debian/changelog

-libsis-base-java (18.08.0+dfsg-2) UNRELEASED; urgency=medium
+libsis-base-java (18.09~pre1+git20180827.fe4953e+dfsg-1) UNRELEASED; urgency=medium
 
-  * Fix watch file
+  * Temporarily use Git HEAD since latest HEAD is needed to package
+    libsis-jhdf5
 
  -- Andreas Tille <tille@debian.org>  Wed, 19 Sep 2018 09:57:55 +0200
 

debian/patches/0001-Change-test-testGetLinkInfoRegularFile-to-precision-.patch

-From: Bernd Rinn <brinn@ethz.ch>
-Date: Tue, 21 Aug 2018 15:20:44 +0200
-Origin: https://sissource.ethz.ch/sispub/base/commit/331b8ccb2d5197393fef09fe4e02febaf0041287
-Subject: Change test testGetLinkInfoRegularFile() to precision of
- 1 second, as some java.io.File.lastModified() on some JREs report the last
- modified time with sub-second resolution.
-
----
- sourceTest/java/ch/systemsx/cisd/base/unix/UnixTests.java | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
---- a/sourceTest/java/ch/systemsx/cisd/base/unix/UnixTests.java
-+++ b/sourceTest/java/ch/systemsx/cisd/base/unix/UnixTests.java
-@@ -56,7 +56,7 @@ public class UnixTests extends AbstractF
-         assertEquals("root", Unix.tryGetUserNameForUid(0));
-         assertEquals(FileLinkType.REGULAR_FILE, info.getLinkType());
-         assertFalse(info.isSymbolicLink());
--        assertEquals(f.lastModified(), 1000 * info.getLastModified());
-+        assertEquals(f.lastModified()/1000, info.getLastModified());
-     }
- 
-     @Test(groups =

debian/patches/fix_tests.patch

-Subject: Tests made assumption user is not root
-Description: Update uid/gid tests assuming non root user.
-Forwarded: no
-Author: Olivier Sallou <osallou@debian.org>
---- a/sourceTest/java/ch/systemsx/cisd/base/unix/UnixTests.java
-+++ b/sourceTest/java/ch/systemsx/cisd/base/unix/UnixTests.java
-@@ -165,14 +165,14 @@ public class UnixTests extends AbstractF
-         { "requires_unix" })
-     public void testGetUid()
-     {
--        assertTrue(Unix.getUid() > 0);
-+        assertTrue(Unix.getUid() >= 0);
-     }
- 
-     @Test(groups =
-         { "requires_unix" })
-     public void testGetEuid()
-     {
--        assertTrue(Unix.getEuid() > 0);
-+        assertTrue(Unix.getEuid() >= 0);
-         assertEquals(Unix.getUid(), Unix.getEuid());
-     }
- 
-@@ -180,14 +180,14 @@ public class UnixTests extends AbstractF
-         { "requires_unix" })
-     public void testGetGid()
-     {
--        assertTrue(Unix.getGid() > 0);
-+        assertTrue(Unix.getGid() >= 0);
-     }
- 
-     @Test(groups =
-         { "requires_unix" })
-     public void testGetEgid()
-     {
--        assertTrue(Unix.getEgid() > 0);
-+        assertTrue(Unix.getEgid() >= 0);
-         assertEquals(Unix.getGid(), Unix.getEgid());
-     }
- 

debian/patches/load_native_debian.patch

@@ -8,7 +8,7 @@ Forwarded: no
 Last-Updated: 2015-08-21
 --- a/source/java/ch/systemsx/cisd/base/convert/NativeData.java
 +++ b/source/java/ch/systemsx/cisd/base/convert/NativeData.java
-@@ -45,7 +45,8 @@
+@@ -45,7 +45,8 @@ public class NativeData
              useNativeLib = false;
          } else
          {
@@ -20,7 +20,7 @@ Last-Updated: 2015-08-21
  
 --- a/source/java/ch/systemsx/cisd/base/unix/Unix.java
 +++ b/source/java/ch/systemsx/cisd/base/unix/Unix.java
-@@ -46,7 +46,8 @@
+@@ -65,7 +65,8 @@ public final class Unix
  
      static
      {

debian/patches/remove_ch_rinn_imports.patch

@@ -13,7 +13,7 @@ Last-Updated: 2015-08-21
  import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
  import ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked;
  import ch.systemsx.cisd.base.utilities.NativeLibraryUtilities;
-@@ -415,13 +414,11 @@ public final class Unix
+@@ -647,13 +646,11 @@ public final class Unix
  
      private static native String strerror();
      
@@ -29,7 +29,7 @@ Last-Updated: 2015-08-21
          try
 --- a/sourceTest/java/ch/systemsx/cisd/base/unix/UnixTests.java
 +++ b/sourceTest/java/ch/systemsx/cisd/base/unix/UnixTests.java
-@@ -25,7 +25,6 @@ import java.nio.charset.Charset;
+@@ -27,7 +27,6 @@ import java.nio.charset.Charset;
  import org.apache.commons.io.FileUtils;
  import org.testng.annotations.Test;
  
@@ -37,11 +37,11 @@ Last-Updated: 2015-08-21
  import ch.systemsx.cisd.base.BuildAndEnvironmentInfo;
  import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
  import ch.systemsx.cisd.base.unix.Unix.Group;
-@@ -37,7 +36,6 @@ import ch.systemsx.cisd.base.unix.Unix.S
+@@ -39,7 +38,6 @@ import ch.systemsx.cisd.base.unix.Unix.S
   * 
   * @author Bernd Rinn
   */
 -@Friend(toClasses = Unix.class)
  public class UnixTests extends AbstractFileSystemTestCase
  {
- 
+     private UnixTests()

debian/patches/series

 remove_ch_rinn_imports.patch
 load_native_debian.patch
-fix_tests.patch
 skip_testGetLinkInfoDirectory.patch
-0001-Change-test-testGetLinkInfoRegularFile-to-precision-.patch

debian/patches/skip_testGetLinkInfoDirectory.patch

@@ -19,7 +19,7 @@ Forwarded-Upstream: Bernd Rinn <brinn@ethz.ch>
 
 --- a/sourceTest/java/ch/systemsx/cisd/base/unix/UnixTests.java
 +++ b/sourceTest/java/ch/systemsx/cisd/base/unix/UnixTests.java
-@@ -79,7 +79,7 @@ public class UnixTests extends AbstractF
+@@ -90,7 +90,7 @@ public class UnixTests extends AbstractF
      }
  
      @Test(groups =

debian/watch

 version=4
 
-opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
-  https://sissource.ethz.ch/sispub/base/tags .*archive/.+/base@ANY_VERSION@@ARCHIVE_EXT@
+# opts="uversionmangle=s/(\d)[_\.\-\+]?((RC|rc|pre|dev|beta|alpha)\d*)$/$1~$2/,repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
+#  https://sissource.ethz.ch/sispub/base/tags .*archive/.+/base@ANY_VERSION@@ARCHIVE_EXT@
+
+opts="mode=git,pretty=18.09~pre1+git%cd.%h,uversionmangle=s/(\d)[_\.\-\+]?((RC|rc|pre|dev|beta|alpha)\d*)$/$1~$2/,repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
+    https://sissource.ethz.ch/sispub/base.git HEAD

source/c/compile_windows_x64.mak → source/c/Makefile_Win64.mak

@@ -6,13 +6,13 @@
 #============================================================================
 
 # Visual C++ directory, for example
-VCPPDIR=C:\Program Files (x86)\Microsoft Visual Studio 9.0\VC
+VCPPDIR=C:\Program Files (x86)\Microsoft Visual Studio\2017\Community\VC
 
 # Directory where JDK is installed (We require JDK 1.6)
-JAVADIR=C:\Program Files\Java\jdk1.6.0_37
+JAVADIR=C:\Program Files\Java\jdk1.8.0_181
 
 # Common parent directory
-PARENTDIR=C:\nativeData
+PARENTDIR=F:\base
 
 # Directory of the HDF Java Products, for example
 SRCDIR=$(PARENTDIR)\c\

source/c/compile_linux_amd64.sh

 #! /bin/bash
 
-gcc -shared -O3 -fPIC unix.c -I/usr/java/jdk1.6.0/include -I/usr/java/jdk1.6.0/include/linux -o libunix.so
+JAVA_INCLUDE=/usr/lib/jvm/java-1.8.0/include 
+gcc -shared -O3 -fPIC unix.c -I$JAVA_INCLUDE -I$JAVA_INCLUDE/linux -o libunix.so
 
 # MACHINE_BYTE_ORDER=1 corresponds to 'little endian'
-gcc -shared -O3 -fPIC -DMACHINE_BYTE_ORDER=1 copy*.c  -I/usr/java/jdk1.6.0/include -I/usr/java/jdk1.6.0/include/linux -o libnativedata.so
+gcc -shared -O3 -fPIC -DMACHINE_BYTE_ORDER=1 copy*.c -I$JAVA_INCLUDE -I$JAVA_INCLUDE/linux -o libnativedata.so

source/c/compile_linux_arm.sh

 #! /bin/bash
 
-gcc -shared -O3 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/usr/java/jdk1.7.0/include -I/usr/java/jdk1.7.0/include/linux unix.c -o libunix.so
+gcc -shared -O3 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/usr/java/jdk1.8.0/include -I/usr/java/jdk1.8.0/include/linux unix.c -o libunix.so
 
 # MACHINE_BYTE_ORDER=1 corresponds to 'little endian'
-gcc -shared -O3 -fPIC -DMACHINE_BYTE_ORDER=1 copy*.c  -I/usr/java/jdk1.7.0/include -I/usr/java/jdk1.7.0/include/linux -o libnativedata.so
+gcc -shared -O3 -fPIC -DMACHINE_BYTE_ORDER=1 copy*.c -I/usr/java/jdk1.8.0/include -I/usr/java/jdk1.8.0/include/linux -o libnativedata.so

source/c/compile_linux_i386.sh

-#! /bin/bash
-
-gcc -m32 -shared -O3 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/usr/java/jdk1.6.0/include -I/usr/java/jdk1.6.0/include/linux unix.c -o libunix.so
-
-# MACHINE_BYTE_ORDER=1 corresponds to 'little endian'
-gcc -m32 -shared -O3 -fPIC -DMACHINE_BYTE_ORDER=1 copy*.c  -I/usr/java/jdk1.6.0/include -I/usr/java/jdk1.6.0/include/linux -o libnativedata.so

source/c/compile_macosx_i386.sh

-#! /bin/bash
-
-gcc -m32 -mmacosx-version-min=10.6 -bundle -O3 unix.c -I/System/Library/Frameworks/JavaVM.framework/Versions/Current/Headers -o libunix.jnilib
-
-# MACHINE_BYTE_ORDER=1 corresponds to 'little endian'
-gcc -m32 -mmacosx-version-min=10.6 -bundle -O3 -DMACHINE_BYTE_ORDER=1 copy*.c -I/System/Library/Frameworks/JavaVM.framework/Versions/Current/Headers -o libnativedata.jnilib

source/c/compile_macosx_x86_64.sh

 #! /bin/bash
 
-gcc -m64 -mmacosx-version-min=10.6 -dynamiclib -D_DARWIN_USE_64_BIT_INODE -O3 unix.c -I/System/Library/Frameworks/JavaVM.framework/Versions/Current/Headers -o libunix.jnilib
+gcc -m64 -mmacosx-version-min=10.11 -dynamiclib -D_DARWIN_USE_64_BIT_INODE -O3 unix.c -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/System/Library/Frameworks/JavaVM.framework/Versions/Current/Headers -o libunix.jnilib
 
 # MACHINE_BYTE_ORDER=1 corresponds to 'little endian'
-gcc -m64 -mmacosx-version-min=10.6 -dynamiclib -O3 -DMACHINE_BYTE_ORDER=1 copy*.c -I/System/Library/Frameworks/JavaVM.framework/Versions/Current/Headers -o libnativedata.jnilib
+gcc -m64 -mmacosx-version-min=10.11 -dynamiclib -O3 -DMACHINE_BYTE_ORDER=1 copy*.c -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/System/Library/Frameworks/JavaVM.framework/Versions/Current/Headers -o libnativedata.jnilib

source/c/compile_solaris_amd64.sh

-#! /bin/bash
-
-cc -G -KPIC -fast -m64 -I/usr/java/include -I/usr/java/include/solaris unix.c -o libunix.so
-
-# MACHINE_BYTE_ORDER=1 corresponds to 'little endian'
-cc -G -KPIC -fast -m64 -DMACHINE_BYTE_ORDER=1 copy*.c  -I/usr/java/include -I/usr/java/include/solaris -o libnativedata.so

source/c/compile_solaris_sparc.sh

-#! /bin/bash
-
-cc -G -KPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/usr/java/include -I/usr/java/include/solaris unix.c -o libunix.so
-
-# MACHINE_BYTE_ORDER=2 corresponds to 'big endian'
-cc -G -KPIC -DMACHINE_BYTE_ORDER=2 copy*.c  -I/usr/java/include -I/usr/java/include/solaris -o libnativedata.so

source/c/compile_solaris_sparcv9.sh

-#! /bin/bash
-
-cc -G -KPIC -fast -m64 -I/usr/java/include -I/usr/java/include/solaris unix.c -o libunix.so
-
-# MACHINE_BYTE_ORDER=2 corresponds to 'big endian'
-cc -G -KPIC -fast -m64 -DMACHINE_BYTE_ORDER=2 copy*.c  -I/usr/java/include -I/usr/java/include/solaris -o libnativedata.so

source/c/compile_solaris_x86.sh

-#! /bin/bash
-
-cc -G -KPIC -fast -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/usr/java/include -I/usr/java/include/solaris unix.c -o libunix.so
-
-# MACHINE_BYTE_ORDER=1 corresponds to 'little endian'
-cc -G -KPIC -fast -DMACHINE_BYTE_ORDER=1 copy*.c  -I/usr/java/include -I/usr/java/include/solaris -o libnativedata.so

source/c/compile_windows_i386.mak

-#============================================================================
-#
-#              Makefile to compile the 'nativedata' native library
-#              Usage: nmake /f compile_windows_i386.mak
-#
-#============================================================================
-
-# Visual C++ directory, for example
-VCPPDIR=C:\Program Files\Microsoft Visual Studio 9.0\VC
-
-# Directory where JDK is installed (We require JDK 1.6)
-JAVADIR=C:\Program Files\Java\jdk1.6.0_37
-
-# Common parent directory
-PARENTDIR=C:\nativeData
-
-# Directory of the HDF Java Products, for example
-SRCDIR=$(PARENTDIR)\c\
-
-#===========================================================================
-#   Do not make any change below this line unless you know what you do
-#===========================================================================
-PATH=$(PATH);$(VCPPDIR)\BIN
-SRCDIR=$(SRCDIR)
-
-VALID_PATH_SET=YES
-#-------------------------------------------------------
-# Test if all path is valid
-
-!IF EXISTS("$(VCPPDIR)")
-!ELSE
-!MESSAGE ERROR: Visual C++ directory $(VCPPDIR) does not exist
-VALID_PATH_SET=NO 
-!ENDIF
-
-!IF EXISTS("$(JAVADIR)")
-!ELSE
-!MESSAGE ERROR: JDK directory $(JAVADIR) does not exist
-VALID_PATH_SET=NO 
-!ENDIF
-
-!IF EXISTS("$(SRCDIR)")
-!ELSE
-!MESSAGE ERROR: C source directory $(SRCDIR) does not exist
-VALID_PATH_SET=NO 
-!ENDIF
-
-#-------------------------------------------------------
-
-
-!IF "$(VALID_PATH_SET)" == "YES"
-
-!IF "$(OS)" == "Windows_NT"
-NULL=
-!ELSE 
-NULL=nul
-!ENDIF 
-
-INTDIR=.\nativedata\Release
-OUTDIR=$(SRCDIR)\lib\win
-
-INCLUDES =  \
-	"$(JAVADIR)\include\jni.h" \
-	"$(JAVADIR)\include\win32\jni_md.h"
-
-
-ALL : "$(OUTDIR)\nativedata.dll"
-
-"$(INTDIR)" :
-    if not exist "$(INTDIR)/$(NULL)" mkdir "$(INTDIR)"
-
-"$(OUTDIR)" :
-    if not exist "$(OUTDIR)/$(NULL)" mkdir "$(OUTDIR)"
-
-CPP=cl.exe
-CPP_PROJ=/nologo /W3 /EHsc /O2 /I "$(JAVADIR)\include" /I "$(JAVADIR)\include\win32" /D "WIN32" /D "NDEBUG" /D "_WINDOWS" /D "MACHINE_BYTE_ORDER=1" /Fp"$(INTDIR)\nativedata.pch" /Fo"$(INTDIR)\\" /Fd"$(INTDIR)\\" /FD /c 
-
-.c{$(INTDIR)}.obj::
-   $(CPP) @<<
-   $(CPP_PROJ) $< 
-<<
-
-.cpp{$(INTDIR)}.obj::
-   $(CPP) @<<
-   $(CPP_PROJ) $< 
-<<
-
-.cxx{$(INTDIR)}.obj::
-   $(CPP) @<<
-   $(CPP_PROJ) $< 
-<<
-
-.c{$(INTDIR)}.sbr::
-   $(CPP) @<<
-   $(CPP_PROJ) $< 
-<<
-
-.cpp{$(INTDIR)}.sbr::
-   $(CPP) @<<
-   $(CPP_PROJ) $< 
-<<
-
-.cxx{$(INTDIR)}.sbr::
-   $(CPP) @<<
-   $(CPP_PROJ) $< 
-<<
-
-MTL=midl.exe
-MTL_PROJ=/nologo /D "NDEBUG" /mktyplib203 /win32 
-RSC=rc.exe
-BSC32=bscmake.exe
-BSC32_FLAGS=/nologo /o"$(INTDIR)\nativedata.bsc" 
-BSC32_SBRS= \
-	
-LINK=link.exe
-LINK_FLAGS=/nologo /dll /nodefaultlib:msvcrt /incremental:no /pdb:"$(INTDIR)\nativedata.pdb" /machine:I386 /out:"$(OUTDIR)\nativedata.dll" /implib:"$(INTDIR)\nativedata.lib" 
-LINK_OBJS= \
-	"$(INTDIR)\copyCommon.obj" \
-	"$(INTDIR)\copyByteDouble.obj" \
-	"$(INTDIR)\copyByteFloat.obj" \
-	"$(INTDIR)\copyByteInt.obj" \
-	"$(INTDIR)\copyByteLong.obj" \
-	"$(INTDIR)\copyByteShort.obj" \
-	"$(INTDIR)\copyByteChar.obj"
-
-"$(OUTDIR)\nativedata.dll" : "$(OUTDIR)" $(DEF_FILE) $(LINK_OBJS)
-    $(LINK) @<<
-  $(LINK_FLAGS) $(LINK_OBJS)
-<<
-
-
-SOURCE=$(SRCDIR)\copyCommon.c
-
-"$(INTDIR)\copyCommon.obj" : $(SOURCE) $(INCLUDES) "$(INTDIR)"
-	$(CPP) $(CPP_PROJ) $(SOURCE)
-
-
-SOURCE=$(SRCDIR)\copyByteDouble.c
-
-"$(INTDIR)\copyByteDouble.obj" : $(SOURCE) $(INCLUDES) "$(INTDIR)"
-	$(CPP) $(CPP_PROJ) $(SOURCE)
-
-SOURCE=$(SRCDIR)\copyByteFloat.c
-
-"$(INTDIR)\copyByteFloat.obj" : $(SOURCE) $(INCLUDES) "$(INTDIR)"
-	$(CPP) $(CPP_PROJ) $(SOURCE)
-
-SOURCE=$(SRCDIR)\copyByteInt.c
-
-"$(INTDIR)\copyByteInt.obj" : $(SOURCE) $(INCLUDES) "$(INTDIR)"
-	$(CPP) $(CPP_PROJ) $(SOURCE)
-
-SOURCE=$(SRCDIR)\copyByteLong.c
-
-"$(INTDIR)\copyByteLong.obj" : $(SOURCE) $(INCLUDES) "$(INTDIR)"
-	$(CPP) $(CPP_PROJ) $(SOURCE)
-
-SOURCE=$(SRCDIR)\copyByteShort.c
-
-"$(INTDIR)\copyByteShort.obj" : $(SOURCE) $(INCLUDES) "$(INTDIR)"
-	$(CPP) $(CPP_PROJ) $(SOURCE)
-
-SOURCE=$(SRCDIR)\copyByteChar.c
-
-"$(INTDIR)\copyByteChar.obj" : $(SOURCE) $(INCLUDES) "$(INTDIR)"
-	$(CPP) $(CPP_PROJ) $(SOURCE)
-
-CLEAN :
-	-@erase "$(INTDIR)\copyCommon.obj"
-	-@erase "$(INTDIR)\copyByteDouble.obj"
-	-@erase "$(INTDIR)\copyByteFloat.obj"
-	-@erase "$(INTDIR)\copyByteInt.obj"
-	-@erase "$(INTDIR)\copyByteLong.obj"
-	-@erase "$(INTDIR)\copyByteShort.obj"
-	-@erase "$(INTDIR)\copyByteChar.obj"
-	-@erase "$(INTDIR)\vc90.idb"
-	-@erase "$(INTDIR)\nativedata.exp"
-	-@erase "$(INTDIR)\nativedata.lib"
-	-@erase "$(OUTDIR)\nativedata.dll"
-
-!ENDIF

source/c/unix.c

@@ -13,6 +13,7 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
+#include <time.h>
 #include <unistd.h>
 #include <errno.h>
 #include <string.h>
@@ -20,6 +21,7 @@
 #include <grp.h>
 #include <sys/types.h>
 #include <sys/stat.h>
+#include <sys/time.h>
 #include <jni.h>
 
 /* Types of links. Keep in sync with Java enum. */
@@ -28,6 +30,17 @@
 #define SYMLINK 2
 #define OTHER 3
 
+/* Field name for nano second precission of file stat times. */
+#ifdef __MACH__
+#define ST_ATIME_NANO st_atimespec.tv_nsec
+#define ST_MTIME_NANO st_mtimespec.tv_nsec
+#define ST_CTIME_NANO st_ctimespec.tv_nsec
+#else
+#define ST_ATIME_NANO st_atim.tv_nsec
+#define ST_MTIME_NANO st_mtim.tv_nsec
+#define ST_CTIME_NANO st_ctim.tv_nsec
+#endif
+
 #ifndef __STAT
 #define __STAT stat
 #endif
@@ -44,6 +57,82 @@ jclass groupClass;
 jmethodID groupConstructorID;
 jclass statClass;
 jmethodID statConstructorID;
+jboolean statConstructorHasNanos;
+
+/* 
+ * Error and Exception Handling 
+ */
+ 
+#define THROWEXCEPTION(className,args) {                                    \
+    jclass     jc;                                                          \
+    jmethodID  jm;                                                          \
+    jobject    ex;                                                          \
+    jc = (*env)->FindClass(env, (className));                               \
+    if (jc == NULL) {                                                       \
+        return JNI_FALSE;                                                   \
+    }                                                                       \
+    jm = (*env)->GetMethodID(env, jc, "<init>", "(Ljava/lang/String;)V");   \
+    if (jm == NULL) {                                                       \
+        printf("THROWEXCEPTION FATAL ERROR: GetMethodID failed\n");         \
+        return JNI_FALSE;                                                   \
+    }                                                                       \
+    ex = (*env)->NewObjectA (env, jc, jm, (jvalue*)(args));                 \
+    if (ex == NULL) {                                                       \
+        printf("THROWEXCEPTION FATAL ERROR:  %s: Creation failed\n", (className)); \
+        return JNI_FALSE;                                                   \
+    }                                                                       \
+    if ((*env)->Throw(env, (jthrowable)ex) < 0) {                           \
+        printf("THROWEXCEPTION FATAL ERROR:  %s: Throw failed\n", (className));    \
+        return JNI_FALSE;                                                   \
+    }                                                                       \
+    return JNI_TRUE;                                                        \
+}
+
+/*
+ *  Routine to raise particular Java exceptions from C
+ */
+static jboolean
+jni_error_class
+    (JNIEnv *env, const char *message, const char *className)
+{
+    char *args[2];
+    jstring str = (*env)->NewStringUTF(env, message);
+    args[0] = (char *)str;
+    args[1] = 0;
+
+    THROWEXCEPTION(className, args);
+} /* end jni_error_class() */
+
+/*
+ *  A NULL argument in an HDF5 call
+ *  Create and throw an 'NullPointerException'
+ *
+ *  Note:  This routine never returns from the 'throw',
+ *  and the Java native method immediately raises the
+ *  exception.
+ */
+jboolean null_pointer_exception(JNIEnv *env, const char *functName)
+{
+    return jni_error_class(env, functName, "java/lang/NullPointerException");
+} /* end null_pointer_exception() */
+
+/*
+ *  A fatal error in a JNI call
+ *  Create and throw an 'InternalError'
+ *
+ *  Note:  This routine never returns from the 'throw',
+ *  and the Java native method immediately raises the
+ *  exception.
+ */
+jboolean internal_error(JNIEnv *env, const char *functName)
+{
+    return jni_error_class(env, functName, "java/lang/InternalError");
+} /* end iternal_error() */
+
+
+/*
+ * End Error and Exception Handling 
+ */
 
 JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_base_unix_Unix_init
   (JNIEnv *env, jclass clss)
@@ -82,11 +171,18 @@ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_base_unix_Unix_init
         return -1;
     }
     statClass = (*env)->NewGlobalRef(env, statClass);
+    statConstructorHasNanos = JNI_TRUE;
+    statConstructorID = (*env)->GetMethodID(env, statClass, "<init>", "(JJSBIIIJJJJJJJJI)V");
+    if (statConstructorID == NULL) /* We have an old Java class without the "microsecond constructor". */
+    {
+        (*env)->ExceptionClear(env);
+	    statConstructorHasNanos = JNI_FALSE;
 	    statConstructorID = (*env)->GetMethodID(env, statClass, "<init>", "(JJSBIIIJJJJJI)V");
-    if (groupConstructorID == NULL) /* Really shouldn't happen, will throw NoSuchMethodError. */
+	    if (statConstructorID == NULL) /* Really shouldn't happen, will throw NoSuchMethodError. */
 	    {
 	        return -1;
 	    }
+	}
     return 0;
 }
 
@@ -165,10 +261,20 @@ jobject call_stat(JNIEnv *env, jclass clss, jstring filename, stat_func_ptr stat
         {
             type = OTHER;
         }
+        if (statConstructorHasNanos)
+        {
+            result = (*env)->NewObject(env, statClass, statConstructorID, (jlong) s.st_dev, (jlong) s.st_ino, 
+                       (jshort) (s.st_mode & 07777), (jbyte) type, (jint) s.st_nlink, 
+                       (jint) s.st_uid, (jint) s.st_gid, (jlong) s.st_atime, (jlong) s.ST_ATIME_NANO, 
+                       (jlong) s.st_mtime, (jlong) s.ST_MTIME_NANO, (jlong) s.st_ctime, (jlong) s.ST_CTIME_NANO, 
+                       (jlong) s.st_size, (jlong) s.st_blocks, (jint) s.st_blksize);
+        } else
+        {
             result = (*env)->NewObject(env, statClass, statConstructorID, (jlong) s.st_dev, (jlong) s.st_ino, 
                        (jshort) (s.st_mode & 07777), (jbyte) type, (jint) s.st_nlink, 
                        (jint) s.st_uid, (jint) s.st_gid, (jlong) s.st_atime, (jlong) s.st_mtime, 
                        (jlong) s.st_ctime, (jlong) s.st_size, (jlong) s.st_blocks, (jint) s.st_blksize);
+        }
         return result;
     }
 }
@@ -236,6 +342,23 @@ JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_base_unix_Unix_chown(JNIEnv *env, j
     }
 }
 
+JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_base_unix_Unix_lchown(JNIEnv *env, jclass clss, jstring linkname, jint uid, jint gid)
+{
+    const char* plinkname;
+    int retval;
+	
+    plinkname = (char *)(*env)->GetStringUTFChars(env, linkname, NULL);
+    retval = lchown(plinkname, uid, gid);
+    (*env)->ReleaseStringUTFChars(env, linkname, plinkname);
+    if (retval < 0)
+    {
+		    return -errno;
+    } else
+    {
+        return 0;
+    }
+}
+
 JNIEXPORT jstring JNICALL Java_ch_systemsx_cisd_base_unix_Unix_getuser(JNIEnv *env, jclass clss, jint uid)
 {
     struct passwd *pw;
@@ -444,3 +567,133 @@ JNIEXPORT jstring JNICALL Java_ch_systemsx_cisd_base_unix_Unix_strerror__(JNIEnv
 {
     return (*env)->NewStringUTF(env, strerror(errno));
 }
+
+JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_base_unix_Unix_lutimes
+  (JNIEnv *env, jclass clss, jstring filename, jlong accessTimeSecs, jlong accessTimeMicroSecs, jlong modificationTimeSecs, jlong modificationTimeMicroSecs)
+{
+    const char* pfilename;
+    struct timeval times[2];
+    int retval;
+
+    pfilename = (char *)(*env)->GetStringUTFChars(env, filename, NULL);
+    times[0].tv_sec = accessTimeSecs;
+    times[0].tv_usec = accessTimeMicroSecs;
+    times[1].tv_sec = modificationTimeSecs;
+    times[1].tv_usec = modificationTimeMicroSecs;
+
+    retval = lutimes(pfilename, times);
+    if (retval < 0)
+    {
+        retval = -errno;
+    }
+
+    (*env)->ReleaseStringUTFChars(env, filename, pfilename);
+
+   return retval;
+}
+
+JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_base_unix_Unix_utimes
+  (JNIEnv *env, jclass clss, jstring filename, jlong accessTimeSecs, jlong accessTimeMicroSecs, jlong modificationTimeSecs, jlong modificationTimeMicroSecs)
+{
+    const char* pfilename;
+    struct timeval times[2];
+    int retval;
+
+    pfilename = (char *)(*env)->GetStringUTFChars(env, filename, NULL);
+    times[0].tv_sec = accessTimeSecs;
+    times[0].tv_usec = accessTimeMicroSecs;
+    times[1].tv_sec = modificationTimeSecs;
+    times[1].tv_usec = modificationTimeMicroSecs;
+
+    retval = utimes(pfilename, times);
+    if (retval < 0)
+    {
+        retval = -errno;
+    }
+
+    (*env)->ReleaseStringUTFChars(env, filename, pfilename);
+
+   return retval;
+}
+
+JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_base_unix_Unix_clock_1gettime
+  (JNIEnv *env, jclass clss, jlongArray time)
+{
+    struct timespec spec;
+    jlong   *timeP;
+    jboolean isCopy;
+    int retval;
+    
+    if (time == NULL) 
+    {
+        null_pointer_exception(env, "clock_gettime: time is NULL");
+    } /* end if */
+    timeP = (jlong*)(*env)->GetPrimitiveArrayCritical(env, time, &isCopy);
+    if (timeP == NULL) 
+    {
+        internal_error(env, "clock_gettime: time not pinned");
+    } /* end if */
+
+
+    retval = clock_gettime(CLOCK_REALTIME, &spec);
+    if (retval < 0)
+    {
+        retval = -errno;
+    } else
+    {
+	    timeP[0] = spec.tv_sec;
+	    timeP[1] = spec.tv_nsec;
+	}
+
+    (*env)->ReleasePrimitiveArrayCritical(env, time, timeP, 0);    
+    
+    return retval;
+}
+
+int clock_gettime2(int clk_id, struct timespec* t) {
+    struct timeval now;
+    
+    int rv = gettimeofday(&now, NULL);
+    if (rv) 
+    {
+        return rv;
+    }
+    t->tv_sec  = now.tv_sec;
+    t->tv_nsec = now.tv_usec * 1000;
+    
+    return 0;
+}
+
+JNIEXPORT jint JNICALL Java_ch_systemsx_cisd_base_unix_Unix_clock_1gettime2
+  (JNIEnv *env, jclass clss, jlongArray time)
+{
+    struct timespec spec;
+    jlong   *timeP;
+    jboolean isCopy;
+    int retval;
+    
+    if (time == NULL) 
+    {
+        null_pointer_exception(env, "clock_gettime: time is NULL");
+    } /* end if */
+    timeP = (jlong*)(*env)->GetPrimitiveArrayCritical(env, time, &isCopy);
+    if (timeP == NULL) 
+    {
+        internal_error(env, "clock_gettime: time not pinned");
+    } /* end if */
+
+
+    retval = clock_gettime2(CLOCK_REALTIME, &spec);
+    if (retval < 0)
+    {
+        retval = -errno;
+    } else
+    {
+	    timeP[0] = spec.tv_sec;
+	    timeP[1] = spec.tv_nsec;
+	}
+
+    (*env)->ReleasePrimitiveArrayCritical(env, time, timeP, 0);    
+    
+    return retval;
+}