Author: tbooth-guest
Date: 2015-08-17 16:46:45 +0000 (Mon, 17 Aug 2015)
New Revision: 19970
Added:
trunk/packages/libsis-jhdf5-java/trunk/debian/libsis-jhdf5-jni.install
trunk/packages/libsis-jhdf5-java/trunk/debian/patches/load_native_debian.patch
Removed:
trunk/packages/libsis-jhdf5-java/trunk/debian/libsis-jhdf5.install
trunk/packages/libsis-jhdf5-java/trunk/debian/patches/fix_link_error.patch
trunk/packages/libsis-jhdf5-java/trunk/debian/patches/rename_jni_library.patch
trunk/packages/libsis-jhdf5-java/trunk/debian/patches/sort_exceptions.patch
Modified:
trunk/packages/libsis-jhdf5-java/trunk/debian/changelog
trunk/packages/libsis-jhdf5-java/trunk/debian/control
trunk/packages/libsis-jhdf5-java/trunk/debian/patches/series
trunk/packages/libsis-jhdf5-java/trunk/debian/rules
Log:
I'm not sure if this is an improvement or not. It compiles, links and
runs the tests (or at least a subset) but there are failures. Also,
I'm not running all of the tests just now. Olivier was running more.
One test failure is an OutOfMemoryError that just seems to happen
whatever you set the memory size to in the JVM. Tried with hdf5 from
both Sid and Experimental.
Modified: trunk/packages/libsis-jhdf5-java/trunk/debian/changelog
===================================================================
--- trunk/packages/libsis-jhdf5-java/trunk/debian/changelog 2015-08-17
12:13:53 UTC (rev 19969)
+++ trunk/packages/libsis-jhdf5-java/trunk/debian/changelog 2015-08-17
16:46:45 UTC (rev 19970)
@@ -1,8 +1,5 @@
libsis-jhdf5-java (14.12.1-1) UNRELEASED; urgency=medium
- This build is totally broken. If you attempt to make it work without
reading
- the README.source you are wasting your time.
-
* [ Team upload ]
First package
Modified: trunk/packages/libsis-jhdf5-java/trunk/debian/control
===================================================================
--- trunk/packages/libsis-jhdf5-java/trunk/debian/control 2015-08-17
12:13:53 UTC (rev 19969)
+++ trunk/packages/libsis-jhdf5-java/trunk/debian/control 2015-08-17
16:46:45 UTC (rev 19970)
@@ -6,27 +6,27 @@
libcommons-lang-java,
libcommons-io-java,
libsis-base-java,
- libjhdf5-jni ( >> 2.9-3 ),
+ libhdf5-dev ( >> 1.8.13),
libhdf5-dev,
- junit4, testng, libjmock-java
+ junit4,
+ testng
+# libjmock-java
Standards-Version: 3.9.6
Homepage:
http://svncisd.ethz.ch/repos/cisd/jhdf5/tags/release/14.12.x/14.12.1/jhdf5
Vcs-Svn:
svn://anonscm.debian.org/debian-med/trunk/packages/libsis-jhdf5-java/trunk/
Vcs-Browser:
http://anonscm.debian.org/viewvc/debian-med/trunk/packages/libsis-jhdf5-java/trunk/
-
Package: libsis-jhdf5-java
-Architecture: any
-Depends: ${misc:Depends}, ${java:Depends}, libjhdf5-jni, libsis-jhdf5
+Architecture: all
+Depends: ${misc:Depends}, ${java:Depends}, libsis-jhdf5-jni (=
${binary:Version})
Description: easy-to-use HDF library for Java
JHDF5 is a Java binding to the HDF Group library for HDF5 focusing on
ease-of-use, which was developed by CISD and is now maintained by ETH SIS.
The library uses HDF5 1.8 from the HDF Group and files created with
JHDF5 are fully compatible with HDF5 1.6/1.8 (as you choose).
-Package: libsis-jhdf5
-Section: libs
+Package: libsis-jhdf5-jni
Architecture: any
Depends: ${misc:Depends}, ${shlibs:Depends}
-Description: native libs used by libsis-jhdf5-java
- bla bla bla
+Description: native libs used by libsis-jhdf5-java package
+ This package is only useful with libsis-jhdf5-java.
Added: trunk/packages/libsis-jhdf5-java/trunk/debian/libsis-jhdf5-jni.install
===================================================================
--- trunk/packages/libsis-jhdf5-java/trunk/debian/libsis-jhdf5-jni.install
(rev 0)
+++ trunk/packages/libsis-jhdf5-java/trunk/debian/libsis-jhdf5-jni.install
2015-08-17 16:46:45 UTC (rev 19970)
@@ -0,0 +1 @@
+libsis_jhdf5.so /usr/lib/jni
Deleted: trunk/packages/libsis-jhdf5-java/trunk/debian/libsis-jhdf5.install
===================================================================
--- trunk/packages/libsis-jhdf5-java/trunk/debian/libsis-jhdf5.install
2015-08-17 12:13:53 UTC (rev 19969)
+++ trunk/packages/libsis-jhdf5-java/trunk/debian/libsis-jhdf5.install
2015-08-17 16:46:45 UTC (rev 19970)
@@ -1,3 +0,0 @@
-source/c/hdf-java/.libs/lib*.so.* usr/lib/sis-jhdf5/
-source/c/jhdf5/.libs/lib*.so.* usr/lib/sis-jhdf5/
-
Deleted:
trunk/packages/libsis-jhdf5-java/trunk/debian/patches/fix_link_error.patch
===================================================================
--- trunk/packages/libsis-jhdf5-java/trunk/debian/patches/fix_link_error.patch
2015-08-17 12:13:53 UTC (rev 19969)
+++ trunk/packages/libsis-jhdf5-java/trunk/debian/patches/fix_link_error.patch
2015-08-17 16:46:45 UTC (rev 19970)
@@ -1,52 +0,0 @@
---- a/source/java/ch/systemsx/cisd/hdf5/hdf5lib/H5.java
-+++ b/source/java/ch/systemsx/cisd/hdf5/hdf5lib/H5.java
-@@ -14,9 +14,11 @@
- import ncsa.hdf.hdf5lib.exceptions.HDF5Exception;
- import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException;
- import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException;
-+import ncsa.hdf.hdf5lib.H5.*;
-
- import ch.systemsx.cisd.base.utilities.NativeLibraryUtilities;
-
-+
- /**
- * The low-level C function wrappers. These functions are <i>not</i>
thread-safe and need to be used
- * through thread-safe wrappers.
-@@ -159,7 +161,7 @@
- * @return a non-negative value if successful
- * @exception HDF5LibraryException - Error from the HDF-5 Library.
- */
-- private static native int H5dont_atexit() throws HDF5LibraryException;
-+ public static native int H5dont_atexit() throws HDF5LibraryException;
-
- /**
- * H5get_libversion retrieves the major, minor, and release numbers of
the version of the HDF
-@@ -1946,7 +1948,7 @@
- // //
- // ////////////////////////////////////////////////////////////
-
-- private static native int H5Rcreate(byte[] ref, int loc_id, String name,
int ref_type,
-+ public static native int H5Rcreate(byte[] ref, int loc_id, String name,
int ref_type,
- int space_id) throws HDF5LibraryException, NullPointerException,
- IllegalArgumentException;
-
---- a/source/java/ncsa/hdf/hdf5lib/H5.java
-+++ b/source/java/ncsa/hdf/hdf5lib/H5.java
-@@ -356,7 +356,7 @@
- * @exception HDF5LibraryException
- * - Error from the HDF-5 Library.
- **/
--private synchronized static native int H5dont_atexit()
-+public synchronized static native int H5dont_atexit()
- throws HDF5LibraryException;
-
- /**
-@@ -6861,7 +6861,7 @@
- ////
- //////////////////////////////////////////////////////////////
-
--private synchronized static native int H5Rcreate(byte[] ref, int loc_id,
-+public synchronized static native int H5Rcreate(byte[] ref, int loc_id,
- String name, int ref_type, int space_id)
- throws HDF5LibraryException, NullPointerException,
IllegalArgumentException;
-
Added:
trunk/packages/libsis-jhdf5-java/trunk/debian/patches/load_native_debian.patch
===================================================================
---
trunk/packages/libsis-jhdf5-java/trunk/debian/patches/load_native_debian.patch
(rev 0)
+++
trunk/packages/libsis-jhdf5-java/trunk/debian/patches/load_native_debian.patch
2015-08-17 16:46:45 UTC (rev 19970)
@@ -0,0 +1,20 @@
+There is already a libjhdf5.so on the system. This is an incompatible fork.
+Since the .so is tightly bound to the Java library there seems no harm in
simply
+renaming this one; nothing outside this package should want to link to it.
+
+Also, skip the library loader utility class since it doesn't help us. Note
that
+on modern java, multiple calls to System.loadLibrary() are idempotent too.
+--- a/source/java/ch/systemsx/cisd/hdf5/hdf5lib/H5.java
++++ b/source/java/ch/systemsx/cisd/hdf5/hdf5lib/H5.java
+@@ -36,10 +36,7 @@
+
+ static
+ {
+- if (NativeLibraryUtilities.loadNativeLibrary("jhdf5") == false)
+- {
+- throw new UnsupportedOperationException("No suitable HDF5 native
library found for this platform.");
+- }
++ System.loadLibrary("sis-jhdf5");
+
+ // Important! Exit quietly
+ try
Deleted:
trunk/packages/libsis-jhdf5-java/trunk/debian/patches/rename_jni_library.patch
===================================================================
---
trunk/packages/libsis-jhdf5-java/trunk/debian/patches/rename_jni_library.patch
2015-08-17 12:13:53 UTC (rev 19969)
+++
trunk/packages/libsis-jhdf5-java/trunk/debian/patches/rename_jni_library.patch
2015-08-17 16:46:45 UTC (rev 19970)
@@ -1,14 +0,0 @@
-There is already a libjhdf5.so on the system. This is an incompatible fork.
-Since the .so is tightly bound to the Java library there seems no harm in
simply
-renaming this one; nothing outside this package should want to link to it.
---- a/source/java/ch/systemsx/cisd/hdf5/hdf5lib/H5.java
-+++ b/source/java/ch/systemsx/cisd/hdf5/hdf5lib/H5.java
-@@ -36,7 +36,7 @@
-
- static
- {
-- if (NativeLibraryUtilities.loadNativeLibrary("jhdf5") == false)
-+ if (NativeLibraryUtilities.loadNativeLibrary("sis-jhdf5") == false)
- {
- throw new UnsupportedOperationException("No suitable HDF5 native
library found for this platform.");
- }
Modified: trunk/packages/libsis-jhdf5-java/trunk/debian/patches/series
===================================================================
--- trunk/packages/libsis-jhdf5-java/trunk/debian/patches/series
2015-08-17 12:13:53 UTC (rev 19969)
+++ trunk/packages/libsis-jhdf5-java/trunk/debian/patches/series
2015-08-17 16:46:45 UTC (rev 19970)
@@ -1,3 +1,3 @@
fix_dodgy_cast.patch
remove_ch_rinn_imports.patch
-rename_jni_library.patch
+load_native_debian.patch
Deleted:
trunk/packages/libsis-jhdf5-java/trunk/debian/patches/sort_exceptions.patch
===================================================================
--- trunk/packages/libsis-jhdf5-java/trunk/debian/patches/sort_exceptions.patch
2015-08-17 12:13:53 UTC (rev 19969)
+++ trunk/packages/libsis-jhdf5-java/trunk/debian/patches/sort_exceptions.patch
2015-08-17 16:46:45 UTC (rev 19970)
@@ -1,364 +0,0 @@
-This is my initial attempt to get the code to compile against
/usr/share/java/jhdf5.jar that is
-in /usr/share/java/jhdf5.jar, but I realised the amount of pacthing was
getting silly.
-
-I'm leaving this partial patch in the package for info.
-
-Index: sis-jhdf5-14.12.1/ch/systemsx/cisd/hdf5/HDF5Utils.java
-===================================================================
---- sis-jhdf5-14.12.1.orig/source/java/ch/systemsx/cisd/hdf5/HDF5Utils.java
2015-08-10 17:27:59.874762864 +0100
-+++ sis-jhdf5-14.12.1/source/java/ch/systemsx/cisd/hdf5/HDF5Utils.java
2015-08-10 17:27:59.866762864 +0100
-@@ -344,7 +344,7 @@
- *
- * @throws HDF5JavaException If <var>dimensions</var> do not define a
one-dimensional array.
- */
-- static int getOneDimensionalArraySize(final int[] dimensions)
-+ static int getOneDimensionalArraySize(final int[] dimensions) throws
HDF5JavaException
- {
- assert dimensions != null;
-
-@@ -366,7 +366,7 @@
- * @throws HDF5JavaException If <var>dimensions</var> do not define a
one-dimensional array or
- * if <code>dimensions[0]</code> overflows the
<code>int</code> type.
- */
-- static int getOneDimensionalArraySize(final long[] dimensions)
-+ static int getOneDimensionalArraySize(final long[] dimensions) throws
HDF5JavaException
- {
- assert dimensions != null;
-
-Index: sis-jhdf5-14.12.1/ch/systemsx/cisd/hdf5/HDF5BaseReader.java
-===================================================================
---- sis-jhdf5-14.12.1.orig/ch/systemsx/cisd/hdf5/HDF5BaseReader.java
2015-08-10 17:27:59.874762864 +0100
-+++ sis-jhdf5-14.12.1/ch/systemsx/cisd/hdf5/HDF5BaseReader.java
2015-08-10 17:48:16.774795452 +0100
-@@ -114,7 +114,7 @@
- final CharacterEncoding encodingForNewDataSets;
-
- HDF5BaseReader(File hdf5File, boolean performNumericConversions, boolean
autoDereference,
-- FileFormat fileFormat, boolean overwrite, String
preferredHouseKeepingNameSuffix)
-+ FileFormat fileFormat, boolean overwrite, String
preferredHouseKeepingNameSuffix) throws HDF5FileNotFoundException
- {
- this(hdf5File, performNumericConversions, false, autoDereference,
fileFormat, overwrite,
- preferredHouseKeepingNameSuffix);
-@@ -122,7 +122,7 @@
-
- HDF5BaseReader(File hdf5File, boolean performNumericConversions, boolean
useUTF8CharEncoding,
- boolean autoDereference, FileFormat fileFormat, boolean overwrite,
-- String preferredHouseKeepingNameSuffix)
-+ String preferredHouseKeepingNameSuffix) throws
HDF5FileNotFoundException
- {
- assert hdf5File != null;
- assert preferredHouseKeepingNameSuffix != null;
-@@ -176,7 +176,7 @@
- }
- }
-
-- int openFile(FileFormat fileFormat, boolean overwrite)
-+ int openFile(FileFormat fileFormat, boolean overwrite) throws
HDF5FileNotFoundException
- {
- if (hdf5File.exists() == false)
- {
-@@ -465,7 +465,7 @@
- * <code>nullWhenOutside == true</code>.
- */
- DataSpaceParameters tryGetSpaceParameters(final int dataSetId, final long
offset,
-- final int blockSize, boolean nullWhenOutside, ICleanUpRegistry
registry)
-+ final int blockSize, boolean nullWhenOutside, ICleanUpRegistry
registry) throws HDF5JavaException
- {
- return tryGetSpaceParameters(dataSetId, 0, offset, blockSize,
nullWhenOutside, registry);
- }
-@@ -474,7 +474,7 @@
- * Returns the {@link DataSpaceParameters} for a 1d block of the given
<var>dataSetId</var>.
- */
- DataSpaceParameters getSpaceParameters(final int dataSetId, final long
offset,
-- final int blockSize, ICleanUpRegistry registry)
-+ final int blockSize, ICleanUpRegistry registry) throws
HDF5JavaException
- {
- return tryGetSpaceParameters(dataSetId, 0, offset, blockSize, false,
registry);
- }
-@@ -483,7 +483,7 @@
- * Returns the {@link DataSpaceParameters} for a 1d block of the given
<var>dataSetId</var>.
- */
- DataSpaceParameters getSpaceParameters(final int dataSetId, final long
memoryOffset,
-- final long offset, final int blockSize, ICleanUpRegistry registry)
-+ final long offset, final int blockSize, ICleanUpRegistry
registry) throws HDF5JavaException
- {
- return tryGetSpaceParameters(dataSetId, memoryOffset, offset,
blockSize, false, registry);
- }
-@@ -493,7 +493,7 @@
- */
- DataSpaceParameters tryGetSpaceParameters(final int dataSetId, final long
memoryOffset,
- final long offset, final int blockSize, boolean nullWhenOutside,
-- ICleanUpRegistry registry)
-+ ICleanUpRegistry registry) throws HDF5JavaException
- {
- final int memorySpaceId;
- final int dataSpaceId;
-@@ -551,7 +551,7 @@
- * <var>dataSetId</var>.
- */
- DataSpaceParameters getSpaceParameters(final int dataSetId, final long[]
offset,
-- final int[] blockDimensionsOrNull, ICleanUpRegistry registry)
-+ final int[] blockDimensionsOrNull, ICleanUpRegistry registry)
throws HDF5JavaException
- {
- return tryGetSpaceParameters(dataSetId, offset,
blockDimensionsOrNull, false, registry);
- }
-@@ -561,7 +561,7 @@
- * <var>dataSetId</var>.
- */
- DataSpaceParameters tryGetSpaceParameters(final int dataSetId, final
long[] offset,
-- final int[] blockDimensionsOrNull, boolean nullWhenOutside,
ICleanUpRegistry registry)
-+ final int[] blockDimensionsOrNull, boolean nullWhenOutside,
ICleanUpRegistry registry) throws HDF5JavaException
- {
- final int memorySpaceId;
- final int dataSpaceId;
-@@ -610,7 +610,7 @@
- * mapped to a block in memory.
- */
- DataSpaceParameters getBlockSpaceParameters(final int dataSetId, final
int[] memoryOffset,
-- final int[] memoryDimensions, ICleanUpRegistry registry)
-+ final int[] memoryDimensions, ICleanUpRegistry registry) throws
HDF5JavaException
- {
- return tryGetBlockSpaceParameters(dataSetId, memoryOffset,
memoryDimensions, false,
- registry);
-@@ -621,7 +621,7 @@
- * mapped to a block in memory.
- */
- DataSpaceParameters tryGetBlockSpaceParameters(final int dataSetId, final
int[] memoryOffset,
-- final int[] memoryDimensions, final boolean nullWhenOutside,
ICleanUpRegistry registry)
-+ final int[] memoryDimensions, final boolean nullWhenOutside,
ICleanUpRegistry registry) throws HDF5JavaException
- {
- assert memoryOffset != null;
- assert memoryDimensions != null;
-@@ -653,7 +653,7 @@
- */
- DataSpaceParameters getBlockSpaceParameters(final int dataSetId, final
int[] memoryOffset,
- final int[] memoryDimensions, final long[] offset, final int[]
blockDimensions,
-- ICleanUpRegistry registry)
-+ ICleanUpRegistry registry) throws HDF5JavaException
- {
- return tryGetBlockSpaceParameters(dataSetId, memoryOffset,
memoryDimensions, offset,
- blockDimensions, false, registry);
-@@ -665,7 +665,7 @@
- */
- DataSpaceParameters tryGetBlockSpaceParameters(final int dataSetId, final
int[] memoryOffset,
- final int[] memoryDimensions, final long[] offset, final int[]
blockDimensions,
-- final boolean nullWhenOutside, ICleanUpRegistry registry)
-+ final boolean nullWhenOutside, ICleanUpRegistry registry) throws
HDF5JavaException
- {
- assert memoryOffset != null;
- assert memoryDimensions != null;
-@@ -790,7 +790,7 @@
- * @param dataSetPath The name (including path information) of the data
set to return
- * information about.
- */
-- HDF5DataSetInformation getDataSetInformation(final String dataSetPath)
-+ HDF5DataSetInformation getDataSetInformation(final String dataSetPath)
throws HDF5JavaException
- {
- return getDataSetInformation(dataSetPath,
DataTypeInfoOptions.DEFAULT, true);
- }
-@@ -806,7 +806,7 @@
- * @param fillDimensions If <code>true</code>, fill in the dimensions of
the dataset
- */
- HDF5DataSetInformation getDataSetInformation(final String dataSetPath,
-- final DataTypeInfoOptions options, final boolean fillDimensions)
-+ final DataTypeInfoOptions options, final boolean fillDimensions)
throws HDF5JavaException
- {
- assert dataSetPath != null;
-
-@@ -814,7 +814,7 @@
- new ICallableWithCleanUp<HDF5DataSetInformation>()
- {
- @Override
-- public HDF5DataSetInformation call(ICleanUpRegistry
registry)
-+ public HDF5DataSetInformation call(ICleanUpRegistry
registry) throws HDF5JavaException
- {
- final int dataSetId = h5.openDataSet(fileId,
dataSetPath, registry);
- final int dataTypeId =
h5.getDataTypeForDataSet(dataSetId, registry);
-@@ -872,7 +872,7 @@
- * the array rank into one rank. It is a failure condition if the
<var>objectPath</var> does not
- * exist or does not identify a data set. This method follows symbolic
links.
- */
-- int getRank(String dataSetPath)
-+ int getRank(String dataSetPath) throws HDF5JavaException
- {
- final HDF5DataSetInformation info =
- getDataSetInformation(dataSetPath,
DataTypeInfoOptions.MINIMAL, true);
-@@ -885,7 +885,7 @@
- * space). It is a failure condition if the <var>objectPath</var> does
not exist or does not
- * identify a data set. This method follows symbolic links.
- */
-- long[] getDimensions(String dataSetPath)
-+ long[] getDimensions(String dataSetPath) throws HDF5JavaException
- {
- assert dataSetPath != null;
-
-@@ -918,7 +918,7 @@
- return runner.call(informationDeterminationRunnable);
- }
-
-- HDF5DataTypeVariant tryGetTypeVariant(final String objectPath)
-+ HDF5DataTypeVariant tryGetTypeVariant(final String objectPath) throws
HDF5JavaException
- {
- assert objectPath != null;
-
-@@ -926,7 +926,7 @@
- new ICallableWithCleanUp<HDF5DataTypeVariant>()
- {
- @Override
-- public HDF5DataTypeVariant call(ICleanUpRegistry
registry)
-+ public HDF5DataTypeVariant call(ICleanUpRegistry
registry) throws HDF5JavaException
- {
- final int objectId = h5.openObject(fileId,
objectPath, registry);
- return tryGetTypeVariant(objectId, registry);
-@@ -936,7 +936,7 @@
- return runner.call(readRunnable);
- }
-
-- HDF5DataTypeVariant tryGetTypeVariant(final String objectPath, final
String attributeName)
-+ HDF5DataTypeVariant tryGetTypeVariant(final String objectPath, final
String attributeName) throws HDF5JavaException
- {
- assert objectPath != null;
-
-@@ -944,7 +944,7 @@
- new ICallableWithCleanUp<HDF5DataTypeVariant>()
- {
- @Override
-- public HDF5DataTypeVariant call(ICleanUpRegistry
registry)
-+ public HDF5DataTypeVariant call(ICleanUpRegistry
registry) throws HDF5JavaException
- {
- final int objectId = h5.openObject(fileId,
objectPath, registry);
- return tryGetTypeVariant(objectId, attributeName,
registry);
-@@ -955,7 +955,7 @@
- }
-
- HDF5EnumerationValueArray getEnumValueArray(final int attributeId, final
String objectPath,
-- final String attributeName, ICleanUpRegistry registry)
-+ final String attributeName, ICleanUpRegistry registry) throws
HDF5JavaException
- {
- final int storageDataTypeId = h5.getDataTypeForAttribute(attributeId,
registry);
- final int nativeDataTypeId = h5.getNativeDataType(storageDataTypeId,
registry);
-@@ -1000,7 +1000,7 @@
- }
-
- HDF5EnumerationValueMDArray getEnumValueMDArray(final int attributeId,
final String objectPath,
-- final String attributeName, ICleanUpRegistry registry)
-+ final String attributeName, ICleanUpRegistry registry) throws
HDF5JavaException
- {
- final int storageDataTypeId = h5.getDataTypeForAttribute(attributeId,
registry);
- final int nativeDataTypeId = h5.getNativeDataType(storageDataTypeId,
registry);
-@@ -1054,7 +1054,7 @@
- }
-
- HDF5DataTypeVariant[] tryGetTypeVariantForCompoundMembers(String
dataTypePathOrNull,
-- ICleanUpRegistry registry)
-+ ICleanUpRegistry registry) throws HDF5JavaException
- {
- if (dataTypePathOrNull == null)
- {
-@@ -1089,14 +1089,14 @@
- }
- }
-
-- HDF5DataTypeVariant tryGetTypeVariant(final int objectId,
ICleanUpRegistry registry)
-+ HDF5DataTypeVariant tryGetTypeVariant(final int objectId,
ICleanUpRegistry registry) throws HDF5JavaException
- {
- final int typeVariantOrdinal = getAttributeTypeVariant(objectId,
registry);
- return typeVariantOrdinal < 0 ? null :
HDF5DataTypeVariant.values()[typeVariantOrdinal];
- }
-
- HDF5DataTypeVariant tryGetTypeVariant(final int objectId, String
attributeName,
-- ICleanUpRegistry registry)
-+ ICleanUpRegistry registry) throws HDF5JavaException
- {
- final int typeVariantOrdinal = getAttributeTypeVariant(objectId,
attributeName, registry);
- return typeVariantOrdinal < 0 ? null :
HDF5DataTypeVariant.values()[typeVariantOrdinal];
-@@ -1109,7 +1109,7 @@
- * @param objectId The id of the data set object in the file.
- * @return The ordinal of the type variant or <code>null</code>.
- */
-- int getAttributeTypeVariant(final int objectId, ICleanUpRegistry registry)
-+ int getAttributeTypeVariant(final int objectId, ICleanUpRegistry
registry) throws HDF5JavaException
- {
- checkOpen();
- final String dataTypeVariantAttributeName =
-@@ -1130,7 +1130,7 @@
- * @param attributeName The name of the attribute to get the type variant
for.
- * @return The ordinal of the type variant or <code>null</code>.
- */
-- int getAttributeTypeVariant(final int objectId, String attributeName,
ICleanUpRegistry registry)
-+ int getAttributeTypeVariant(final int objectId, String attributeName,
ICleanUpRegistry registry) throws HDF5JavaException
- {
- checkOpen();
- final String typeVariantAttrName =
-@@ -1380,7 +1380,7 @@
-
- HDF5EnumerationType getEnumTypeForStorageDataType(final String nameOrNull,
- final int storageDataTypeId, final boolean resolveName, final
String objectPathOrNull,
-- final String attributeNameOrNull, final ICleanUpRegistry registry)
-+ final String attributeNameOrNull, final ICleanUpRegistry
registry) throws HDF5JavaException
- {
- int classType = h5.getClassType(storageDataTypeId);
- final boolean isArray = (classType == H5T_ARRAY);
-@@ -1423,7 +1423,7 @@
- values, this);
- }
-
-- void checkEnumValues(int dataTypeId, final String[] values, final String
nameOrNull)
-+ void checkEnumValues(int dataTypeId, final String[] values, final String
nameOrNull) throws HDF5JavaException
- {
- final String[] valuesStored =
h5.getNamesForEnumOrCompoundMembers(dataTypeId);
- if (valuesStored.length != values.length)
-@@ -1462,13 +1462,13 @@
- }
- }
-
-- boolean isScaledEnum(final int objectId, final ICleanUpRegistry registry)
-+ boolean isScaledEnum(final int objectId, final ICleanUpRegistry registry)
throws HDF5JavaException
- {
- final HDF5DataTypeVariant typeVariantOrNull =
tryGetTypeVariant(objectId, registry);
- return (HDF5DataTypeVariant.ENUM == typeVariantOrNull);
- }
-
-- boolean isScaledBitField(final int objectId, final ICleanUpRegistry
registry)
-+ boolean isScaledBitField(final int objectId, final ICleanUpRegistry
registry) throws HDF5JavaException
- {
- final HDF5DataTypeVariant typeVariantOrNull =
tryGetTypeVariant(objectId, registry);
- return (HDF5DataTypeVariant.BITFIELD == typeVariantOrNull);
-@@ -1518,7 +1518,7 @@
- }
-
- String[] getStringArrayAttribute(final int objectId, final String
objectPath,
-- final String attributeName, final boolean readRaw, final
ICleanUpRegistry registry)
-+ final String attributeName, final boolean readRaw, final
ICleanUpRegistry registry) throws HDF5JavaException
- {
- final int attributeId = h5.openAttribute(objectId, attributeName,
registry);
- final int stringArrayDataTypeId =
h5.getDataTypeForAttribute(attributeId, registry);
-@@ -1568,7 +1568,7 @@
- }
-
- MDArray<String> getStringMDArrayAttribute(final int objectId, final
String objectPath,
-- final String attributeName, final boolean readRaw, final
ICleanUpRegistry registry)
-+ final String attributeName, final boolean readRaw, final
ICleanUpRegistry registry) throws HDF5JavaException
- {
- final int attributeId = h5.openAttribute(objectId, attributeName,
registry);
- final int stringArrayDataTypeId =
h5.getDataTypeForAttribute(attributeId, registry);
-Index:
sis-jhdf5-14.12.1/ch/systemsx/cisd/hdf5/cleanup/ICallableWithCleanUp.java
-===================================================================
----
sis-jhdf5-14.12.1.orig/ch/systemsx/cisd/hdf5/cleanup/ICallableWithCleanUp.java
2015-02-22 10:46:50.000000000 +0000
-+++ sis-jhdf5-14.12.1/ch/systemsx/cisd/hdf5/cleanup/ICallableWithCleanUp.java
2015-08-10 17:42:56.198786867 +0100
-@@ -16,6 +16,8 @@
-
- package ch.systemsx.cisd.hdf5.cleanup;
-
-+import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException;
-+
- /**
- * A role that calls a method which requires one or more clean-up steps that
need to be run reliably
- * at the end of the method regardless of whether the method is finished
normally or whether it
-@@ -29,6 +31,6 @@
- {
-
- /** Calls the method requiring clean-up. */
-- public T call(ICleanUpRegistry registry);
-+ public T call(ICleanUpRegistry registry) throws HDF5JavaException;
-
- }
Modified: trunk/packages/libsis-jhdf5-java/trunk/debian/rules
===================================================================
--- trunk/packages/libsis-jhdf5-java/trunk/debian/rules 2015-08-17 12:13:53 UTC
(rev 19969)
+++ trunk/packages/libsis-jhdf5-java/trunk/debian/rules 2015-08-17 16:46:45 UTC
(rev 19970)
@@ -3,7 +3,7 @@
# Uncomment this to turn on verbose mode.
#export DH_VERBOSE=1
-export
CLASSPATH=/usr/share/java/commons-lang.jar:/usr/share/java/commons-io.jar:/usr/share/java/sis-base.jar:/usr/share/java/testng.jar:/usr/share/java/junit4.jar:/usr/share/java/jmock.jar
+export
CLASSPATH=/usr/share/java/commons-lang.jar:/usr/share/java/commons-io.jar:/usr/share/java/sis-base.jar
DPKG_EXPORT_BUILDFLAGS = 1
include /usr/share/dpkg/buildflags.mk
@@ -12,44 +12,33 @@
%:
dh $@ --with javahelper
-override_dh_auto_configure:
- cp debian/build_native/hdf-java/* source/c/hdf-java
- cd source/c/hdf-java && autoreconf -i
- cp debian/build_native/jhdf5/* source/c/jhdf5
- cd source/c/jhdf5 && autoreconf -i
- dh_auto_configure
-
-
override_dh_auto_clean:
- if test -e source/c/hdf-java/Makefile; then cd source/c/hdf-java; make
clean; fi
- rm -f source/c/hdf-java/AUTHORS source/c/hdf-java/NEWS
source/c/hdf-java/README source/c/hdf-java/ChangeLog
- rm -rf source/c/hdf-java/configure* source/c/hdf-java/Makefile*
source/c/hdf-java/autom4te.cache
- if test -e source/c/jhdf5/Makefile; then cd source/c/jhdf5; make clean;
fi
- rm -f source/c/jhdf5/AUTHORS source/c/jhdf5/NEWS source/c/jhdf5/README
source/c/jhdf5/ChangeLog
- rm -rf source/c/jhdf5/configure* source/c/jhdf5/Makefile*
source/c/jhdf5/autom4te.cache
- rm -rf src lib build *.jar test
+ rm -rf jsrc lib build *.jar
+ rm -rf source/c/*.log
+ rm -rf source/c/*.so
+ cd debian/test && rm -f *.h5 *.class
+ cd sourceTest/java && rm -f *.hdf
#find test -name '*.class' -delete
override_dh_auto_build:
- # Avoids jh_build thinking that files in .svn or .pc are things it
- # needs to compile.
- mkdir src ; cp -r source/java/* src
- # See README.source about this file being removed
- rm src/ch/systemsx/cisd/hdf5/h5ar/HDF5ArchiverMain.java
- # This I cannot adequately explain:
-# perl debian/i_hate_java.perl < ch/systemsx/cisd/hdf5/hdf5lib/H5.java \
-# > src/ch/systemsx/cisd/hdf5/hdf5lib/H5.java
- jh_build sis-jhdf5.jar src
- cd source/c/hdf-java ; ./configure && make
- cd source/c/jhdf5 ; ./configure && make
+ # C build
+ cd source/c && \
+ $(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -shared -fPIC
-Wl,--exclude-libs,ALL \
+ -I/usr/lib/jvm/default-java/include/ -I/usr/include/hdf5/serial
\
+ jhdf5/*.c hdf-java/*.c -o libsis-jhdf5.so -lz -lhdf5_serial
+ # Java build - see README.source about the file being removed
+ mkdir jsrc ; cp -r source/java/ch source/java/ncsa jsrc
+ rm jsrc/ch/systemsx/cisd/hdf5/h5ar/HDF5ArchiverMain.java
+ # This line is still needed on Ubuntu 14.04
+ jh_build sis-jhdf5.jar jsrc
override_dh_auto_test:
- dh_auto_test
- mkdir test ; cp -r source/java/* test ; cp -r sourceTest/java/* test
- # See README.source about this file being removed
- rm -f test/ch/systemsx/cisd/hdf5/h5ar/HDF5ArchiverMain.java
- # libmock-java does not match full API
- rm -f test/ch/systemsx/cisd/hdf5/h5ar/DirectoryIndexUpdaterTest.java
- jh_build sis-jhdf5-test.jar test
- cp source/c/hdf-java/.libs/*.so* source/c/jhdf5/.libs/*.so* test/
- java -Dnative.libpath=test -classpath
/usr/share/java/junit4.jar:sis-jhdf5-test.jar:/usr/share/java/sis-base.jar:/usr/share/java/jhdf5.jar
org.junit.runner.JUnitCore test.hdf5lib.TestAll
+ # Run the tests that come with the upstream source.
+ # The contortions with the CLASSPATH are to try and ensure that the
MANIFEST is
+ # supplying the correct deps automatically.
+ export CLASSPATH=".:`readlink -f
sis-jhdf5.jar`:/usr/share/java/junit4.jar" JNIPATH="`readlink -f source/c`" ; \
+ cd sourceTest/java && \
+ ln -s test/hdf5lib/h5ex_g_iterate.hdf . && \
+ find test -name '*.java' | env CLASSPATH="$$CLASSPATH:$(CLASSPATH)"
xargs javac && \
+ java -Xmx2048M -Djava.library.path="$$JNIPATH"
org.junit.runner.JUnitCore test.hdf5lib.TestAll
+
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