Codebase list libsbml / 82165fe6-c4b6-4ec3-8814-4fdd5c922eab/main
Refresh patches. Debian Janitor 4 years ago
10 changed file(s) with 99 addition(s) and 59 deletion(s). Raw diff Collapse all Expand all
88 ---
99 Last-Update: <2015-01-12>
1010
11 --- a/docs/CMakeLists.txt
12 +++ b/docs/CMakeLists.txt
11 Index: libsbml/docs/CMakeLists.txt
12 ===================================================================
13 --- libsbml.orig/docs/CMakeLists.txt
14 +++ libsbml/docs/CMakeLists.txt
1315 @@ -101,7 +101,7 @@ macro(createManual lang)
1416 file(TO_NATIVE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/formatted/${lang}-api output_path)
1517 file(TO_NATIVE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/formatted/${lang}-api/search search_path)
22 Description: Avoid error
33 TypeError: '>=' not supported between instances of 'str' and 'int'
44
5 --- a/src/bindings/swig/swigdoc.py
6 +++ b/src/bindings/swig/swigdoc.py
5 Index: libsbml/src/bindings/swig/swigdoc.py
6 ===================================================================
7 --- libsbml.orig/src/bindings/swig/swigdoc.py
8 +++ libsbml/src/bindings/swig/swigdoc.py
79 @@ -467,7 +467,7 @@ class Method:
810 # this fixes a real problem in the Java documentation for libSBML.
911
22 Description: Desperately trying to fix CMake config by simply
33 commenting the line which causes an error
44
5 --- a/src/bindings/r/CMakeLists.txt
6 +++ b/src/bindings/r/CMakeLists.txt
5 Index: libsbml/src/bindings/r/CMakeLists.txt
6 ===================================================================
7 --- libsbml.orig/src/bindings/r/CMakeLists.txt
8 +++ libsbml/src/bindings/r/CMakeLists.txt
79 @@ -336,7 +336,12 @@ configure_file (
810 "${CMAKE_CURRENT_BINARY_DIR}/libSBML/NAMESPACE"
911 )
77 ---
88 Last-Update: <2015-01-09>
99
10 --- a/config/makefile-common-actions.mk
11 +++ b/config/makefile-common-actions.mk
10 Index: libsbml/config/makefile-common-actions.mk
11 ===================================================================
12 --- libsbml.orig/config/makefile-common-actions.mk
13 +++ libsbml/config/makefile-common-actions.mk
1214 @@ -77,6 +77,15 @@ endif
1315 # here is only to remove duplicates, which the 'sort' function does as a
1416 # documented side-effect.)
2527 compile ?= $(LIBTOOL) --mode=compile --tag=CC $(CC) $(sort $(default_includes) $(INCLUDES)) $(CPPFLAGS) \
2628 $(extra_CPPFLAGS) $(CFLAGS) $(extra_CFLAGS)
2729
28 --- a/src/bindings/matlab/Makefile.in
29 +++ b/src/bindings/matlab/Makefile.in
30 Index: libsbml/src/bindings/matlab/Makefile.in
31 ===================================================================
32 --- libsbml.orig/src/bindings/matlab/Makefile.in
33 +++ libsbml/src/bindings/matlab/Makefile.in
3034 @@ -150,7 +150,7 @@ endif
3135 # is really necessary, but it seems prudent.
3236
3640 $(LIBTOOL) -dlopen $(TOP_BUILDDIR)/src/libsbml.la --mode=execute $(1)
3741 endef
3842
39 --- a/src/bindings/perl/Makefile.in
40 +++ b/src/bindings/perl/Makefile.in
43 Index: libsbml/src/bindings/perl/Makefile.in
44 ===================================================================
45 --- libsbml.orig/src/bindings/perl/Makefile.in
46 +++ libsbml/src/bindings/perl/Makefile.in
4147 @@ -185,6 +185,7 @@ ifeq (GCC,$(findstring GCC,$(shell $(CXX
4248 CXXFLAGS += -fno-strict-aliasing
4349 endif
88 Author: Andreas Tille <tille@debian.org>
99 Last-Update: Mon, 14 May 2018 10:55:58 +0200
1010
11 --- a/docs/src/SBMLDoclet.java
12 +++ b/docs/src/SBMLDoclet.java
11 Index: libsbml/docs/src/SBMLDoclet.java
12 ===================================================================
13 --- libsbml.orig/docs/src/SBMLDoclet.java
14 +++ libsbml/docs/src/SBMLDoclet.java
1315 @@ -111,7 +111,7 @@ import java.util.*;
1416 import java.lang.reflect.*;
1517 import com.sun.tools.doclets.standard.Standard;
44 Andreas Tille <tille@debian.org>
55 Last-Update: Sun, 18 Mar 2018 19:39:40 +0100
66
7 --- a/docs/CMakeLists.txt
8 +++ b/docs/CMakeLists.txt
7 Index: libsbml/docs/CMakeLists.txt
8 ===================================================================
9 --- libsbml.orig/docs/CMakeLists.txt
10 +++ libsbml/docs/CMakeLists.txt
911 @@ -208,10 +208,6 @@ if (WITH_JAVA)
1012 endif()
1113 set(Java_JAVADOC_JAR ${Java_JAVADOC_JAR} CACHE FILEPATH "Location of javadoc jar")
66 .
77 With this patch we was able to build package on lemote loongson 3a.
88
9 --- a/src/bindings/perl/CMakeLists.txt
10 +++ b/src/bindings/perl/CMakeLists.txt
9 Index: libsbml/src/bindings/perl/CMakeLists.txt
10 ===================================================================
11 --- libsbml.orig/src/bindings/perl/CMakeLists.txt
12 +++ libsbml/src/bindings/perl/CMakeLists.txt
1113 @@ -176,6 +176,12 @@ if (LIBSBML_REMOVE_WRAPPERS)
1214 endforeach()
1315 endif(LIBSBML_REMOVE_WRAPPERS)
11 Last-Update: Tue, 01 May 2018 19:03:21 +0200
22 Description: Install Perl modules in correct dir
33
4 --- a/src/bindings/perl/Makefile.PL.in
5 +++ b/src/bindings/perl/Makefile.PL.in
4 Index: libsbml/src/bindings/perl/Makefile.PL.in
5 ===================================================================
6 --- libsbml.orig/src/bindings/perl/Makefile.PL.in
7 +++ libsbml/src/bindings/perl/Makefile.PL.in
68 @@ -58,7 +58,6 @@ WriteMakefile(
79 NAME => "LibSBML",
810 PREFIX => "@prefix@",
1113 LIBS => "@XERCES_LDFLAGS@ @EXPAT_LDFLAGS@ @LIBXML_LDFLAGS@ @XERCES_LIBS@ @EXPAT_LIBS@ @LIBXML_LIBS@ @ZLIB_LIBS@ @BZ2_LIBS@ @LIBS@ -lm",
1214 LDDLFLAGS => $lddlflags,
1315 CC => "@CXX@",
14 --- a/src/bindings/perl/CMakeLists.txt
15 +++ b/src/bindings/perl/CMakeLists.txt
16 Index: libsbml/src/bindings/perl/CMakeLists.txt
17 ===================================================================
18 --- libsbml.orig/src/bindings/perl/CMakeLists.txt
19 +++ libsbml/src/bindings/perl/CMakeLists.txt
1620 @@ -232,8 +232,14 @@ Could not determine Perl version, please
1721 string(REPLACE "'" "" PERL_PLATFORM ${PERL_PLATFORM})
1822 string(REPLACE ";" "" PERL_PLATFORM ${PERL_PLATFORM})
22 Author: Andreas Tille <tille@debian.org>
33 Last-Update: Mon, 14 May 2018 10:55:58 +0200
44
5 --- a/docs/src/SBMLDoclet.java
5 Index: libsbml/docs/src/SBMLDoclet.java
6 ===================================================================
7 --- libsbml.orig/docs/src/SBMLDoclet.java
68 +++ /dev/null
79 @@ -1,525 +0,0 @@
810 -/**
530532 - }
531533 -
532534 -}
533 --- a/docs/CMakeLists.txt
534 +++ b/docs/CMakeLists.txt
535 Index: libsbml/docs/CMakeLists.txt
536 ===================================================================
537 --- libsbml.orig/docs/CMakeLists.txt
538 +++ libsbml/docs/CMakeLists.txt
535539 @@ -229,67 +229,10 @@ if (WITH_JAVA)
536540 file(COPY ${graphic} DESTINATION ${CMAKE_CURRENT_SOURCE_DIR}/formatted/java-api/org/sbml/libsbml/)
537541 endforeach()
22 Bug-Debian: https://bugs.debian.org/805584
33 Description: Build with SWIG 3.x
44
5 --- a/src/bindings/csharp/local.i
6 +++ b/src/bindings/csharp/local.i
7 @@ -117,13 +117,13 @@ static SWIG_CSharpWStringHelperCallback
5 Index: libsbml/src/bindings/csharp/local.i
6 ===================================================================
7 --- libsbml.orig/src/bindings/csharp/local.i
8 +++ libsbml/src/bindings/csharp/local.i
9 @@ -121,13 +121,13 @@ static SWIG_CSharpWStringHelperCallback
810 %pragma(csharp) imclasscode=%{
911 protected class SWIGWStringHelper {
1012
2123 string ustr = System.Runtime.InteropServices.Marshal.PtrToStringUni(cString);
2224 return System.Runtime.InteropServices.Marshal.StringToHGlobalUni(ustr);
2325 }
24 @@ -203,15 +203,15 @@ SWIGEXPORT void SWIGSTDCALL SWIGRegister
26 @@ -207,15 +207,15 @@ SWIGEXPORT void SWIGSTDCALL SWIGRegister
2527 */
2628 %typemap(cscode) SBMLExtension
2729 %{
4143 return new SBase(cPtr, owner);
4244 }
4345 %}
44 @@ -224,9 +224,9 @@ SWIGEXPORT void SWIGSTDCALL SWIGRegister
46 @@ -228,9 +228,9 @@ SWIGEXPORT void SWIGSTDCALL SWIGRegister
4547 %pragma(csharp) modulecode =
4648 %{
4749
5355
5456 SBMLExtension ext = new SBMLExtension(cPtr, false);
5557 string pkgName = ext.getName();
56 @@ -237,9 +237,9 @@ SWIGEXPORT void SWIGSTDCALL SWIGRegister
58 @@ -241,9 +241,9 @@ SWIGEXPORT void SWIGSTDCALL SWIGRegister
5759 return new SBMLExtension(cPtr,owner);
5860 }
5961
6567
6668 SBMLNamespaces sbn = new SBMLNamespaces(cPtr, false);
6769 if (sbn != null)
68 @@ -289,9 +289,9 @@ SWIGEXPORT void SWIGSTDCALL SWIGRegister
70 @@ -293,9 +293,9 @@ SWIGEXPORT void SWIGSTDCALL SWIGRegister
6971 return new SBMLConverter(cPtr,owner);
7072 }
7173
7779
7880 SBasePlugin sbp = new SBasePlugin(cPtr, false);
7981 string pkgName = sbp.getPackageName();
80 @@ -306,9 +306,9 @@ SWIGEXPORT void SWIGSTDCALL SWIGRegister
82 @@ -310,9 +310,9 @@ SWIGEXPORT void SWIGSTDCALL SWIGRegister
8183 }
8284
8385
8991
9092 SBase sb = new SBase(cPtr, false);
9193 string pkgName = sb.getPackageName();
92 @@ -637,23 +637,23 @@ SWIGEXPORT void SWIGSTDCALL SWIGRegister
94 @@ -641,23 +641,23 @@ SWIGEXPORT void SWIGSTDCALL SWIGRegister
9395
9496 %typemap(csbody) TYPENAME
9597 %{
120122
121123 if (obj != null)
122124 {
123 @@ -670,22 +670,22 @@ SWIGEXPORT void SWIGSTDCALL SWIGRegister
125 @@ -674,22 +674,22 @@ SWIGEXPORT void SWIGSTDCALL SWIGRegister
124126
125127 %typemap(csbody_derived) TYPENAME
126128 %{
150152
151153 if (obj != null)
152154 {
153 @@ -701,22 +701,22 @@ SWIGEXPORT void SWIGSTDCALL SWIGRegister
155 @@ -705,22 +705,22 @@ SWIGEXPORT void SWIGSTDCALL SWIGRegister
154156
155157 %typemap(csbody_derived) TYPENAME
156158 %{
180182
181183 if (obj != null)
182184 {
183 @@ -981,10 +981,10 @@ COVARIANT_GETID(InitialAssignment)
185 @@ -985,10 +985,10 @@ COVARIANT_GETID(InitialAssignment)
184186 %typemap(csbase) SBMLConstructorException "System.ArgumentException";
185187 %typemap(cscode) SBMLConstructorException
186188 %{
193195 }
194196
195197 public SBMLConstructorException(string v) :
196 @@ -995,10 +995,10 @@ COVARIANT_GETID(InitialAssignment)
198 @@ -999,10 +999,10 @@ COVARIANT_GETID(InitialAssignment)
197199 %typemap(csbase) XMLConstructorException "System.ArgumentException";
198200 %typemap(cscode) XMLConstructorException
199201 %{
206208 }
207209
208210 public XMLConstructorException(string v) :
209 @@ -1037,7 +1037,7 @@ COVARIANT_GETID(InitialAssignment)
211 @@ -1041,7 +1041,7 @@ COVARIANT_GETID(InitialAssignment)
210212 static CustomExceptionDelegate customDelegate =
211213 new CustomExceptionDelegate(SetPendingCustomException);
212214
215217 public static extern
216218 void CustomExceptionRegisterCallback(CustomExceptionDelegate customCallback);
217219
218 @@ -1389,8 +1389,8 @@ XMLCONSTRUCTOR_EXCEPTION(XMLTripple)
220 @@ -1393,8 +1393,8 @@ XMLCONSTRUCTOR_EXCEPTION(XMLTripple)
219221 %typemap(cstype) List* _FNAME_ %{ _TYPENAME_ ## List %}
220222 %typemap(csout) List* _FNAME_
221223 {
226228 }
227229 %typemap(out) List* _FNAME_
228230 {
229 --- a/src/bindings/csharp/local-packages-arrays.i
230 +++ b/src/bindings/csharp/local-packages-arrays.i
231 @@ -39,9 +39,9 @@
231 Index: libsbml/src/bindings/csharp/local-packages-arrays.i
232 ===================================================================
233 --- libsbml.orig/src/bindings/csharp/local-packages-arrays.i
234 +++ libsbml/src/bindings/csharp/local-packages-arrays.i
235 @@ -43,9 +43,9 @@
232236 */
233237 %typemap(cscode) ArraysExtension
234238 %{
240244
241245 SBasePlugin sbp = new SBasePlugin(cPtr, false);
242246 SBase sb = sbp.getParentSBMLObject();
243 @@ -53,9 +53,9 @@
247 @@ -57,9 +57,9 @@
244248 }
245249 }
246250
252256
253257 SBase sb = new SBase(cPtr, false);
254258 switch( sb.getTypeCode() )
255 --- a/src/bindings/csharp/local-packages-groups.i
256 +++ b/src/bindings/csharp/local-packages-groups.i
259 Index: libsbml/src/bindings/csharp/local-packages-groups.i
260 ===================================================================
261 --- libsbml.orig/src/bindings/csharp/local-packages-groups.i
262 +++ libsbml/src/bindings/csharp/local-packages-groups.i
257263 @@ -40,9 +40,9 @@
258264 */
259265 %typemap(cscode) GroupsExtension
278284
279285 SBase sb = new SBase(cPtr, false);
280286 switch( sb.getTypeCode() )
281 --- a/src/bindings/csharp/local-packages-layout.i
282 +++ b/src/bindings/csharp/local-packages-layout.i
287 Index: libsbml/src/bindings/csharp/local-packages-layout.i
288 ===================================================================
289 --- libsbml.orig/src/bindings/csharp/local-packages-layout.i
290 +++ libsbml/src/bindings/csharp/local-packages-layout.i
283291 @@ -33,9 +33,9 @@
284292 */
285293 %typemap(cscode) LayoutExtension
304312
305313 SBase sb = new SBase(cPtr, false);
306314 switch( sb.getTypeCode() )
307 --- a/src/bindings/csharp/local-packages-render.i
308 +++ b/src/bindings/csharp/local-packages-render.i
315 Index: libsbml/src/bindings/csharp/local-packages-render.i
316 ===================================================================
317 --- libsbml.orig/src/bindings/csharp/local-packages-render.i
318 +++ libsbml/src/bindings/csharp/local-packages-render.i
309319 @@ -32,9 +32,9 @@ COVARIANT_RTYPE_FUNCTION(GradientBase, g
310320 */
311321 %typemap(cscode) RenderExtension
330340
331341 SBase sb = new SBase(cPtr, false);
332342 switch( sb.getTypeCode() )
333 --- a/src/bindings/csharp/local-packages-req.i
334 +++ b/src/bindings/csharp/local-packages-req.i
335 @@ -38,9 +38,9 @@
343 Index: libsbml/src/bindings/csharp/local-packages-req.i
344 ===================================================================
345 --- libsbml.orig/src/bindings/csharp/local-packages-req.i
346 +++ libsbml/src/bindings/csharp/local-packages-req.i
347 @@ -42,9 +42,9 @@
336348 */
337349 %typemap(cscode) ReqExtension
338350 %{
344356
345357 SBasePlugin sbp = new SBasePlugin(cPtr, false);
346358 SBase sb = sbp.getParentSBMLObject();
347 @@ -53,9 +53,9 @@
359 @@ -57,9 +57,9 @@
348360 }
349361 }
350362
356368
357369 SBase sb = new SBase(cPtr, false);
358370 switch( sb.getTypeCode() )
359 --- a/src/bindings/csharp/local-packages-spatial.i
360 +++ b/src/bindings/csharp/local-packages-spatial.i
361 @@ -62,9 +62,9 @@ void SampledField::getUncompressed(int *
371 Index: libsbml/src/bindings/csharp/local-packages-spatial.i
372 ===================================================================
373 --- libsbml.orig/src/bindings/csharp/local-packages-spatial.i
374 +++ libsbml/src/bindings/csharp/local-packages-spatial.i
375 @@ -68,9 +68,9 @@ void SampledField::getUncompressed(int *
362376 */
363377 %typemap(cscode) SpatialExtension
364378 %{
370384
371385 SBasePlugin sbp = new SBasePlugin(cPtr, false);
372386 SBase sb = sbp.getParentSBMLObject();
373 @@ -96,9 +96,9 @@ void SampledField::getUncompressed(int *
387 @@ -102,9 +102,9 @@ void SampledField::getUncompressed(int *
374388 }
375389 }
376390
381395 + if (cPtr.Equals(global::System.IntPtr.Zero)) return null;
382396
383397 SBase sb = new SBase(cPtr, false);
384 switch( sb.getTypeCode() )
398 switch ( sb.getTypeCode() )