Package: src:scilab
Version: 5.5.2-2
Severity: important
Tags: patch
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Hi,
Please find attached a patch to support building against HDF5-1.10 currently in
experimental. This patch partly comes from upstream ticket #14539 [1].
[1] https://bugzilla.scilab.org/show_bug.cgi?id=14539
I intend to request a transition slot this week, and will upload if need be, as
member of the Debian Science team.
Thanks,
_g.
- -- System Information:
Debian Release: stretch/sid
APT prefers testing
APT policy: (500, 'testing')
Architecture: amd64 (x86_64)
Foreign Architectures: i386
Kernel: Linux 4.6.0-1-amd64 (SMP w/2 CPU cores)
Locale: LANG=fr_FR.UTF-8, LC_CTYPE=fr_FR.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
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diff -Nru scilab-5.5.2/debian/changelog scilab-5.5.2/debian/changelog
--- scilab-5.5.2/debian/changelog 2015-10-30 10:22:41.000000000 +0100
+++ scilab-5.5.2/debian/changelog 2016-10-22 15:54:38.000000000 +0200
@@ -1,3 +1,9 @@
+scilab (5.5.2-3) unstable; urgency=medium
+
+ * New patch to support HDF5-1.10
+
+ -- Gilles Filippini <p...@debian.org> Sat, 22 Oct 2016 15:54:20 +0200
+
scilab (5.5.2-2) unstable; urgency=medium
* Team upload.
diff -Nru scilab-5.5.2/debian/patches/hdf5-1.10-api.patch scilab-5.5.2/debian/patches/hdf5-1.10-api.patch
--- scilab-5.5.2/debian/patches/hdf5-1.10-api.patch 1970-01-01 01:00:00.000000000 +0100
+++ scilab-5.5.2/debian/patches/hdf5-1.10-api.patch 2016-10-24 21:14:57.000000000 +0200
@@ -0,0 +1,331 @@
+Index: scilab-5.5.2/m4/hdf5.m4
+===================================================================
+--- scilab-5.5.2.orig/m4/hdf5.m4
++++ scilab-5.5.2/m4/hdf5.m4
+@@ -65,6 +65,11 @@ if test "x$with_hdf5_library" != "xyes";
+ [AC_MSG_ERROR([libhdf5 or libhdf5_hl: library missing. (Cannot find symbol H5Fopen) in $with_hdf5_library. Check if libhdf5 is installed and if the version is correct])],
+ [-lz]
+ )
++ AC_CHECK_LIB([hdf5], [H5Rdereference2],
++ [FORCE_HDF_1_10_API="-DH5Rdereference_vers=2"],
++ [],
++ [-lz]
++ )
+ else
+ if $WITH_DEVTOOLS; then # Scilab thirparties
+ HDF5_LIBS="-L$DEVTOOLS_LIBDIR -lhdf5 -lhdf5_hl"
+@@ -93,6 +98,7 @@ LIBS="$save_LIBS"
+
+ AC_SUBST(HDF5_LIBS)
+ AC_SUBST(HDF5_CFLAGS)
++AC_SUBST(FORCE_HDF_1_10_API)
+
+ AC_DEFINE([WITH_HDF5], [], [With the HDF5 library])
+
+Index: scilab-5.5.2/modules/hdf5/Makefile.am
+===================================================================
+--- scilab-5.5.2.orig/modules/hdf5/Makefile.am
++++ scilab-5.5.2/modules/hdf5/Makefile.am
+@@ -86,6 +86,8 @@ FORCE_HDF_1.8_API = -DH5Dopen_vers=2 -D
+ -DH5Gcreate_vers=2 -DH5Gopen_vers=2 -DH5Tget_array_dims_vers=2 \
+ -DH5Acreate_vers=2 -DNO_DEPRECATED_SYMBOLS
+
++FORCE_HDF_1.10_API = @FORCE_HDF_1_10_API@
++
+ libscihdf5_la_CPPFLAGS = -I$(srcdir)/includes/ \
+ -I$(srcdir)/src/c/ \
+ -I$(srcdir)/src/cpp/ \
+@@ -98,7 +100,8 @@ libscihdf5_la_CPPFLAGS = -I$(srcdir)/inc
+ $(JAVA_JNI_INCLUDE) \
+ $(HDF5_CFLAGS) \
+ $(AM_CPPFLAGS) \
+- $(FORCE_HDF_1.8_API)
++ $(FORCE_HDF_1.8_API) \
++ $(FORCE_HDF_1.10_API)
+
+
+
+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";
diff -Nru scilab-5.5.2/debian/patches/series scilab-5.5.2/debian/patches/series
--- scilab-5.5.2/debian/patches/series 2015-10-18 22:53:53.000000000 +0200
+++ scilab-5.5.2/debian/patches/series 2016-10-24 21:08:16.000000000 +0200
@@ -11,3 +11,4 @@
jvm-archdir-ppc64le.diff
aarch64-detection.patch
libjogl2-java-2.3.2.diff
+hdf5-1.10-api.patch
