Fix compilation with recent hdf5

Also disable modelica as the compilation fails with it

3 files changed, 295 insertions, 9 deletions

diff --git a/.SRCINFO b/.SRCINFO
index 24ae7ff5c82f..48dd67057efb 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,9 +1,9 @@
 # Generated by mksrcinfo v8
-# Sat May 14 16:07:17 UTC 2016
+# Tue Aug  9 14:52:09 UTC 2016
 pkgbase = scilab
 	pkgdesc = A scientific software package for numerical computations.
 	pkgver = 5.5.2
-	pkgrel = 10
+	pkgrel = 11
 	url = https://www.scilab.org
 	arch = i686
 	arch = x86_64
@@ -16,7 +16,7 @@ pkgbase = scilab
 	depends = suitesparse>=4.4.1
 	depends = arpack
 	depends = fftw
-	depends = hdf5-1.8
+	depends = hdf5
 	depends = libmatio
 	depends = tk
 	depends = curl
@@ -46,12 +46,14 @@ pkgbase = scilab
 	source = https://www.scilab.org/download/5.5.2/scilab-5.5.2-src.tar.gz
 	source = scilab-5.5.2-batik-1.8.patch
 	source = scilab-5.5.2-fop-2.0.patch
+	source = scilab-5.5.2-hdf5-1.8.10.patch::http://bugzilla.scilab.org/attachment.cgi?id=4382
 	source = scilab-5.5.2-xmlgraphics-common-2.0.patch
 	source = scilab-5.5.2-strict-jar.patch
 	source = scilab-5.5.2-jogl.patch
 	sha256sums = a734519de96d35b8f081768a5584086e46db089ab11c021744897b22ec4d0f5e
 	sha256sums = 4f243e32be0aa2755405e121e7a23a370276c98e00d1b016bd43df56a76782ca
 	sha256sums = a8e03352cdaa5955414945e3fc8f56a035793869934345eef301cc6124b7ec95
+	sha256sums = ed8572b978ef7ad5d22b7f7346af139d771c7397cd0de2220e49621b59521bca
 	sha256sums = 64de4a044fb7228cae7003e6f86f6f0958ea10049f2fb24a11a07b0087e4ef36
 	sha256sums = cda2635f25a56f3c423f7a88791222aae3caad53c086cedc0cfe48011936a5a8
 	sha256sums = 1796919522e00f6f0a38677ba1b79498822a9e75a7e7da2c31ebaa935153d92e
diff --git a/PKGBUILD b/PKGBUILD
index 3838e95ec70e..ea9e8465860a 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -4,13 +4,13 @@
 
 pkgname=scilab
 pkgver=5.5.2
-pkgrel=10
+pkgrel=11
 pkgdesc='A scientific software package for numerical computations.'
 arch=('i686' 'x86_64')
 url='https://www.scilab.org'
 license=('BSD' 'custom:CeCILL')
 depends=('suitesparse>=4.4.1'  'arpack' 'fftw'
-         'hdf5-1.8'
+         'hdf5'
          'libmatio' 'tk' 'curl'
          'java-runtime=7'
          'beanshell2' 'eclipse-ecj' 'java-flexdock>=1.2.4' 'fop-hyph'
@@ -26,12 +26,14 @@ conflicts=('scilab-git' 'scilab-bin')
 source=("${url}/download/${pkgver}/${pkgname}-${pkgver}-src.tar.gz"
         "${pkgname}-${pkgver}-batik-1.8.patch"
         "${pkgname}-${pkgver}-fop-2.0.patch"
+        "${pkgname}-${pkgver}-hdf5-1.8.10.patch::http://bugzilla.scilab.org/attachment.cgi?id=4382"
         "${pkgname}-${pkgver}-xmlgraphics-common-2.0.patch"
         "${pkgname}-${pkgver}-strict-jar.patch"
         "${pkgname}-${pkgver}-jogl.patch")
 sha256sums=('a734519de96d35b8f081768a5584086e46db089ab11c021744897b22ec4d0f5e'
             '4f243e32be0aa2755405e121e7a23a370276c98e00d1b016bd43df56a76782ca'
             'a8e03352cdaa5955414945e3fc8f56a035793869934345eef301cc6124b7ec95'
+            'ed8572b978ef7ad5d22b7f7346af139d771c7397cd0de2220e49621b59521bca'
             '64de4a044fb7228cae7003e6f86f6f0958ea10049f2fb24a11a07b0087e4ef36'
             'cda2635f25a56f3c423f7a88791222aae3caad53c086cedc0cfe48011936a5a8'
             '1796919522e00f6f0a38677ba1b79498822a9e75a7e7da2c31ebaa935153d92e')
@@ -50,7 +52,7 @@ prepare(){
   # Linked to https://codereview.scilab.org/#/c/18089/
   patch < "${srcdir}"/${pkgname}-${pkgver}-strict-jar.patch
   # http://bugzilla.scilab.org/show_bug.cgi?id=14539
-  # hdf5-1.8
+  patch -p1 < "${srcdir}"/${pkgname}-${pkgver}-hdf5-1.8.10.patch
 }
 
 build() {
@@ -67,9 +69,7 @@ build() {
     --with-matio \
     --with-umfpack \
     --with-fftw \
-    --with-modelica \
-    --with-hdf5-include=/opt/hdf5-1.8/include \
-    --with-hdf5-library=/opt/hdf5-1.8/lib \
+    --without-modelica \
     --with-install-help-xml \
     --enable-build-help \
     --enable-build-localization \
diff --git a/scilab-5.5.2-hdf5-1.8.10.patch b/scilab-5.5.2-hdf5-1.8.10.patch
new file mode 100644
index 000000000000..ac51e90895d0
--- /dev/null
+++ b/scilab-5.5.2-hdf5-1.8.10.patch
@@ -0,0 +1,284 @@
+Index: scilab-5.5.2/modules/hdf5/src/c/h5_readDataFromFile.c

+===================================================================

+--- scilab-5.5.2.orig/modules/hdf5/src/c/h5_readDataFromFile.c

++++ scilab-5.5.2/modules/hdf5/src/c/h5_readDataFromFile.c

+@@ -716,7 +716,11 @@ int readCommonPolyMatrix(int _iDatasetId

+         /*

+          * Open the referenced object, get its name and type.

+          */

+-        obj = H5Rdereference(_iDatasetId, H5R_OBJECT, &pData[i]);

++        obj = H5Rdereference(_iDatasetId,

++    #if H5_VERSION_GE(1,10,0)

++                             H5P_DATASET_ACCESS_DEFAULT,

++    #endif

++                             H5R_OBJECT, &pData[i]);

+         if (_iComplex)

+         {

+             status = readComplexPoly(obj, &_piNbCoef[i], &_pdblReal[i], &_pdblImg[i]);

+@@ -950,7 +954,11 @@ int readCommonSparseComplexMatrix(int _i

+     }

+ 

+     //read Row data

+-    obj = H5Rdereference(_iDatasetId, H5R_OBJECT, &pRef[0]);

++    obj = H5Rdereference(_iDatasetId,

++#if H5_VERSION_GE(1,10,0)

++                         H5P_DATASET_ACCESS_DEFAULT,

++#endif

++                         H5R_OBJECT, &pRef[0]);

+     status = readInteger32Matrix(obj, _piNbItemRow);

+     if (status < 0)

+     {

+@@ -958,7 +966,11 @@ int readCommonSparseComplexMatrix(int _i

+     }

+ 

+     //read cols data

+-    obj = H5Rdereference(_iDatasetId, H5R_OBJECT, &pRef[1]);

++    obj = H5Rdereference(_iDatasetId,

++#if H5_VERSION_GE(1,10,0)

++                         H5P_DATASET_ACCESS_DEFAULT,

++#endif

++                         H5R_OBJECT, &pRef[1]);

+     status = readInteger32Matrix(obj, _piColPos);

+     if (status < 0)

+     {

+@@ -966,7 +978,11 @@ int readCommonSparseComplexMatrix(int _i

+     }

+ 

+     //read sparse data

+-    obj = H5Rdereference(_iDatasetId, H5R_OBJECT, &pRef[2]);

++    obj = H5Rdereference(_iDatasetId,

++#if H5_VERSION_GE(1,10,0)

++                         H5P_DATASET_ACCESS_DEFAULT,

++#endif

++                         H5R_OBJECT, &pRef[2]);

+ 

+     if (_iComplex)

+     {

+@@ -1017,7 +1033,11 @@ int readBooleanSparseMatrix(int _iDatase

+     }

+ 

+     //read Row data

+-    obj = H5Rdereference(_iDatasetId, H5R_OBJECT, &pRef[0]);

++    obj = H5Rdereference(_iDatasetId,

++#if H5_VERSION_GE(1,10,0)

++                         H5P_DATASET_ACCESS_DEFAULT,

++#endif

++                         H5R_OBJECT, &pRef[0]);

+     status = readInteger32Matrix(obj, _piNbItemRow);

+     if (status < 0)

+     {

+@@ -1027,7 +1047,11 @@ int readBooleanSparseMatrix(int _iDatase

+     if (_iNbItem != 0)

+     {

+         //read cols data

+-        obj = H5Rdereference(_iDatasetId, H5R_OBJECT, &pRef[1]);

++        obj = H5Rdereference(_iDatasetId,

++    #if H5_VERSION_GE(1,10,0)

++                             H5P_DATASET_ACCESS_DEFAULT,

++    #endif

++                             H5R_OBJECT, &pRef[1]);

+         status = readInteger32Matrix(obj, _piColPos);

+         if (status < 0)

+         {

+@@ -1132,7 +1156,11 @@ int getListItemDataset(int _iDatasetId,

+ {

+     hobj_ref_t poRef = ((hobj_ref_t *) _piItemRef)[_iItemPos];

+ 

+-    *_piItemDataset = H5Rdereference(_iDatasetId, H5R_OBJECT, &poRef);

++    *_piItemDataset = H5Rdereference(_iDatasetId,

++#if H5_VERSION_GE(1,10,0)

++                                     H5P_DATASET_ACCESS_DEFAULT,

++#endif

++                                     H5R_OBJECT, &poRef);

+ 

+     if (*_piItemDataset == 0)

+     {

+Index: scilab-5.5.2/modules/hdf5/src/c/h5_readDataFromFile_v1.c

+===================================================================

+--- scilab-5.5.2.orig/modules/hdf5/src/c/h5_readDataFromFile_v1.c

++++ scilab-5.5.2/modules/hdf5/src/c/h5_readDataFromFile_v1.c

+@@ -471,7 +471,11 @@ int readDoubleMatrix_v1(int _iDatasetId,

+         }

+ 

+         //Open the referenced object, get its name and type.

+-        obj = H5Rdereference(_iDatasetId, H5R_OBJECT, &Ref);

++        obj = H5Rdereference(_iDatasetId,

++    #if H5_VERSION_GE(1,10,0)

++                             H5P_DATASET_ACCESS_DEFAULT,

++    #endif

++                             H5R_OBJECT, &Ref);

+         readDouble_v1(obj, _iRows, _iCols, _pdblData);

+     }

+ 

+@@ -498,14 +502,22 @@ int readDoubleComplexMatrix_v1(int _iDat

+     }

+ 

+     //Open the referenced object, get its name and type.

+-    obj = H5Rdereference(_iDatasetId, H5R_OBJECT, &pRef[0]);

++    obj = H5Rdereference(_iDatasetId,

++#if H5_VERSION_GE(1,10,0)

++                         H5P_DATASET_ACCESS_DEFAULT,

++#endif

++                         H5R_OBJECT, &pRef[0]);

+     status = readDouble_v1(obj, _iRows, _iCols, _pdblReal);

+     if (status < 0)

+     {

+         return -1;

+     }

+ 

+-    obj = H5Rdereference(_iDatasetId, H5R_OBJECT, &pRef[1]);

++    obj = H5Rdereference(_iDatasetId,

++#if H5_VERSION_GE(1,10,0)

++                         H5P_DATASET_ACCESS_DEFAULT,

++#endif

++                         H5R_OBJECT, &pRef[1]);

+     status = readDouble_v1(obj, _iRows, _iCols, _pdblImg);

+     if (status < 0)

+     {

+@@ -831,7 +843,11 @@ int readCommonPolyMatrix_v1(int _iDatase

+         /*

+         * Open the referenced object, get its name and type.

+         */

+-        obj = H5Rdereference(_iDatasetId, H5R_OBJECT, &pData[i]);

++        obj = H5Rdereference(_iDatasetId,

++    #if H5_VERSION_GE(1,10,0)

++                             H5P_DATASET_ACCESS_DEFAULT,

++    #endif

++                             H5R_OBJECT, &pData[i]);

+         if (_iComplex)

+         {

+             status = readComplexPoly_v1(obj, &_piNbCoef[i], &_pdblReal[i], &_pdblImg[i]);

+@@ -1066,7 +1082,11 @@ int readCommonSparseComplexMatrix_v1(int

+     }

+ 

+     //read Row data

+-    obj = H5Rdereference(_iDatasetId, H5R_OBJECT, &pRef[0]);

++    obj = H5Rdereference(_iDatasetId,

++#if H5_VERSION_GE(1,10,0)

++                         H5P_DATASET_ACCESS_DEFAULT,

++#endif

++                         H5R_OBJECT, &pRef[0]);

+     status = readInteger32Matrix_v1(obj, 1, _iRows, _piNbItemRow);

+     if (status < 0)

+     {

+@@ -1074,7 +1094,11 @@ int readCommonSparseComplexMatrix_v1(int

+     }

+ 

+     //read cols data

+-    obj = H5Rdereference(_iDatasetId, H5R_OBJECT, &pRef[1]);

++    obj = H5Rdereference(_iDatasetId,

++#if H5_VERSION_GE(1,10,0)

++                         H5P_DATASET_ACCESS_DEFAULT,

++#endif

++                         H5R_OBJECT, &pRef[1]);

+     status = readInteger32Matrix_v1(obj, 1, _iNbItem, _piColPos);

+     if (status < 0)

+     {

+@@ -1082,7 +1106,11 @@ int readCommonSparseComplexMatrix_v1(int

+     }

+ 

+     //read sparse data

+-    obj = H5Rdereference(_iDatasetId, H5R_OBJECT, &pRef[2]);

++    obj = H5Rdereference(_iDatasetId,

++#if H5_VERSION_GE(1,10,0)

++                         H5P_DATASET_ACCESS_DEFAULT,

++#endif

++                         H5R_OBJECT, &pRef[2]);

+ 

+     if (_iComplex)

+     {

+@@ -1128,7 +1156,11 @@ int readBooleanSparseMatrix_v1(int _iDat

+     }

+ 

+     //read Row data

+-    obj = H5Rdereference(_iDatasetId, H5R_OBJECT, &pRef[0]);

++    obj = H5Rdereference(_iDatasetId,

++#if H5_VERSION_GE(1,10,0)

++                         H5P_DATASET_ACCESS_DEFAULT,

++#endif

++                         H5R_OBJECT, &pRef[0]);

+     status = readInteger32Matrix_v1(obj, 1, _iRows, _piNbItemRow);

+     if (status < 0)

+     {

+@@ -1136,7 +1168,11 @@ int readBooleanSparseMatrix_v1(int _iDat

+     }

+ 

+     //read cols data

+-    obj = H5Rdereference(_iDatasetId, H5R_OBJECT, &pRef[1]);

++    obj = H5Rdereference(_iDatasetId,

++#if H5_VERSION_GE(1,10,0)

++                         H5P_DATASET_ACCESS_DEFAULT,

++#endif

++                         H5R_OBJECT, &pRef[1]);

+     status = readInteger32Matrix_v1(obj, 1, _iNbItem, _piColPos);

+     if (status < 0)

+     {

+@@ -1235,7 +1271,11 @@ int getListItemDataset_v1(int _iDatasetI

+ {

+     hobj_ref_t poRef = ((hobj_ref_t *) _piItemRef)[_iItemPos];

+ 

+-    *_piItemDataset = H5Rdereference(_iDatasetId, H5R_OBJECT, &poRef);

++    *_piItemDataset = H5Rdereference(_iDatasetId,

++#if H5_VERSION_GE(1,10,0)

++                                     H5P_DATASET_ACCESS_DEFAULT,

++#endif

++                                     H5R_OBJECT, &poRef);

+ 

+     if (*_piItemDataset == 0)

+     {

+Index: scilab-5.5.2/modules/hdf5/src/cpp/H5ReferenceData.cpp

+===================================================================

+--- scilab-5.5.2.orig/modules/hdf5/src/cpp/H5ReferenceData.cpp

++++ scilab-5.5.2/modules/hdf5/src/cpp/H5ReferenceData.cpp

+@@ -39,7 +39,11 @@ const char ** H5ReferenceData::getRefere

+     for (int i = 0; i < totalSize; i++)

+     {

+         void * ref = &(((void **)cdata)[i]);

+-        hid_t obj = H5Rdereference(file, datasetReference ? H5R_DATASET_REGION : H5R_OBJECT, ref);

++        hid_t obj = H5Rdereference(file,

++    #if H5_VERSION_GE(1,10,0)

++                                   H5P_DATASET_ACCESS_DEFAULT,

++    #endif

++                                   datasetReference ? H5R_DATASET_REGION : H5R_OBJECT, ref);

+         H5O_info_t info;

+         H5Oget_info(obj, &info);

+         H5Oclose(obj);

+@@ -81,7 +85,11 @@ H5Object & H5ReferenceData::getData(cons

+ 

+     file = getFile().getH5Id();

+     ref = &(((void **)cdata)[0]);

+-    obj = H5Rdereference(file, datasetReference ? H5R_DATASET_REGION : H5R_OBJECT, ref);

++    obj = H5Rdereference(file,

++#if H5_VERSION_GE(1,10,0)

++                         H5P_DATASET_ACCESS_DEFAULT,

++#endif

++                         datasetReference ? H5R_DATASET_REGION : H5R_OBJECT, ref);

+     if (obj < 0)

+     {

+         throw H5Exception(__LINE__, __FILE__, _("Cannot open object at the given position."));

+@@ -123,7 +131,11 @@ H5Object ** H5ReferenceData::getReferenc

+     for (int i = 0; i < totalSize; i++)

+     {

+         void * ref = &(((void **)cdata)[i]);

+-        hid_t obj = H5Rdereference(file, datasetReference ? H5R_DATASET_REGION : H5R_OBJECT, ref);

++        hid_t obj = H5Rdereference(file,

++    #if H5_VERSION_GE(1,10,0)

++                                   H5P_DATASET_ACCESS_DEFAULT,

++    #endif

++                                   datasetReference ? H5R_DATASET_REGION : H5R_OBJECT, ref);

+         objs[i] = &H5Object::getObject(getParent(), obj);

+     }

+ 

+@@ -178,7 +190,11 @@ void H5ReferenceData::printData(std::ost

+     char * cdata = static_cast<char *>(data) + offset + pos * (stride ? stride : dataSize);

+     void ** ref = &(((void **)cdata)[0]);

+     hid_t file = getFile().getH5Id();

+-    hid_t obj = H5Rdereference(file, datasetReference ? H5R_DATASET_REGION : H5R_OBJECT, ref);

++    hid_t obj = H5Rdereference(file,

++#if H5_VERSION_GE(1,10,0)

++                               H5P_DATASET_ACCESS_DEFAULT,

++#endif

++                               datasetReference ? H5R_DATASET_REGION : H5R_OBJECT, ref);

+     if (obj < 0)

+     {

+         os << "NULL";
\ No newline at end of file