Fix for new hdf5 and LD_LIBRARY_PATH

4 files changed, 341 insertions, 7 deletions

diff --git a/.SRCINFO b/.SRCINFO
index 3fe349bc9c8e..d2ca953b7e1f 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,8 +1,8 @@
 # Generated by mksrcinfo v8
-# Fri Jul 29 21:41:49 UTC 2016
+# Tue Aug  9 14:28:05 UTC 2016
 pkgbase = scilab-git
 	pkgdesc = A scientific software package for numerical computations
-	pkgver = 6.0.0.beta.2.r107.g742e0b0
+	pkgver = 6.0.0.beta.2.r122.g028d997
 	pkgrel = 1
 	url = https://www.scilab.org/
 	arch = i686
@@ -21,7 +21,7 @@ pkgbase = scilab-git
 	depends = libmatio
 	depends = tk
 	depends = curl
-	depends = hdf5_18
+	depends = hdf5
 	depends = java-runtime>=8
 	depends = beanshell2
 	depends = eclipse-ecj
@@ -47,10 +47,14 @@ pkgbase = scilab-git
 	source = git://git.scilab.org/scilab
 	source = scilab-git_strict-jar.patch
 	source = scilab-git_jogl.patch::http://gitweb.scilab.org/?p=scilab.git;a=patch;h=db79126ed25fc254e83f8a96b164cb2dbf0d6204
+	source = scilab-git-hdf5-1.8.10.patch
+	source = scilab-git_LD_LIBRARY_PATH.patch
 	source = scilab-git_java-default-dir.patch
 	sha256sums = SKIP
 	sha256sums = 38aa094951338fa1d267dc6f397552e175213b0f8ba7b35727c178607861f6dd
 	sha256sums = 7777f0e5fedb3f71f8869a20c448f139501caab17537786db37b999d5c76e618
+	sha256sums = 87e4c7b182755cf557a370820d880aaacfb4be2d3be6255f533668d8e677fd31
+	sha256sums = 37f649fea0196b255e5a8576dd1e8c5fd219c6e8c600b703b35303fb90b6a7e0
 	sha256sums = a2eb7888bf52862fdba300e113667ad4d3f95512dbf1a99b661eb54b68038948
 
 pkgname = scilab-git
diff --git a/PKGBUILD b/PKGBUILD
index d6bbeb843d28..01791a279ee3 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -2,7 +2,7 @@
 
 _pkgname=scilab
 pkgname=scilab-git
-pkgver=6.0.0.beta.2.r107.g742e0b0
+pkgver=6.0.0.beta.2.r122.g028d997
 pkgrel=1
 pkgdesc='A scientific software package for numerical computations'
 arch=('i686' 'x86_64')
@@ -11,7 +11,7 @@ license=('custom:CeCILL' 'BSD')
 makedepends=('apache-ant' 'git' 'ocaml' 'java-environment>=8' 'gcc-fortran')
 depends=('suitesparse>=4.4.1'  'arpack' 'fftw' 'eigen'
          'libmatio' 'tk' 'curl'
-         'hdf5_18'
+         'hdf5'
          'java-runtime>=8'
          'beanshell2' 'eclipse-ecj' 'java-flexdock>=1.2.4' 'fop-hyph'
          'java-freehep-vectorgraphics' 'jeuclid-core' 'jgraphx>=2.0.0.1' 'javahelp2'
@@ -23,11 +23,16 @@ conflicts=('scilab')
 source=("git://git.scilab.org/scilab"
         "${pkgname}_strict-jar.patch"
         "${pkgname}_jogl.patch::http://gitweb.scilab.org/?p=scilab.git;a=patch;h=db79126ed25fc254e83f8a96b164cb2dbf0d6204"
+        "${pkgname}-hdf5-1.8.10.patch"
+        "${pkgname}_LD_LIBRARY_PATH.patch"
         "${pkgname}_java-default-dir.patch")
 sha256sums=('SKIP'
             '38aa094951338fa1d267dc6f397552e175213b0f8ba7b35727c178607861f6dd'
             '7777f0e5fedb3f71f8869a20c448f139501caab17537786db37b999d5c76e618'
+            '87e4c7b182755cf557a370820d880aaacfb4be2d3be6255f533668d8e677fd31'
+            '37f649fea0196b255e5a8576dd1e8c5fd219c6e8c600b703b35303fb90b6a7e0'
             'a2eb7888bf52862fdba300e113667ad4d3f95512dbf1a99b661eb54b68038948')
+
 pkgver() {
   cd "${srcdir}/${_pkgname}/${_pkgname}"
 
@@ -43,6 +48,10 @@ prepare(){
   patch < "${srcdir}"/${pkgname}_strict-jar.patch
   # Fix path for Java
   patch -p1 < "${srcdir}"/${pkgname}_java-default-dir.patch
+  # http://bugzilla.scilab.org/show_bug.cgi?id=14539
+  patch -p1 < "${srcdir}"/${pkgname}-hdf5-1.8.10.patch
+  # Fix for LD_LIBRARY_PATH
+  patch bin/scilab "${srcdir}"/${pkgname}_LD_LIBRARY_PATH.patch
 }
 
 build() {
@@ -52,8 +61,6 @@ build() {
     --prefix=/usr \
     --with-gcc \
     --with-gfortran \
-    --with-hdf5-include=/usr/include/hdf5_18 \
-    --with-hdf5-library=/usr/lib/hdf5_18 \
     --with-jdk=/usr/lib/jvm/java-8-openjdk \
     --with-mpi \
     --with-matio \
diff --git a/scilab-git-hdf5-1.8.10.patch b/scilab-git-hdf5-1.8.10.patch
new file mode 100644
index 000000000000..f145896b84bc
--- /dev/null
+++ b/scilab-git-hdf5-1.8.10.patch
@@ -0,0 +1,312 @@
+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";
+--- scilab/modules/hdf5/sci_gateway/cpp/sci_hdf5_load_v3.cpp.old	2016-08-09 16:02:51.829103999 +0200
++++ scilab/modules/hdf5/sci_gateway/cpp/sci_hdf5_load_v3.cpp	2016-08-09 16:07:48.226497997 +0200
+@@ -638,7 +638,11 @@
+         //import field
+         for (int j = 0; j < refcount; ++j)
+         {
++#if H5_VERSION_GE(1,10,0)
++            int data = H5Rdereference(refs, H5P_DATASET_ACCESS_DEFAULT, H5R_OBJECT, &vrefs[j]);
++#else
+             int data = H5Rdereference(refs, H5R_OBJECT, &vrefs[j]);
++#endif
+             if (data < 0)
+             {
+                 freeStringMatrix(dfield, fields.data());
+--- scilab/modules/hdf5/sci_gateway/cpp/sci_hdf5_listvar_v3.cpp.old	2016-08-09 16:03:33.795871083 +0200
++++ scilab/modules/hdf5/sci_gateway/cpp/sci_hdf5_listvar_v3.cpp	2016-08-09 16:07:48.039830860 +0200
+@@ -706,7 +706,11 @@
+             //import field
+             for (int j = 0; j < refcount; ++j)
+             {
++#if H5_VERSION_GE(1,10,0)
++                int data = H5Rdereference(refs, H5P_DATASET_ACCESS_DEFAULT, H5R_OBJECT, &vrefs[j]);
++#else
+                 int data = H5Rdereference(refs, H5R_OBJECT, &vrefs[j]);
++#endif
+                 if (data < 0)
+                 {
+                     return false;
diff --git a/scilab-git_LD_LIBRARY_PATH.patch b/scilab-git_LD_LIBRARY_PATH.patch
new file mode 100644
index 000000000000..222dff3b8806
--- /dev/null
+++ b/scilab-git_LD_LIBRARY_PATH.patch
@@ -0,0 +1,11 @@
+--- bin/scilab	2016-08-09 15:08:31.708445393 +0200
++++ bin/scilab	2016-08-09 15:10:30.285575525 +0200
+@@ -808,7 +808,7 @@
+ if test -d $SCI/lib/thirdparty; then
+     SCILIB=$SCI/lib/thirdparty:$SCILIB;
+ fi
+-LD_LIBRARY_PATH=$SCILIB${LD_LIBRARY_PATH+:$LD_LIBRARY_PATH}
++LD_LIBRARY_PATH=$SCILIB${LD_LIBRARY_PATH+:$LD_LIBRARY_PATH}:/usr/lib/scilab
+ 
+ case $OS in
+     *darwin* | *Darwin*) # MacOS X