
+ * returns an empty string.
+ */
+ virtual const char* getPreamble ();
+Index: libsbml-5.4.1/src/sbml/validator/constraints/KineticLawUnitsCheck.h
+===================================================================
+--- libsbml-5.4.1.orig/src/sbml/validator/constraints/KineticLawUnitsCheck.h 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/sbml/validator/constraints/KineticLawUnitsCheck.h 2012-03-30 13:03:03.000000000 +0200
+@@ -79,7 +79,7 @@
+
+ /**
+ * @return the preamble to use when logging constraint violations. The
+- * preamble will be prepended to each log message. If not overriden,
++ * preamble will be prepended to each log message. If not overridden,
+ * returns an empty string.
+ */
+ virtual const char* getPreamble ();
+Index: libsbml-5.4.1/src/sbml/validator/constraints/KineticLawUnitsCheck.cpp
+===================================================================
+--- libsbml-5.4.1.orig/src/sbml/validator/constraints/KineticLawUnitsCheck.cpp 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/sbml/validator/constraints/KineticLawUnitsCheck.cpp 2012-03-30 13:03:03.000000000 +0200
+@@ -80,7 +80,7 @@
+
+ /**
+ * @return the preamble to use when logging constraint violations. The
+- * preamble will be prepended to each log message. If not overriden,
++ * preamble will be prepended to each log message. If not overridden,
+ * returns an empty string.
+ */
+ const char*
+Index: libsbml-5.4.1/src/sbml/validator/constraints/IdBase.h
+===================================================================
+--- libsbml-5.4.1.orig/src/sbml/validator/constraints/IdBase.h 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/sbml/validator/constraints/IdBase.h 2012-03-30 13:03:03.000000000 +0200
+@@ -112,7 +112,7 @@
+
+ /**
+ * @return the preamble to use when logging constraint violations. The
+- * preamble will be prepended to each log message. If not overriden,
++ * preamble will be prepended to each log message. If not overridden,
+ * returns an empty string.
+ */
+ virtual const char* getPreamble ();
+Index: libsbml-5.4.1/src/sbml/validator/constraints/IdBase.cpp
+===================================================================
+--- libsbml-5.4.1.orig/src/sbml/validator/constraints/IdBase.cpp 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/sbml/validator/constraints/IdBase.cpp 2012-03-30 13:03:03.000000000 +0200
+@@ -68,7 +68,7 @@
+
+ /**
+ * @return the preamble to use when logging constraint violations. The
+- * preamble will be prepended to each log message. If not overriden,
++ * preamble will be prepended to each log message. If not overridden,
+ * returns an empty string.
+ */
+ const char*
+Index: libsbml-5.4.1/src/sbml/validator/constraints/FunctionNoArgsMathCheck.h
+===================================================================
+--- libsbml-5.4.1.orig/src/sbml/validator/constraints/FunctionNoArgsMathCheck.h 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/sbml/validator/constraints/FunctionNoArgsMathCheck.h 2012-03-30 13:03:03.000000000 +0200
+@@ -74,7 +74,7 @@
+
+ /**
+ * @return the preamble to use when logging constraint violations. The
+- * preamble will be prepended to each log message. If not overriden,
++ * preamble will be prepended to each log message. If not overridden,
+ * returns an empty string.
+ */
+ virtual const char* getPreamble ();
+Index: libsbml-5.4.1/src/sbml/validator/constraints/FunctionApplyMathCheck.h
+===================================================================
+--- libsbml-5.4.1.orig/src/sbml/validator/constraints/FunctionApplyMathCheck.h 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/sbml/validator/constraints/FunctionApplyMathCheck.h 2012-03-30 13:03:03.000000000 +0200
+@@ -74,7 +74,7 @@
+
+ /**
+ * @return the preamble to use when logging constraint violations. The
+- * preamble will be prepended to each log message. If not overriden,
++ * preamble will be prepended to each log message. If not overridden,
+ * returns an empty string.
+ */
+ virtual const char* getPreamble ();
+Index: libsbml-5.4.1/src/sbml/validator/constraints/ExponentUnitsCheck.h
+===================================================================
+--- libsbml-5.4.1.orig/src/sbml/validator/constraints/ExponentUnitsCheck.h 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/sbml/validator/constraints/ExponentUnitsCheck.h 2012-03-30 13:03:03.000000000 +0200
+@@ -75,7 +75,7 @@
+
+ /**
+ * @return the preamble to use when logging constraint violations. The
+- * preamble will be prepended to each log message. If not overriden,
++ * preamble will be prepended to each log message. If not overridden,
+ * returns an empty string.
+ */
+ virtual const char* getPreamble ();
+Index: libsbml-5.4.1/src/sbml/validator/constraints/EqualityArgsMathCheck.h
+===================================================================
+--- libsbml-5.4.1.orig/src/sbml/validator/constraints/EqualityArgsMathCheck.h 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/sbml/validator/constraints/EqualityArgsMathCheck.h 2012-03-30 13:03:03.000000000 +0200
+@@ -74,7 +74,7 @@
+
+ /**
+ * @return the preamble to use when logging constraint violations. The
+- * preamble will be prepended to each log message. If not overriden,
++ * preamble will be prepended to each log message. If not overridden,
+ * returns an empty string.
+ */
+ virtual const char* getPreamble ();
+Index: libsbml-5.4.1/src/sbml/validator/constraints/CiElementMathCheck.h
+===================================================================
+--- libsbml-5.4.1.orig/src/sbml/validator/constraints/CiElementMathCheck.h 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/sbml/validator/constraints/CiElementMathCheck.h 2012-03-30 13:03:03.000000000 +0200
+@@ -74,7 +74,7 @@
+
+ /**
+ * @return the preamble to use when logging constraint violations. The
+- * preamble will be prepended to each log message. If not overriden,
++ * preamble will be prepended to each log message. If not overridden,
+ * returns an empty string.
+ */
+ virtual const char* getPreamble ();
+Index: libsbml-5.4.1/src/sbml/validator/constraints/ArgumentsUnitsCheckWarnings.h
+===================================================================
+--- libsbml-5.4.1.orig/src/sbml/validator/constraints/ArgumentsUnitsCheckWarnings.h 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/sbml/validator/constraints/ArgumentsUnitsCheckWarnings.h 2012-03-30 13:03:03.000000000 +0200
+@@ -75,7 +75,7 @@
+
+ /**
+ * @return the preamble to use when logging constraint violations. The
+- * preamble will be prepended to each log message. If not overriden,
++ * preamble will be prepended to each log message. If not overridden,
+ * returns an empty string.
+ */
+ virtual const char* getPreamble ();
+Index: libsbml-5.4.1/src/sbml/validator/constraints/ArgumentsUnitsCheck.h
+===================================================================
+--- libsbml-5.4.1.orig/src/sbml/validator/constraints/ArgumentsUnitsCheck.h 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/sbml/validator/constraints/ArgumentsUnitsCheck.h 2012-03-30 13:03:03.000000000 +0200
+@@ -75,7 +75,7 @@
+
+ /**
+ * @return the preamble to use when logging constraint violations. The
+- * preamble will be prepended to each log message. If not overriden,
++ * preamble will be prepended to each log message. If not overridden,
+ * returns an empty string.
+ */
+ virtual const char* getPreamble ();
+Index: libsbml-5.4.1/src/sbml/packages/layout/sbml/TextGlyph.h
+===================================================================
+--- libsbml-5.4.1.orig/src/sbml/packages/layout/sbml/TextGlyph.h 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/sbml/packages/layout/sbml/TextGlyph.h 2012-03-30 13:03:03.000000000 +0200
+@@ -240,7 +240,7 @@
+ * SBMLTypeCode_t if this object is defined in SBML core package,
+ * return values will be one of SBMLLayoutTypeCode_t if this object is
+ * defined in Layout extension (i.e. similar enum types are defined in
+- * each pacakge extension for each SBase subclass)
++ * each package extension for each SBase subclass)
+ * The value of each typecode can be duplicated between those of
+ * different packages. Thus, to distinguish the typecodes of different
+ * packages, not only the return value of getTypeCode() but also that of
+Index: libsbml-5.4.1/src/sbml/packages/layout/sbml/SpeciesReferenceGlyph.h
+===================================================================
+--- libsbml-5.4.1.orig/src/sbml/packages/layout/sbml/SpeciesReferenceGlyph.h 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/sbml/packages/layout/sbml/SpeciesReferenceGlyph.h 2012-03-30 13:03:03.000000000 +0200
+@@ -298,7 +298,7 @@
+ * SBMLTypeCode_t if this object is defined in SBML core package,
+ * return values will be one of SBMLLayoutTypeCode_t if this object is
+ * defined in Layout extension (i.e. similar enum types are defined in
+- * each pacakge extension for each SBase subclass)
++ * each package extension for each SBase subclass)
+ * The value of each typecode can be duplicated between those of
+ * different packages. Thus, to distinguish the typecodes of different
+ * packages, not only the return value of getTypeCode() but also that of
+Index: libsbml-5.4.1/src/sbml/packages/layout/sbml/SpeciesGlyph.h
+===================================================================
+--- libsbml-5.4.1.orig/src/sbml/packages/layout/sbml/SpeciesGlyph.h 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/sbml/packages/layout/sbml/SpeciesGlyph.h 2012-03-30 13:03:03.000000000 +0200
+@@ -194,7 +194,7 @@
+ * SBMLTypeCode_t if this object is defined in SBML core package,
+ * return values will be one of SBMLLayoutTypeCode_t if this object is
+ * defined in Layout extension (i.e. similar enum types are defined in
+- * each pacakge extension for each SBase subclass)
++ * each package extension for each SBase subclass)
+ * The value of each typecode can be duplicated between those of
+ * different packages. Thus, to distinguish the typecodes of different
+ * packages, not only the return value of getTypeCode() but also that of
+Index: libsbml-5.4.1/src/sbml/packages/layout/sbml/ReactionGlyph.h
+===================================================================
+--- libsbml-5.4.1.orig/src/sbml/packages/layout/sbml/ReactionGlyph.h 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/sbml/packages/layout/sbml/ReactionGlyph.h 2012-03-30 13:03:03.000000000 +0200
+@@ -454,7 +454,7 @@
+ * SBMLTypeCode_t if this object is defined in SBML core package,
+ * return values will be one of SBMLLayoutTypeCode_t if this object is
+ * defined in Layout extension (i.e. similar enum types are defined in
+- * each pacakge extension for each SBase subclass)
++ * each package extension for each SBase subclass)
+ * The value of each typecode can be duplicated between those of
+ * different packages. Thus, to distinguish the typecodes of different
+ * packages, not only the return value of getTypeCode() but also that of
+Index: libsbml-5.4.1/src/sbml/packages/layout/sbml/Point.h
+===================================================================
+--- libsbml-5.4.1.orig/src/sbml/packages/layout/sbml/Point.h 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/sbml/packages/layout/sbml/Point.h 2012-03-30 13:03:03.000000000 +0200
+@@ -275,7 +275,7 @@
+ * SBMLTypeCode_t if this object is defined in SBML core package,
+ * return values will be one of SBMLLayoutTypeCode_t if this object is
+ * defined in Layout extension (i.e. similar enum types are defined in
+- * each pacakge extension for each SBase subclass)
++ * each package extension for each SBase subclass)
+ * The value of each typecode can be duplicated between those of
+ * different packages. Thus, to distinguish the typecodes of different
+ * packages, not only the return value of getTypeCode() but also that of
+Index: libsbml-5.4.1/src/sbml/packages/layout/sbml/LineSegment.h
+===================================================================
+--- libsbml-5.4.1.orig/src/sbml/packages/layout/sbml/LineSegment.h 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/sbml/packages/layout/sbml/LineSegment.h 2012-03-30 13:03:03.000000000 +0200
+@@ -225,7 +225,7 @@
+ * SBMLTypeCode_t if this object is defined in SBML core package,
+ * return values will be one of SBMLLayoutTypeCode_t if this object is
+ * defined in Layout extension (i.e. similar enum types are defined in
+- * each pacakge extension for each SBase subclass)
++ * each package extension for each SBase subclass)
+ * The value of each typecode can be duplicated between those of
+ * different packages. Thus, to distinguish the typecodes of different
+ * packages, not only the return value of getTypeCode() but also that of
+Index: libsbml-5.4.1/src/sbml/packages/layout/sbml/Layout.h
+===================================================================
+--- libsbml-5.4.1.orig/src/sbml/packages/layout/sbml/Layout.h 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/sbml/packages/layout/sbml/Layout.h 2012-03-30 13:03:03.000000000 +0200
+@@ -1347,7 +1347,7 @@
+ * SBMLTypeCode_t if this object is defined in SBML core package,
+ * return values will be one of SBMLLayoutTypeCode_t if this object is
+ * defined in Layout extension (i.e. similar enum types are defined in
+- * each pacakge extension for each SBase subclass)
++ * each package extension for each SBase subclass)
+ * The value of each typecode can be duplicated between those of
+ * different packages. Thus, to distinguish the typecodes of different
+ * packages, not only the return value of getTypeCode() but also that of
+Index: libsbml-5.4.1/src/sbml/packages/layout/sbml/GraphicalObject.h
+===================================================================
+--- libsbml-5.4.1.orig/src/sbml/packages/layout/sbml/GraphicalObject.h 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/sbml/packages/layout/sbml/GraphicalObject.h 2012-03-30 13:03:03.000000000 +0200
+@@ -259,7 +259,7 @@
+ * SBMLTypeCode_t if this object is defined in SBML core package,
+ * return values will be one of SBMLLayoutTypeCode_t if this object is
+ * defined in Layout extension (i.e. similar enum types are defined in
+- * each pacakge extension for each SBase subclass)
++ * each package extension for each SBase subclass)
+ * The value of each typecode can be duplicated between those of
+ * different packages. Thus, to distinguish the typecodes of different
+ * packages, not only the return value of getTypeCode() but also that of
+Index: libsbml-5.4.1/src/sbml/packages/layout/sbml/Dimensions.h
+===================================================================
+--- libsbml-5.4.1.orig/src/sbml/packages/layout/sbml/Dimensions.h 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/sbml/packages/layout/sbml/Dimensions.h 2012-03-30 13:03:03.000000000 +0200
+@@ -248,7 +248,7 @@
+ * SBMLTypeCode_t if this object is defined in SBML core package,
+ * return values will be one of SBMLLayoutTypeCode_t if this object is
+ * defined in Layout extension (i.e. similar enum types are defined in
+- * each pacakge extension for each SBase subclass)
++ * each package extension for each SBase subclass)
+ * The value of each typecode can be duplicated between those of
+ * different packages. Thus, to distinguish the typecodes of different
+ * packages, not only the return value of getTypeCode() but also that of
+Index: libsbml-5.4.1/src/sbml/packages/layout/sbml/Curve.h
+===================================================================
+--- libsbml-5.4.1.orig/src/sbml/packages/layout/sbml/Curve.h 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/sbml/packages/layout/sbml/Curve.h 2012-03-30 13:03:03.000000000 +0200
+@@ -302,7 +302,7 @@
+ * SBMLTypeCode_t if this object is defined in SBML core package,
+ * return values will be one of SBMLLayoutTypeCode_t if this object is
+ * defined in Layout extension (i.e. similar enum types are defined in
+- * each pacakge extension for each SBase subclass)
++ * each package extension for each SBase subclass)
+ * The value of each typecode can be duplicated between those of
+ * different packages. Thus, to distinguish the typecodes of different
+ * packages, not only the return value of getTypeCode() but also that of
+Index: libsbml-5.4.1/src/sbml/packages/layout/sbml/CubicBezier.h
+===================================================================
+--- libsbml-5.4.1.orig/src/sbml/packages/layout/sbml/CubicBezier.h 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/sbml/packages/layout/sbml/CubicBezier.h 2012-03-30 13:03:03.000000000 +0200
+@@ -265,7 +265,7 @@
+ * SBMLTypeCode_t if this object is defined in SBML core package,
+ * return values will be one of SBMLLayoutTypeCode_t if this object is
+ * defined in Layout extension (i.e. similar enum types are defined in
+- * each pacakge extension for each SBase subclass)
++ * each package extension for each SBase subclass)
+ * The value of each typecode can be duplicated between those of
+ * different packages. Thus, to distinguish the typecodes of different
+ * packages, not only the return value of getTypeCode() but also that of
+Index: libsbml-5.4.1/src/sbml/packages/layout/sbml/CompartmentGlyph.h
+===================================================================
+--- libsbml-5.4.1.orig/src/sbml/packages/layout/sbml/CompartmentGlyph.h 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/sbml/packages/layout/sbml/CompartmentGlyph.h 2012-03-30 13:03:03.000000000 +0200
+@@ -196,7 +196,7 @@
+ * SBMLTypeCode_t if this object is defined in SBML core package,
+ * return values will be one of SBMLLayoutTypeCode_t if this object is
+ * defined in Layout extension (i.e. similar enum types are defined in
+- * each pacakge extension for each SBase subclass)
++ * each package extension for each SBase subclass)
+ * The value of each typecode can be duplicated between those of
+ * different packages. Thus, to distinguish the typecodes of different
+ * packages, not only the return value of getTypeCode() but also that of
+Index: libsbml-5.4.1/src/sbml/packages/layout/sbml/BoundingBox.h
+===================================================================
+--- libsbml-5.4.1.orig/src/sbml/packages/layout/sbml/BoundingBox.h 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/sbml/packages/layout/sbml/BoundingBox.h 2012-03-30 13:03:03.000000000 +0200
+@@ -344,7 +344,7 @@
+ * SBMLTypeCode_t if this object is defined in SBML core package,
+ * return values will be one of SBMLLayoutTypeCode_t if this object is
+ * defined in Layout extension (i.e. similar enum types are defined in
+- * each pacakge extension for each SBase subclass)
++ * each package extension for each SBase subclass)
+ * The value of each typecode can be duplicated between those of
+ * different packages. Thus, to distinguish the typecodes of different
+ * packages, not only the return value of getTypeCode() but also that of
+Index: libsbml-5.4.1/src/sbml/packages/layout/extension/LayoutExtension.cpp
+===================================================================
+--- libsbml-5.4.1.orig/src/sbml/packages/layout/extension/LayoutExtension.cpp 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/sbml/packages/layout/extension/LayoutExtension.cpp 2012-03-30 13:03:03.000000000 +0200
+@@ -342,7 +342,7 @@
+ {
+ //-------------------------------------------------------------------------
+ //
+- // 1. Checks if the layout pacakge has already been registered.
++ // 1. Checks if the layout package has already been registered.
+ //
+ //-------------------------------------------------------------------------
+
+Index: libsbml-5.4.1/src/sbml/extension/SBMLExtensionRegistry.h
+===================================================================
+--- libsbml-5.4.1.orig/src/sbml/extension/SBMLExtensionRegistry.h 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/sbml/extension/SBMLExtensionRegistry.h 2012-03-30 13:03:03.000000000 +0200
+@@ -98,13 +98,13 @@
+
+ /**
+ * Remove all L2 Extension namespaces from the namespace list. This will call all
+- * overriden SBMLExtension::removeL2Namespaces methods.
++ * overridden SBMLExtension::removeL2Namespaces methods.
+ */
+ void removeL2Namespaces(XMLNamespaces *xmlns) const;
+
+ /**
+ * adds all L2 Extension namespaces to the namespace list. This will call all
+- * overriden SBMLExtension::addL2Namespaces methods.
++ * overridden SBMLExtension::addL2Namespaces methods.
+ */
+ void addL2Namespaces(XMLNamespaces *xmlns) const;
+
+Index: libsbml-5.4.1/src/sbml/extension/SBMLExtensionRegistry.cpp
+===================================================================
+--- libsbml-5.4.1.orig/src/sbml/extension/SBMLExtensionRegistry.cpp 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/sbml/extension/SBMLExtensionRegistry.cpp 2012-03-30 13:03:03.000000000 +0200
+@@ -304,7 +304,7 @@
+
+ /**
+ * adds all L2 Extension namespaces to the namespace list. This will call all
+- * overriden SBMLExtension::addL2Namespaces methods.
++ * overridden SBMLExtension::addL2Namespaces methods.
+ */
+ void
+ SBMLExtensionRegistry::addL2Namespaces(XMLNamespaces *xmlns) const
+Index: libsbml-5.4.1/src/sbml/extension/SBMLExtension.h
+===================================================================
+--- libsbml-5.4.1.orig/src/sbml/extension/SBMLExtension.h 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/sbml/extension/SBMLExtension.h 2012-03-30 13:03:03.000000000 +0200
+@@ -43,8 +43,8 @@
+ * The extended class is implemented based on the following steps:
+ *
+ * (NOTE:
+- * "src/pacakges/groups/extension/GroupsExtension.{h,cpp}" and
+- * "src/pacakges/layout/extension/LayoutExtension.{h,cpp}" are
++ * "src/packages/groups/extension/GroupsExtension.{h,cpp}" and
++ * "src/packages/layout/extension/LayoutExtension.{h,cpp}" are
+ * example files in which SBMLExtension derived classes are implemented)
+ *
+ * <ol>
+@@ -390,7 +390,7 @@
+ {
+ //-------------------------------------------------------------------------
+ //
+- // 1. Checks if the groups pacakge has already been registered.
++ // 1. Checks if the groups package has already been registered.
+ //
+ //-------------------------------------------------------------------------
+
+@@ -708,7 +708,7 @@
+ *
+ * Returns the ith URI (the supported package version)
+ *
+- * @param i the index of the list of URI (the list of supporeted pacakge versions)
++ * @param i the index of the list of URI (the list of supporeted package versions)
+ * @return the URI of supported package version with the given index.
+ */
+ const std::string& getSupportedPackageURI(unsigned int i) const;
+Index: libsbml-5.4.1/src/bindings/python/pydoc-normal.i
+===================================================================
+--- libsbml-5.4.1.orig/src/bindings/python/pydoc-normal.i 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/bindings/python/pydoc-normal.i 2012-03-30 13:03:03.000000000 +0200
+@@ -39783,8 +39783,8 @@
+ extension). The extended class is implemented based on the following
+ steps:
+
+- (NOTE: 'src/pacakges/groups/extension/GroupsExtension.{h,cpp}'
+- and 'src/pacakges/layout/extension/LayoutExtension.{h,cpp}' are
++ (NOTE: 'src/packages/groups/extension/GroupsExtension.{h,cpp}'
++ and 'src/packages/layout/extension/LayoutExtension.{h,cpp}' are
+ example files in which SBMLExtension derived classes are implemented)
+
+ <ol>
+@@ -40112,7 +40112,7 @@
+ {
+ //-------------------------------------------------------------------------
+ //
+- // 1. Checks if the groups pacakge has already been registered.
++ // 1. Checks if the groups package has already been registered.
+ //
+ //-------------------------------------------------------------------------
+
+@@ -40254,7 +40254,7 @@
+ Returns the ith URI (the supported package version)
+
+ Parameter 'i' is the index of the list of URI (the list of supporeted
+- pacakge versions) Returns the URI of supported package version with
++ package versions) Returns the URI of supported package version with
+ the given index.
+ ";
+
+@@ -40474,13 +40474,13 @@
+
+ %feature("docstring") SBMLExtensionRegistry::removeL2Namespaces "
+ Remove all L2 Extension namespaces from the namespace list. This will
+- call all overriden SBMLExtension::removeL2Namespaces methods.
++ call all overridden SBMLExtension::removeL2Namespaces methods.
+ ";
+
+
+ %feature("docstring") SBMLExtensionRegistry::addL2Namespaces "
+ adds all L2 Extension namespaces to the namespace list. This will
+- call all overriden SBMLExtension::addL2Namespaces methods.
++ call all overridden SBMLExtension::addL2Namespaces methods.
+ ";
+
+
+Index: libsbml-5.4.1/src/bindings/python/pydoc-doxygen.i
+===================================================================
+--- libsbml-5.4.1.orig/src/bindings/python/pydoc-doxygen.i 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/bindings/python/pydoc-doxygen.i 2012-03-30 13:03:03.000000000 +0200
+@@ -40975,8 +40975,8 @@
+ The extended class is implemented based on the following steps:
+
+ (NOTE:
+- \'src/pacakges/groups/extension/GroupsExtension.{h,cpp}\' and
+- \'src/pacakges/layout/extension/LayoutExtension.{h,cpp}\' are
++ \'src/packages/groups/extension/GroupsExtension.{h,cpp}\' and
++ \'src/packages/layout/extension/LayoutExtension.{h,cpp}\' are
+ example files in which SBMLExtension derived classes are implemented)
+
+ <ol>
+@@ -41322,7 +41322,7 @@
+ {
+ //-------------------------------------------------------------------------
+ //
+- // 1. Checks if the groups pacakge has already been registered.
++ // 1. Checks if the groups package has already been registered.
+ //
+ //-------------------------------------------------------------------------
+
+@@ -41464,7 +41464,7 @@
+ %feature("docstring") SBMLExtension::getSupportedPackageURI "
+ Returns the ith URI (the supported package version)
+
+- @param i the index of the list of URI (the list of supporeted pacakge versions)
++ @param i the index of the list of URI (the list of supporeted package versions)
+ @return the URI of supported package version with the given index.
+ ";
+
+@@ -41668,13 +41668,13 @@
+
+ %feature("docstring") SBMLExtensionRegistry::removeL2Namespaces "
+ Remove all L2 Extension namespaces from the namespace list. This will call all
+- overriden SBMLExtension::removeL2Namespaces methods.
++ overridden SBMLExtension::removeL2Namespaces methods.
+ ";
+
+
+ %feature("docstring") SBMLExtensionRegistry::addL2Namespaces "
+ adds all L2 Extension namespaces to the namespace list. This will call all
+- overriden SBMLExtension::addL2Namespaces methods.
++ overridden SBMLExtension::addL2Namespaces methods.
+ ";
+
+
+Index: libsbml-5.4.1/src/bindings/python/libsbml_wrap.cpp
+===================================================================
+--- libsbml-5.4.1.orig/src/bindings/python/libsbml_wrap.cpp 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/bindings/python/libsbml_wrap.cpp 2012-03-30 13:03:03.000000000 +0200
+@@ -128575,7 +128575,7 @@
+ "Returns the ith URI (the supported package version)\n"
+ "\n"
+ "Parameter 'i' is the index of the list of URI (the list of supporeted\n"
+- "pacakge versions) Returns the URI of supported package version with\n"
++ "package versions) Returns the URI of supported package version with\n"
+ "the given index.\n"
+ "\n"
+ ""},
+@@ -128805,14 +128805,14 @@
+ "SBMLExtensionRegistry_removeL2Namespaces(SBMLExtensionRegistry self, XMLNamespaces xmlns)\n"
+ "\n"
+ "Remove all L2 Extension namespaces from the namespace list. This will\n"
+- "call all overriden SBMLExtension::removeL2Namespaces methods.\n"
++ "call all overridden SBMLExtension::removeL2Namespaces methods.\n"
+ "\n"
+ ""},
+ { (char *)"SBMLExtensionRegistry_addL2Namespaces", _wrap_SBMLExtensionRegistry_addL2Namespaces, METH_VARARGS, (char *)"\n"
+ "SBMLExtensionRegistry_addL2Namespaces(SBMLExtensionRegistry self, XMLNamespaces xmlns)\n"
+ "\n"
+ "adds all L2 Extension namespaces to the namespace list. This will\n"
+- "call all overriden SBMLExtension::addL2Namespaces methods.\n"
++ "call all overridden SBMLExtension::addL2Namespaces methods.\n"
+ "\n"
+ ""},
+ { (char *)"SBMLExtensionRegistry_enableL2NamespaceForDocument", _wrap_SBMLExtensionRegistry_enableL2NamespaceForDocument, METH_VARARGS, (char *)"\n"
+Index: libsbml-5.4.1/src/bindings/python/libsbml.py
+===================================================================
+--- libsbml-5.4.1.orig/src/bindings/python/libsbml.py 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/bindings/python/libsbml.py 2012-03-30 13:03:03.000000000 +0200
+@@ -48908,8 +48908,8 @@
+ extension). The extended class is implemented based on the following
+ steps:
+
+- (NOTE: 'src/pacakges/groups/extension/GroupsExtension.{h,cpp}'
+- and 'src/pacakges/layout/extension/LayoutExtension.{h,cpp}' are
++ (NOTE: 'src/packages/groups/extension/GroupsExtension.{h,cpp}'
++ and 'src/packages/layout/extension/LayoutExtension.{h,cpp}' are
+ example files in which SBMLExtension derived classes are implemented)
+
+ <ol>
+@@ -49237,7 +49237,7 @@
+ {
+ //-------------------------------------------------------------------------
+ //
+- // 1. Checks if the groups pacakge has already been registered.
++ // 1. Checks if the groups package has already been registered.
+ //
+ //-------------------------------------------------------------------------
+
+@@ -49381,7 +49381,7 @@
+ Returns the ith URI (the supported package version)
+
+ Parameter 'i' is the index of the list of URI (the list of supporeted
+- pacakge versions) Returns the URI of supported package version with
++ package versions) Returns the URI of supported package version with
+ the given index.
+
+ """
+@@ -49704,7 +49704,7 @@
+ removeL2Namespaces(self, XMLNamespaces xmlns)
+
+ Remove all L2 Extension namespaces from the namespace list. This will
+- call all overriden SBMLExtension::removeL2Namespaces methods.
++ call all overridden SBMLExtension::removeL2Namespaces methods.
+
+ """
+ return _libsbml.SBMLExtensionRegistry_removeL2Namespaces(self, *args)
+@@ -49714,7 +49714,7 @@
+ addL2Namespaces(self, XMLNamespaces xmlns)
+
+ adds all L2 Extension namespaces to the namespace list. This will
+- call all overriden SBMLExtension::addL2Namespaces methods.
++ call all overridden SBMLExtension::addL2Namespaces methods.
+
+ """
+ return _libsbml.SBMLExtensionRegistry_addL2Namespaces(self, *args)
+Index: libsbml-5.4.1/src/bindings/python/libsbml-doxygen.py
+===================================================================
+--- libsbml-5.4.1.orig/src/bindings/python/libsbml-doxygen.py 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/bindings/python/libsbml-doxygen.py 2012-03-30 13:03:03.000000000 +0200
+@@ -48342,8 +48342,8 @@
+ The extended class is implemented based on the following steps:
+
+ (NOTE:
+- 'src/pacakges/groups/extension/GroupsExtension.{h,cpp}' and
+- 'src/pacakges/layout/extension/LayoutExtension.{h,cpp}' are
++ 'src/packages/groups/extension/GroupsExtension.{h,cpp}' and
++ 'src/packages/layout/extension/LayoutExtension.{h,cpp}' are
+ example files in which SBMLExtension derived classes are implemented)
+
+ <ol>
+@@ -48689,7 +48689,7 @@
+ {
+ //-------------------------------------------------------------------------
+ //
+- // 1. Checks if the groups pacakge has already been registered.
++ // 1. Checks if the groups package has already been registered.
+ //
+ //-------------------------------------------------------------------------
+
+@@ -48834,7 +48834,7 @@
+
+ Returns the ith URI (the supported package version)
+
+- @param i the index of the list of URI (the list of supporeted pacakge versions)
++ @param i the index of the list of URI (the list of supporeted package versions)
+ @return the URI of supported package version with the given index.
+
+ """
+@@ -49141,7 +49141,7 @@
+ removeL2Namespaces(self, XMLNamespaces xmlns)
+
+ Remove all L2 Extension namespaces from the namespace list. This will call all
+- overriden SBMLExtension::removeL2Namespaces methods.
++ overridden SBMLExtension::removeL2Namespaces methods.
+
+ """
+ return _libsbml.SBMLExtensionRegistry_removeL2Namespaces(self, *args)
+@@ -49151,7 +49151,7 @@
+ addL2Namespaces(self, XMLNamespaces xmlns)
+
+ adds all L2 Extension namespaces to the namespace list. This will call all
+- overriden SBMLExtension::addL2Namespaces methods.
++ overridden SBMLExtension::addL2Namespaces methods.
+
+ """
+ return _libsbml.SBMLExtensionRegistry_addL2Namespaces(self, *args)
+Index: libsbml-5.4.1/src/bindings/perl/LibSBML.pod
+===================================================================
+--- libsbml-5.4.1.orig/src/bindings/perl/LibSBML.pod 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/bindings/perl/LibSBML.pod 2012-03-30 13:03:03.000000000 +0200
+@@ -38126,8 +38126,8 @@
+ their packages (e.g. GroupsExtension class is implemented for groups extension).
+ The extended class is implemented based on the following steps:
+ (NOTE:
+-"src/pacakges/groups/extension/GroupsExtension.{h,cpp}" and
+-"src/pacakges/layout/extension/LayoutExtension.{h,cpp}" are
++"src/packages/groups/extension/GroupsExtension.{h,cpp}" and
++"src/packages/layout/extension/LayoutExtension.{h,cpp}" are
+ example files in which SBMLExtension derived classes are implemented)
+ <ol>
+
+@@ -38505,7 +38505,7 @@
+ {
+ //-------------------------------------------------------------------------
+ //
+-// 1. Checks if the groups pacakge has already been registered.
++// 1. Checks if the groups package has already been registered.
+ //
+ //-------------------------------------------------------------------------
+ if (SBMLExtensionRegistry::getInstance().isRegistered(getPackageName()))
+@@ -38626,7 +38626,7 @@
+ =item SBMLExtension::getSupportedPackageURI
+
+ Returns the ith URI (the supported package version)
+- at param i the index of the list of URI (the list of supporeted pacakge versions)
++ at param i the index of the list of URI (the list of supporeted package versions)
+ Returns the URI of supported package version with the given index.
+
+
+@@ -38804,13 +38804,13 @@
+ =item SBMLExtensionRegistry::removeL2Namespaces
+
+ Remove all L2 Extension namespaces from the namespace list. This will call all
+-overriden SBMLExtension::removeL2Namespaces methods.
++overridden SBMLExtension::removeL2Namespaces methods.
+
+
+ =item SBMLExtensionRegistry::addL2Namespaces
+
+ adds all L2 Extension namespaces to the namespace list. This will call all
+-overriden SBMLExtension::addL2Namespaces methods.
++overridden SBMLExtension::addL2Namespaces methods.
+
+
+ =item SBMLExtensionRegistry::enableL2NamespaceForDocument
+Index: libsbml-5.4.1/src/bindings/perl/LibSBML.pm
+===================================================================
+--- libsbml-5.4.1.orig/src/bindings/perl/LibSBML.pm 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/bindings/perl/LibSBML.pm 2012-03-30 13:03:03.000000000 +0200
+@@ -38139,8 +38139,8 @@
+ their packages (e.g. GroupsExtension class is implemented for groups extension).
+ The extended class is implemented based on the following steps:
+ (NOTE:
+-"src/pacakges/groups/extension/GroupsExtension.{h,cpp}" and
+-"src/pacakges/layout/extension/LayoutExtension.{h,cpp}" are
++"src/packages/groups/extension/GroupsExtension.{h,cpp}" and
++"src/packages/layout/extension/LayoutExtension.{h,cpp}" are
+ example files in which SBMLExtension derived classes are implemented)
+ <ol>
+
+@@ -38518,7 +38518,7 @@
+ {
+ //-------------------------------------------------------------------------
+ //
+-// 1. Checks if the groups pacakge has already been registered.
++// 1. Checks if the groups package has already been registered.
+ //
+ //-------------------------------------------------------------------------
+ if (SBMLExtensionRegistry::getInstance().isRegistered(getPackageName()))
+@@ -38639,7 +38639,7 @@
+ =item SBMLExtension::getSupportedPackageURI
+
+ Returns the ith URI (the supported package version)
+- at param i the index of the list of URI (the list of supporeted pacakge versions)
++ at param i the index of the list of URI (the list of supporeted package versions)
+ Returns the URI of supported package version with the given index.
+
+
+@@ -38817,13 +38817,13 @@
+ =item SBMLExtensionRegistry::removeL2Namespaces
+
+ Remove all L2 Extension namespaces from the namespace list. This will call all
+-overriden SBMLExtension::removeL2Namespaces methods.
++overridden SBMLExtension::removeL2Namespaces methods.
+
+
+ =item SBMLExtensionRegistry::addL2Namespaces
+
+ adds all L2 Extension namespaces to the namespace list. This will call all
+-overriden SBMLExtension::addL2Namespaces methods.
++overridden SBMLExtension::addL2Namespaces methods.
+
+
+ =item SBMLExtensionRegistry::enableL2NamespaceForDocument
+Index: libsbml-5.4.1/src/bindings/java/javadoc.i
+===================================================================
+--- libsbml-5.4.1.orig/src/bindings/java/javadoc.i 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/bindings/java/javadoc.i 2012-03-30 13:03:03.000000000 +0200
+@@ -48634,8 +48634,8 @@
+ * The extended class is implemented based on the following steps:
+ * <p>
+ * (NOTE:
+- * \'src/pacakges/groups/extension/GroupsExtension.{h,cpp}\' and
+- * \'src/pacakges/layout/extension/LayoutExtension.{h,cpp}\' are
++ * \'src/packages/groups/extension/GroupsExtension.{h,cpp}\' and
++ * \'src/packages/layout/extension/LayoutExtension.{h,cpp}\' are
+ * example files in which {@link SBMLExtension} derived classes are implemented)
+ * <p>
+ * <ol>
+@@ -48981,7 +48981,7 @@
+ {
+ //-------------------------------------------------------------------------
+ //
+- // 1. Checks if the groups pacakge has already been registered.
++ // 1. Checks if the groups package has already been registered.
+ //
+ //-------------------------------------------------------------------------
+
+@@ -49128,7 +49128,7 @@
+ * <p>
+ * Returns the ith URI (the supported package version)
+ * <p>
+- * @param i the index of the list of URI (the list of supporeted pacakge versions)
++ * @param i the index of the list of URI (the list of supporeted package versions)
+ * @return the URI of supported package version with the given index.
+ */ public
+ ";
+@@ -49378,7 +49378,7 @@
+ %javamethodmodifiers SBMLExtensionRegistry::removeL2Namespaces(XMLNamespaces *xmlns) const "
+ /**
+ * Remove all L2 Extension namespaces from the namespace list. This will call all
+- * overriden SBMLExtension.removeL2Namespaces methods.
++ * overridden SBMLExtension.removeL2Namespaces methods.
+ */ public
+ ";
+
+@@ -49386,7 +49386,7 @@
+ %javamethodmodifiers SBMLExtensionRegistry::addL2Namespaces(XMLNamespaces *xmlns) const "
+ /**
+ * adds all L2 Extension namespaces to the namespace list. This will call all
+- * overriden SBMLExtension.addL2Namespaces methods.
++ * overridden SBMLExtension.addL2Namespaces methods.
+ */ public
+ ";
+
+Index: libsbml-5.4.1/src/bindings/java/java-files/org/sbml/libsbml/SBMLExtensionRegistry.java
+===================================================================
+--- libsbml-5.4.1.orig/src/bindings/java/java-files/org/sbml/libsbml/SBMLExtensionRegistry.java 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/bindings/java/java-files/org/sbml/libsbml/SBMLExtensionRegistry.java 2012-03-30 13:03:03.000000000 +0200
+@@ -96,7 +96,7 @@
+
+ /**
+ * Remove all L2 Extension namespaces from the namespace list. This will call all
+- * overriden SBMLExtension.removeL2Namespaces methods.
++ * overridden SBMLExtension.removeL2Namespaces methods.
+ */ public
+ void removeL2Namespaces(XMLNamespaces xmlns) {
+ libsbmlJNI.SBMLExtensionRegistry_removeL2Namespaces(swigCPtr, this, XMLNamespaces.getCPtr(xmlns), xmlns);
+@@ -105,7 +105,7 @@
+
+ /**
+ * adds all L2 Extension namespaces to the namespace list. This will call all
+- * overriden SBMLExtension.addL2Namespaces methods.
++ * overridden SBMLExtension.addL2Namespaces methods.
+ */ public
+ void addL2Namespaces(XMLNamespaces xmlns) {
+ libsbmlJNI.SBMLExtensionRegistry_addL2Namespaces(swigCPtr, this, XMLNamespaces.getCPtr(xmlns), xmlns);
+Index: libsbml-5.4.1/src/bindings/java/java-files/org/sbml/libsbml/SBMLExtension.java
+===================================================================
+--- libsbml-5.4.1.orig/src/bindings/java/java-files/org/sbml/libsbml/SBMLExtension.java 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/bindings/java/java-files/org/sbml/libsbml/SBMLExtension.java 2012-03-30 13:03:03.000000000 +0200
+@@ -26,8 +26,8 @@
+ * The extended class is implemented based on the following steps:
+ * <p>
+ * (NOTE:
+- * 'src/pacakges/groups/extension/GroupsExtension.{h,cpp}' and
+- * 'src/pacakges/layout/extension/LayoutExtension.{h,cpp}' are
++ * 'src/packages/groups/extension/GroupsExtension.{h,cpp}' and
++ * 'src/packages/layout/extension/LayoutExtension.{h,cpp}' are
+ * example files in which {@link SBMLExtension} derived classes are implemented)
+ * <p>
+ * <ol>
+@@ -373,7 +373,7 @@
+ {
+ //-------------------------------------------------------------------------
+ //
+- // 1. Checks if the groups pacakge has already been registered.
++ // 1. Checks if the groups package has already been registered.
+ //
+ //-------------------------------------------------------------------------
+
+@@ -570,7 +570,7 @@
+ * <p>
+ * Returns the ith URI (the supported package version)
+ * <p>
+- * @param i the index of the list of URI (the list of supporeted pacakge versions)
++ * @param i the index of the list of URI (the list of supporeted package versions)
+ * @return the URI of supported package version with the given index.
+ */ public
+ String getSupportedPackageURI(long i) {
+Index: libsbml-5.4.1/src/bindings/csharp/csdoc.i
+===================================================================
+--- libsbml-5.4.1.orig/src/bindings/csharp/csdoc.i 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/bindings/csharp/csdoc.i 2012-03-30 13:03:03.000000000 +0200
+@@ -46447,8 +46447,8 @@
+ * The extended class is implemented based on the following steps:
+ *
+ * (NOTE:
+- * \'src/pacakges/groups/extension/GroupsExtension.{h,cpp}\' and
+- * \'src/pacakges/layout/extension/LayoutExtension.{h,cpp}\' are
++ * \'src/packages/groups/extension/GroupsExtension.{h,cpp}\' and
++ * \'src/packages/layout/extension/LayoutExtension.{h,cpp}\' are
+ * example files in which SBMLExtension derived classes are implemented)
+ *
+ * <ol>
+@@ -46794,7 +46794,7 @@
+ {
+ //-------------------------------------------------------------------------
+ //
+- // 1. Checks if the groups pacakge has already been registered.
++ // 1. Checks if the groups package has already been registered.
+ //
+ //-------------------------------------------------------------------------
+
+@@ -46941,7 +46941,7 @@
+ *
+ * Returns the ith URI (the supported package version)
+ *
+- * @param i the index of the list of URI (the list of supporeted pacakge versions)
++ * @param i the index of the list of URI (the list of supporeted package versions)
+ * @return the URI of supported package version with the given index.
+ */ public
+ ";
+@@ -47192,7 +47192,7 @@
+ %csmethodmodifiers SBMLExtensionRegistry::removeL2Namespaces(XMLNamespaces *xmlns) const "
+ /**
+ * Remove all L2 Extension namespaces from the namespace list. This will call all
+- * overriden SBMLExtension::removeL2Namespaces methods.
++ * overridden SBMLExtension::removeL2Namespaces methods.
+ */ public
+ ";
+
+@@ -47200,7 +47200,7 @@
+ %csmethodmodifiers SBMLExtensionRegistry::addL2Namespaces(XMLNamespaces *xmlns) const "
+ /**
+ * adds all L2 Extension namespaces to the namespace list. This will call all
+- * overriden SBMLExtension::addL2Namespaces methods.
++ * overridden SBMLExtension::addL2Namespaces methods.
+ */ public
+ ";
+
+Index: libsbml-5.4.1/src/bindings/csharp/csharp-files-win/SBMLExtensionRegistry.cs
+===================================================================
+--- libsbml-5.4.1.orig/src/bindings/csharp/csharp-files-win/SBMLExtensionRegistry.cs 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/bindings/csharp/csharp-files-win/SBMLExtensionRegistry.cs 2012-03-30 13:03:03.000000000 +0200
+@@ -104,7 +104,7 @@
+
+ /**
+ * Remove all L2 Extension namespaces from the namespace list. This will call all
+- * overriden SBMLExtension::removeL2Namespaces methods.
++ * overridden SBMLExtension::removeL2Namespaces methods.
+ */ public
+ void removeL2Namespaces(XMLNamespaces xmlns) {
+ libsbmlPINVOKE.SBMLExtensionRegistry_removeL2Namespaces(swigCPtr, XMLNamespaces.getCPtr(xmlns));
+@@ -113,7 +113,7 @@
+
+ /**
+ * adds all L2 Extension namespaces to the namespace list. This will call all
+- * overriden SBMLExtension::addL2Namespaces methods.
++ * overridden SBMLExtension::addL2Namespaces methods.
+ */ public
+ void addL2Namespaces(XMLNamespaces xmlns) {
+ libsbmlPINVOKE.SBMLExtensionRegistry_addL2Namespaces(swigCPtr, XMLNamespaces.getCPtr(xmlns));
+Index: libsbml-5.4.1/src/bindings/csharp/csharp-files-win/SBMLExtension.cs
+===================================================================
+--- libsbml-5.4.1.orig/src/bindings/csharp/csharp-files-win/SBMLExtension.cs 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/bindings/csharp/csharp-files-win/SBMLExtension.cs 2012-03-30 13:03:03.000000000 +0200
+@@ -29,8 +29,8 @@
+ * The extended class is implemented based on the following steps:
+ *
+ * (NOTE:
+- * 'src/pacakges/groups/extension/GroupsExtension.{h,cpp}' and
+- * 'src/pacakges/layout/extension/LayoutExtension.{h,cpp}' are
++ * 'src/packages/groups/extension/GroupsExtension.{h,cpp}' and
++ * 'src/packages/layout/extension/LayoutExtension.{h,cpp}' are
+ * example files in which SBMLExtension derived classes are implemented)
+ *
+ * <ol>
+@@ -376,7 +376,7 @@
+ {
+ //-------------------------------------------------------------------------
+ //
+- // 1. Checks if the groups pacakge has already been registered.
++ // 1. Checks if the groups package has already been registered.
+ //
+ //-------------------------------------------------------------------------
+
+@@ -567,7 +567,7 @@
+ *
+ * Returns the ith URI (the supported package version)
+ *
+- * @param i the index of the list of URI (the list of supporeted pacakge versions)
++ * @param i the index of the list of URI (the list of supporeted package versions)
+ * @return the URI of supported package version with the given index.
+ */ public
+ string getSupportedPackageURI(long i) {
+Index: libsbml-5.4.1/src/bindings/csharp/csharp-files/SBMLExtensionRegistry.cs
+===================================================================
+--- libsbml-5.4.1.orig/src/bindings/csharp/csharp-files/SBMLExtensionRegistry.cs 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/bindings/csharp/csharp-files/SBMLExtensionRegistry.cs 2012-03-30 13:03:03.000000000 +0200
+@@ -105,7 +105,7 @@
+
+ /**
+ * Remove all L2 Extension namespaces from the namespace list. This will call all
+- * overriden SBMLExtension::removeL2Namespaces methods.
++ * overridden SBMLExtension::removeL2Namespaces methods.
+ */ public
+ void removeL2Namespaces(XMLNamespaces xmlns) {
+ libsbmlPINVOKE.SBMLExtensionRegistry_removeL2Namespaces(swigCPtr, XMLNamespaces.getCPtr(xmlns));
+@@ -114,7 +114,7 @@
+
+ /**
+ * adds all L2 Extension namespaces to the namespace list. This will call all
+- * overriden SBMLExtension::addL2Namespaces methods.
++ * overridden SBMLExtension::addL2Namespaces methods.
+ */ public
+ void addL2Namespaces(XMLNamespaces xmlns) {
+ libsbmlPINVOKE.SBMLExtensionRegistry_addL2Namespaces(swigCPtr, XMLNamespaces.getCPtr(xmlns));
+Index: libsbml-5.4.1/src/bindings/csharp/csharp-files/SBMLExtension.cs
+===================================================================
+--- libsbml-5.4.1.orig/src/bindings/csharp/csharp-files/SBMLExtension.cs 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/src/bindings/csharp/csharp-files/SBMLExtension.cs 2012-03-30 13:03:03.000000000 +0200
+@@ -29,8 +29,8 @@
+ * The extended class is implemented based on the following steps:
+ *
+ * (NOTE:
+- * 'src/pacakges/groups/extension/GroupsExtension.{h,cpp}' and
+- * 'src/pacakges/layout/extension/LayoutExtension.{h,cpp}' are
++ * 'src/packages/groups/extension/GroupsExtension.{h,cpp}' and
++ * 'src/packages/layout/extension/LayoutExtension.{h,cpp}' are
+ * example files in which SBMLExtension derived classes are implemented)
+ *
+ * <ol>
+@@ -376,7 +376,7 @@
+ {
+ //-------------------------------------------------------------------------
+ //
+- // 1. Checks if the groups pacakge has already been registered.
++ // 1. Checks if the groups package has already been registered.
+ //
+ //-------------------------------------------------------------------------
+
+@@ -568,7 +568,7 @@
+ *
+ * Returns the ith URI (the supported package version)
+ *
+- * @param i the index of the list of URI (the list of supporeted pacakge versions)
++ * @param i the index of the list of URI (the list of supporeted package versions)
+ * @return the URI of supported package version with the given index.
+ */ public
+ string getSupportedPackageURI(long i) {
+Index: libsbml-5.4.1/docs/00README-HowToUsePackageExtension.txt
+===================================================================
+--- libsbml-5.4.1.orig/docs/00README-HowToUsePackageExtension.txt 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/docs/00README-HowToUsePackageExtension.txt 2012-03-30 13:03:03.000000000 +0200
+@@ -37,7 +37,7 @@
+ (e.g. Group, ListOfGroups, Member, and ListOfMembers are the SBase
+ derived classes of the groups package.)
+
+- Each pacakge extension provides a single header file which serves to include
++ Each package extension provides a single header file which serves to include
+ most of the above header files in a similar fashion to the SBMLTypes.h file
+ in libSBML core.
+ For example, GroupsExtensionTypes.h is provided by the groups package.
+@@ -94,7 +94,7 @@
+ For example, two SBasePlugin derived classes, SBMLDocumentPlugin and
+ GroupsModelPlugin, are used by the groups extension.
+ SBMLDocumentPlugin, which is plugged in the sbml element, is a common plugin
+- class for pacakge extensions which use only 'required' attribute in the
++ class for package extensions which use only 'required' attribute in the
+ SBMLDocument class, and thus the class is basically not used in user's
+ code (**).
+ On the other hand, GroupsModelPlugin, which is plugged into the model element,
+Index: libsbml-5.4.1/docs/00README-HowToImplementPackageExtension.txt
+===================================================================
+--- libsbml-5.4.1.orig/docs/00README-HowToImplementPackageExtension.txt 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/docs/00README-HowToImplementPackageExtension.txt 2012-03-30 13:03:03.000000000 +0200
+@@ -34,8 +34,8 @@
+ ----------------------------------------------------------------------
+ (NOTE)
+
+- "src/pacakges/groups/extension/GroupsExtension.{h,cpp}" and
+- "src/pacakges/layout/extension/LayoutExtension.{h,cpp}" are
++ "src/packages/groups/extension/GroupsExtension.{h,cpp}" and
++ "src/packages/layout/extension/LayoutExtension.{h,cpp}" are
+ example files in which SBMLExtension derived classes are implemented.
+ ----------------------------------------------------------------------
+
+@@ -484,7 +484,7 @@
+ ----------------------------------------------------------------------
+ (NOTE)
+
+- - default level, default version, and default pacakge version
++ - default level, default version, and default package version
+ should be given as default arguments.
+ (This may change in the future release).
+
+@@ -527,7 +527,7 @@
+ // connect child elements to this element
+ connectToChild();
+
+- // load pacakge extensions bound with this object (if any)
++ // load package extensions bound with this object (if any)
+ loadPlugins(groupsns);
+ }
+
+@@ -794,7 +794,7 @@
+ 3. Implement one or more SBasePlugin derived classes
+ --------------------------------------------------------------------------------
+
+-Thirdly, SBasePlugin derived classes for the pacakge needs to be implemented.
++Thirdly, SBasePlugin derived classes for the package needs to be implemented.
+
+ ------------------------------------------------------------------------------
+ 3-1) Identify which core SBML elements (e.g. Model, Reaction,..) to be extended
+Index: libsbml-5.4.1/docs/00README-ExtensionSupportClasses.txt
+===================================================================
+--- libsbml-5.4.1.orig/docs/00README-ExtensionSupportClasses.txt 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/docs/00README-ExtensionSupportClasses.txt 2012-03-30 13:03:03.000000000 +0200
+@@ -316,7 +316,7 @@
+ 8) SBMLExtensionException class
+
+ SBMLExtensionException class is a exception class which can be thrown
+- when an exception about pacakge extension occurs (e.g. required package
++ when an exception about package extension occurs (e.g. required package
+ is not registered).
+
+ Currently, the exception can be thrown in the following functions if
+Index: libsbml-5.4.1/docs/00README-ChangesInSBase.txt
+===================================================================
+--- libsbml-5.4.1.orig/docs/00README-ChangesInSBase.txt 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/docs/00README-ChangesInSBase.txt 2012-03-30 13:03:03.000000000 +0200
+@@ -68,12 +68,12 @@
+
+ 3) XMLAttributes mAttributesOfUnknownPkg
+
+- An XMLAttributes object containing attributes of unknown pacakges.
++ An XMLAttributes object containing attributes of unknown packages.
+
+
+ 4) XMLNode mElementsOfUnknownPkg
+
+- An XMLNode object containing elements of unknown pacakges.
++ An XMLNode object containing elements of unknown packages.
+
+ ---------------------------------------------------------------------------
+ 2. Added member functions in SBase class
+@@ -319,7 +319,7 @@
+ (NOTE)
+
+ In summary, each SBase derived class that represents a top-level
+- element of its pacakge extension must override this function.
++ element of its package extension must override this function.
+ ------------------------------------------------------------
+
+
+Index: libsbml-5.4.1/docs/src/libsbml-howto-implement-extension.txt
+===================================================================
+--- libsbml-5.4.1.orig/docs/src/libsbml-howto-implement-extension.txt 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/docs/src/libsbml-howto-implement-extension.txt 2012-03-30 13:03:03.000000000 +0200
+@@ -141,7 +141,7 @@
+ <p><em>NOTE</em></p>
+ <ul>
+ <li>
+- default level, default version, and default pacakge version
++ default level, default version, and default package version
+ should be given as default arguments.
+ (This may change in the future release).
+
+@@ -187,7 +187,7 @@
+ // connect child elements to this element
+ connectToChild();
+
+- // load pacakge extensions bound with this object (if any)
++ // load package extensions bound with this object (if any)
+ loadPlugins(groupsns);
+ }
+ @endverbatim
+@@ -479,7 +479,7 @@
+ <h3><a class="anchor" name="i3">3. Implement SBasePlugin derived classes</a></h3>
+
+ <p>
+-Thirdly, SBasePlugin derived classes for the pacakge needs to be implemented.
++Thirdly, SBasePlugin derived classes for the package needs to be implemented.
+
+ <h4><a class="anchor" name="i3-1">3-1. Identify which core SBML elements (e.g. Model, Reaction,..) to be extended (i.e. adding attributes and/or elements) for your package extensions.</a></h4>
+ <p>
+Index: libsbml-5.4.1/docs/src/libsbml-extension-support-classes.txt
+===================================================================
+--- libsbml-5.4.1.orig/docs/src/libsbml-extension-support-classes.txt 2012-03-30 13:03:03.000000000 +0200
++++ libsbml-5.4.1/docs/src/libsbml-extension-support-classes.txt 2012-03-30 13:03:03.000000000 +0200
+@@ -90,7 +90,7 @@
+ </li>
+
+ <li> <a href="#SBMLExtensionException"> SBMLExtensionException</a> class is a exception class
+-which can be thrown when an exception about pacakge extension occurs.
++which can be thrown when an exception about package extension occurs.
+ </li>
+ </ul>
+
+@@ -574,7 +574,7 @@
+
+ <p>
+ SBMLExtensionException class is an exception class which can be thrown
+- when an exception about pacakge extension occurs (e.g., required package
++ when an exception about package extension occurs (e.g., required package
+ is not registered).
+ </p>
+
Modified: trunk/packages/libsbml/trunk/debian/rules
===================================================================
--- trunk/packages/libsbml/trunk/debian/rules 2012-03-30 10:34:48 UTC (rev 10188)
+++ trunk/packages/libsbml/trunk/debian/rules 2012-03-30 12:16:20 UTC (rev 10189)
@@ -89,8 +89,9 @@
rm -f build-stamp
# Add here commands to clean up after the build process.
[ ! -f Makefile ] || $(MAKE) distclean
- ### remove the during build created debian/libsbml5-octave.install ###
+ ### remove the by debian/rules created files ###
rm -f debian/libsbml5-octave.install
+ rm -f changelog
### the clean target of the libsbml makefile is highly b0rken ###
### verx ugly ###
find src/bindings -name "*Glyph*" -exec rm -f {} +
@@ -197,6 +198,7 @@
strip --strip-unneeded $(debtmp)/$(OCTAVE_PATH)/*.mex || true
strip --strip-unneeded $(debtmp)/$(OCTAVE_PATH)/*.mex || true
echo $(OCTAVE_PATH) >debian/libsbml5-octave.install
+ cp NEWS.txt changelog
# Build architecture-independent files here.
binary-indep: build install
@@ -213,6 +215,8 @@
dh_installman
dh_link
dh_strip --dbg-package=${dbgpack}
+ strip --remove-section=.comment debian/libsbml5-matlab/usr/lib/*.mexa64
+ strip --remove-section=.comment debian/libsbml5-octave/$(OCTAVE_PATH)/*.mex
dh_compress
dh_fixperms
dh_makeshlibs
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