Codebase list libsbml / 93d32ee
Update patches Andreas Tille 3 years ago
3 changed file(s) with 96 addition(s) and 118 deletion(s). Raw diff Collapse all Expand all
+0
-21
debian/patches/fix_cmake_configuration.patch less more
0 Author: Andreas Tille <tille@debian.org>
1 Last-Update: Mon, 03 Dec 2018 16:11:35 +0100
2 Description: Desperately trying to fix CMake config by simply
3 commenting the line which causes an error
4
5 --- a/src/bindings/r/CMakeLists.txt
6 +++ b/src/bindings/r/CMakeLists.txt
7 @@ -336,7 +336,12 @@ configure_file (
8 "${CMAKE_CURRENT_BINARY_DIR}/libSBML/NAMESPACE"
9 )
10
11 -get_target_property(LIBSBML_R_NATIVELIB binding_r_lib LOCATION)
12 +# get_target_property(LIBSBML_R_NATIVELIB binding_r_lib LOCATION)
13 +# Commented since it leads to
14 +#CMake Error at src/bindings/r/CMakeLists.txt:339 (get_target_property):
15 +# The LOCATION property may not be read from target "binding_r_lib". Use the
16 +# target name directly with add_custom_command, or use the generator
17 +# expression $<TARGET_FILE>, as appropriate.
18
19 if (APPLE AND ENABLE_UNIVERSAL)
20
+0
-1
debian/patches/series less more
77 javadoc_java9.patch
88 javadoc.patch
99 remove_SBMLDoclet.patch
10 fix_cmake_configuration.patch
1110 fix_build_issue.patch
1211 fix_python_interpreter.patch
+96
-96
debian/patches/swig-3.x.patch less more
44
55 --- a/src/bindings/csharp/local.i
66 +++ b/src/bindings/csharp/local.i
7 @@ -121,13 +121,13 @@ static SWIG_CSharpWStringHelperCallback
7 @@ -129,13 +129,13 @@ static SWIG_CSharpWStringHelperCallback
88 %pragma(csharp) imclasscode=%{
99 protected class SWIGWStringHelper {
1010
2121 string ustr = System.Runtime.InteropServices.Marshal.PtrToStringUni(cString);
2222 return System.Runtime.InteropServices.Marshal.StringToHGlobalUni(ustr);
2323 }
24 @@ -207,15 +207,15 @@ SWIGEXPORT void SWIGSTDCALL SWIGRegister
24 @@ -215,15 +215,15 @@ SWIGEXPORT void SWIGSTDCALL SWIGRegister
2525 */
2626 %typemap(cscode) SBMLExtension
2727 %{
4141 return new SBase(cPtr, owner);
4242 }
4343 %}
44 @@ -228,9 +228,9 @@ SWIGEXPORT void SWIGSTDCALL SWIGRegister
44 @@ -236,9 +236,9 @@ SWIGEXPORT void SWIGSTDCALL SWIGRegister
4545 %pragma(csharp) modulecode =
4646 %{
4747
5353
5454 SBMLExtension ext = new SBMLExtension(cPtr, false);
5555 string pkgName = ext.getName();
56 @@ -241,9 +241,9 @@ SWIGEXPORT void SWIGSTDCALL SWIGRegister
56 @@ -249,9 +249,9 @@ SWIGEXPORT void SWIGSTDCALL SWIGRegister
5757 return new SBMLExtension(cPtr,owner);
5858 }
5959
6565
6666 SBMLNamespaces sbn = new SBMLNamespaces(cPtr, false);
6767 if (sbn != null)
68 @@ -293,9 +293,9 @@ SWIGEXPORT void SWIGSTDCALL SWIGRegister
68 @@ -301,9 +301,9 @@ SWIGEXPORT void SWIGSTDCALL SWIGRegister
6969 return new SBMLConverter(cPtr,owner);
7070 }
7171
7777
7878 SBasePlugin sbp = new SBasePlugin(cPtr, false);
7979 string pkgName = sbp.getPackageName();
80 @@ -310,9 +310,9 @@ SWIGEXPORT void SWIGSTDCALL SWIGRegister
80 @@ -318,9 +318,9 @@ SWIGEXPORT void SWIGSTDCALL SWIGRegister
8181 }
8282
8383
8989
9090 SBase sb = new SBase(cPtr, false);
9191 string pkgName = sb.getPackageName();
92 @@ -641,23 +641,23 @@ SWIGEXPORT void SWIGSTDCALL SWIGRegister
92 @@ -649,23 +649,23 @@ SWIGEXPORT void SWIGSTDCALL SWIGRegister
9393
9494 %typemap(csbody) TYPENAME
9595 %{
120120
121121 if (obj != null)
122122 {
123 @@ -674,22 +674,22 @@ SWIGEXPORT void SWIGSTDCALL SWIGRegister
123 @@ -682,22 +682,22 @@ SWIGEXPORT void SWIGSTDCALL SWIGRegister
124124
125125 %typemap(csbody_derived) TYPENAME
126126 %{
150150
151151 if (obj != null)
152152 {
153 @@ -705,22 +705,22 @@ SWIGEXPORT void SWIGSTDCALL SWIGRegister
153 @@ -713,22 +713,22 @@ SWIGEXPORT void SWIGSTDCALL SWIGRegister
154154
155155 %typemap(csbody_derived) TYPENAME
156156 %{
180180
181181 if (obj != null)
182182 {
183 @@ -985,10 +985,10 @@ COVARIANT_GETID(InitialAssignment)
183 @@ -993,10 +993,10 @@ COVARIANT_GETID(InitialAssignment)
184184 %typemap(csbase) SBMLConstructorException "System.ArgumentException";
185185 %typemap(cscode) SBMLConstructorException
186186 %{
193193 }
194194
195195 public SBMLConstructorException(string v) :
196 @@ -999,10 +999,10 @@ COVARIANT_GETID(InitialAssignment)
196 @@ -1007,10 +1007,10 @@ COVARIANT_GETID(InitialAssignment)
197197 %typemap(csbase) XMLConstructorException "System.ArgumentException";
198198 %typemap(cscode) XMLConstructorException
199199 %{
206206 }
207207
208208 public XMLConstructorException(string v) :
209 @@ -1041,7 +1041,7 @@ COVARIANT_GETID(InitialAssignment)
209 @@ -1049,7 +1049,7 @@ COVARIANT_GETID(InitialAssignment)
210210 static CustomExceptionDelegate customDelegate =
211211 new CustomExceptionDelegate(SetPendingCustomException);
212212
215215 public static extern
216216 void CustomExceptionRegisterCallback(CustomExceptionDelegate customCallback);
217217
218 @@ -1393,8 +1393,8 @@ XMLCONSTRUCTOR_EXCEPTION(XMLTripple)
218 @@ -1401,8 +1401,8 @@ XMLCONSTRUCTOR_EXCEPTION(XMLTripple)
219219 %typemap(cstype) List* _FNAME_ %{ _TYPENAME_ ## List %}
220220 %typemap(csout) List* _FNAME_
221221 {
228228 {
229229 --- a/src/bindings/csharp/local-packages-arrays.i
230230 +++ b/src/bindings/csharp/local-packages-arrays.i
231 @@ -43,9 +43,9 @@
231 @@ -48,9 +48,9 @@
232 */
233 %typemap(cscode) ArraysExtension
234 %{
235 - public override SBasePlugin DowncastSBasePlugin(IntPtr cPtr, bool owner)
236 + public override SBasePlugin DowncastSBasePlugin(global::System.IntPtr cPtr, bool owner)
237 {
238 - if (cPtr.Equals(IntPtr.Zero)) return null;
239 + if (cPtr.Equals(global::System.IntPtr.Zero)) return null;
240
241 SBasePlugin sbp = new SBasePlugin(cPtr, false);
242 SBase sb = sbp.getParentSBMLObject();
243 @@ -62,9 +62,9 @@
244 }
245 }
246
247 - public override SBase DowncastSBase(IntPtr cPtr, bool owner)
248 + public override SBase DowncastSBase(global::System.IntPtr cPtr, bool owner)
249 {
250 - if (cPtr.Equals(IntPtr.Zero)) return null;
251 + if (cPtr.Equals(global::System.IntPtr.Zero)) return null;
252
253 SBase sb = new SBase(cPtr, false);
254 switch( sb.getTypeCode() )
255 --- a/src/bindings/csharp/local-packages-groups.i
256 +++ b/src/bindings/csharp/local-packages-groups.i
257 @@ -45,9 +45,9 @@
258 */
259 %typemap(cscode) GroupsExtension
260 %{
261 - public override SBasePlugin DowncastSBasePlugin(IntPtr cPtr, bool owner)
262 + public override SBasePlugin DowncastSBasePlugin(global::System.IntPtr cPtr, bool owner)
263 {
264 - if (cPtr.Equals(IntPtr.Zero)) return null;
265 + if (cPtr.Equals(global::System.IntPtr.Zero)) return null;
266
267 SBasePlugin sbp = new SBasePlugin(cPtr, false);
268 SBase sb = sbp.getParentSBMLObject();
269 @@ -66,9 +66,9 @@
270 }
271 }
272
273 - public override SBase DowncastSBase(IntPtr cPtr, bool owner)
274 + public override SBase DowncastSBase(global::System.IntPtr cPtr, bool owner)
275 {
276 - if (cPtr.Equals(IntPtr.Zero)) return null;
277 + if (cPtr.Equals(global::System.IntPtr.Zero)) return null;
278
279 SBase sb = new SBase(cPtr, false);
280 switch( sb.getTypeCode() )
281 --- a/src/bindings/csharp/local-packages-layout.i
282 +++ b/src/bindings/csharp/local-packages-layout.i
283 @@ -38,9 +38,9 @@
232284 */
233 %typemap(cscode) ArraysExtension
285 %typemap(cscode) LayoutExtension
234286 %{
235287 - public override SBasePlugin DowncastSBasePlugin(IntPtr cPtr, bool owner)
236288 + public override SBasePlugin DowncastSBasePlugin(global::System.IntPtr cPtr, bool owner)
240292
241293 SBasePlugin sbp = new SBasePlugin(cPtr, false);
242294 SBase sb = sbp.getParentSBMLObject();
243 @@ -57,9 +57,9 @@
244 }
245 }
246
247 - public override SBase DowncastSBase(IntPtr cPtr, bool owner)
248 + public override SBase DowncastSBase(global::System.IntPtr cPtr, bool owner)
249 {
250 - if (cPtr.Equals(IntPtr.Zero)) return null;
251 + if (cPtr.Equals(global::System.IntPtr.Zero)) return null;
252
253 SBase sb = new SBase(cPtr, false);
254 switch( sb.getTypeCode() )
255 --- a/src/bindings/csharp/local-packages-groups.i
256 +++ b/src/bindings/csharp/local-packages-groups.i
257 @@ -40,9 +40,9 @@
258 */
259 %typemap(cscode) GroupsExtension
260 %{
261 - public override SBasePlugin DowncastSBasePlugin(IntPtr cPtr, bool owner)
262 + public override SBasePlugin DowncastSBasePlugin(global::System.IntPtr cPtr, bool owner)
263 {
264 - if (cPtr.Equals(IntPtr.Zero)) return null;
265 + if (cPtr.Equals(global::System.IntPtr.Zero)) return null;
266
267 SBasePlugin sbp = new SBasePlugin(cPtr, false);
268 SBase sb = sbp.getParentSBMLObject();
269 @@ -61,9 +61,9 @@
270 }
271 }
272
273 - public override SBase DowncastSBase(IntPtr cPtr, bool owner)
274 + public override SBase DowncastSBase(global::System.IntPtr cPtr, bool owner)
275 {
276 - if (cPtr.Equals(IntPtr.Zero)) return null;
277 + if (cPtr.Equals(global::System.IntPtr.Zero)) return null;
278
279 SBase sb = new SBase(cPtr, false);
280 switch( sb.getTypeCode() )
281 --- a/src/bindings/csharp/local-packages-layout.i
282 +++ b/src/bindings/csharp/local-packages-layout.i
283 @@ -33,9 +33,9 @@
284 */
285 %typemap(cscode) LayoutExtension
286 %{
287 - public override SBasePlugin DowncastSBasePlugin(IntPtr cPtr, bool owner)
288 + public override SBasePlugin DowncastSBasePlugin(global::System.IntPtr cPtr, bool owner)
289 {
290 - if (cPtr.Equals(IntPtr.Zero)) return null;
291 + if (cPtr.Equals(global::System.IntPtr.Zero)) return null;
292
293 SBasePlugin sbp = new SBasePlugin(cPtr, false);
294 SBase sb = sbp.getParentSBMLObject();
295 @@ -57,9 +57,9 @@
295 @@ -62,9 +62,9 @@
296296 }
297297 }
298298
306306 switch( sb.getTypeCode() )
307307 --- a/src/bindings/csharp/local-packages-render.i
308308 +++ b/src/bindings/csharp/local-packages-render.i
309 @@ -32,9 +32,9 @@ COVARIANT_RTYPE_FUNCTION(GradientBase, g
310 */
311 %typemap(cscode) RenderExtension
312 %{
313 - public override SBasePlugin DowncastSBasePlugin(IntPtr cPtr, bool owner)
314 + public override SBasePlugin DowncastSBasePlugin(global::System.IntPtr cPtr, bool owner)
315 {
316 - if (cPtr.Equals(IntPtr.Zero)) return null;
317 + if (cPtr.Equals(global::System.IntPtr.Zero)) return null;
318
319 SBasePlugin sbp = new SBasePlugin(cPtr, false);
320 SBase sb = sbp.getParentSBMLObject();
321 @@ -59,9 +59,9 @@ COVARIANT_RTYPE_FUNCTION(GradientBase, g
322 }
323 }
324
325 - public override SBase DowncastSBase(IntPtr cPtr, bool owner)
326 + public override SBase DowncastSBase(global::System.IntPtr cPtr, bool owner)
327 {
328 - if (cPtr.Equals(IntPtr.Zero)) return null;
329 + if (cPtr.Equals(global::System.IntPtr.Zero)) return null;
330
331 SBase sb = new SBase(cPtr, false);
332 switch( sb.getTypeCode() )
309 @@ -37,9 +37,9 @@ COVARIANT_RTYPE_FUNCTION(GradientBase, g
310 */
311 %typemap(cscode) RenderExtension
312 %{
313 - public override SBasePlugin DowncastSBasePlugin(IntPtr cPtr, bool owner)
314 + public override SBasePlugin DowncastSBasePlugin(global::System.IntPtr cPtr, bool owner)
315 {
316 - if (cPtr.Equals(IntPtr.Zero)) return null;
317 + if (cPtr.Equals(global::System.IntPtr.Zero)) return null;
318
319 SBasePlugin sbp = new SBasePlugin(cPtr, false);
320 SBase sb = sbp.getParentSBMLObject();
321 @@ -64,9 +64,9 @@ COVARIANT_RTYPE_FUNCTION(GradientBase, g
322 }
323 }
324
325 - public override SBase DowncastSBase(IntPtr cPtr, bool owner)
326 + public override SBase DowncastSBase(global::System.IntPtr cPtr, bool owner)
327 {
328 - if (cPtr.Equals(IntPtr.Zero)) return null;
329 + if (cPtr.Equals(global::System.IntPtr.Zero)) return null;
330
331 SBase sb = new SBase(cPtr, false);
332 switch( sb.getTypeCode() )
333333 --- a/src/bindings/csharp/local-packages-req.i
334334 +++ b/src/bindings/csharp/local-packages-req.i
335 @@ -42,9 +42,9 @@
335 @@ -47,9 +47,9 @@
336336 */
337337 %typemap(cscode) ReqExtension
338338 %{
344344
345345 SBasePlugin sbp = new SBasePlugin(cPtr, false);
346346 SBase sb = sbp.getParentSBMLObject();
347 @@ -57,9 +57,9 @@
347 @@ -62,9 +62,9 @@
348348 }
349349 }
350350
358358 switch( sb.getTypeCode() )
359359 --- a/src/bindings/csharp/local-packages-spatial.i
360360 +++ b/src/bindings/csharp/local-packages-spatial.i
361 @@ -68,9 +68,9 @@ void SampledField::getUncompressed(int *
361 @@ -73,9 +73,9 @@ void SampledField::getUncompressed(int *
362362 */
363363 %typemap(cscode) SpatialExtension
364364 %{
370370
371371 SBasePlugin sbp = new SBasePlugin(cPtr, false);
372372 SBase sb = sbp.getParentSBMLObject();
373 @@ -102,9 +102,9 @@ void SampledField::getUncompressed(int *
373 @@ -107,9 +107,9 @@ void SampledField::getUncompressed(int *
374374 }
375375 }
376376