Merge pull request #1227 in HDFFV/hdf5 from ~BYRN/hdf5_adb:hdf5_1_10 to hdf5_1_10

* commit 'd8ec4df92880d98907b12af8fc9fff86e0631270':
  Update system commands with HD prefix and whitespace

5 files changed, 27 insertions, 24 deletions

diff --git a/java/examples/groups/JavaGroupExample.sh.in b/java/examples/groups/JavaGroupExample.sh.in
index a2cc4b7..9d68a58 100644
--- a/java/examples/groups/JavaGroupExample.sh.in
+++ b/java/examples/groups/JavaGroupExample.sh.in
@@ -34,13 +34,13 @@ nerrors=0
 # where the libs exist
 HDFLIB_HOME="$top_srcdir/java/lib"
 BLDLIBDIR="$top_builddir/hdf5/lib"
-BLDREFDIR="./groups"
+BLDITERDIR="./groups"
 BLDDIR="."
 HDFTEST_HOME="$top_srcdir/java/examples/groups"
 JARFILE=jar@PACKAGE_TARNAME@-@PACKAGE_VERSION@.jar
 TESTJARFILE=jar@PACKAGE_TARNAME@groups.jar
 test -d $BLDLIBDIR || mkdir -p $BLDLIBDIR
-test -d $BLDREFDIR || mkdir -p $BLDREFDIR
+test -d $BLDITERDIR || mkdir -p $BLDITERDIR
 
 ######################################################################
 # library files
@@ -59,9 +59,11 @@ LIST_JAR_TESTFILES="
 $HDFLIB_HOME/slf4j-api-1.7.25.jar
 $HDFLIB_HOME/ext/slf4j-simple-1.7.25.jar
 "
-LIST_DATA_FILES="
+LIST_ITER_FILES="
 $HDFTEST_HOME/h5ex_g_iterate.h5
 $HDFTEST_HOME/h5ex_g_visit.h5
+"
+LIST_DATA_FILES="
 $HDFTEST_HOME/../testfiles/examples.groups.H5Ex_G_Create.txt
 $HDFTEST_HOME/../testfiles/examples.groups.H5Ex_G_Iterate.txt
 $HDFTEST_HOME/../testfiles/examples.groups.H5Ex_G_Compact.txt
@@ -146,6 +148,7 @@ CLEAN_LIBFILES_AND_BLDLIBDIR()
 }
 
 COPY_DATAFILES="$LIST_DATA_FILES"
+COPY_ITERFILES="$LIST_ITER_FILES"
 
 COPY_DATAFILES_TO_BLDDIR()
 {
@@ -190,12 +193,12 @@ CLEAN_DATAFILES_AND_BLDDIR()
         fi
 }
 
-COPY_REFFILES="$LIST_REF_FILES"
+COPY_ITERFILES="$LIST_ITER_FILES"
 
-COPY_REFFILES_TO_BLDREFDIR()
+COPY_ITERFILES_TO_BLDITERDIR()
 {
     # copy test files. Used -f to make sure get a new copy
-    for tstfile in $COPY_REFFILES
+    for tstfile in $COPY_ITERFILES
     do
         # ignore '#' comment
         echo $tstfile | tr -d ' ' | grep '^#' > /dev/null
@@ -206,9 +209,9 @@ COPY_REFFILES_TO_BLDREFDIR()
             # make cp fail
             SDIR=`$DIRNAME $tstfile`
             INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'`
-            INODE_DDIR=`$LS -i -d $BLDREFDIR | $AWK -F' ' '{print $1}'`
+            INODE_DDIR=`$LS -i -d $BLDITERDIR | $AWK -F' ' '{print $1}'`
             if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then
-                $CP -f $tstfile $BLDREFDIR
+                $CP -f $tstfile $BLDITERDIR
                 if [ $? -ne 0 ]; then
                     echo "Error: FAILED to copy $tstfile ."
 
@@ -220,16 +223,16 @@ COPY_REFFILES_TO_BLDREFDIR()
     done
 }
 
-CLEAN_REFFILES_AND_BLDREFDIR()
+CLEAN_ITERFILES_AND_BLDITERDIR()
 {
     # skip rm if srcdir is same as destdir
     # this occurs when build/test performed in source dir and
     # make cp fail
     SDIR=`$DIRNAME $HDFTEST_HOME/h5ex_g_iterate.h5`
     INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'`
-    INODE_DDIR=`$LS -i -d $BLDREFDIR | $AWK -F' ' '{print $1}'`
+    INODE_DDIR=`$LS -i -d $BLDITERDIR | $AWK -F' ' '{print $1}'`
     if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then
-        $RM $BLDREFDIR
+        $RM $BLDITERDIR
     fi
 }
 
@@ -252,7 +255,7 @@ JAVAEXEFLAGS=@H5_JAVAFLAGS@
 # prepare for test
 COPY_LIBFILES_TO_BLDLIBDIR
 COPY_DATAFILES_TO_BLDDIR
-COPY_REFFILES_TO_BLDREFDIR
+COPY_REFFILES_TO_BLDITERDIR
 
 CPATH=".:"$BLDLIBDIR"/"$JARFILE":"$BLDLIBDIR"/slf4j-api-1.7.25.jar:"$BLDLIBDIR"/slf4j-simple-1.7.25.jar:"$TESTJARFILE""
 
@@ -368,7 +371,7 @@ fi
 # Clean up temporary files/directories
 CLEAN_LIBFILES_AND_BLDLIBDIR
 CLEAN_DATAFILES_AND_BLDDIR
-CLEAN_REFFILES_AND_BLDREFDIR
+CLEAN_ITERFILES_AND_BLDITERDIR
 
 # Report test results and exit
 if test $nerrors -eq 0 ; then
diff --git a/java/src/jni/h5dImp.c b/java/src/jni/h5dImp.c
index f984948..652c873 100644
--- a/java/src/jni/h5dImp.c
+++ b/java/src/jni/h5dImp.c
@@ -1109,7 +1109,7 @@ Java_hdf_hdf5lib_H5_H5Dwrite_1string
                     const char *utf8 = ENVPTR->GetStringUTFChars(ENVPAR obj, 0);
 
                     if (utf8) {
-                        strncpy(&c_buf[i * str_len], utf8, str_len);
+                        HDstrncpy(&c_buf[i * str_len], utf8, str_len);
                     } /* end if */
 
                     ENVPTR->ReleaseStringUTFChars(ENVPAR obj, utf8);
diff --git a/java/src/jni/h5pImp.c b/java/src/jni/h5pImp.c
index e6d1be8..52008ce 100644
--- a/java/src/jni/h5pImp.c
+++ b/java/src/jni/h5pImp.c
@@ -3881,7 +3881,7 @@ Java_hdf_hdf5lib_H5_H5Pset_1fapl_1multi
                 const char *utf8 = ENVPTR->GetStringUTFChars(ENVPAR obj, 0);
 
                 if (utf8) {
-                    member_name[i] = (char*)HDmalloc(strlen(utf8) + 1);
+                    member_name[i] = (char*)HDmalloc(HDstrlen(utf8) + 1);
                     if (member_name[i]) {
                         strcpy(member_name[i], utf8);
                     } /* end if */
@@ -4189,7 +4189,7 @@ Java_hdf_hdf5lib_H5_H5Pset_1mdc_1config
         h5JNIFatalError(env, "H5Pset_mdc_config: out of memory trace_file_name");
         return;
     } /* end if */
-    strncpy(cacheinfo.trace_file_name, str, 1025);
+    HDstrncpy(cacheinfo.trace_file_name, str, 1025);
     ENVPTR->ReleaseStringUTFChars(ENVPAR j_str, str);
     if(ENVPTR->ExceptionOccurred(ENVONLY)) {
         h5JNIFatalError(env, "H5Pset_mdc_config: loading trace_file_name failed");
diff --git a/java/src/jni/h5sImp.c b/java/src/jni/h5sImp.c
index a4b4848..65cdd7b 100644
--- a/java/src/jni/h5sImp.c
+++ b/java/src/jni/h5sImp.c
@@ -571,7 +571,7 @@ Java_hdf_hdf5lib_H5_H5Sset_1extent_1simple
         h5JNIFatalError(env, "H5Pset_simple_extent:  dims not pinned");
         return -1;
     } /* end if */
-    sa = lp = (hsize_t *) malloc((size_t)rank * sizeof(hsize_t));
+    sa = lp = (hsize_t *) HDmalloc((size_t)rank * sizeof(hsize_t));
     if (sa == NULL) {
         ENVPTR->ReleaseLongArrayElements(ENVPAR dims, dimsP, JNI_ABORT);
         h5JNIFatalError(env, "H5Sset_simple_extent:  dims not converted to hsize_t");
@@ -1017,7 +1017,7 @@ Java_hdf_hdf5lib_H5_H5Sget_1select_1hyper_1blocklist
                 h5JNIFatalError(env, "H5Sget_select_hyper_blocklist:  buf not pinned");
             } /* end if */
             else {
-                ba = (hsize_t *) malloc((size_t)nb * 2 * (size_t)rank * sizeof(hsize_t));
+                ba = (hsize_t *) HDmalloc((size_t)nb * 2 * (size_t)rank * sizeof(hsize_t));
                 if (ba == NULL) {
                     ENVPTR->ReleaseLongArrayElements(ENVPAR buf, bufP, JNI_ABORT);
                     h5JNIFatalError(env, "H5Screate-simple:  buffer not converted to hsize_t");
@@ -1135,7 +1135,7 @@ Java_hdf_hdf5lib_H5_H5Sget_1select_1bounds
             return -1;
         } /* end if */
         rank = (int) ENVPTR->GetArrayLength(ENVPAR start);
-        strt = (hsize_t *)malloc((size_t)rank * sizeof(hsize_t));
+        strt = (hsize_t *)HDmalloc((size_t)rank * sizeof(hsize_t));
         if (strt == NULL) {
             ENVPTR->ReleaseLongArrayElements(ENVPAR start, startP, JNI_ABORT);
             h5JNIFatalError(env, "H5Sget_select_bounds:  start not converted to hsize_t");
diff --git a/java/src/jni/h5util.c b/java/src/jni/h5util.c
index 42f8a5c..fd34ba1 100644
--- a/java/src/jni/h5util.c
+++ b/java/src/jni/h5util.c
@@ -1768,7 +1768,7 @@ h5str_render_bin_output
                         if (H5Tis_variable_str(tid)) {
                             s = *(char**) mem;
                             if (s != NULL)
-                                size = strlen(s);
+                                size = HDstrlen(s);
                         }
                         else {
                             s = (char *) mem;
@@ -2129,11 +2129,11 @@ render_bin_output_region_data_points
                     ret_value = -1;
 
                 HDfree(dims1);
-            } /* end if((dims1 = (hsize_t *) malloc(sizeof(hsize_t) * ndims)) != NULL) */
+            } /* end if((dims1 = (hsize_t *) HDmalloc(sizeof(hsize_t) * ndims)) != NULL) */
             else
                 ret_value = -1;
             HDfree(region_buf);
-        } /* end if((region_buf = malloc(type_size * (size_t)npoints)) != NULL) */
+        } /* end if((region_buf = HDmalloc(type_size * (size_t)npoints)) != NULL) */
         else
             ret_value = -1;
 
@@ -2436,7 +2436,7 @@ Java_hdf_hdf5lib_H5_H5AreadComplex
     H5Tclose(p_type);
 
     n = ENVPTR->GetArrayLength(ENVPAR buf);
-    rdata = (char *)malloc((size_t)n * size);
+    rdata = (char *)HDmalloc((size_t)n * size);
     if (rdata == NULL) {
         h5JNIFatalError(env, "H5AreadComplex:  failed to allocate buff for read");
     } /* end if */
@@ -2952,7 +2952,7 @@ obj_info_all
     if (retVal < 0) {
         *(datainfo->otype+datainfo->count) = -1;
         *(datainfo->ltype+datainfo->count) = -1;
-        *(datainfo->objname+datainfo->count) = (char *)HDmalloc(strlen(name)+1);
+        *(datainfo->objname+datainfo->count) = (char *)HDmalloc(HDstrlen(name)+1);
         HDstrcpy(*(datainfo->objname+datainfo->count), name);
         *(datainfo->objno+datainfo->count) = (unsigned long)-1;
     } /* end if */