| Patch |
File delta |
Description |
| perl installdirs.patch | (download) |
src/bindings/perl/CMakeLists.txt |
8 7 + 1 - 0 !
src/bindings/perl/Makefile.PL.in |
1 0 + 1 - 0 !
2 files changed, 7 insertions(+), 2 deletions(-) |
install perl modules in correct dir
|
| hardening.patch | (download) |
config/makefile-common-actions.mk |
9 9 + 0 - 0 !
src/bindings/matlab/Makefile.in |
2 1 + 1 - 0 !
src/bindings/perl/Makefile.in |
1 1 + 0 - 0 !
3 files changed, 11 insertions(+), 1 deletion(-) |
hardening
.
libsbml (5.11.0+dfsg-1sid1) UNRELEASED; urgency=medium
.
* update from upstream
|
| doxygen.patch | (download) |
docs/CMakeLists.txt |
2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-) |
fix a wrong file name
docs/CmakeLists.txt contains a wrong path to right-arrow-2x.png
.
libsbml (5.11.0+dfsg-1sid1) UNRELEASED; urgency=medium
.
* update from upstream
|
| swig 3.x.patch | (download) |
src/bindings/csharp/local-packages-arrays.i |
8 4 + 4 - 0 !
src/bindings/csharp/local-packages-groups.i |
8 4 + 4 - 0 !
src/bindings/csharp/local-packages-layout.i |
8 4 + 4 - 0 !
src/bindings/csharp/local-packages-render.i |
8 4 + 4 - 0 !
src/bindings/csharp/local-packages-req.i |
8 4 + 4 - 0 !
src/bindings/csharp/local-packages-spatial.i |
8 4 + 4 - 0 !
src/bindings/csharp/local.i |
86 43 + 43 - 0 !
7 files changed, 67 insertions(+), 67 deletions(-) |
build with swig 3.x
|
| mips compile with O1.patch | (download) |
src/bindings/perl/CMakeLists.txt |
6 6 + 0 - 0 !
1 file changed, 6 insertions(+) |
package libsbml ftbfs on mipsel
We have successfully built libsbml using -O1 optimization level.
-O1 is used for mips/mipsel, for critical part of package.
.
With this patch we was able to build package on lemote loongson 3a.
|
| javadoc_java9.patch | (download) |
docs/CMakeLists.txt |
4 0 + 4 - 0 !
1 file changed, 4 deletions(-) |
work around javadoc issue with java 9
See https://lists.debian.org/debian-java/2018/03/msg00023.html
Bug-Debian: https://bugs.debian.org/893298
|
| javadoc.patch | (download) |
docs/src/SBMLDoclet.java |
2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-) |
deal with issue in doclets
/build/libsbml-5.16.0+dfsg/docs/src/SBMLDoclet.java:112: error: package com.sun.tools.doclets.standard is not visible
import com.sun.tools.doclets.standard.Standard;
^
(package com.sun.tools.doclets.standard is declared in module jdk.javadoc, which does not export it)
.
This web page brought the idea for the patch:
https://docs.oracle.com/javase/9/docs/api/com/sun/javadoc/class-use/LanguageVersion.html
|
| remove_SBMLDoclet.patch | (download) |
docs/CMakeLists.txt |
63 3 + 60 - 0 !
docs/src/SBMLDoclet.java |
525 0 + 525 - 0 !
2 files changed, 3 insertions(+), 585 deletions(-) |
deal with issue in doclets by removing docs/src/sbmldoclet.java
Bug-Debian: https://bugs.debian.org/896531
|
| fix_build_issue.patch | (download) |
src/bindings/swig/swigdoc.py |
2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-) |
avoid error
TypeError: '>=' not supported between instances of 'str' and 'int'
|
| fix_python_interpreter.patch | (download) |
docs/src/filters/doc-filter-c.py |
2 1 + 1 - 0 !
docs/src/filters/doc-filter-csharp.py |
2 1 + 1 - 0 !
docs/src/filters/doc-filter-python.py |
2 1 + 1 - 0 !
docs/src/utilities/compare-classes.py |
2 1 + 1 - 0 !
docs/src/utilities/compare-constants.py |
2 1 + 1 - 0 !
docs/src/utilities/generate-class-name-list.py |
2 1 + 1 - 0 !
docs/src/utilities/generate-converters-list.py |
2 1 + 1 - 0 !
docs/src/utilities/generate-cplusplus-class-names.py |
2 1 + 1 - 0 !
docs/src/utilities/generate-extensions-summary.py |
2 1 + 1 - 0 !
docs/src/utilities/generate-pkg-stylesheet.py |
2 1 + 1 - 0 !
docs/src/utilities/pythondocpreprocessor.py |
2 1 + 1 - 0 !
examples/python/addCVTerms.py |
2 1 + 1 - 0 !
examples/python/addCustomValidator.py |
2 1 + 1 - 0 !
examples/python/addModelHistory.py |
2 1 + 1 - 0 !
examples/python/addingEvidenceCodes_1.py |
2 1 + 1 - 0 !
examples/python/addingEvidenceCodes_2.py |
2 1 + 1 - 0 !
examples/python/appendAnnotation.py |
2 1 + 1 - 0 !
examples/python/append_to_note.py |
2 1 + 1 - 0 !
examples/python/arrays/flattenArrays.py |
2 1 + 1 - 0 !
examples/python/callExternalValidator.py |
2 1 + 1 - 0 !
examples/python/comp/flattenModel.py |
2 1 + 1 - 0 !
examples/python/convertSBML.py |
2 1 + 1 - 0 !
examples/python/createExampleSBML.py |
2 1 + 1 - 0 !
examples/python/createSimpleModel.py |
2 1 + 1 - 0 !
examples/python/distrib/createNormalExample.py |
2 1 + 1 - 0 !
examples/python/echoSBML.py |
2 1 + 1 - 0 !
examples/python/evaluateCustomMath.py |
2 1 + 1 - 0 !
examples/python/fbc/convertCobraToFbc.py |
2 1 + 1 - 0 !
examples/python/fbc/convertFbcToCobra.py |
2 1 + 1 - 0 !
examples/python/fbc/fbc_example1.py |
2 1 + 1 - 0 !
examples/python/fbc/print_gene_product_association.py |
2 1 + 1 - 0 !
examples/python/getAllElementsWithNotes.py |
2 1 + 1 - 0 !
examples/python/groups/groups_example1.py |
2 1 + 1 - 0 !
examples/python/groups/print_groups.py |
2 1 + 1 - 0 !
examples/python/inlineFunctionDefinitions.py |
2 1 + 1 - 0 !
examples/python/inlineInitialAssignments.py |
2 1 + 1 - 0 !
examples/python/layout/convertLayout.py |
2 1 + 1 - 0 !
examples/python/layout/example1-L3.py |
2 1 + 1 - 0 !
examples/python/layout/example1.py |
2 1 + 1 - 0 !
examples/python/printAnnotation.py |
2 1 + 1 - 0 !
examples/python/printMath.py |
2 1 + 1 - 0 !
examples/python/printNotes.py |
2 1 + 1 - 0 !
examples/python/printRegisteredPackages.py |
2 1 + 1 - 0 !
examples/python/printSBML.py |
2 1 + 1 - 0 !
examples/python/printUnits.py |
2 1 + 1 - 0 !
examples/python/printsupported.py |
2 1 + 1 - 0 !
examples/python/promoteParameters.py |
2 1 + 1 - 0 !
examples/python/qual/qual_example1.py |
2 1 + 1 - 0 !
examples/python/readSBML.py |
2 1 + 1 - 0 !
examples/python/replaceOneFD.py |
2 1 + 1 - 0 !
examples/python/setIdFromNames.py |
2 1 + 1 - 0 !
examples/python/stringInput.py |
2 1 + 1 - 0 !
examples/python/stripPackage.py |
2 1 + 1 - 0 !
examples/python/translateMath.py |
2 1 + 1 - 0 !
examples/python/unsetAnnotation.py |
2 1 + 1 - 0 !
examples/python/unsetNotes.py |
2 1 + 1 - 0 !
examples/python/validateSBML.py |
2 1 + 1 - 0 !
examples/python/validateSBMLWithCallback.py |
2 1 + 1 - 0 !
src/bindings/python/doc-converter/prettytable.py |
2 1 + 1 - 0 !
src/bindings/python/doc-converter/rewrite_pydoc.py |
2 1 + 1 - 0 !
src/bindings/python/test.py |
2 1 + 1 - 0 !
src/bindings/swig/libsbmlutils.py |
2 1 + 1 - 0 !
src/bindings/swig/swigdoc.py |
2 1 + 1 - 0 !
63 files changed, 63 insertions(+), 63 deletions(-) |
---
|
| wrong_import_in_AutoTestRunner.patch | (download) |
src/bindings/java/AutoTestRunner.java |
5 4 + 1 - 0 !
1 file changed, 4 insertions(+), 1 deletion(-) |
there is no class in org/sbml/libsbml/test, looking in its
subdirectories instead
|
| missing_header.patch | (download) |
src/bindings/matlab/StructureFields.cpp |
3 3 + 0 - 0 !
1 file changed, 3 insertions(+) |
the fbcassociation header has to be included in the matlab
bindings, as they use the FbcAssociation class
|
