[med-svn] r18964 - in trunk/packages/libsbml/trunk/debian: . patches
Ivo Maintz
ivomaintz-guest at moszumanska.debian.org
Fri Mar 13 13:04:08 UTC 2015
Author: ivomaintz-guest
Date: 2015-03-13 13:04:07 +0000 (Fri, 13 Mar 2015)
New Revision: 18964
Added:
trunk/packages/libsbml/trunk/debian/libsbml5-cil-doc.doc-base
trunk/packages/libsbml/trunk/debian/libsbml5-doc.doc-base
trunk/packages/libsbml/trunk/debian/libsbml5-java-doc.doc-base
trunk/packages/libsbml/trunk/debian/libsbml5-perl-doc.doc-base
trunk/packages/libsbml/trunk/debian/libsbml5-python-doc.doc-base
trunk/packages/libsbml/trunk/debian/patches/perl-installdirs.patch
Removed:
trunk/packages/libsbml/trunk/debian/libsbml5-octave.links.amd64
trunk/packages/libsbml/trunk/debian/libsbml5-octave.links.i386
trunk/packages/libsbml/trunk/debian/patches/mexext.patch
trunk/packages/libsbml/trunk/debian/patches/perl-installdirs.patch
Modified:
trunk/packages/libsbml/trunk/debian/README.source
trunk/packages/libsbml/trunk/debian/changelog
trunk/packages/libsbml/trunk/debian/control
trunk/packages/libsbml/trunk/debian/control.in
trunk/packages/libsbml/trunk/debian/libsbml5-doc.docs
trunk/packages/libsbml/trunk/debian/libsbml5-octave.install
trunk/packages/libsbml/trunk/debian/libsbml5-python-doc.docs
trunk/packages/libsbml/trunk/debian/patches/doxygen.patch
trunk/packages/libsbml/trunk/debian/patches/hardening.patch
trunk/packages/libsbml/trunk/debian/patches/series
trunk/packages/libsbml/trunk/debian/patches/spelling.patch
trunk/packages/libsbml/trunk/debian/rules
Log:
* Upstream update
* install of octave bindings is more robust (could work also on other
architectures than amd64/i386)
* some work to get more lintian-compiant...
Modified: trunk/packages/libsbml/trunk/debian/README.source
===================================================================
--- trunk/packages/libsbml/trunk/debian/README.source 2015-03-12 08:46:56 UTC (rev 18963)
+++ trunk/packages/libsbml/trunk/debian/README.source 2015-03-13 13:04:07 UTC (rev 18964)
@@ -1,3 +1,9 @@
+libsbml (5.11.0)
+ * find all misspelled words with this string:
+ find -type f -exec sed -i 's/multiple /multiple /g;s/another /another /g;s/functions /functions /g;s/absolute /absolute /g;s/explicitly /explicitly /g;s/information /information /g;s/program /program /g;s/privileges /privileges /g;s/the /the /g' {} +
+
+ -- Ivo Maintz <ivo at maintz.de> Fri, 09 Jan 2015 16:51:09 +0100
+
libsbml (5.9.2)
* render extension is now included in the source distribution, no extra work to do
* the original tarball must be re-created to exclude unwanted files (actually docs/src/prettify/*);
Modified: trunk/packages/libsbml/trunk/debian/changelog
===================================================================
--- trunk/packages/libsbml/trunk/debian/changelog 2015-03-12 08:46:56 UTC (rev 18963)
+++ trunk/packages/libsbml/trunk/debian/changelog 2015-03-13 13:04:07 UTC (rev 18964)
@@ -1,10 +1,25 @@
+libsbml (5.11.2+dfsg-1) UNRELEASED; urgency=medium
+
+ * New upstream version
+ * debian/*doc-base: added doc-base integration for the *doc packages
+ * debian/control.in: fixed some spelling errors
+ * debian/libsbml5-octave.install: turned into a script to install into the
+ right location
+ * debian/rules: use octave itself do set OCTAVE_PATH
+ debian/libsbml5-octave.links.* are obsolete
+ install index.html to the proper location
+ remove wastful *.md5 files
+
+ -- Ivo Maintz <ivo at maintz.de> Wed, 11 Mar 2015 15:45:42 +0100
+
libsbml (5.10.0+dfsg-2) UNRELEASED; urgency=medium
+ [ Andreas Tille ]
* According to https://lists.debian.org/debian-bsd/2014/09/msg00133.html
libsbml requires openjdk - so we drop all alternatives from the
dependency list
- -- Andreas Tille <tille at debian.org> Wed, 17 Sep 2014 08:47:46 +0200
+ -- Ivo Maintz <ivo at maintz.de> Mon, 22 Sep 2014 10:11:35 +0200
libsbml (5.10.0+dfsg-1) unstable; urgency=medium
Modified: trunk/packages/libsbml/trunk/debian/control
===================================================================
--- trunk/packages/libsbml/trunk/debian/control 2015-03-12 08:46:56 UTC (rev 18963)
+++ trunk/packages/libsbml/trunk/debian/control 2015-03-13 13:04:07 UTC (rev 18964)
@@ -14,7 +14,7 @@
python-dev,
perl,
libperl-dev,
- openjdk-7-jdk,
+ default-jdk | openjdk-7-jdk,
octave-pkg-dev,
r-base-dev,
r-base-core,
@@ -27,7 +27,7 @@
cli-runtime,
dpkg-dev (>= 1.16.1~),
texlive-latex-base
-Standards-Version: 3.9.5
+Standards-Version: 3.9.6
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/
Homepage: http://www.sbml.org/
@@ -68,7 +68,7 @@
Section: libs
Depends: ${shlibs:Depends},
${misc:Depends}
-Pre-Depends: multiarch-support
+Pre-Depends: ${misc:Pre-Depends}
Conflicts: libsbml3
Provides: libsbml
Description: System Biology Markup Language library
@@ -88,12 +88,12 @@
libsbml-python
Provides: python-sbml,
libsbml-python
-Description: System Biology Markup Language library - Python bindings
+Description: System Biology Markup Language library - python 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 Python bindings of LibSBML.
+ This package contains the python bindings of LibSBML.
Package: libsbml5-matlab
Section: contrib/math
@@ -101,12 +101,12 @@
Conflicts: libsbml4-matlab
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}
-Description: System Biology Markup Language library - Matlab bindings
+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 Matlab bindings of LibSBML.
+ This package contains the matlab bindings of LibSBML.
Package: libsbml5-java
Architecture: any
@@ -114,16 +114,16 @@
Depends: ${shlibs:Depends},
${misc:Depends},
jarwrapper
-Pre-Depends: multiarch-support
+Pre-Depends: ${misc:Pre-Depends}
Conflicts: libsbml3-java,
libsbml4-java
Provides: libsbml-java
-Description: System Biology Markup Language library - Java binding
+Description: System Biology Markup Language library - java 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 Java binding of LibSBML.
+ This Package contains the java bindings of LibSBML.
Package: libsbml5-perl
Architecture: any
@@ -133,12 +133,12 @@
${misc:Depends}
Conflicts: libsbml3-perl
Provides: libsbml-perl
-Description: System Biology Markup Language library - Perl binding
+Description: System Biology Markup Language library - perl 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 Perl binding of LibSBML.
+ This package contains the perl bindings of LibSBML.
Package: libsbml5-octave
Architecture: any
@@ -147,12 +147,12 @@
${misc:Depends},
octave
Provides: libsbml-octave
-Description: System Biology Markup Language library - Octave binding
+Description: System Biology Markup Language library - octave 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 Octave binding of LibSBML.
+ This package contains the octave bindings of LibSBML.
Package: libsbml5-cil
Architecture: any
@@ -161,12 +161,12 @@
${misc:Depends},
libsbml5-dev
Provides: libsbml-cil
-Description: System Biology Markup Language library - CLR binding
+Description: System Biology Markup Language library - cil 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 CLR binding of LibSBML.
+ This package contains the cil bindings of LibSBML.
Package: libsbml5-examples
Architecture: all
@@ -178,14 +178,14 @@
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 C/C++, Java, Perl and layout examples.
+ This package contains C/C++, java, perl and layout examples.
Package: libsbml5-doc
Architecture: all
Section: doc
Depends: ${misc:Depends}
Suggests: libsbml5-dev (= ${binary:Version})
-Description: System Biology Markup Language library -- Documentation
+Description: System Biology Markup Language library -- documentation
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),
@@ -197,7 +197,7 @@
Section: doc
Depends: ${misc:Depends}
Suggests: libsbml5-dev (= ${binary:Version})
-Description: System Biology Markup Language library -- CIL Documentation
+Description: System Biology Markup Language library -- cil documentation
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),
@@ -209,7 +209,7 @@
Section: doc
Depends: ${misc:Depends}
Suggests: libsbml5-dev (= ${binary:Version})
-Description: System Biology Markup Language library -- Java Documentation
+Description: System Biology Markup Language library -- java documentation
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),
@@ -221,7 +221,7 @@
Section: doc
Depends: ${misc:Depends}
Suggests: libsbml5-dev (= ${binary:Version})
-Description: System Biology Markup Language library -- Perl Documentation
+Description: System Biology Markup Language library -- perl documentation
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),
@@ -233,7 +233,7 @@
Section: doc
Depends: ${misc:Depends}
Suggests: libsbml5-dev (= ${binary:Version})
-Description: System Biology Markup Language library -- Python Documentation
+Description: System Biology Markup Language library -- python documentation
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),
Modified: trunk/packages/libsbml/trunk/debian/control.in
===================================================================
--- trunk/packages/libsbml/trunk/debian/control.in 2015-03-12 08:46:56 UTC (rev 18963)
+++ trunk/packages/libsbml/trunk/debian/control.in 2015-03-13 13:04:07 UTC (rev 18964)
@@ -27,7 +27,7 @@
cli-runtime,
dpkg-dev (>= 1.16.1~),
texlive-latex-base
-Standards-Version: 3.9.5
+Standards-Version: 3.9.6
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/
Homepage: http://www.sbml.org/
@@ -45,6 +45,7 @@
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 files necessary for development with libsbml.
Package: libsbml5-dbg
@@ -61,6 +62,7 @@
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 th debugging symbols for libsbml.
Package: libsbml5
@@ -68,7 +70,7 @@
Section: libs
Depends: ${shlibs:Depends},
${misc:Depends}
-Pre-Depends: multiarch-support
+Pre-Depends: ${misc:Pre-Depends}
Conflicts: libsbml3
Provides: libsbml
Description: System Biology Markup Language library
@@ -114,16 +116,16 @@
Depends: ${shlibs:Depends},
${misc:Depends},
jarwrapper
-Pre-Depends: multiarch-support
+Pre-Depends: ${misc:Pre-Depends}
Conflicts: libsbml3-java,
libsbml4-java
Provides: libsbml-java
-Description: System Biology Markup Language library - Java binding
+Description: System Biology Markup Language library - Java 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 Java binding of LibSBML.
+ This Package contains the Java bindings of LibSBML.
Package: libsbml5-perl
Architecture: any
@@ -133,12 +135,12 @@
${misc:Depends}
Conflicts: libsbml3-perl
Provides: libsbml-perl
-Description: System Biology Markup Language library - Perl binding
+Description: System Biology Markup Language library - Perl 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 Perl binding of LibSBML.
+ This package contains the Perl bindings of LibSBML.
Package: libsbml5-octave
Architecture: any
@@ -147,12 +149,12 @@
${misc:Depends},
octave
Provides: libsbml-octave
-Description: System Biology Markup Language library - Octave binding
+Description: System Biology Markup Language library - Octave 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 Octave binding of LibSBML.
+ This package contains the Octave bindings of LibSBML.
Package: libsbml5-cil
Architecture: any
@@ -161,12 +163,12 @@
${misc:Depends},
libsbml5-dev
Provides: libsbml-cil
-Description: System Biology Markup Language library - CLR binding
+Description: System Biology Markup Language library - CLI 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 CLR binding of LibSBML.
+ This package contains the CLI bindings of LibSBML.
Package: libsbml5-examples
Architecture: all
@@ -185,7 +187,7 @@
Section: doc
Depends: ${misc:Depends}
Suggests: libsbml5-dev (= ${binary:Version})
-Description: System Biology Markup Language library -- Documentation
+Description: System Biology Markup Language library -- documentation
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),
@@ -197,45 +199,45 @@
Section: doc
Depends: ${misc:Depends}
Suggests: libsbml5-dev (= ${binary:Version})
-Description: System Biology Markup Language library -- CIL Documentation
+Description: System Biology Markup Language library -- CIL documentation
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 documentation for mono/cil bindings
+ This package contains documentation for MONO/CLI bindings
Package: libsbml5-java-doc
Architecture: all
Section: doc
Depends: ${misc:Depends}
Suggests: libsbml5-dev (= ${binary:Version})
-Description: System Biology Markup Language library -- Java Documentation
+Description: System Biology Markup Language library -- Java documentation
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 documentation for java bindings
+ This package contains documentation for Java bindings
Package: libsbml5-perl-doc
Architecture: all
Section: doc
Depends: ${misc:Depends}
Suggests: libsbml5-dev (= ${binary:Version})
-Description: System Biology Markup Language library -- Perl Documentation
+Description: System Biology Markup Language library -- Perl documentation
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 documentation for perl bindings
+ This package contains documentation for Perl bindings
Package: libsbml5-python-doc
Architecture: all
Section: doc
Depends: ${misc:Depends}
Suggests: libsbml5-dev (= ${binary:Version})
-Description: System Biology Markup Language library -- Python Documentation
+Description: System Biology Markup Language library -- Python documentation
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 documentation for python bindings
+ This package contains documentation for Python bindings
Added: trunk/packages/libsbml/trunk/debian/libsbml5-cil-doc.doc-base
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-cil-doc.doc-base (rev 0)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-cil-doc.doc-base 2015-03-13 13:04:07 UTC (rev 18964)
@@ -0,0 +1,12 @@
+Document: libsbml5-cil
+Title: libsbml5 csharp API
+Abstract: System Biology Markup Language library
+ 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.
+Section: Programming
+
+Format: HTML
+Files: /usr/share/doc/libsbml5-cil-doc/csharp-api/*.html
+Index: /usr/share/doc/libsbml5-cil-doc/csharp-api/index.html
Added: trunk/packages/libsbml/trunk/debian/libsbml5-doc.doc-base
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-doc.doc-base (rev 0)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-doc.doc-base 2015-03-13 13:04:07 UTC (rev 18964)
@@ -0,0 +1,12 @@
+Document: libsbml5
+Title: libsbml5 documentation
+Abstract: System Biology Markup Language library
+ 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.
+Section: Science/Biology
+
+Format: HTML
+Files: /usr/share/doc/libsbml5-doc/*api/ /usr/share/doc/libsbml5-doc/index.html
+Index: /usr/share/doc/libsbml5-doc/index.html
Modified: trunk/packages/libsbml/trunk/debian/libsbml5-doc.docs
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-doc.docs 2015-03-12 08:46:56 UTC (rev 18963)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-doc.docs 2015-03-13 13:04:07 UTC (rev 18964)
@@ -1,2 +1,4 @@
debian/tmp/usr/share/libsbml/docs/c-api
debian/tmp/usr/share/libsbml/docs/cpp-api
+debian/tmp/usr/share/libsbml/docs/index.html
+docs/.graphics
Added: trunk/packages/libsbml/trunk/debian/libsbml5-java-doc.doc-base
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-java-doc.doc-base (rev 0)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-java-doc.doc-base 2015-03-13 13:04:07 UTC (rev 18964)
@@ -0,0 +1,12 @@
+Document: libsbml5-java
+Title: libsbml5 java API
+Abstract: System Biology Markup Language library
+ 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.
+Section: Programming/Java
+
+Format: HTML
+Files: /usr/share/doc/libsbml5-java-doc/java-api/*.html
+Index: /usr/share/doc/libsbml5-java-doc/java-api/index.html
Modified: trunk/packages/libsbml/trunk/debian/libsbml5-octave.install
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-octave.install 2015-03-12 08:46:56 UTC (rev 18963)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-octave.install 2015-03-13 13:04:07 UTC (rev 18964)
@@ -1,2 +1,4 @@
-usr/lib/octave/site/oct/*/*.mex
-usr/lib/octave/site/oct/*/*.m usr/share/octave/site/m/libsbml-5.10.0
+#!/bin/sh
+
+echo "usr/lib/octave/site/oct/*/*.mex $(octave-config -p LOCALOCTFILEDIR)/libsbml5"
+echo "usr/lib/octave/site/oct/*/*.m $(octave-config -p LOCALFCNFILEDIR)/libsbml5"
Deleted: trunk/packages/libsbml/trunk/debian/libsbml5-octave.links.amd64
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-octave.links.amd64 2015-03-12 08:46:56 UTC (rev 18963)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-octave.links.amd64 2015-03-13 13:04:07 UTC (rev 18964)
@@ -1,2 +0,0 @@
-usr/lib/octave/site/oct/x86_64-pc-linux-gnu/OutputSBML.mex usr/share/octave/site/libsbml-5.10.0/OutputSBML.mex
-usr/lib/octave/site/oct/x86_64-pc-linux-gnu/TranslateSBML.mex usr/share/octave/site/libsbml-5.10.0/TranslateSBML.mex
Deleted: trunk/packages/libsbml/trunk/debian/libsbml5-octave.links.i386
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-octave.links.i386 2015-03-12 08:46:56 UTC (rev 18963)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-octave.links.i386 2015-03-13 13:04:07 UTC (rev 18964)
@@ -1,2 +0,0 @@
-usr/lib/octave/site/oct/i386-linux-gnu/OutputSBML.mex usr/share/octave/site/libsbml-5.10.0/OutputSBML.mex
-usr/lib/octave/site/oct/i386-linux-gnu/TranslateSBML.mex usr/share/octave/site/libsbml-5.10.0/TranslateSBML.mex
Added: trunk/packages/libsbml/trunk/debian/libsbml5-perl-doc.doc-base
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-perl-doc.doc-base (rev 0)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-perl-doc.doc-base 2015-03-13 13:04:07 UTC (rev 18964)
@@ -0,0 +1,12 @@
+Document: libsbml5-perl
+Title: libsbml5 perl API
+Abstract: System Biology Markup Language library
+ 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.
+Section: Programming/Perl
+
+Format: HTML
+Files: /usr/share/doc/libsbml5-perl-doc/perl-api/*.html
+Index: /usr/share/doc/libsbml5-perl-doc/perl-api/index.html
Added: trunk/packages/libsbml/trunk/debian/libsbml5-python-doc.doc-base
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-python-doc.doc-base (rev 0)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-python-doc.doc-base 2015-03-13 13:04:07 UTC (rev 18964)
@@ -0,0 +1,12 @@
+Document: libsbml5-python
+Title: libsbml5 Python API
+Abstract: System Biology Markup Language library
+ 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.
+Section: Programming/Python
+
+Format: HTML
+Files: /usr/share/doc/libsbml5-python-doc/python-api/*.html
+Index: /usr/share/doc/libsbml5-python-doc/python-api/index.html
Modified: trunk/packages/libsbml/trunk/debian/libsbml5-python-doc.docs
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-python-doc.docs 2015-03-12 08:46:56 UTC (rev 18963)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-python-doc.docs 2015-03-13 13:04:07 UTC (rev 18964)
@@ -1 +1 @@
-debian/tmp/usr/share/libsbml/docs/python-api/
+debian/tmp/usr/share/libsbml/docs/python-api
Modified: trunk/packages/libsbml/trunk/debian/patches/doxygen.patch
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/doxygen.patch 2015-03-12 08:46:56 UTC (rev 18963)
+++ trunk/packages/libsbml/trunk/debian/patches/doxygen.patch 2015-03-13 13:04:07 UTC (rev 18964)
@@ -1,37 +1,22 @@
Description: fix a wrong file name
- docs/CMakeLists.txt contains a wrong file name: doxygen-tabs.css instead of libsbml-doxygen-tabs.css
+ docs/CmakeLists.txt contains a wrong path to right-arrow-2x.png
.
- libsbml (5.10.0-1) UNRELEASED; urgency=medium
+ libsbml (5.11.0+dfsg-1sid1) UNRELEASED; urgency=medium
.
- * New upstream version
+ * update from upstream
Author: Ivo Maintz <ivo at maintz.de>
---
-Last-Update: 2014-02-27
+Last-Update: <2015-01-12>
-Index: libsbml-5.10.0/docs/CMakeLists.txt
-===================================================================
---- libsbml-5.10.0.orig/docs/CMakeLists.txt 2014-04-16 09:50:09.860337829 +0200
-+++ libsbml-5.10.0/docs/CMakeLists.txt 2014-04-16 09:51:51.893469161 +0200
-@@ -104,9 +104,9 @@
+--- libsbml-5.11.0+dfsg.orig/docs/CMakeLists.txt
++++ libsbml-5.11.0+dfsg/docs/CMakeLists.txt
+@@ -101,7 +101,7 @@ macro(createManual lang)
+ file(TO_NATIVE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/formatted/${lang}-api output_path)
+ file(TO_NATIVE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/formatted/${lang}-api/search search_path)
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/css/right-arrow-2x.png right_arrow)
++ file(TO_NATIVE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/src/common-graphics/right-arrow-2x.png 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)
-
-@@ -168,7 +168,7 @@
- ADD_CUSTOM_COMMAND(
- OUTPUT ${CMAKE_CURRENT_SOURCE_DIR}/src/libsbml.py
- COMMAND ${PYTHON_EXECUTABLE}
-- ARGS pythondocpreprocessor.py
-+ ARGS utilities/pythondocpreprocessor.py
- ${CMAKE_CURRENT_BINARY_DIR}/../src/bindings/python/libsbml-doxygen.py
- libsbml.py
- ${PYTHON_SUBSTITUTIONS}
+ file(TO_NATIVE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/src/doxygen-tabs.css tabs_css)
+ file(TO_NATIVE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/src/css/search.png search_png)
Modified: trunk/packages/libsbml/trunk/debian/patches/hardening.patch
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/hardening.patch 2015-03-12 08:46:56 UTC (rev 18963)
+++ trunk/packages/libsbml/trunk/debian/patches/hardening.patch 2015-03-13 13:04:07 UTC (rev 18964)
@@ -1,77 +1,16 @@
Description: hardening
.
- libsbml (5.10.0-1) UNRELEASED; urgency=low
+ libsbml (5.11.0+dfsg-1sid1) UNRELEASED; urgency=medium
.
* update from upstream
Author: Ivo Maintz <ivo at maintz.de>
---
-Last-Update: <2013-01-22>
+Last-Update: <2015-01-09>
-Index: libsbml-5.10.0/src/bindings/matlab/Makefile.in
-===================================================================
---- libsbml-5.10.0.orig/src/bindings/matlab/Makefile.in 2013-11-28 14:51:16.191345434 +0100
-+++ libsbml-5.10.0/src/bindings/matlab/Makefile.in 2013-11-28 14:51:16.183345349 +0100
-@@ -70,12 +70,7 @@
- installSBML.m \
- isoctave.m \
- matlab-tags-regexp.txt \
-- mexopts-R2007.sh \
-- mexopts-R2008.sh \
-- mexopts-R2009-R2010.sh \
-- mexopts-xcode43.sh \
-- mexopts-xcode45.sh \
-- mexopts-lion.sh \
-+ mexopts-R2009-2010.sh \
- test.xml \
- test/CMakeLists.txt
-
-@@ -142,7 +137,7 @@
- # is really necessary, but it seems prudent.
-
- define matlabrun
-- env CFLAGS="$(CFLAGS)" srcdir=. \
-+ env CFLAGS="$(shell dpkg-buildflags --get CFLAGS)" srcdir=. \
- $(LIBTOOL) -dlopen $(TOP_BUILDDIR)/src/libsbml.la --mode=execute $(1)
- endef
-
-Index: libsbml-5.10.0/src/bindings/matlab/mexopts-R2009-R2010.sh
-===================================================================
---- libsbml-5.10.0.orig/src/bindings/matlab/mexopts-R2009-R2010.sh 2013-11-28 14:51:16.191345434 +0100
-+++ libsbml-5.10.0/src/bindings/matlab/mexopts-R2009-R2010.sh 2013-11-28 14:51:16.183345349 +0100
-@@ -324,7 +324,13 @@
- #
- #----------------------------------------------------------------------------
- # CC="$CC"
--# CFLAGS="$CFLAGS"
-+ CFLAGS = $(shell dpkg-buildflags --get CFLAGS)
-+ CFLAGS += -Wall
-+ CXXFLAGS = $(shell dpkg-buildflags --get CXXFLAGS)
-+ CXXFLAGS += -Wall
-+ LDFLAGS = $(shell dpkg-buildflags --get LDFLAGS)
-+ CPPFLAGS = $(shell dpkg-buildflags --get CPPFLAGS)
-+ CCFLAGS = $(shell dpkg-buildflags --get CCFLAGS)
- # COPTIMFLAGS="$COPTIMFLAGS"
- # CDEBUGFLAGS="$CDEBUGFLAGS"
- # CLIBS="$CLIBS"
-Index: libsbml-5.10.0/src/bindings/perl/Makefile.in
-===================================================================
---- libsbml-5.10.0.orig/src/bindings/perl/Makefile.in 2013-11-28 14:51:16.191345434 +0100
-+++ libsbml-5.10.0/src/bindings/perl/Makefile.in 2013-11-28 14:51:16.183345349 +0100
-@@ -177,6 +177,8 @@
- endif
-
-
-+CXXFLAGS = $(shell dpkg-buildflags --get CXXFLAGS)
-+
- # If the last run was made with --enable-layout and this one isn't, or
- # vice-versa, the swig wrap files will be wrong for this run. However, you
- # can't tell just by looking at file mod times, so you can't use normal
-Index: libsbml-5.10.0/config/makefile-common-actions.mk
-===================================================================
---- libsbml-5.10.0.orig/config/makefile-common-actions.mk 2013-11-28 14:51:16.191345434 +0100
-+++ libsbml-5.10.0/config/makefile-common-actions.mk 2013-11-28 14:51:16.183345349 +0100
-@@ -72,6 +72,15 @@
+--- libsbml-5.11.0+dfsg.orig/config/makefile-common-actions.mk
++++ libsbml-5.11.0+dfsg/config/makefile-common-actions.mk
+@@ -77,6 +77,15 @@ endif
# here is only to remove duplicates, which the 'sort' function does as a
# documented side-effect.)
@@ -87,3 +26,24 @@
compile ?= $(LIBTOOL) --mode=compile --tag=CC $(CC) $(sort $(default_includes) $(INCLUDES)) $(CPPFLAGS) \
$(extra_CPPFLAGS) $(CFLAGS) $(extra_CFLAGS)
+--- libsbml-5.11.0+dfsg.orig/src/bindings/matlab/Makefile.in
++++ libsbml-5.11.0+dfsg/src/bindings/matlab/Makefile.in
+@@ -150,7 +150,7 @@ endif
+ # is really necessary, but it seems prudent.
+
+ define matlabrun
+- env CFLAGS="$(CFLAGS)" srcdir=. \
++ env CFLAGS="$(shell dpkg-buildflags --get CFLAGS)" srcdir=. \
+ $(LIBTOOL) -dlopen $(TOP_BUILDDIR)/src/libsbml.la --mode=execute $(1)
+ endef
+
+--- libsbml-5.11.0+dfsg.orig/src/bindings/perl/Makefile.in
++++ libsbml-5.11.0+dfsg/src/bindings/perl/Makefile.in
+@@ -178,6 +178,7 @@ ifeq (GCC,$(findstring GCC,$(shell $(CXX
+ CXXFLAGS += -fno-strict-aliasing
+ endif
+
++CXXFLAGS = $(shell dpkg-buildflags --get CXXFLAGS)
+
+ # 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
Deleted: trunk/packages/libsbml/trunk/debian/patches/mexext.patch
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/mexext.patch 2015-03-12 08:46:56 UTC (rev 18963)
+++ trunk/packages/libsbml/trunk/debian/patches/mexext.patch 2015-03-13 13:04:07 UTC (rev 18964)
@@ -1,19 +0,0 @@
-Description: get the matching mex extension
- Matlabs script $MATLABROOT/bin/mexext fails in an chrooted environment.
- .
-Author: Ivo Maintz <ivo at maintz.de>
-
----
-Last-Update: <2014-03-01>
-
---- libsbml-5.10.0.orig/src/bindings/matlab/FindMatlab.cmake
-+++ libsbml-5.10.0/src/bindings/matlab/FindMatlab.cmake
-@@ -162,7 +162,7 @@ IF(WIN32)
- SET(MATLAB_MATLAB_COMMAND "${MATLAB_ROOT_PATH}/bin/matlab.bat")
- ELSE (WIN32)
- SET(MATLAB_MEX_COMMAND "${MATLAB_ROOT_PATH}/bin/mex")
-- SET(MATLAB_MEXEXT ${MATLAB_ROOT_PATH}/bin/mexext)
-+ SET(MATLAB_MEXEXT "${CMAKE_SOURCE_DIR}/debian/bin/mexext")
- SET(MATLAB_MATLAB_COMMAND "${MATLAB_ROOT_PATH}/bin/matlab")
- MESSAGE(STATUS ${MATLAB_ROOT_PATH}/bin/maci64/)
- if(APPLE)
Deleted: trunk/packages/libsbml/trunk/debian/patches/perl-installdirs.patch
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/perl-installdirs.patch 2015-03-12 08:46:56 UTC (rev 18963)
+++ trunk/packages/libsbml/trunk/debian/patches/perl-installdirs.patch 2015-03-13 13:04:07 UTC (rev 18964)
@@ -1,32 +0,0 @@
-Author: gregor herrmann <gregoa at debian.org>
-Last-Update: Fri, 12 Sep 2014 14:42:36 +0200
-Bug-Debian: http://bugs.debian.org/761134
-Description: Fix Perl installation path
-
---- a/src/bindings/perl/Makefile.PL.in
-+++ b/src/bindings/perl/Makefile.PL.in
-@@ -58,7 +58,6 @@
- NAME => "LibSBML",
- PREFIX => "@prefix@",
- MAKEFILE => 'Makefile-perl',
-- INSTALLDIRS => "site",
- LIBS => "@XERCES_LDFLAGS@ @EXPAT_LDFLAGS@ @LIBXML_LDFLAGS@ @XERCES_LIBS@ @EXPAT_LIBS@ @LIBXML_LIBS@ @ZLIB_LIBS@ @BZ2_LIBS@ @LIBS@ -lm",
- LDDLFLAGS => $lddlflags,
- CC => "@CXX@",
---- a/src/bindings/perl/CMakeLists.txt
-+++ b/src/bindings/perl/CMakeLists.txt
-@@ -168,7 +168,13 @@
- string(REPLACE "'" "" PERL_PLATFORM ${PERL_PLATFORM})
- string(REPLACE ";" "" PERL_PLATFORM ${PERL_PLATFORM})
- string(REPLACE "archname=" "" PERL_PLATFORM ${PERL_PLATFORM})
-- set(PERL_PACKAGE_INSTALL_DIR ${CMAKE_INSTALL_LIBDIR}/perl5/site_perl/${PERL_VERSION}/${PERL_PLATFORM})
-+ execute_process(COMMAND "${PERL_EXECUTABLE}" -V:vendorarch
-+ OUTPUT_VARIABLE PERL_VENDORARCH OUTPUT_STRIP_TRAILING_WHITESPACE)
-+ string(REPLACE " " "" PERL_VENDORARCH ${PERL_VENDORARCH})
-+ string(REPLACE "'" "" PERL_VENDORARCH ${PERL_VENDORARCH})
-+ string(REPLACE ";" "" PERL_VENDORARCH ${PERL_VENDORARCH})
-+ string(REPLACE "vendorarch=/usr/lib/" "" PERL_VENDORARCH ${PERL_VENDORARCH})
-+ set(PERL_PACKAGE_INSTALL_DIR ${CMAKE_INSTALL_LIBDIR}/${PERL_VENDORARCH})
- set(PERL_PACKAGE_INSTALL_BIN_DIR ${PERL_PACKAGE_INSTALL_DIR}/auto/libSBML)
- else()
- set(PERL_PACKAGE_INSTALL_DIR ${MISC_PREFIX}bindings/perl)
Added: trunk/packages/libsbml/trunk/debian/patches/perl-installdirs.patch
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/perl-installdirs.patch (rev 0)
+++ trunk/packages/libsbml/trunk/debian/patches/perl-installdirs.patch 2015-03-13 13:04:07 UTC (rev 18964)
@@ -0,0 +1,27 @@
+--- a/src/bindings/perl/Makefile.PL.in
++++ b/src/bindings/perl/Makefile.PL.in
+@@ -58,7 +58,6 @@
+ NAME => "LibSBML",
+ PREFIX => "@prefix@",
+ MAKEFILE => 'Makefile-perl',
+- INSTALLDIRS => "site",
+ LIBS => "@XERCES_LDFLAGS@ @EXPAT_LDFLAGS@ @LIBXML_LDFLAGS@ @XERCES_LIBS@ @EXPAT_LIBS@ @LIBXML_LIBS@ @ZLIB_LIBS@ @BZ2_LIBS@ @LIBS@ -lm",
+ LDDLFLAGS => $lddlflags,
+ CC => "@CXX@",
+--- a/src/bindings/perl/CMakeLists.txt
++++ b/src/bindings/perl/CMakeLists.txt
+@@ -168,7 +168,13 @@
+ string(REPLACE "'" "" PERL_PLATFORM ${PERL_PLATFORM})
+ string(REPLACE ";" "" PERL_PLATFORM ${PERL_PLATFORM})
+ string(REPLACE "archname=" "" PERL_PLATFORM ${PERL_PLATFORM})
+- set(PERL_PACKAGE_INSTALL_DIR ${CMAKE_INSTALL_LIBDIR}/perl5/site_perl/${PERL_VERSION}/${PERL_PLATFORM})
++ execute_process(COMMAND "${PERL_EXECUTABLE}" -V:vendorarch
++ OUTPUT_VARIABLE PERL_VENDORARCH OUTPUT_STRIP_TRAILING_WHITESPACE)
++ string(REPLACE " " "" PERL_VENDORARCH ${PERL_VENDORARCH})
++ string(REPLACE "'" "" PERL_VENDORARCH ${PERL_VENDORARCH})
++ string(REPLACE ";" "" PERL_VENDORARCH ${PERL_VENDORARCH})
++ string(REPLACE "vendorarch=/usr/lib/" "" PERL_VENDORARCH ${PERL_VENDORARCH})
++ set(PERL_PACKAGE_INSTALL_DIR ${CMAKE_INSTALL_LIBDIR}/${PERL_VENDORARCH})
+ set(PERL_PACKAGE_INSTALL_BIN_DIR ${PERL_PACKAGE_INSTALL_DIR}/auto/libSBML)
+ else()
+ set(PERL_PACKAGE_INSTALL_DIR ${MISC_PREFIX}bindings/perl)
Modified: trunk/packages/libsbml/trunk/debian/patches/series
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/series 2015-03-12 08:46:56 UTC (rev 18963)
+++ trunk/packages/libsbml/trunk/debian/patches/series 2015-03-13 13:04:07 UTC (rev 18964)
@@ -1,5 +1,4 @@
+perl-installdirs.patch
hardening.patch
-mexext.patch
doxygen.patch
spelling.patch
-perl-installdirs.patch
Modified: trunk/packages/libsbml/trunk/debian/patches/spelling.patch
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/spelling.patch 2015-03-12 08:46:56 UTC (rev 18963)
+++ trunk/packages/libsbml/trunk/debian/patches/spelling.patch 2015-03-13 13:04:07 UTC (rev 18964)
@@ -1,59 +1,64 @@
Description: fixes spelling errors
This patch fixes spelling errors; lintian informed about "spelling-error-in-binary"
.
- libsbml (5.10.0-1) UNRELEASED; urgency=medium
+ libsbml (5.11.0+dfsg-1sid1) UNRELEASED; urgency=medium
.
- [Ivo Maintz]
- * New upstream version
+ * update from upstream
Author: Ivo Maintz <ivo at maintz.de>
---
-Last-Update: 2014-04-16
+Last-Update: <2015-01-12>
---- libsbml-5.10.0.orig/OLD_NEWS.txt
-+++ libsbml-5.10.0/OLD_NEWS.txt
-@@ -1102,7 +1102,7 @@ Version 3.1.1 (released 2008-02-25)
- Thanks to Chris Meyers for reporting this.
+--- libsbml-5.11.0+dfsg.orig/docs/src/common-text/libsbml-import-for-python.html
++++ libsbml-5.11.0+dfsg/docs/src/common-text/libsbml-import-for-python.html
+@@ -67,6 +67,6 @@ probably means that <code>PYTHONPATH</co
+ It may also mean that the read/write permissions of the installed library
+ files or a directory in the hierarchy containing them are such that you are
+ not allowed to access the files. In that case, please consult your systems
+-administrator or (if you have administrator priviledges) reset the
++administrator or (if you have administrator privileges) reset the
+ permissions yourself.
- - Tracker issue #1880570.
-- The previous fix for a piecewise without an otherwise statement
-+ The previous fix for a piecewise without anotherwise statement
- did not propagate for the use of piecewise within a lambda
- function. This is now fixed and multiple tests included to catch
- this and similar potential failures.
---- libsbml-5.10.0.orig/docs/src/libsbml-accessing.html
-+++ libsbml-5.10.0/docs/src/libsbml-accessing.html
-@@ -366,7 +366,7 @@ correctly. It may also mean that the re
- installed library files or a directory in the hierarchy containing them are
- such that you are not allowed to access the files. In that case, please
- 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-5.10.0.orig/src/bindings/csharp/csdoc.i
-+++ libsbml-5.10.0/src/bindings/csharp/csdoc.i
-@@ -246,7 +246,7 @@
- * appear first. The error code @if clike (a value drawn from the enumeration
- * #XMLErrorCode_t) @endif can provide a clue about what happened. For example,
- * a file might be unreadable (either because it does not actually exist
-- * 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:
-@@ -404,7 +404,7 @@
- * appear first. The error code @if clike (a value drawn from the enumeration
- * #XMLErrorCode_t)@endif can provide a clue about what happened. For example,
- * a file might be unreadable (either because it does not actually exist
-- * 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:
-@@ -4074,7 +4074,7 @@ s.setNotes(\'<body xmlns=\'http://www.w3
- * Hierarchical Model Composition (“comp”) package, and
+--- libsbml-5.11.0+dfsg.orig/src/bindings/csharp/csdoc.i
++++ libsbml-5.11.0+dfsg/src/bindings/csharp/csdoc.i
+@@ -324,7 +324,7 @@
+ * 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 read it) or some sort of file operation error may have been
++ * 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:
+ * @if cpp
+@@ -525,7 +525,7 @@ if (doc.getNumErrors() > 0)
+ * enumeration #XMLErrorCode_t)@endif can provide a clue about what
+ * happened. For example, a file might be unreadable (either because it does
+ * not actually exist or because the user does not have the necessary access
+- * priviledges to read it) or some sort of file operation error may have been
++ * 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:
+ * @if cpp
+@@ -819,7 +819,7 @@ if (doc.getNumErrors() > 0)
+ * enumeration #XMLErrorCode_t)@endif can provide a clue about what
+ * happened. For example, a file might be unreadable (either because it does
+ * not actually exist or because the user does not have the necessary access
+- * priviledges to read it) or some sort of file operation error may have been
++ * 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:
+ * @if cpp
+@@ -993,7 +993,7 @@ if (doc.getNumErrors() > 0)
+ * enumeration #XMLErrorCode_t)@endif can provide a clue about what
+ * happened. For example, a file might be unreadable (either because it does
+ * not actually exist or because the user does not have the necessary access
+- * priviledges to read it) or some sort of file operation error may have been
++ * 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:
+ * @if cpp
+@@ -4869,7 +4869,7 @@ void example (SBase sb)
+ * Hierarchical %Model Composition (“comp”) package, and
* extracted parts of that model in order to construct a new model in
* memory. The new, in-memory model will not accept a component drawn from
- * an other SBMLDocument with different package namespace declarations.
@@ -61,241 +66,155 @@
* 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:
-@@ -25953,7 +25953,7 @@ sp.setId(\'MySpecies\');
- * This attribute is optional in SBML Level 2, with a default of @c
- * false; it is mandatory in SBML Level 3 (with no default value). It
- * is used to indicate that a reaction occurs on a vastly faster time scale
-- * 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
-@@ -49145,7 +49145,7 @@ else:
- <td class=\'s-na\'>N</td>
- <td class=\'s-error\'>E</td></tr>
- <tr><td><code>@link libsbmlcs.libsbml.CompNoMultipleReferences CompNoMultipleReferences @endlink</code></td>
--<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>
-@@ -49469,7 +49469,7 @@ else:
- <td class=\'s-na\'>N</td>
- <td class=\'s-error\'>E</td></tr>
- <tr><td><code>@link libsbmlcs.libsbml.CompDeprecatedReplaceFunction CompDeprecatedReplaceFunction @endlink</code></td>
--<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-5.10.0.orig/src/bindings/csharp/csharp-files-win/Reaction.cs
-+++ libsbml-5.10.0/src/bindings/csharp/csharp-files-win/Reaction.cs
-@@ -96,7 +96,7 @@ namespace libsbml {
- * This attribute is optional in SBML Level 2, with a default of @c
- * false; it is mandatory in SBML Level 3 (with no default value). It
- * 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-5.10.0.orig/src/bindings/csharp/csharp-files-win/SBMLError.cs
-+++ libsbml-5.10.0/src/bindings/csharp/csharp-files-win/SBMLError.cs
-@@ -4530,7 +4530,7 @@ namespace libsbml {
- <td class='s-na'>N</td>
- <td class='s-error'>E</td></tr>
- <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-5.10.0.orig/src/bindings/csharp/csharp-files-win/SBMLReader.cs
-+++ libsbml-5.10.0/src/bindings/csharp/csharp-files-win/SBMLReader.cs
-@@ -179,7 +179,7 @@ public class SBMLReader : IDisposable {
- * appear first. The error code @if clike (a value drawn from the enumeration
- * #XMLErrorCode_t) @endif can provide a clue about what happened. For example,
- * 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-5.10.0.orig/src/bindings/csharp/csharp-files-win/SBase.cs
-+++ libsbml-5.10.0/src/bindings/csharp/csharp-files-win/SBase.cs
-@@ -2901,7 +2901,7 @@ s.setNotes('<body xmlns='http://www.w3.o
+@@ -55313,7 +55313,7 @@ on yyyy-MM-dd HH:mm with libSBML version
+ <td class=\'s-error\'></td>
+ </tr>
+ <tr><td class=\'code\'>@link libsbml#CompNoMultipleReferences CompNoMultipleReferences at endlink</td>
+-<td class=\'meaning\'>Objects may not be referenced by mutiple SBaseRef constructs.</td>
++<td class=\'meaning\'>Objects may not be referenced by multiple SBaseRef constructs.</td>
+ <td class=\'s-na\'></td>
+ <td class=\'s-na\'></td>
+ <td class=\'s-na\'></td>
+@@ -55673,7 +55673,7 @@ on yyyy-MM-dd HH:mm with libSBML version
+ <td class=\'s-error\'></td>
+ </tr>
+ <tr><td class=\'code\'>@link libsbml#CompDeprecatedReplaceFunction CompDeprecatedReplaceFunction at endlink</td>
+-<td class=\'meaning\'>The performReplacementsAndConversions fuctions is deprecated.</td>
++<td class=\'meaning\'>The performReplacementsAndConversions functions is deprecated.</td>
+ <td class=\'s-na\'></td>
+ <td class=\'s-na\'></td>
+ <td class=\'s-na\'></td>
+@@ -65167,7 +65167,7 @@ if (doc->getLevel() == 2)
+ * <h3><a class=\'anchor\' name=\'math-history\'>Historical notes</a></h3>
+ *
+ * Readers may wonder why this part of libSBML uses a seemingly less
+- * object-oriented design than other parts. Originally, much of libSBML was
++ * object-oriented design thanother parts. Originally, much of libSBML was
+ * written in C. All subsequent development was done in C++, but the
+ * complexity of some of the functionality for converting between infix, AST
+ * and MathML, coupled with the desire to maintain stability and backward
+--- libsbml-5.11.0+dfsg.orig/src/bindings/java/java-files/org/sbml/libsbml/ASTNode.java
++++ libsbml-5.11.0+dfsg/src/bindings/java/java-files/org/sbml/libsbml/ASTNode.java
+@@ -211,7 +211,7 @@ defined in SBML.
+ * <h3><a class='anchor' name='math-history'>Historical notes</a></h3>
+ <p>
+ * Readers may wonder why this part of libSBML uses a seemingly less
+- * object-oriented design than other parts. Originally, much of libSBML was
++ * object-oriented design thanother parts. Originally, much of libSBML was
+ * written in C. All subsequent development was done in C++, but the
+ * complexity of some of the functionality for converting between infix, AST
+ * and MathML, coupled with the desire to maintain stability and backward
+--- libsbml-5.11.0+dfsg.orig/src/bindings/java/java-files/org/sbml/libsbml/SBMLError.java
++++ libsbml-5.11.0+dfsg/src/bindings/java/java-files/org/sbml/libsbml/SBMLError.java
+@@ -5350,7 +5350,7 @@ defined in SBML.
+ <td class='s-error'></td>
+ </tr>
+ <tr><td class='code'>{@link libsbmlConstants#CompNoMultipleReferences CompNoMultipleReferences}</td>
+-<td class='meaning'>Objects may not be referenced by mutiple SBaseRef constructs.</td>
++<td class='meaning'>Objects may not be referenced by multiple SBaseRef constructs.</td>
+ <td class='s-na'></td>
+ <td class='s-na'></td>
+ <td class='s-na'></td>
+@@ -5710,7 +5710,7 @@ defined in SBML.
+ <td class='s-error'></td>
+ </tr>
+ <tr><td class='code'>{@link libsbmlConstants#CompDeprecatedReplaceFunction CompDeprecatedReplaceFunction}</td>
+-<td class='meaning'>The performReplacementsAndConversions fuctions is deprecated.</td>
++<td class='meaning'>The performReplacementsAndConversions functions is deprecated.</td>
+ <td class='s-na'></td>
+ <td class='s-na'></td>
+ <td class='s-na'></td>
+--- libsbml-5.11.0+dfsg.orig/src/bindings/java/java-files/org/sbml/libsbml/SBMLReader.java
++++ libsbml-5.11.0+dfsg/src/bindings/java/java-files/org/sbml/libsbml/SBMLReader.java
+@@ -197,7 +197,7 @@ public class SBMLReader {
+ * appear first. The error code can provide a clue about what
+ * happened. For example, a file might be unreadable (either because it does
+ * 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 been
++ * 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:
+ <p>
+@@ -302,7 +302,7 @@ if (doc.getNumErrors() > 0)
+ * appear first. The error code can provide a clue about what
+ * happened. For example, a file might be unreadable (either because it does
+ * not actually exist or because the user does not have the necessary access
+- * priviledges to read it) or some sort of file operation error may have been
++ * 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:
+ <p>
+--- libsbml-5.11.0+dfsg.orig/src/bindings/java/java-files/org/sbml/libsbml/SBase.java
++++ libsbml-5.11.0+dfsg/src/bindings/java/java-files/org/sbml/libsbml/SBase.java
+@@ -2952,7 +2952,7 @@ void example (SBase sb)
* 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-5.10.0.orig/src/bindings/csharp/csharp-files/Reaction.cs
-+++ libsbml-5.10.0/src/bindings/csharp/csharp-files/Reaction.cs
-@@ -96,7 +96,7 @@ namespace libsbmlcs {
- * This attribute is optional in SBML Level 2, with a default of @c
- * false; it is mandatory in SBML Level 3 (with no default value). It
- * 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-5.10.0.orig/src/bindings/csharp/csharp-files/SBMLError.cs
-+++ libsbml-5.10.0/src/bindings/csharp/csharp-files/SBMLError.cs
-@@ -4530,7 +4530,7 @@ namespace libsbmlcs {
- <td class='s-na'>N</td>
- <td class='s-error'>E</td></tr>
- <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-5.10.0.orig/src/bindings/csharp/csharp-files/SBMLReader.cs
-+++ libsbml-5.10.0/src/bindings/csharp/csharp-files/SBMLReader.cs
-@@ -179,7 +179,7 @@ public class SBMLReader : IDisposable {
- * appear first. The error code @if clike (a value drawn from the enumeration
- * #XMLErrorCode_t) @endif can provide a clue about what happened. For example,
- * 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-5.10.0.orig/src/bindings/csharp/csharp-files/SBase.cs
-+++ libsbml-5.10.0/src/bindings/csharp/csharp-files/SBase.cs
-@@ -2931,7 +2931,7 @@ s.setNotes('<body xmlns='http://www.w3.o
- * Hierarchical Model Composition (“comp”) package, and
- * extracted parts of that model in order to construct a new model in
- * memory. The new, in-memory model will not accept a component drawn from
-- * 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-5.10.0.orig/src/bindings/java/java-files/org/sbml/libsbml/Reaction.java
-+++ libsbml-5.10.0/src/bindings/java/java-files/org/sbml/libsbml/Reaction.java
-@@ -91,7 +91,7 @@ package org.sbml.libsbml;
- * This attribute is optional in SBML Level 2, with a default of
- * <code>false</code>; it is mandatory in SBML Level 3 (with no default value). It
- * 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-5.10.0.orig/src/bindings/java/java-files/org/sbml/libsbml/SBMLError.java
-+++ libsbml-5.10.0/src/bindings/java/java-files/org/sbml/libsbml/SBMLError.java
-@@ -4438,7 +4438,7 @@ defined in SBML.
- <td class='s-na'>N</td>
- <td class='s-error'>E</td></tr>
- <tr><td><code>{@link libsbmlConstants#CompNoMultipleReferences CompNoMultipleReferences }</code></td>
--<td> Objects may not be referenced by mutiple 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>
-@@ -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-5.10.0.orig/src/bindings/java/java-files/org/sbml/libsbml/SBMLReader.java
-+++ libsbml-5.10.0/src/bindings/java/java-files/org/sbml/libsbml/SBMLReader.java
-@@ -193,7 +193,7 @@ public class SBMLReader {
- * If the file <code>filename</code> could not be read, the file-reading error will
- * appear first. The error code can provide a clue about what happened. For example,
- * 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-5.10.0.orig/src/bindings/java/java-files/org/sbml/libsbml/SBase.java
-+++ libsbml-5.10.0/src/bindings/java/java-files/org/sbml/libsbml/SBase.java
-@@ -2790,7 +2790,7 @@ appears in the documentation.
- * Hierarchical {@link Model} Composition (“comp”) package, and
- * extracted parts of that model in order to construct a new model in
- * memory. The new, in-memory model will not accept a component drawn from
- * 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-5.10.0.orig/src/bindings/java/javadoc.i
-+++ libsbml-5.10.0/src/bindings/java/javadoc.i
-@@ -235,7 +235,7 @@ defined in SBML.
- * If the file <code>filename</code> could not be read, the file-reading error will
- * appear first. The error code can provide a clue about what happened. For example,
- * a file might be unreadable (either because it does not actually exist
-- * 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:
-@@ -328,7 +328,7 @@ defined in SBML.
- * If the file <code>filename</code> could not be read, the file-reading error will
- * appear first. The error code can provide a clue about what happened. For example,
- * a file might be unreadable (either because it does not actually exist
-- * 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:
-@@ -3882,7 +3882,7 @@ appears in the documentation.
- * Hierarchical {@link Model} Composition (“comp”) package, and
+--- libsbml-5.11.0+dfsg.orig/src/bindings/java/java-files/org/sbml/libsbml/libsbml.java
++++ libsbml-5.11.0+dfsg/src/bindings/java/java-files/org/sbml/libsbml/libsbml.java
+@@ -590,7 +590,7 @@ public class libsbml implements libsbmlC
+ * 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 been
++ * 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:
+ <p>
+@@ -666,7 +666,7 @@ if (doc.getNumErrors() > 0)
+ * appear first. The error code can provide a clue about what
+ * happened. For example, a file might be unreadable (either because it does
+ * not actually exist or because the user does not have the necessary access
+- * priviledges to read it) or some sort of file operation error may have been
++ * 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:
+ <p>
+--- libsbml-5.11.0+dfsg.orig/src/bindings/java/javadoc.i
++++ libsbml-5.11.0+dfsg/src/bindings/java/javadoc.i
+@@ -311,7 +311,7 @@ defined in SBML.
+ * appear first. The error code can provide a clue about what
+ * happened. For example, a file might be unreadable (either because it does
+ * 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 been
++ * 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:
+ <p>
+@@ -414,7 +414,7 @@ if (doc.getNumErrors() > 0)
+ * appear first. The error code can provide a clue about what
+ * happened. For example, a file might be unreadable (either because it does
+ * not actually exist or because the user does not have the necessary access
+- * priviledges to read it) or some sort of file operation error may have been
++ * 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:
+ <p>
+@@ -590,7 +590,7 @@ if (doc.getNumErrors() > 0)
+ * appear first. The error code can provide a clue about what
+ * happened. For example, a file might be unreadable (either because it does
+ * not actually exist or because the user does not have the necessary access
+- * priviledges to read it) or some sort of file operation error may have been
++ * 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:
+ <p>
+@@ -664,7 +664,7 @@ if (doc.getNumErrors() > 0)
+ * appear first. The error code can provide a clue about what
+ * happened. For example, a file might be unreadable (either because it does
+ * not actually exist or because the user does not have the necessary access
+- * priviledges to read it) or some sort of file operation error may have been
++ * 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:
+ <p>
+@@ -4180,7 +4180,7 @@ void example (SBase sb)
+ * Hierarchical Model Composition (“comp”) package, and
* extracted parts of that model in order to construct a new model in
* memory. The new, in-memory model will not accept a component drawn from
- * an other {@link SBMLDocument} with different package namespace declarations.
@@ -303,54 +222,36 @@
* 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:
-@@ -25033,7 +25033,7 @@ attributes.</caption>
- * This attribute is optional in SBML Level 2, with a default of
- * <code>false</code>; it is mandatory in SBML Level 3 (with no default value). It
- * is used to indicate that a reaction occurs on a vastly faster time scale
-- * 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
-@@ -48043,7 +48043,7 @@ defined in SBML.
- <td class=\'s-na\'>N</td>
- <td class=\'s-error\'>E</td></tr>
- <tr><td><code>{@link libsbmlConstants#CompNoMultipleReferences CompNoMultipleReferences }</code></td>
--<td> Objects may not be referenced by mutiple 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>
-@@ -48367,7 +48367,7 @@ defined in SBML.
- <td class=\'s-na\'>N</td>
- <td class=\'s-error\'>E</td></tr>
- <tr><td><code>{@link libsbmlConstants#CompDeprecatedReplaceFunction CompDeprecatedReplaceFunction }</code></td>
--<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-5.10.0.orig/src/bindings/perl/LibSBML.pm
-+++ libsbml-5.10.0/src/bindings/perl/LibSBML.pm
-@@ -261,7 +261,7 @@ If the file C<filename> could not be rea
- appear first. The error code @if clike (a value drawn from the enumeration
- #XMLErrorCode_t) @endif@~ can provide a clue about what happened. For example,
- a file might be unreadable (either because it does not actually exist
--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:
-@@ -367,7 +367,7 @@ If the file C<filename> could not be rea
- appear first. The error code @if clike (a value drawn from the enumeration
- #XMLErrorCode_t)@endif@~ can provide a clue about what happened. For example,
- a file might be unreadable (either because it does not actually exist
--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:
-@@ -2835,7 +2835,7 @@ application read an SBML document contai
+@@ -51755,7 +51755,7 @@ defined in SBML.
+ <td class=\'s-error\'></td>
+ </tr>
+ <tr><td class=\'code\'>{@link libsbmlConstants#CompNoMultipleReferences CompNoMultipleReferences}</td>
+-<td class=\'meaning\'>Objects may not be referenced by mutiple SBaseRef constructs.</td>
++<td class=\'meaning\'>Objects may not be referenced by multiple SBaseRef constructs.</td>
+ <td class=\'s-na\'></td>
+ <td class=\'s-na\'></td>
+ <td class=\'s-na\'></td>
+@@ -52115,7 +52115,7 @@ defined in SBML.
+ <td class=\'s-error\'></td>
+ </tr>
+ <tr><td class=\'code\'>{@link libsbmlConstants#CompDeprecatedReplaceFunction CompDeprecatedReplaceFunction}</td>
+-<td class=\'meaning\'>The performReplacementsAndConversions fuctions is deprecated.</td>
++<td class=\'meaning\'>The performReplacementsAndConversions functions is deprecated.</td>
+ <td class=\'s-na\'></td>
+ <td class=\'s-na\'></td>
+ <td class=\'s-na\'></td>
+@@ -60788,7 +60788,7 @@ defined in SBML.
+ * <h3><a class=\'anchor\' name=\'math-history\'>Historical notes</a></h3>
+ <p>
+ * Readers may wonder why this part of libSBML uses a seemingly less
+- * object-oriented design than other parts. Originally, much of libSBML was
++ * object-oriented design thanother parts. Originally, much of libSBML was
+ * written in C. All subsequent development was done in C++, but the
+ * complexity of some of the functionality for converting between infix, AST
+ * and MathML, coupled with the desire to maintain stability and backward
+--- libsbml-5.11.0+dfsg.orig/src/bindings/perl/LibSBML.pm
++++ libsbml-5.11.0+dfsg/src/bindings/perl/LibSBML.pm
+@@ -2565,7 +2565,7 @@ application read an SBML document contai
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
@@ -359,36 +260,18 @@
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:
-@@ -17001,7 +17001,7 @@ The Reaction object class has another bo
- This attribute is optional in SBML Level 2, with a default of @c
- false; it is mandatory in SBML Level 3 (with no default value). It
- is used to indicate that a reaction occurs on a vastly faster time scale
--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-5.10.0.orig/src/bindings/perl/LibSBML.pod
-+++ libsbml-5.10.0/src/bindings/perl/LibSBML.pod
-@@ -248,7 +248,7 @@ If the file C<filename> could not be rea
- appear first. The error code @if clike (a value drawn from the enumeration
- #XMLErrorCode_t) @endif@~ can provide a clue about what happened. For example,
- a file might be unreadable (either because it does not actually exist
--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:
-@@ -354,7 +354,7 @@ If the file C<filename> could not be rea
- appear first. The error code @if clike (a value drawn from the enumeration
- #XMLErrorCode_t)@endif@~ can provide a clue about what happened. For example,
- a file might be unreadable (either because it does not actually exist
--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:
-@@ -2822,7 +2822,7 @@ application read an SBML document contai
+@@ -33142,7 +33142,7 @@ ASTNode} and @sbmlfunction{parseL3Formul
+ explanations of the infix syntax they accept.
+ <h3><a class="anchor" name="math-history">Historical notes</a></h3>
+ Readers may wonder why this part of libSBML uses a seemingly less
+-object-oriented design than other parts. Originally, much of libSBML was
++object-oriented design thanother parts. Originally, much of libSBML was
+ written in C. All subsequent development was done in C++, but the
+ complexity of some of the functionality for converting between infix, AST
+ and MathML, coupled with the desire to maintain stability and backward
+--- libsbml-5.11.0+dfsg.orig/src/bindings/perl/LibSBML.pod
++++ libsbml-5.11.0+dfsg/src/bindings/perl/LibSBML.pod
+@@ -2552,7 +2552,7 @@ application read an SBML document contai
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
@@ -397,46 +280,55 @@
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:
-@@ -16988,7 +16988,7 @@ The Reaction object class has another bo
- This attribute is optional in SBML Level 2, with a default of @c
- false; it is mandatory in SBML Level 3 (with no default value). It
- is used to indicate that a reaction occurs on a vastly faster time scale
--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-5.10.0.orig/src/bindings/python/libsbml-doxygen.py
-+++ libsbml-5.10.0/src/bindings/python/libsbml-doxygen.py
-@@ -781,7 +781,7 @@ def readSBML(*args):
- appear first. The error code can provide a clue about what happened.
- For example, a file might be unreadable (either because it does not
- 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:
-
-@@ -1245,7 +1245,7 @@ class SBMLReader(_object):
- appear first. The error code can provide a clue about what happened.
- For example, a file might be unreadable (either because it does not
- actually exist or because the user does not have the necessary access
-- 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:
-
-@@ -1329,7 +1329,7 @@ class SBMLReader(_object):
- appear first. The error code can provide a clue about what happened.
- For example, a file might be unreadable (either because it does not
- actually exist or because the user does not have the necessary access
-- 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:
-
-@@ -4831,7 +4831,7 @@ class SBase(_object):
- Hierarchical Model Composition (“comp”) package, and
+@@ -33129,7 +33129,7 @@ ASTNode} and @sbmlfunction{parseL3Formul
+ explanations of the infix syntax they accept.
+ <h3><a class="anchor" name="math-history">Historical notes</a></h3>
+ Readers may wonder why this part of libSBML uses a seemingly less
+-object-oriented design than other parts. Originally, much of libSBML was
++object-oriented design thanother parts. Originally, much of libSBML was
+ written in C. All subsequent development was done in C++, but the
+ complexity of some of the functionality for converting between infix, AST
+ and MathML, coupled with the desire to maintain stability and backward
+--- libsbml-5.11.0+dfsg.orig/src/bindings/python/libsbml-doxygen.py
++++ libsbml-5.11.0+dfsg/src/bindings/python/libsbml-doxygen.py
+@@ -1187,7 +1187,7 @@ class SBMLReader(_object):
+ 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 read it) or some sort of file operation error may have been
++ 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:
+ @if cpp
+@@ -1378,7 +1378,7 @@ class SBMLReader(_object):
+ enumeration #XMLErrorCode_t)@endif@~ can provide a clue about what
+ happened. For example, a file might be unreadable (either because it does
+ not actually exist or because the user does not have the necessary access
+- priviledges to read it) or some sort of file operation error may have been
++ 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:
+ @if cpp
+@@ -1721,7 +1721,7 @@ def readSBML(*args):
+ enumeration #XMLErrorCode_t)@endif@~ can provide a clue about what
+ happened. For example, a file might be unreadable (either because it does
+ not actually exist or because the user does not have the necessary access
+- priviledges to read it) or some sort of file operation error may have been
++ 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:
+ @if cpp
+@@ -1888,7 +1888,7 @@ def readSBMLFromFile(*args):
+ enumeration #XMLErrorCode_t)@endif@~ can provide a clue about what
+ happened. For example, a file might be unreadable (either because it does
+ not actually exist or because the user does not have the necessary access
+- priviledges to read it) or some sort of file operation error may have been
++ 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:
+ @if cpp
+@@ -5524,7 +5524,7 @@ 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.
@@ -444,36 +336,36 @@
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:
-@@ -26201,7 +26201,7 @@ class Reaction(SBase):
- This attribute is optional in SBML Level 2, with a default of @c
- false; it is mandatory in SBML Level 3 (with no default value). It
- is used to indicate that a reaction occurs on a vastly faster time scale
-- 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
-@@ -50681,7 +50681,7 @@ class SBMLError(XMLError):
- <td class='s-na'>N</td>
- <td class='s-error'>E</td></tr>
- <tr><td><code>@link libsbml.CompNoMultipleReferences CompNoMultipleReferences @endlink</code></td>
-- <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>
-@@ -51005,7 +51005,7 @@ class SBMLError(XMLError):
- <td class='s-na'>N</td>
- <td class='s-error'>E</td></tr>
- <tr><td><code>@link libsbml.CompDeprecatedReplaceFunction CompDeprecatedReplaceFunction @endlink</code></td>
-- <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-5.10.0.orig/src/bindings/python/libsbml.py
-+++ libsbml-5.10.0/src/bindings/python/libsbml.py
-@@ -782,7 +782,7 @@ def readSBML(*args):
+@@ -56749,7 +56749,7 @@ class SBMLError(XMLError):
+ <td class='s-error'></td>
+ </tr>
+ <tr><td class='code'>@link libsbml#CompNoMultipleReferences CompNoMultipleReferences at endlink</td>
+- <td class='meaning'>Objects may not be referenced by mutiple SBaseRef constructs.</td>
++ <td class='meaning'>Objects may not be referenced by multiple SBaseRef constructs.</td>
+ <td class='s-na'></td>
+ <td class='s-na'></td>
+ <td class='s-na'></td>
+@@ -57109,7 +57109,7 @@ class SBMLError(XMLError):
+ <td class='s-error'></td>
+ </tr>
+ <tr><td class='code'>@link libsbml#CompDeprecatedReplaceFunction CompDeprecatedReplaceFunction at endlink</td>
+- <td class='meaning'>The performReplacementsAndConversions fuctions is deprecated.</td>
++ <td class='meaning'>The performReplacementsAndConversions functions is deprecated.</td>
+ <td class='s-na'></td>
+ <td class='s-na'></td>
+ <td class='s-na'></td>
+@@ -67516,7 +67516,7 @@ class ASTNode(ASTBase):
+ <h3><a class='anchor' name='math-history'>Historical notes</a></h3>
+
+ Readers may wonder why this part of libSBML uses a seemingly less
+- object-oriented design than other parts. Originally, much of libSBML was
++ object-oriented design thanother parts. Originally, much of libSBML was
+ written in C. All subsequent development was done in C++, but the
+ complexity of some of the functionality for converting between infix, AST
+ and MathML, coupled with the desire to maintain stability and backward
+--- libsbml-5.11.0+dfsg.orig/src/bindings/python/libsbml.py
++++ libsbml-5.11.0+dfsg/src/bindings/python/libsbml.py
+@@ -812,7 +812,7 @@ def readSBML(*args):
appear first. The error code can provide a clue about what happened.
For example, a file might be unreadable (either because it does not
actually exist or because the user does not have the necessary access
@@ -482,7 +374,7 @@
been reported by the underlying operating system. Callers can check
for these situations using a program fragment such as the following:
-@@ -1209,7 +1209,7 @@ class SBMLReader(_object):
+@@ -1264,7 +1264,7 @@ 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
@@ -491,8 +383,8 @@
been reported by the underlying operating system. Callers can check
for these situations using a program fragment such as the following:
-@@ -1293,7 +1293,7 @@ class SBMLReader(_object):
- appear first. The error code can provide a clue about what happened.
+@@ -1344,7 +1344,7 @@ 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
@@ -500,36 +392,45 @@
been reported by the underlying operating system. Callers can check
for these situations using a program fragment such as the following:
-@@ -4255,7 +4255,7 @@ class SBase(_object):
- SBML Hierarchical Model Composition (“comp”) package, and
- extracted parts of that model in order to construct a new model in
- memory. The new, in-memory model will not accept a component drawn
-- 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
-@@ -44795,7 +44795,7 @@ class SBMLError(XMLError):
- |libsbml.CompDeprecatedSBaseRefSpelling |The spelling 'sbaseRef' is deprecated |N |N |N |N |N |N |W |
- |libsbml.CompSBaseRefMustReferenceObject |An SBaseRef must reference an object. |N |N |N |N |N |N |E |
- |libsbml.CompSBaseRefMustReferenceOnlyOneObject |An SBaseRef must reference only one other object. |N |N |N |N |N |N |E |
-- |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 |
-@@ -44831,7 +44831,7 @@ class SBMLError(XMLError):
- |libsbml.CompFlatteningNotImplementedReqd |Flattening not implemented for required package. |N |N |N |N |N |N |W |
- |libsbml.CompFlatteningWarning |Flattening reference may come from package. |N |N |N |N |N |N |W |
- |libsbml.CompDeprecatedDeleteFunction |The performDeletions functions is deprecated. |N |N |N |N |N |N |E |
-- |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-5.10.0.orig/src/bindings/python/libsbml_wrap.cpp
-+++ libsbml-5.10.0/src/bindings/python/libsbml_wrap.cpp
-@@ -111129,7 +111129,7 @@ static PyMethodDef SwigMethods[] = {
+@@ -1569,7 +1569,7 @@ def readSBMLFromFile(*args):
+ appear first. The error code can provide a clue about what happened.
+ For example, a file might be unreadable (either because it does not
+ actually exist or because the user does not have the necessary access
+- 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:
+
+@@ -48695,7 +48695,7 @@ class SBMLError(XMLError):
+ |CompDeprecatedSBaseRefSpelling |The spelling 'sbaseRef' is deprecated | | | | | | | |
+ |CompSBaseRefMustReferenceObject |An SBaseRef must reference an object. | | | | | | | |
+ |CompSBaseRefMustReferenceOnlyOneObject |An SBaseRef must reference only one other object. | | | | | | | |
+- |CompNoMultipleReferences |Objects may not be referenced by mutiple SBaseRef constructs. | | | | | | | |
++ |CompNoMultipleReferences |Objects may not be referenced by multiple SBaseRef constructs. | | | | | | | |
+ |CompPortMustReferenceObject |Port must reference an object | | | | | | | |
+ |CompPortMustReferenceOnlyOneObject |Port must reference only one other object. | | | | | | | |
+ |CompPortAllowedAttributes |Allowed attributes on a Port | | | | | | | |
+@@ -48731,7 +48731,7 @@ class SBMLError(XMLError):
+ |CompFlatteningNotImplementedReqd |Flattening not implemented for required package. | | | | | | | |
+ |CompFlatteningWarning |Flattening reference may come from package. | | | | | | | |
+ |CompDeprecatedDeleteFunction |The performDeletions functions is deprecated. | | | | | | | |
+- |CompDeprecatedReplaceFunction |The performReplacementsAndConversions fuctions is deprecated. | | | | | | | |
++ |CompDeprecatedReplaceFunction |The performReplacementsAndConversions functions is deprecated. | | | | | | | |
+ |CompDeletedReplacement |Element deleted before a subelement could be replaced. | | | | | | | |
+ |CompIdRefMayReferenceUnknownPackage |The 'comp:idRef' attribute must be the 'id' of a model element | | | | | | | |
+ |CompMetaIdRefMayReferenceUnknownPkg |The 'comp:metaIdRef' attribute must be the 'metaid' of a model element | | | | | | | |
+@@ -55596,7 +55596,7 @@ class ASTNode(ASTBase):
+ ......................................................................
+
+ Readers may wonder why this part of libSBML uses a seemingly less
+- object-oriented design than other parts. Originally, much of libSBML
++ object-oriented design thanother parts. Originally, much of libSBML
+ was written in C. All subsequent development was done in C++, but the
+ complexity of some of the functionality for converting between infix,
+ AST and MathML, coupled with the desire to maintain stability and
+--- libsbml-5.11.0+dfsg.orig/src/bindings/python/libsbml_wrap.cpp
++++ libsbml-5.11.0+dfsg/src/bindings/python/libsbml_wrap.cpp
+@@ -115177,7 +115177,7 @@ static PyMethodDef SwigMethods[] = {
"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"
@@ -538,7 +439,7 @@
"been reported by the underlying operating system. Callers can check\n"
"for these situations using a program fragment such as the following:\n"
"\n"
-@@ -111207,7 +111207,7 @@ static PyMethodDef SwigMethods[] = {
+@@ -115258,7 +115258,7 @@ 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"
@@ -547,18 +448,18 @@
"been reported by the underlying operating system. Callers can check\n"
"for these situations using a program fragment such as the following:\n"
"\n"
-@@ -113545,7 +113545,7 @@ static PyMethodDef SwigMethods[] = {
- "SBML Hierarchical Model Composition (“comp”) package, and\n"
- "extracted parts of that model in order to construct a new model in\n"
- "memory. The new, in-memory model will not accept a component drawn\n"
-- "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-5.10.0.orig/src/bindings/python/local.i
-+++ libsbml-5.10.0/src/bindings/python/local.i
-@@ -592,7 +592,7 @@ SBMLReader::readSBML(const std::string&)
+@@ -115419,7 +115419,7 @@ 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"
+--- libsbml-5.11.0+dfsg.orig/src/bindings/python/local.i
++++ libsbml-5.11.0+dfsg/src/bindings/python/local.i
+@@ -605,7 +605,7 @@ SBMLReader::readSBML(const std::string&)
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
@@ -567,8 +468,8 @@
been reported by the underlying operating system. Callers can check
for these situations using a program fragment such as the following:
-@@ -679,7 +679,7 @@ SBMLReader::readSBMLFromFile(const std::
- appear first. The error code can provide a clue about what happened.
+@@ -688,7 +688,7 @@ 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
@@ -576,7 +477,7 @@
been reported by the underlying operating system. Callers can check
for these situations using a program fragment such as the following:
-@@ -777,7 +777,7 @@ def readSBML(*args):
+@@ -769,7 +769,7 @@ 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
@@ -585,28 +486,46 @@
been reported by the underlying operating system. Callers can check
for these situations using a program fragment such as the following:
---- libsbml-5.10.0.orig/src/bindings/python/pydoc-doxygen.i
-+++ libsbml-5.10.0/src/bindings/python/pydoc-doxygen.i
-@@ -215,7 +215,7 @@ If the file @p filename could not be rea
- appear first. The error code @if clike (a value drawn from the enumeration
- #XMLErrorCode_t) @endif@~ can provide a clue about what happened. For example,
- a file might be unreadable (either because it does not actually exist
--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
+--- libsbml-5.11.0+dfsg.orig/src/bindings/python/pydoc-doxygen.i
++++ libsbml-5.11.0+dfsg/src/bindings/python/pydoc-doxygen.i
+@@ -284,7 +284,7 @@ appear first. The error code @if clike
+ enumeration #XMLErrorCode_t)@endif@~ can provide a clue about what
+ happened. For example, a file might be unreadable (either because it does
+ 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 been
++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:
-@@ -365,7 +365,7 @@ If the file @p filename could not be rea
- appear first. The error code @if clike (a value drawn from the enumeration
- #XMLErrorCode_t)@endif@~ can provide a clue about what happened. For example,
- a file might be unreadable (either because it does not actually exist
--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
+ @if cpp
+@@ -471,7 +471,7 @@ appear first. The error code @if clike
+ enumeration #XMLErrorCode_t)@endif@~ can provide a clue about what
+ happened. For example, a file might be unreadable (either because it does
+ 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 been
++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:
-@@ -3427,7 +3427,7 @@ application read an SBML document contai
- Hierarchical Model Composition (“comp”) package, and
+ @if cpp
+@@ -737,7 +737,7 @@ appear first. The error code @if clike
+ enumeration #XMLErrorCode_t)@endif@~ can provide a clue about what
+ happened. For example, a file might be unreadable (either because it does
+ 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 been
++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:
+ @if cpp
+@@ -900,7 +900,7 @@ appear first. The error code @if clike
+ enumeration #XMLErrorCode_t)@endif@~ can provide a clue about what
+ happened. For example, a file might be unreadable (either because it does
+ 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 been
++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:
+ @if cpp
+@@ -4030,7 +4030,7 @@ 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.
@@ -614,36 +533,36 @@
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:
-@@ -22938,7 +22938,7 @@ The Reaction object class has another bo
- This attribute is optional in SBML Level 2, with a default of @c
- false; it is mandatory in SBML Level 3 (with no default value). It
- is used to indicate that a reaction occurs on a vastly faster time scale
--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
-@@ -44129,7 +44129,7 @@ from libSBML core. at endif
- <td class=\'s-na\'>N</td>
- <td class=\'s-error\'>E</td></tr>
- <tr><td><code>@link libsbml.CompNoMultipleReferences CompNoMultipleReferences @endlink</code></td>
--<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>
-@@ -44453,7 +44453,7 @@ from libSBML core. at endif
- <td class=\'s-na\'>N</td>
- <td class=\'s-error\'>E</td></tr>
- <tr><td><code>@link libsbml.CompDeprecatedReplaceFunction CompDeprecatedReplaceFunction @endlink</code></td>
--<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-5.10.0.orig/src/bindings/python/pydoc-normal.i
-+++ libsbml-5.10.0/src/bindings/python/pydoc-normal.i
-@@ -187,7 +187,7 @@ If the file 'filename' could not be read
+@@ -49596,7 +49596,7 @@ from libSBML core. at endif
+ <td class=\'s-error\'></td>
+ </tr>
+ <tr><td class=\'code\'>@link libsbml#CompNoMultipleReferences CompNoMultipleReferences at endlink</td>
+-<td class=\'meaning\'>Objects may not be referenced by mutiple SBaseRef constructs.</td>
++<td class=\'meaning\'>Objects may not be referenced by multiple SBaseRef constructs.</td>
+ <td class=\'s-na\'></td>
+ <td class=\'s-na\'></td>
+ <td class=\'s-na\'></td>
+@@ -49956,7 +49956,7 @@ from libSBML core. at endif
+ <td class=\'s-error\'></td>
+ </tr>
+ <tr><td class=\'code\'>@link libsbml#CompDeprecatedReplaceFunction CompDeprecatedReplaceFunction at endlink</td>
+-<td class=\'meaning\'>The performReplacementsAndConversions fuctions is deprecated.</td>
++<td class=\'meaning\'>The performReplacementsAndConversions functions is deprecated.</td>
+ <td class=\'s-na\'></td>
+ <td class=\'s-na\'></td>
+ <td class=\'s-na\'></td>
+@@ -58742,7 +58742,7 @@ explanations of the infix syntax they ac
+ <h3><a class=\'anchor\' name=\'math-history\'>Historical notes</a></h3>
+
+ Readers may wonder why this part of libSBML uses a seemingly less
+-object-oriented design than other parts. Originally, much of libSBML was
++object-oriented design thanother parts. Originally, much of libSBML was
+ written in C. All subsequent development was done in C++, but the
+ complexity of some of the functionality for converting between infix, AST
+ and MathML, coupled with the desire to maintain stability and backward
+--- libsbml-5.11.0+dfsg.orig/src/bindings/python/pydoc-normal.i
++++ libsbml-5.11.0+dfsg/src/bindings/python/pydoc-normal.i
+@@ -265,7 +265,7 @@ If the file 'filename' could not be read
appear first. The error code can provide a clue about what happened.
For example, a file might be unreadable (either because it does not
actually exist or because the user does not have the necessary access
@@ -652,7 +571,7 @@
been reported by the underlying operating system. Callers can check
for these situations using a program fragment such as the following:
-@@ -264,7 +264,7 @@ If the file 'filename' could not be read
+@@ -345,7 +345,7 @@ 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
@@ -661,79 +580,66 @@
been reported by the underlying operating system. Callers can check
for these situations using a program fragment such as the following:
-@@ -2693,7 +2693,7 @@ application read an SBML document contai
- SBML Hierarchical Model Composition (“comp”) package, and
- extracted parts of that model in order to construct a new model in
- memory. The new, in-memory model will not accept a component drawn
--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
-@@ -36352,7 +36352,7 @@ If the name of a code does not begin wit
- |libsbml.CompDeprecatedSBaseRefSpelling |The spelling 'sbaseRef' is deprecated |N |N |N |N |N |N |W |
- |libsbml.CompSBaseRefMustReferenceObject |An SBaseRef must reference an object. |N |N |N |N |N |N |E |
- |libsbml.CompSBaseRefMustReferenceOnlyOneObject |An SBaseRef must reference only one other object. |N |N |N |N |N |N |E |
-- |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 |
-@@ -36388,7 +36388,7 @@ If the name of a code does not begin wit
- |libsbml.CompFlatteningNotImplementedReqd |Flattening not implemented for required package. |N |N |N |N |N |N |W |
- |libsbml.CompFlatteningWarning |Flattening reference may come from package. |N |N |N |N |N |N |W |
- |libsbml.CompDeprecatedDeleteFunction |The performDeletions functions is deprecated. |N |N |N |N |N |N |E |
-- |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-5.10.0.orig/src/sbml/Reaction.h
-+++ libsbml-5.10.0/src/sbml/Reaction.h
-@@ -113,7 +113,7 @@
- * This attribute is optional in SBML Level 2, with a default of @c
- * false; it is mandatory in SBML Level 3 (with no default value). It
- * is used to indicate that a reaction occurs on a vastly faster time scale
-- * 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-5.10.0.orig/src/sbml/SBMLReader.cpp
-+++ libsbml-5.10.0/src/sbml/SBMLReader.cpp
-@@ -238,7 +238,7 @@ SBMLReader::readInternal (const char* co
- if (stream.isError())
- {
- // If we encountered an error, some parsers will report it sooner
-- // 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-5.10.0.orig/src/sbml/SBMLReader.h
-+++ libsbml-5.10.0/src/sbml/SBMLReader.h
-@@ -185,7 +185,7 @@ public:
- * appear first. The error code @if clike (a value drawn from the enumeration
- * #XMLErrorCode_t) @endif@~ can provide a clue about what happened. For example,
- * a file might be unreadable (either because it does not actually exist
-- * 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:
-@@ -306,7 +306,7 @@ public:
- * appear first. The error code @if clike (a value drawn from the enumeration
- * #XMLErrorCode_t)@endif@~ can provide a clue about what happened. For example,
- * a file might be unreadable (either because it does not actually exist
-- * 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-5.10.0.orig/src/sbml/SBase.h
-+++ libsbml-5.10.0/src/sbml/SBase.h
-@@ -2724,7 +2724,7 @@ s.setNotes("<body xmlns='http://www.w3.o
- * Hierarchical Model Composition (“comp”) package, and
+@@ -506,7 +506,7 @@ 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:
+
+@@ -559,7 +559,7 @@ 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:
+
+@@ -40642,7 +40642,7 @@ If the name of a code does not begin wit
+ |CompDeprecatedSBaseRefSpelling |The spelling 'sbaseRef' is deprecated | | | | | | | |
+ |CompSBaseRefMustReferenceObject |An SBaseRef must reference an object. | | | | | | | |
+ |CompSBaseRefMustReferenceOnlyOneObject |An SBaseRef must reference only one other object. | | | | | | | |
+- |CompNoMultipleReferences |Objects may not be referenced by mutiple SBaseRef constructs. | | | | | | | |
++ |CompNoMultipleReferences |Objects may not be referenced by multiple SBaseRef constructs. | | | | | | | |
+ |CompPortMustReferenceObject |Port must reference an object | | | | | | | |
+ |CompPortMustReferenceOnlyOneObject |Port must reference only one other object. | | | | | | | |
+ |CompPortAllowedAttributes |Allowed attributes on a Port | | | | | | | |
+@@ -40678,7 +40678,7 @@ If the name of a code does not begin wit
+ |CompFlatteningNotImplementedReqd |Flattening not implemented for required package. | | | | | | | |
+ |CompFlatteningWarning |Flattening reference may come from package. | | | | | | | |
+ |CompDeprecatedDeleteFunction |The performDeletions functions is deprecated. | | | | | | | |
+- |CompDeprecatedReplaceFunction |The performReplacementsAndConversions fuctions is deprecated. | | | | | | | |
++ |CompDeprecatedReplaceFunction |The performReplacementsAndConversions functions is deprecated. | | | | | | | |
+ |CompDeletedReplacement |Element deleted before a subelement could be replaced. | | | | | | | |
+ |CompIdRefMayReferenceUnknownPackage |The 'comp:idRef' attribute must be the 'id' of a model element | | | | | | | |
+ |CompMetaIdRefMayReferenceUnknownPkg |The 'comp:metaIdRef' attribute must be the 'metaid' of a model element | | | | | | | |
+@@ -45871,7 +45871,7 @@ Historical notes
+ ......................................................................
+
+ Readers may wonder why this part of libSBML uses a seemingly less
+-object-oriented design than other parts. Originally, much of libSBML
++object-oriented design thanother parts. Originally, much of libSBML
+ was written in C. All subsequent development was done in C++, but the
+ complexity of some of the functionality for converting between infix,
+ AST and MathML, coupled with the desire to maintain stability and
+--- libsbml-5.11.0+dfsg.orig/src/sbml/SBMLReader.h
++++ libsbml-5.11.0+dfsg/src/sbml/SBMLReader.h
+@@ -152,7 +152,7 @@
+ * enumeration #XMLErrorCode_t)@endif@~ can provide a clue about what
+ * happened. For example, a file might be unreadable (either because it does
+ * 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 been
++ * 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:
+ * @if cpp
+--- libsbml-5.11.0+dfsg.orig/src/sbml/SBase.h
++++ libsbml-5.11.0+dfsg/src/sbml/SBase.h
+@@ -2748,7 +2748,7 @@ s.setNotes("<body xmlns='http://www.w3.o
+ * 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.
@@ -741,28 +647,39 @@
* 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-5.10.0.orig/src/sbml/common/common-documentation.h
-+++ libsbml-5.10.0/src/sbml/common/common-documentation.h
-@@ -5414,7 +5414,7 @@ e><a href="libsbml.html#parseL3Formula(j
- <td class="s-na">N</td>
- <td class="s-error">E</td></tr>
- <tr><td><code>@link CompSBMLErrorCode_t#CompNoMultipleReferences CompNoMultipleReferences @endlink</code></td>
--<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>
-@@ -5738,7 +5738,7 @@ e><a href="libsbml.html#parseL3Formula(j
- <td class="s-na">N</td>
- <td class="s-error">E</td></tr>
- <tr><td><code>@link CompSBMLErrorCode_t#CompDeprecatedReplaceFunction CompDeprecatedReplaceFunction @endlink</code></td>
--<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-5.10.0.orig/src/sbml/packages/comp/validator/CompSBMLError.h
-+++ libsbml-5.10.0/src/sbml/packages/comp/validator/CompSBMLError.h
+--- libsbml-5.11.0+dfsg.orig/src/sbml/common/common-sbmlerror-codes.h
++++ libsbml-5.11.0+dfsg/src/sbml/common/common-sbmlerror-codes.h
+@@ -5197,7 +5197,7 @@
+ <td class="s-error"></td>
+ </tr>
+ <tr><td class="code">@sbmlconstant{CompNoMultipleReferences, SBMLErrorCode_t}</td>
+-<td class="meaning">Objects may not be referenced by mutiple SBaseRef constructs.</td>
++<td class="meaning">Objects may not be referenced by multiple SBaseRef constructs.</td>
+ <td class="s-na"></td>
+ <td class="s-na"></td>
+ <td class="s-na"></td>
+@@ -5557,7 +5557,7 @@
+ <td class="s-error"></td>
+ </tr>
+ <tr><td class="code">@sbmlconstant{CompDeprecatedReplaceFunction, SBMLErrorCode_t}</td>
+-<td class="meaning">The performReplacementsAndConversions fuctions is deprecated.</td>
++<td class="meaning">The performReplacementsAndConversions functions is deprecated.</td>
+ <td class="s-na"></td>
+ <td class="s-na"></td>
+ <td class="s-na"></td>
+--- libsbml-5.11.0+dfsg.orig/src/sbml/math/ASTNode.h
++++ libsbml-5.11.0+dfsg/src/sbml/math/ASTNode.h
+@@ -71,7 +71,7 @@
+ * <h3><a class="anchor" name="math-history">Historical notes</a></h3>
+ *
+ * Readers may wonder why this part of libSBML uses a seemingly less
+- * object-oriented design than other parts. Originally, much of libSBML was
++ * object-oriented design thanother parts. Originally, much of libSBML was
+ * written in C. All subsequent development was done in C++, but the
+ * complexity of some of the functionality for converting between infix, AST
+ * and MathML, coupled with the desire to maintain stability and backward
+--- libsbml-5.11.0+dfsg.orig/src/sbml/packages/comp/validator/CompSBMLError.h
++++ libsbml-5.11.0+dfsg/src/sbml/packages/comp/validator/CompSBMLError.h
@@ -124,7 +124,7 @@ typedef enum
, CompDeprecatedSBaseRefSpelling = 1020711 /*!< The spelling 'sbaseRef' is deprecated */
, CompSBaseRefMustReferenceObject = 1020712 /*!< An SBaseRef must reference an object. */
@@ -781,8 +698,8 @@
, 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-5.10.0.orig/src/sbml/packages/comp/validator/CompSBMLErrorTable.h
-+++ libsbml-5.10.0/src/sbml/packages/comp/validator/CompSBMLErrorTable.h
+--- libsbml-5.11.0+dfsg.orig/src/sbml/packages/comp/validator/CompSBMLErrorTable.h
++++ libsbml-5.11.0+dfsg/src/sbml/packages/comp/validator/CompSBMLErrorTable.h
@@ -949,7 +949,7 @@ static const packageErrorTableEntry comp
// 1020714
@@ -801,3 +718,770 @@
LIBSBML_CAT_GENERAL_CONSISTENCY,
LIBSBML_SEV_ERROR,
"The software used to process this hierarchical model used the deprecated "
+--- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/ColorDefinition.cpp
++++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/ColorDefinition.cpp
+@@ -117,7 +117,7 @@ ColorDefinition::ColorDefinition (Render
+ * The XMLNode object has to contain a valid XML representation of a
+ * ColorDefinition object as defined in the render extension specification.
+ * This method is normally called when render information is read from a file and
+- * should normally not have to be called explicitely.
++ * should normally not have to be called explicitly.
+ *
+ * @param node the XMLNode object reference that describes the ColorDefinition
+ * object to be instantiated.
+@@ -634,7 +634,7 @@ bool ColorDefinition::accept (SBMLVisito
+ * The XMLNode object has to contain a valid XML representation of a
+ * ListOfColorDefinitions object as defined in the render extension specification.
+ * This method is normally called when render information is read from a file and
+- * should normally not have to be called explicitely.
++ * should normally not have to be called explicitly.
+ *
+ * @param node the XMLNode object reference that describes the ListOfColorDefinitions
+ * object to be instantiated.
+--- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/ColorDefinition.h
++++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/ColorDefinition.h
+@@ -112,7 +112,7 @@ public:
+ * The XMLNode object has to contain a valid XML representation of a
+ * ColorDefinition object as defined in the render extension specification.
+ * This method is normally called when render information is read from a file and
+- * should normally not have to be called explicitely.
++ * should normally not have to be called explicitly.
+ *
+ *
+ * (FOR BACKWARD COMPATIBILITY)
+@@ -441,7 +441,7 @@ public:
+ * The XMLNode object has to contain a valid XML representation of a
+ * ListOfColorDefinitions object as defined in the render extension specification.
+ * This method is normally called when render information is read from a file and
+- * should normally not have to be called explicitely.
++ * should normally not have to be called explicitly.
+ *
+ * @param node the XMLNode object reference that describes the ListOfColorDefinitions
+ * object to be instantiated.
+--- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/Ellipse.cpp
++++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/Ellipse.cpp
+@@ -93,7 +93,7 @@ Ellipse::Ellipse (RenderPkgNamespaces* r
+ * The XMLNode object has to contain a valid XML representation of a
+ * RadialGradient object as defined in the render extension specification.
+ * This method is normally called when render information is read from a file and
+- * should normally not have to be called explicitely.
++ * should normally not have to be called explicitly.
+ *
+ * @param node the XMLNode object reference that describes the RadialGradient
+ * object to be instantiated.
+--- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/Ellipse.h
++++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/Ellipse.h
+@@ -97,7 +97,7 @@ public:
+ * The XMLNode object has to contain a valid XML representation of a
+ * RadialGradient object as defined in the render extension specification.
+ * This method is normally called when render information is read from a file and
+- * should normally not have to be called explicitely.
++ * should normally not have to be called explicitly.
+ *
+ * @param node the XMLNode object reference that describes the RadialGradient
+ * object to be instantiated.
+--- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/GlobalStyle.cpp
++++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/GlobalStyle.cpp
+@@ -88,7 +88,7 @@ GlobalStyle::GlobalStyle (RenderPkgNames
+ * The XMLNode object has to contain a valid XML representation of a
+ * GlobalStyle object as defined in the render extension specification.
+ * This method is normally called when render information is read from a file and
+- * should normally not have to be called explicitely.
++ * should normally not have to be called explicitly.
+ *
+ * @param node the XMLNode object reference that describes the GlobalStyle
+ * object to be instantiated.
+@@ -282,7 +282,7 @@ ListOfGlobalStyles::ListOfGlobalStyles(u
+ * The XMLNode object has to contain a valid XML representation of a
+ * ListOfGlobalStyles object as defined in the render extension specification.
+ * This method is normally called when render information is read from a file and
+- * should normally not have to be called explicitely.
++ * should normally not have to be called explicitly.
+ *
+ * @param node the XMLNode object reference that describes the ListOfGlobalStyles
+ * object to be instantiated.
+--- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/GlobalStyle.h
++++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/GlobalStyle.h
+@@ -92,7 +92,7 @@ public:
+ * The XMLNode object has to contain a valid XML representation of a
+ * GlobalStyle object as defined in the render extension specification.
+ * This method is normally called when render information is read from a file and
+- * should normally not have to be called explicitely.
++ * should normally not have to be called explicitly.
+ *
+ * @param node the XMLNode object reference that describes the GlobalStyle
+ * object to be instantiated.
+@@ -182,7 +182,7 @@ class LIBSBML_EXTERN ListOfGlobalStyles
+ * The XMLNode object has to contain a valid XML representation of a
+ * ListOfGlobalStyles object as defined in the render extension specification.
+ * This method is normally called when render information is read from a file and
+- * should normally not have to be called explicitely.
++ * should normally not have to be called explicitly.
+ *
+ * @param node the XMLNode object reference that describes the ListOfGlobalStyles
+ * object to be instantiated.
+--- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/GradientBase.cpp
++++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/GradientBase.cpp
+@@ -108,7 +108,7 @@ GradientBase::GradientBase (RenderPkgNam
+ * The XMLNode object has to contain a valid XML representation of a
+ * GradientBase object as defined in the render extension specification.
+ * This method is normally called when render information is read from a file and
+- * should normally not have to be called explicitely.
++ * should normally not have to be called explicitly.
+ *
+ * @param node the XMLNode object reference that describes the GradientBase
+ * object to be instantiated.
+@@ -733,7 +733,7 @@ bool GradientBase::accept (SBMLVisitor&
+ * The XMLNode object has to contain a valid XML representation of a
+ * ListOfGradientDefinitions object as defined in the render extension specification.
+ * This method is normally called when render information is read from a file and
+- * should normally not have to be called explicitely.
++ * should normally not have to be called explicitly.
+ *
+ * @param node the XMLNode object reference that describes the ListOfGradientDefinitions
+ * object to be instantiated.
+--- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/GradientBase.h
++++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/GradientBase.h
+@@ -117,7 +117,7 @@ protected:
+ * The XMLNode object has to contain a valid XML representation of a
+ * GradientBase object as defined in the render extension specification.
+ * This method is normally called when render information is read from a file and
+- * should normally not have to be called explicitely.
++ * should normally not have to be called explicitly.
+ *
+ * @param node the XMLNode object reference that describes the GradientBase
+ * object to be instantiated.
+@@ -503,7 +503,7 @@ public:
+ * The XMLNode object has to contain a valid XML representation of a
+ * ListOfGradientDefinitions object as defined in the render extension specification.
+ * This method is normally called when render information is read from a file and
+- * should normally not have to be called explicitely.
++ * should normally not have to be called explicitly.
+ *
+ * @param node the XMLNode object reference that describes the ListOfGradientDefinitions
+ * object to be instantiated.
+--- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/GradientStop.cpp
++++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/GradientStop.cpp
+@@ -134,7 +134,7 @@ ListOfGradientStops::ListOfGradientStops
+ * The XMLNode object has to contain a valid XML representation of a
+ * ListOfGradientStops object as defined in the render extension specification.
+ * This method is normally called when render information is read from a file and
+- * should normally not have to be called explicitely.
++ * should normally not have to be called explicitly.
+ *
+ * @param node the XMLNode object reference that describes the ListOfGradientStops
+ * object to be instantiated.
+@@ -183,7 +183,7 @@ ListOfGradientStops::ListOfGradientStops
+ * The XMLNode object has to contain a valid XML representation of a
+ * GradientStop object as defined in the render extension specification.
+ * This method is normally called when render information is read from a file and
+- * should normally not have to be called explicitely.
++ * should normally not have to be called explicitly.
+ *
+ * @param node the XMLNode object reference that describes the GradientStop
+ * object to be instantiated.
+--- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/GradientStop.h
++++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/GradientStop.h
+@@ -120,7 +120,7 @@ public:
+ * The XMLNode object has to contain a valid XML representation of a
+ * GradientStop object as defined in the render extension specification.
+ * This method is normally called when render information is read from a file and
+- * should normally not have to be called explicitely.
++ * should normally not have to be called explicitly.
+ *
+ * @param node the XMLNode object reference that describes the GradientStop
+ * object to be instantiated.
+@@ -326,7 +326,7 @@ public:
+ * The XMLNode object has to contain a valid XML representation of a
+ * ListOfGradientStops object as defined in the render extension specification.
+ * This method is normally called when render information is read from a file and
+- * should normally not have to be called explicitely.
++ * should normally not have to be called explicitly.
+ *
+ * @param node the XMLNode object reference that describes the ListOfGradientStops
+ * object to be instantiated.
+--- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/GraphicalPrimitive1D.cpp
++++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/GraphicalPrimitive1D.cpp
+@@ -113,7 +113,7 @@ GraphicalPrimitive1D::~GraphicalPrimitiv
+ * The XMLNode object has to contain a valid XML representation of a
+ * GraphicalPrimitive1D object as defined in the render extension specification.
+ * This method is normally called when render information is read from a file and
+- * should normally not have to be called explicitely.
++ * should normally not have to be called explicitly.
+ *
+ * @param node the XMLNode object reference that describes the GraphicalPrimitive1D
+ * object to be instantiated.
+--- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/GraphicalPrimitive1D.h
++++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/GraphicalPrimitive1D.h
+@@ -101,7 +101,7 @@ public:
+ * The XMLNode object has to contain a valid XML representation of a
+ * GraphicalPrimitive1D object as defined in the render extension specification.
+ * This method is normally called when render information is read from a file and
+- * should normally not have to be called explicitely.
++ * should normally not have to be called explicitly.
+ *
+ * @param node the XMLNode object reference that describes the GraphicalPrimitive1D
+ * object to be instantiated.
+--- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/GraphicalPrimitive2D.cpp
++++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/GraphicalPrimitive2D.cpp
+@@ -83,7 +83,7 @@ GraphicalPrimitive2D::GraphicalPrimitive
+ * The XMLNode object has to contain a valid XML representation of a
+ * GraphicalPrimitive2D object as defined in the render extension specification.
+ * This method is normally called when render information is read from a file and
+- * should normally not have to be called explicitely.
++ * should normally not have to be called explicitly.
+ *
+ * @param node the XMLNode object reference that describes the GraphicalPrimitive2D
+ * object to be instantiated.
+@@ -285,7 +285,7 @@ void GraphicalPrimitive2D::writeAttribut
+ stream.writeAttribute("fill-rule", getPrefix(), "inherit");
+ break;
+ case GraphicalPrimitive2D::NONZERO:
+- // if the fill rule has been set explicitely,
++ // if the fill rule has been set explicitly,
+ // we have to write it because otherwise
+ // it is assumed to be inherited.
+ stream.writeAttribute("fill-rule", getPrefix(), "nonzero");
+@@ -317,7 +317,7 @@ void GraphicalPrimitive2D::addGraphicalP
+ att.add("fill-rule","inherit");
+ break;
+ case GraphicalPrimitive2D::NONZERO:
+- // if the fill rule has been set explicitely,
++ // if the fill rule has been set explicitly,
+ // we have to write it because otherwise
+ // it is assumed to be inherited.
+ att.add("fill-rule","nonzero");
+--- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/GraphicalPrimitive2D.h
++++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/GraphicalPrimitive2D.h
+@@ -102,7 +102,7 @@ public:
+ * The XMLNode object has to contain a valid XML representation of a
+ * GraphicalPrimitive2D object as defined in the render extension specification.
+ * This method is normally called when render information is read from a file and
+- * should normally not have to be called explicitely.
++ * should normally not have to be called explicitly.
+ *
+ * @param node the XMLNode object reference that describes the GraphicalPrimitive2D
+ * object to be instantiated.
+--- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/Image.cpp
++++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/Image.cpp
+@@ -104,7 +104,7 @@ Image::Image (RenderPkgNamespaces* rende
+ * The XMLNode object has to contain a valid XML representation of a
+ * Image object as defined in the render extension specification.
+ * This method is normally called when render information is read from a file and
+- * should normally not have to be called explicitely.
++ * should normally not have to be called explicitly.
+ *
+ * @param node the XMLNode object reference that describes the Image
+ * object to be instantiated.
+@@ -347,7 +347,7 @@ const std::string& Image::getImageRefere
+ /** @cond doxygenLibsbmlInternal */
+ /*
+ * Sets the position of the image relative to its viewport.
+- * The position can either be specified in relative or in absolut coordinates
++ * The position can either be specified in relative or in absolute coordinates
+ * or a combination of both.
+ * The z coordinatee can be omitted. In that case it is set to 0.
+ *
+@@ -366,7 +366,7 @@ void Image::setCoordinates(const RelAbsV
+ /** @cond doxygenLibsbmlInternal */
+ /*
+ * Sets the x coordinate of the image position.
+- * The position can either be specified in relative or in absolut coordinates
++ * The position can either be specified in relative or in absolute coordinates
+ * or a combination of both.
+ *
+ * @param x x coordinate of the image position
+@@ -380,7 +380,7 @@ void Image::setX(const RelAbsVector& coo
+ /** @cond doxygenLibsbmlInternal */
+ /*
+ * Sets the y coordinate of the image position.
+- * The position can either be specified in relative or in absolut coordinates
++ * The position can either be specified in relative or in absolute coordinates
+ * or a combination of both.
+ *
+ * @param y y coordinate of the image position
+@@ -394,7 +394,7 @@ void Image::setY(const RelAbsVector& coo
+ /** @cond doxygenLibsbmlInternal */
+ /*
+ * Sets the z coordinate of the image position.
+- * The position can either be specified in relative or in absolut coordinates
++ * The position can either be specified in relative or in absolute coordinates
+ * or a combination of both.
+ *
+ * @param z z coordinate of the image position
+--- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/Image.h
++++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/Image.h
+@@ -103,7 +103,7 @@ public:
+ * The XMLNode object has to contain a valid XML representation of a
+ * Image object as defined in the render extension specification.
+ * This method is normally called when render information is read from a file and
+- * should normally not have to be called explicitely.
++ * should normally not have to be called explicitly.
+ *
+ * @param node the XMLNode object reference that describes the Image
+ * object to be instantiated.
+@@ -135,7 +135,7 @@ public:
+
+ /**
+ * Sets the position of the image relative to its viewport.
+- * The position can either be specified in relative or in absolut coordinates
++ * The position can either be specified in relative or in absolute coordinates
+ * or a combination of both.
+ * The z coordinatee can be omitted. In that case it is set to 0.
+ *
+@@ -147,7 +147,7 @@ public:
+
+ /**
+ * Sets the x coordinate of the image position.
+- * The position can either be specified in relative or in absolut coordinates
++ * The position can either be specified in relative or in absolute coordinates
+ * or a combination of both.
+ *
+ * @param x x coordinate of the image position
+@@ -156,7 +156,7 @@ public:
+
+ /**
+ * Sets the y coordinate of the image position.
+- * The position can either be specified in relative or in absolut coordinates
++ * The position can either be specified in relative or in absolute coordinates
+ * or a combination of both.
+ *
+ * @param y y coordinate of the image position
+@@ -165,7 +165,7 @@ public:
+
+ /**
+ * Sets the z coordinate of the image position.
+- * The position can either be specified in relative or in absolut coordinates
++ * The position can either be specified in relative or in absolute coordinates
+ * or a combination of both.
+ *
+ * @param z z coordinate of the image position
+--- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/LineEnding.cpp
++++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/LineEnding.cpp
+@@ -133,7 +133,7 @@ LineEnding::getAllElements(ElementFilter
+ * The XMLNode object has to contain a valid XML representation of a
+ * ListOfLineEndings object as defined in the render extension specification.
+ * This method is normally called when render information is read from a file and
+- * should normally not have to be called explicitely.
++ * should normally not have to be called explicitly.
+ *
+ * @param node the XMLNode object reference that describes the ListOfLineEndings
+ * object to be instantiated.
+@@ -202,7 +202,7 @@ ListOfLineEndings::ListOfLineEndings(uns
+ * The XMLNode object has to contain a valid XML representation of a
+ * LineEnding object as defined in the render extension specification.
+ * This method is normally called when render information is read from a file and
+- * should normally not have to be called explicitely.
++ * should normally not have to be called explicitly.
+ *
+ * @param node the XMLNode object reference that describes the LineEnding
+ * object to be instantiated.
+--- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/LineEnding.h
++++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/LineEnding.h
+@@ -111,7 +111,7 @@ public:
+ * The XMLNode object has to contain a valid XML representation of a
+ * LineEnding object as defined in the render extension specification.
+ * This method is normally called when render information is read from a file and
+- * should normally not have to be called explicitely.
++ * should normally not have to be called explicitly.
+ *
+ * @param node the XMLNode object reference that describes the LineEnding
+ * object to be instantiated.
+@@ -466,7 +466,7 @@ public:
+ * The XMLNode object has to contain a valid XML representation of a
+ * ListOfLineEndings object as defined in the render extension specification.
+ * This method is normally called when render information is read from a file and
+- * should normally not have to be called explicitely.
++ * should normally not have to be called explicitly.
+ *
+ * @param node the XMLNode object reference that describes the ListOfLineEndings
+ * object to be instantiated.
+--- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/LinearGradient.cpp
++++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/LinearGradient.cpp
+@@ -102,7 +102,7 @@ LinearGradient::LinearGradient (RenderPk
+ * The XMLNode object has to contain a valid XML representation of a
+ * LinearGradient object as defined in the render extension specification.
+ * This method is normally called when render information is read from a file and
+- * should normally not have to be called explicitely.
++ * should normally not have to be called explicitly.
+ *
+ * @param node the XMLNode object reference that describes the LinearGradient
+ * object to be instantiated.
+--- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/LinearGradient.h
++++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/LinearGradient.h
+@@ -99,7 +99,7 @@ public:
+ * The XMLNode object has to contain a valid XML representation of a
+ * LinearGradient object as defined in the render extension specification.
+ * This method is normally called when render information is read from a file and
+- * should normally not have to be called explicitely.
++ * should normally not have to be called explicitly.
+ *
+ * @param node the XMLNode object reference that describes the LinearGradient
+ * object to be instantiated.
+--- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/ListOfCurveElements.cpp
++++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/ListOfCurveElements.cpp
+@@ -51,7 +51,7 @@ const std::string ListOfCurveElements::E
+ * The XMLNode object has to contain a valid XML representation of a
+ * ListOfCurveElements object as defined in the render extension specification.
+ * This method is normally called when render information is read from a file and
+- * should normally not have to be called explicitely.
++ * should normally not have to be called explicitly.
+ *
+ * @param node the XMLNode object reference that describes the ListOfCurveElements
+ * object to be instantiated.
+--- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/ListOfCurveElements.h
++++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/ListOfCurveElements.h
+@@ -60,7 +60,7 @@ public:
+ * The XMLNode object has to contain a valid XML representation of a
+ * ListOfCurveElements object as defined in the render extension specification.
+ * This method is normally called when render information is read from a file and
+- * should normally not have to be called explicitely.
++ * should normally not have to be called explicitly.
+ *
+ * @param node the XMLNode object reference that describes the ListOfCurveElements
+ * object to be instantiated.
+--- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/LocalRenderInformation.h
++++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/LocalRenderInformation.h
+@@ -397,7 +397,7 @@ public:
+ * The XMLNode object has to contain a valid XML representation of a
+ * ListOfLocalRenderInformation object as defined in the render extension specification.
+ * This method is normally called when render information is read from a file and
+- * should normally not have to be called explicitely.
++ * should normally not have to be called explicitly.
+ *
+ * @param node the XMLNode object reference that describes the ListOfLocalRenderInformation
+ * object to be instantiated.
+--- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/LocalStyle.cpp
++++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/LocalStyle.cpp
+@@ -96,7 +96,7 @@ LocalStyle::LocalStyle (RenderPkgNamespa
+ * The XMLNode object has to contain a valid XML representation of a
+ * LocalStyle object as defined in the render extension specification.
+ * This method is normally called when render information is read from a file and
+- * should normally not have to be called explicitely.
++ * should normally not have to be called explicitly.
+ *
+ * @param node the XMLNode object reference that describes the LocalStyle
+ * object to be instantiated.
+@@ -352,7 +352,7 @@ SBase* ListOfLocalStyles::createObject (
+ * The XMLNode object has to contain a valid XML representation of a
+ * ListOfLocalStyles object as defined in the render extension specification.
+ * This method is normally called when render information is read from a file and
+- * should normally not have to be called explicitely.
++ * should normally not have to be called explicitly.
+ *
+ * @param node the XMLNode object reference that describes the ListOfLocalStyles
+ * object to be instantiated.
+--- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/LocalStyle.h
++++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/LocalStyle.h
+@@ -99,7 +99,7 @@ public:
+ * The XMLNode object has to contain a valid XML representation of a
+ * LocalStyle object as defined in the render extension specification.
+ * This method is normally called when render information is read from a file and
+- * should normally not have to be called explicitely.
++ * should normally not have to be called explicitly.
+ *
+ * @param node the XMLNode object reference that describes the LocalStyle
+ * object to be instantiated.
+@@ -299,7 +299,7 @@ public:
+ * The XMLNode object has to contain a valid XML representation of a
+ * ListOfLocalStyles object as defined in the render extension specification.
+ * This method is normally called when render information is read from a file and
+- * should normally not have to be called explicitely.
++ * should normally not have to be called explicitly.
+ *
+ * @param node the XMLNode object reference that describes the ListOfLocalStyles
+ * object to be instantiated.
+--- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/Polygon.cpp
++++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/Polygon.cpp
+@@ -100,7 +100,7 @@ Polygon::Polygon (RenderPkgNamespaces* r
+ * The XMLNode object has to contain a valid XML representation of a
+ * Polygon object as defined in the render extension specification.
+ * This method is normally called when render information is read from a file and
+- * should normally not have to be called explicitely.
++ * should normally not have to be called explicitly.
+ *
+ * @param node the XMLNode object reference that describes the Polygon
+ * object to be instantiated.
+--- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/Polygon.h
++++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/Polygon.h
+@@ -96,7 +96,7 @@ public:
+ * The XMLNode object has to contain a valid XML representation of a
+ * Polygon object as defined in the render extension specification.
+ * This method is normally called when render information is read from a file and
+- * should normally not have to be called explicitely.
++ * should normally not have to be called explicitly.
+ *
+ * @param node the XMLNode object reference that describes the Polygon
+ * object to be instantiated.
+--- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/RadialGradient.cpp
++++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/RadialGradient.cpp
+@@ -108,7 +108,7 @@ RadialGradient::RadialGradient (RenderPk
+ * The XMLNode object has to contain a valid XML representation of a
+ * RadialGradient object as defined in the render extension specification.
+ * This method is normally called when render information is read from a file and
+- * should normally not have to be called explicitely.
++ * should normally not have to be called explicitly.
+ *
+ * @param node the XMLNode object reference that describes the RadialGradient
+ * object to be instantiated.
+--- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/RadialGradient.h
++++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/RadialGradient.h
+@@ -103,7 +103,7 @@ public:
+ * The XMLNode object has to contain a valid XML representation of a
+ * RadialGradient object as defined in the render extension specification.
+ * This method is normally called when render information is read from a file and
+- * should normally not have to be called explicitely.
++ * should normally not have to be called explicitly.
+ *
+ * @param node the XMLNode object reference that describes the RadialGradient
+ * object to be instantiated.
+--- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/Rectangle.cpp
++++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/Rectangle.cpp
+@@ -106,7 +106,7 @@ Rectangle::Rectangle (RenderPkgNamespace
+ * The XMLNode object has to contain a valid XML representation of a
+ * Rectangle object as defined in the render extension specification.
+ * This method is normally called when render information is read from a file and
+- * should normally not have to be called explicitely.
++ * should normally not have to be called explicitly.
+ *
+ * @param node the XMLNode object reference that describes the Rectangle
+ * object to be instantiated.
+--- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/Rectangle.h
++++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/Rectangle.h
+@@ -84,7 +84,7 @@ public:
+ * The XMLNode object has to contain a valid XML representation of a
+ * Rectangle object as defined in the render extension specification.
+ * This method is normally called when render information is read from a file and
+- * should normally not have to be called explicitely.
++ * should normally not have to be called explicitly.
+ *
+ * @param node the XMLNode object reference that describes the Rectangle
+ * object to be instantiated.
+--- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/RenderCubicBezier.cpp
++++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/RenderCubicBezier.cpp
+@@ -192,7 +192,7 @@ bool RenderCubicBezier::operator==(const
+ * The XMLNode object has to contain a valid XML representation of a
+ * RenderCubicBezier object as defined in the render extension specification.
+ * This method is normally called when render information is read from a file and
+- * should normally not have to be called explicitely.
++ * should normally not have to be called explicitly.
+ *
+ * @param node the XMLNode object reference that describes the RenderCubicBezier
+ * object to be instantiated.
+--- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/RenderCubicBezier.h
++++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/RenderCubicBezier.h
+@@ -141,7 +141,7 @@ public:
+ * The XMLNode object has to contain a valid XML representation of a
+ * RenderCubicBezier object as defined in the render extension specification.
+ * This method is normally called when render information is read from a file and
+- * should normally not have to be called explicitely.
++ * should normally not have to be called explicitly.
+ *
+ * @param node the XMLNode object reference that describes the RenderCubicBezier
+ * object to be instantiated.
+--- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/RenderCurve.cpp
++++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/RenderCurve.cpp
+@@ -112,7 +112,7 @@ RenderCurve::RenderCurve (RenderPkgNames
+ * The XMLNode object has to contain a valid XML representation of a
+ * RenderCurve object as defined in the render extension specification.
+ * This method is normally called when render information is read from a file and
+- * should normally not have to be called explicitely.
++ * should normally not have to be called explicitly.
+ *
+ * @param node the XMLNode object reference that describes the RenderCurve
+ * object to be instantiated.
+--- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/RenderCurve.h
++++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/RenderCurve.h
+@@ -100,7 +100,7 @@ public:
+ * The XMLNode object has to contain a valid XML representation of a
+ * RenderCurve object as defined in the render extension specification.
+ * This method is normally called when render information is read from a file and
+- * should normally not have to be called explicitely.
++ * should normally not have to be called explicitly.
+ *
+ * @param node the XMLNode object reference that describes the RenderCurve
+ * object to be instantiated.
+--- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/RenderGroup.cpp
++++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/RenderGroup.cpp
+@@ -258,7 +258,7 @@ void RenderGroup::readAttributes (const
+ * The XMLNode object has to contain a valid XML representation of a
+ * RenderGroup object as defined in the render extension specification.
+ * This method is normally called when render information is read from a file and
+- * should normally not have to be called explicitely.
++ * should normally not have to be called explicitly.
+ *
+ * @param node the XMLNode object reference that describes the RenderGroup
+ * object to be instantiated.
+--- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/RenderGroup.h
++++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/RenderGroup.h
+@@ -294,7 +294,7 @@ public:
+ * The XMLNode object has to contain a valid XML representation of a
+ * RenderGroup object as defined in the render extension specification.
+ * This method is normally called when render information is read from a file and
+- * should normally not have to be called explicitely.
++ * should normally not have to be called explicitly.
+ *
+ * @param node the XMLNode object reference that describes the RenderGroup
+ * object to be instantiated.
+--- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/RenderInformationBase.cpp
++++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/RenderInformationBase.cpp
+@@ -307,9 +307,9 @@ void RenderInformationBase::setProgramVe
+ * Global render information objects can only reference other global
+ * render information objects, local render information objects can reference other local
+ * render information objects from the same list of local render information or other
+- * global render infromation.
++ * global render information.
+ *
+- * @return the id of the referenced render infromation object.
++ * @return the id of the referenced render information object.
+ */
+ const std::string& RenderInformationBase::getReferenceRenderInformationId() const
+ {
+@@ -320,10 +320,10 @@ const std::string& RenderInformationBase
+ /** @cond doxygenLibsbmlInternal */
+ /*
+ * Sets the id of the referenced render information object.
+- * The user has to make sure that render infromation referencing
++ * The user has to make sure that render information referencing
+ * does not create loops.
+ *
+- * @param id the id of the referenced render infromation
++ * @param id the id of the referenced render information
+ */
+ void RenderInformationBase::setReferenceRenderInformationId(const std::string& id)
+ {
+--- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/RenderInformationBase.h
++++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/RenderInformationBase.h
+@@ -195,18 +195,18 @@ public:
+ * Global render information objects can only reference other global
+ * render information objects, local render information objects can reference other local
+ * render information objects from the same list of local render information or other
+- * global render infromation.
++ * global render information.
+ *
+- * @return the id of the referenced render infromation object.
++ * @return the id of the referenced render information object.
+ */
+ const std::string& getReferenceRenderInformationId() const;
+
+ /**
+ * Sets the id of the referenced render information object.
+- * The user has to make sure that render infromation referencing
++ * The user has to make sure that render information referencing
+ * does not create loops.
+ *
+- * @param id the id of the referenced render infromation
++ * @param id the id of the referenced render information
+ */
+ void setReferenceRenderInformationId(const std::string& id);
+
+--- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/RenderPoint.cpp
++++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/RenderPoint.cpp
+@@ -185,7 +185,7 @@ void RenderPoint::initDefaults ()
+ * The XMLNode object has to contain a valid XML representation of a
+ * RenderPoint object as defined in the render extension specification.
+ * This method is normally called when render information is read from a file and
+- * should normally not have to be called explicitely.
++ * should normally not have to be called explicitly.
+ *
+ * @param node the XMLNode object reference that describes the RenderPoint
+ * object to be instantiated.
+--- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/RenderPoint.h
++++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/RenderPoint.h
+@@ -109,7 +109,7 @@ public:
+ * The XMLNode object has to contain a valid XML representation of a
+ * RenderPoint object as defined in the render extension specification.
+ * This method is normally called when render information is read from a file and
+- * should normally not have to be called explicitely.
++ * should normally not have to be called explicitly.
+ *
+ * @param node the XMLNode object reference that describes the RenderPoint
+ * object to be instantiated.
+--- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/Style.cpp
++++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/Style.cpp
+@@ -553,7 +553,7 @@ const std::string& Style::getElementName
+ * The XMLNode object has to contain a valid XML representation of a
+ * Style object as defined in the render extension specification.
+ * This method is normally called when render information is read from a file and
+- * should normally not have to be called explicitely.
++ * should normally not have to be called explicitly.
+ *
+ * @param node the XMLNode object reference that describes the Style
+ * object to be instantiated.
+--- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/Style.h
++++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/Style.h
+@@ -95,7 +95,7 @@ protected:
+ * The XMLNode object has to contain a valid XML representation of a
+ * Style object as defined in the render extension specification.
+ * This method is normally called when render information is read from a file and
+- * should normally not have to be called explicitely.
++ * should normally not have to be called explicitly.
+ *
+ * @param node the XMLNode object reference that describes the Style
+ * object to be instantiated.
+--- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/Text.cpp
++++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/Text.cpp
+@@ -115,7 +115,7 @@ Text::Text (RenderPkgNamespaces* rendern
+ * The XMLNode object has to contain a valid XML representation of a
+ * Text object as defined in the render extension specification.
+ * This method is normally called when render information is read from a file and
+- * should normally not have to be called explicitely.
++ * should normally not have to be called explicitly.
+ *
+ * @param node the XMLNode object reference that describes the Text
+ * object to be instantiated.
+--- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/Text.h
++++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/Text.h
+@@ -128,7 +128,7 @@ public:
+ * The XMLNode object has to contain a valid XML representation of a
+ * Text object as defined in the render extension specification.
+ * This method is normally called when render information is read from a file and
+- * should normally not have to be called explicitely.
++ * should normally not have to be called explicitly.
+ *
+ * @param node the XMLNode object reference that describes the Text
+ * object to be instantiated.
+--- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/Transformation.cpp
++++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/Transformation.cpp
+@@ -113,7 +113,7 @@ Transformation::~Transformation ()
+ * The XMLNode object has to contain a valid XML representation of a
+ * Transformation object as defined in the render extension specification.
+ * This method is normally called when render information is read from a file and
+- * should normally not have to be called explicitely.
++ * should normally not have to be called explicitly.
+ *
+ * @param node the XMLNode object reference that describes the Transformation
+ * object to be instantiated.
+--- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/Transformation.h
++++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/Transformation.h
+@@ -65,7 +65,7 @@ protected:
+ * The XMLNode object has to contain a valid XML representation of a
+ * Transformation object as defined in the render extension specification.
+ * This method is normally called when render information is read from a file and
+- * should normally not have to be called explicitely.
++ * should normally not have to be called explicitly.
+ *
+ * @param node the XMLNode object reference that describes the Transformation
+ * object to be instantiated.
+--- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/Transformation2D.cpp
++++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/Transformation2D.cpp
+@@ -132,7 +132,7 @@ Transformation2D::Transformation2D(Rende
+ * The XMLNode object has to contain a valid XML representation of a
+ * Transformation2D object as defined in the render extension specification.
+ * This method is normally called when render information is read from a file and
+- * should normally not have to be called explicitely.
++ * should normally not have to be called explicitly.
+ *
+ * @param node the XMLNode object reference that describes the Transformation2D
+ * object to be instantiated.
+--- libsbml-5.11.0+dfsg.orig/src/sbml/packages/render/sbml/Transformation2D.h
++++ libsbml-5.11.0+dfsg/src/sbml/packages/render/sbml/Transformation2D.h
+@@ -99,7 +99,7 @@ public:
+ * The XMLNode object has to contain a valid XML representation of a
+ * Transformation2D object as defined in the render extension specification.
+ * This method is normally called when render information is read from a file and
+- * should normally not have to be called explicitely.
++ * should normally not have to be called explicitly.
+ *
+ * @param node the XMLNode object reference that describes the Transformation2D
+ * object to be instantiated.
Modified: trunk/packages/libsbml/trunk/debian/rules
===================================================================
--- trunk/packages/libsbml/trunk/debian/rules 2015-03-12 08:46:56 UTC (rev 18963)
+++ trunk/packages/libsbml/trunk/debian/rules 2015-03-13 13:04:07 UTC (rev 18964)
@@ -3,8 +3,6 @@
# debian/rules for libsbml
### define the VARS ###
-### part 1 of a dirty hack for octave bindings ###
-OCTAVE_PATH ?= usr$(shell grep LOCALOCTFILEDIR config/makefile-common-vars.mk | tr -s ' ' ' ' | cut -d\ -f3)
version := $(shell dpkg-parsechangelog | grep Version | cut -d\ -f2 | cut -d- -f1)
major := $(shell dpkg-parsechangelog | grep Version | cut -d\ -f2 | cut -d. -f1)
libpack := libsbml
@@ -13,6 +11,10 @@
SRC_TMP := $(CURDIR)/SRC_TMP
# Test for matlab
CMAKE_OPTS := $(shell sed '/MATLAB/d' debian/cmake_opts)
+BIND_OCTAVE :=$(shell which otave-config | grep -q ocatve && echo 'yes')
+ifdef BIND_OCTAVE
+OCTAVE_PATH := $(shell octave-config --oct-site-dir)
+endif
BIND_MATLAB := $(shell which matlab | grep -q matlab && echo 'yes')
ifdef BIND_MATLAB
CMAKE_OPTS := $(shell cat debian/cmake_opts)
@@ -37,7 +39,8 @@
docs/src/doxygen-config-csharp.txt docs/src/doxygen-config-perl.txt docs/src/doxygen-config-python.txt \
docs/src/java-substitutions/libsbmlConstants.java docs/src/libsbml-installation.html docs/src/perlmod/DoxyDocs.pm \
docs/src/perlmod/DoxyStructure.pm docs/src/perlmod/Makefile docs/src/perlmod/doxyrules.make \
- src/bindings/matlab/runTests.log docs/src/doxygen-config-c.txt src/bindings/matlab/*.mex*
+ src/bindings/matlab/runTests.log docs/src/doxygen-config-c.txt src/bindings/matlab/*.mex* docs/src/perlmod \
+ docs/src/doxygen_sqlite3.db docs/src/libsbml.py docs/src/common-text/libsbml-version.html
find src/bindings -name "*.pyc" -delete
override_dh_auto_configure:
@@ -59,9 +62,11 @@
override_dh_auto_install:
cd build ; DESTDIR=../debian/tmp make install
+ sed 's#formatted/##g' docs/index.html.in > $(debtmp)/usr/share/libsbml/docs/index.html
dh_auto_install
pyclean $(debtmp)/usr/lib/python*
find $(debtmp)/usr -type f -name "*.js" -delete
+ find $(debtmp)/usr -type f -name "*.md5" -delete
find $(debtmp)/usr -type f -exec chmod 644 {} +
test -e $(debtmp)/usr/lib/python2.7/site-packages && mv $(debtmp)/usr/lib/python2.7/site-packages $(debtmp)/usr/lib/python2.7/dist-packages || true
find $(debtmp)/usr/lib -name "*.mex*" -exec strip --strip-unneeded {} + || true
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