Hdf5 1 10 sync (#1795)

* Branch sync updates and spelling

* Revert format of getenv

6 files changed, 56 insertions, 39 deletions

diff --git a/java/examples/datasets/JavaDatasetExample.sh.in b/java/examples/datasets/JavaDatasetExample.sh.in
index 9a5ddd8..b299ff2 100644
--- a/java/examples/datasets/JavaDatasetExample.sh.in
+++ b/java/examples/datasets/JavaDatasetExample.sh.in
@@ -29,6 +29,7 @@ CMP='cmp'
 DIFF='diff -c'
 CP='cp'
 DIRNAME='dirname'
+BASENAME='basename'
 LS='ls'
 AWK='awk'
 
@@ -103,17 +104,21 @@ COPY_LIBFILES_TO_BLDLIBDIR()
             INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'`
             INODE_DDIR=`$LS -i -d $BLDLIBDIR | $AWK -F' ' '{print $1}'`
             if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then
-                $CP -f $tstfile $BLDLIBDIR
+                $CP -fR $tstfile $BLDLIBDIR
                 if [ $? -ne 0 ]; then
                     echo "Error: FAILED to copy $tstfile ."
 
                     # Comment out this to CREATE expected file
                     exit $EXIT_FAILURE
                 fi
+                BNAME=`$BASENAME $tstfile`
+                if [ "$BNAME" = "libhdf5_java.dylib" ]; then
+                    COPIED_LIBHDF5_JAVA=1
+                fi
             fi
         fi
     done
-    if [ "$IS_DARWIN" = "yes" ]; then
+    if [[ "$IS_DARWIN" = "yes" ]] && [[ $COPIED_LIBHDF5_JAVA -eq 1 ]]; then
        (cd $BLDLIBDIR; \
          install_name_tool -add_rpath @loader_path libhdf5_java.dylib; \
          exist_path=` otool -l libhdf5_java.dylib | grep libhdf5 | grep -v java | awk '{print $2}'`; \
@@ -134,7 +139,7 @@ COPY_LIBFILES_TO_BLDLIBDIR()
             INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'`
             INODE_DDIR=`$LS -i -d $BLDLIBDIR | $AWK -F' ' '{print $1}'`
             if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then
-                $CP -f $tstfile $BLDLIBDIR
+                $CP -fR $tstfile $BLDLIBDIR
                 if [ $? -ne 0 ]; then
                     echo "Error: FAILED to copy $tstfile ."
 
@@ -155,10 +160,7 @@ CLEAN_LIBFILES_AND_BLDLIBDIR()
     INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'`
     INODE_DDIR=`$LS -i -d $BLDLIBDIR | $AWK -F' ' '{print $1}'`
     if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then
-        for tstfile in $COPY_JARTESTFILES
-        do
-            $RM $BLDLIBDIR/tstfile
-        done
+        $RM -rf $BLDLIBDIR
     fi
 }
 
diff --git a/java/examples/datatypes/JavaDatatypeExample.sh.in b/java/examples/datatypes/JavaDatatypeExample.sh.in
index c6f5dbc..a82d883 100644
--- a/java/examples/datatypes/JavaDatatypeExample.sh.in
+++ b/java/examples/datatypes/JavaDatatypeExample.sh.in
@@ -26,6 +26,7 @@ CMP='cmp'
 DIFF='diff -c'
 CP='cp'
 DIRNAME='dirname'
+BASENAME='basename'
 LS='ls'
 AWK='awk'
 
@@ -100,17 +101,21 @@ COPY_LIBFILES_TO_BLDLIBDIR()
             INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'`
             INODE_DDIR=`$LS -i -d $BLDLIBDIR | $AWK -F' ' '{print $1}'`
             if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then
-                $CP -f $tstfile $BLDLIBDIR
+                $CP -fR $tstfile $BLDLIBDIR
                 if [ $? -ne 0 ]; then
                     echo "Error: FAILED to copy $tstfile ."
 
                     # Comment out this to CREATE expected file
                     exit $EXIT_FAILURE
                 fi
+                BNAME=`$BASENAME $tstfile`
+                if [ "$BNAME" = "libhdf5_java.dylib" ]; then
+                    COPIED_LIBHDF5_JAVA=1
+                fi
             fi
         fi
     done
-    if [ "$IS_DARWIN" = "yes" ]; then
+    if [[ "$IS_DARWIN" = "yes" ]] && [[ $COPIED_LIBHDF5_JAVA -eq 1 ]]; then
        (cd $BLDLIBDIR; \
          install_name_tool -add_rpath @loader_path libhdf5_java.dylib; \
          exist_path=` otool -l libhdf5_java.dylib | grep libhdf5 | grep -v java | awk '{print $2}'`; \
@@ -131,7 +136,7 @@ COPY_LIBFILES_TO_BLDLIBDIR()
             INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'`
             INODE_DDIR=`$LS -i -d $BLDLIBDIR | $AWK -F' ' '{print $1}'`
             if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then
-                $CP -f $tstfile $BLDLIBDIR
+                $CP -fR $tstfile $BLDLIBDIR
                 if [ $? -ne 0 ]; then
                     echo "Error: FAILED to copy $tstfile ."
 
@@ -152,10 +157,7 @@ CLEAN_LIBFILES_AND_BLDLIBDIR()
     INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'`
     INODE_DDIR=`$LS -i -d $BLDLIBDIR | $AWK -F' ' '{print $1}'`
     if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then
-        for tstfile in $COPY_JARTESTFILES
-        do
-            $RM $BLDLIBDIR/tstfile
-        done
+        $RM -rf $BLDLIBDIR
     fi
 }
 
diff --git a/java/examples/groups/JavaGroupExample.sh.in b/java/examples/groups/JavaGroupExample.sh.in
index 86f90bf..1b84ed3 100644
--- a/java/examples/groups/JavaGroupExample.sh.in
+++ b/java/examples/groups/JavaGroupExample.sh.in
@@ -26,6 +26,7 @@ CMP='cmp'
 DIFF='diff -c'
 CP='cp'
 DIRNAME='dirname'
+BASENAME='basename'
 LS='ls'
 AWK='awk'
 
@@ -95,17 +96,21 @@ COPY_LIBFILES_TO_BLDLIBDIR()
             INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'`
             INODE_DDIR=`$LS -i -d $BLDLIBDIR | $AWK -F' ' '{print $1}'`
             if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then
-                $CP -f $tstfile $BLDLIBDIR
+                $CP -fR $tstfile $BLDLIBDIR
                 if [ $? -ne 0 ]; then
                     echo "Error: FAILED to copy $tstfile ."
 
                     # Comment out this to CREATE expected file
                     exit $EXIT_FAILURE
                 fi
+                BNAME=`$BASENAME $tstfile`
+                if [ "$BNAME" = "libhdf5_java.dylib" ]; then
+                    COPIED_LIBHDF5_JAVA=1
+                fi
             fi
         fi
     done
-    if [ "$IS_DARWIN" = "yes" ]; then
+    if [[ "$IS_DARWIN" = "yes" ]] && [[ $COPIED_LIBHDF5_JAVA -eq 1 ]]; then
        (cd $BLDLIBDIR; \
          install_name_tool -add_rpath @loader_path libhdf5_java.dylib; \
          exist_path=` otool -l libhdf5_java.dylib | grep libhdf5 | grep -v java | awk '{print $2}'`; \
@@ -126,7 +131,7 @@ COPY_LIBFILES_TO_BLDLIBDIR()
             INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'`
             INODE_DDIR=`$LS -i -d $BLDLIBDIR | $AWK -F' ' '{print $1}'`
             if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then
-                $CP -f $tstfile $BLDLIBDIR
+                $CP -fR $tstfile $BLDLIBDIR
                 if [ $? -ne 0 ]; then
                     echo "Error: FAILED to copy $tstfile ."
 
@@ -147,10 +152,7 @@ CLEAN_LIBFILES_AND_BLDLIBDIR()
     INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'`
     INODE_DDIR=`$LS -i -d $BLDLIBDIR | $AWK -F' ' '{print $1}'`
     if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then
-        for tstfile in $COPY_JARTESTFILES
-        do
-            $RM $BLDLIBDIR/tstfile
-        done
+        $RM -rf $BLDLIBDIR
     fi
 }
 
diff --git a/java/examples/intro/JavaIntroExample.sh.in b/java/examples/intro/JavaIntroExample.sh.in
index a095f27..41ed694 100644
--- a/java/examples/intro/JavaIntroExample.sh.in
+++ b/java/examples/intro/JavaIntroExample.sh.in
@@ -26,6 +26,7 @@ CMP='cmp'
 DIFF='diff -c'
 CP='cp'
 DIRNAME='dirname'
+BASENAME='basename'
 LS='ls'
 AWK='awk'
 
@@ -89,17 +90,21 @@ COPY_LIBFILES_TO_BLDLIBDIR()
             INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'`
             INODE_DDIR=`$LS -i -d $BLDLIBDIR | $AWK -F' ' '{print $1}'`
             if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then
-                $CP -f $tstfile $BLDLIBDIR
+                $CP -fR $tstfile $BLDLIBDIR
                 if [ $? -ne 0 ]; then
                     echo "Error: FAILED to copy $tstfile ."
 
                     # Comment out this to CREATE expected file
                     exit $EXIT_FAILURE
                 fi
+                BNAME=`$BASENAME $tstfile`
+                if [ "$BNAME" = "libhdf5_java.dylib" ]; then
+                    COPIED_LIBHDF5_JAVA=1
+                fi
             fi
         fi
     done
-    if [ "$IS_DARWIN" = "yes" ]; then
+    if [[ "$IS_DARWIN" = "yes" ]] && [[ $COPIED_LIBHDF5_JAVA -eq 1 ]]; then
        (cd $BLDLIBDIR; \
          install_name_tool -add_rpath @loader_path libhdf5_java.dylib; \
          exist_path=` otool -l libhdf5_java.dylib | grep libhdf5 | grep -v java | awk '{print $2}'`; \
@@ -120,7 +125,7 @@ COPY_LIBFILES_TO_BLDLIBDIR()
             INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'`
             INODE_DDIR=`$LS -i -d $BLDLIBDIR | $AWK -F' ' '{print $1}'`
             if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then
-                $CP -f $tstfile $BLDLIBDIR
+                $CP -fR $tstfile $BLDLIBDIR
                 if [ $? -ne 0 ]; then
                     echo "Error: FAILED to copy $tstfile ."
 
@@ -141,10 +146,7 @@ CLEAN_LIBFILES_AND_BLDLIBDIR()
     INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'`
     INODE_DDIR=`$LS -i -d $BLDLIBDIR | $AWK -F' ' '{print $1}'`
     if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then
-        for tstfile in $COPY_JARTESTFILES
-        do
-            $RM $BLDLIBDIR/tstfile
-        done
+        $RM -rf $BLDLIBDIR
     fi
 }
 
diff --git a/java/src/hdf/hdf5lib/HDF5Constants.java b/java/src/hdf/hdf5lib/HDF5Constants.java
index 30035b6..e409cfb 100644
--- a/java/src/hdf/hdf5lib/HDF5Constants.java
+++ b/java/src/hdf/hdf5lib/HDF5Constants.java
@@ -876,6 +876,8 @@ public class HDF5Constants {
     /** */
     public static final int H5R_OBJ_REF_BUF_SIZE = H5R_OBJ_REF_BUF_SIZE();
     /** */
+    public static final int H5R_DSET_REG_REF_BUF_SIZE = H5R_DSET_REG_REF_BUF_SIZE();
+    /** */
     public static final int H5R_OBJECT = H5R_OBJECT();
 
     /** Define atomic datatypes */
@@ -2300,6 +2302,8 @@ public class HDF5Constants {
 
     private static native final int H5R_OBJ_REF_BUF_SIZE();
 
+    private static native final int H5R_DSET_REG_REF_BUF_SIZE();
+
     private static native final int H5R_OBJECT();
 
     private static native final int H5S_ALL();
diff --git a/java/test/junit.sh.in b/java/test/junit.sh.in
index 293067d..9f5334c 100644
--- a/java/test/junit.sh.in
+++ b/java/test/junit.sh.in
@@ -31,6 +31,7 @@ CMP='cmp'
 DIFF='diff -c'
 CP='cp'
 DIRNAME='dirname'
+BASENAME='basename'
 LS='ls'
 AWK='awk'
 
@@ -138,17 +139,21 @@ COPY_LIBFILES_TO_BLDLIBDIR()
             INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'`
             INODE_DDIR=`$LS -i -d $BLDLIBDIR | $AWK -F' ' '{print $1}'`
             if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then
-                $CP -f $tstfile $BLDLIBDIR
+                $CP -fR $tstfile $BLDLIBDIR
                 if [ $? -ne 0 ]; then
                     echo "Error: FAILED to copy $tstfile ."
 
                     # Comment out this to CREATE expected file
                     exit $EXIT_FAILURE
                 fi
+                BNAME=`$BASENAME $tstfile`
+                if [ "$BNAME" = "libhdf5_java.dylib" ]; then
+                    COPIED_LIBHDF5_JAVA=1
+                fi
             fi
         fi
     done
-    if [ "$IS_DARWIN" = "yes" ]; then
+    if [[ "$IS_DARWIN" = "yes" ]] && [[ $COPIED_LIBHDF5_JAVA -eq 1 ]]; then
        (cd testlibs; \
          install_name_tool -add_rpath @loader_path libhdf5_java.dylib; \
          exist_path=` otool -l libhdf5_java.dylib | grep libhdf5 | grep -v java | awk '{print $2}'`; \
@@ -169,7 +174,7 @@ COPY_LIBFILES_TO_BLDLIBDIR()
             INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'`
             INODE_DDIR=`$LS -i -d $BLDLIBDIR | $AWK -F' ' '{print $1}'`
             if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then
-                $CP -f $tstfile $BLDLIBDIR
+                $CP -fR $tstfile $BLDLIBDIR
                 if [ $? -ne 0 ]; then
                     echo "Error: FAILED to copy $tstfile ."
 
@@ -192,7 +197,7 @@ COPY_LIBFILES_TO_BLDLIBDIR()
             INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'`
             INODE_DDIR=`$LS -i -d $BLDLIBDIR | $AWK -F' ' '{print $1}'`
             if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then
-                $CP -f $tstfile $BLDLIBDIR
+                $CP -fR $tstfile $BLDLIBDIR
                 if [ $? -ne 0 ]; then
                     echo "Error: FAILED to copy $tstfile ."
 
@@ -1074,13 +1079,13 @@ if test "X-$BUILD_MODE" = "X-production" ; then
         TESTING JUnit-TestH5E
         ($RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH -ea org.junit.runner.JUnitCore test.TestH5E > JUnit-TestH5E.ext)
 
-        # Extract file name, line number, version and thread IDs because they may be different
-        sed -e 's/thread [0-9]*/thread (IDs)/' -e 's/: .*\.c /: (file name) /' \
-            -e 's/line [0-9]*/line (number)/' \
-            -e 's/Time: [0-9]*[\.,[0-9]*]*/Time:  XXXX/' \
-            -e 's/v[1-9]*\.[0-9]*\./version (number)\./' \
-            -e 's/[1-9]*\.[0-9]*\.[0-9]*[^)]*/version (number)/' \
-            JUnit-TestH5E.ext > JUnit-TestH5E.out
+# Extract file name, line number, version and thread IDs because they may be different
+sed -e 's/thread [0-9]*/thread (IDs)/' -e 's/: .*\.c /: (file name) /' \
+    -e 's/line [0-9]*/line (number)/' \
+    -e 's/Time: [0-9]*[\.,[0-9]*]*/Time:  XXXX/' \
+    -e 's/v[1-9]*\.[0-9]*\./version (number)\./' \
+    -e 's/[1-9]*\.[0-9]*\.[0-9]*[^)]*/version (number)/' \
+    JUnit-TestH5E.ext > JUnit-TestH5E.out
 
         if diff JUnit-TestH5E.out JUnit-TestH5E.txt > /dev/null; then
             echo "  PASSED      JUnit-TestH5E"