[svn-r22004] Reduced warnings and fixed conflicts resulting from including h5tools.h

Tested: local linux

19 files changed, 189 insertions, 176 deletions

diff --git a/tools/h5copy/h5copy.c b/tools/h5copy/h5copy.c
index 1a9a8eb..574ba94 100644
--- a/tools/h5copy/h5copy.c
+++ b/tools/h5copy/h5copy.c
@@ -465,7 +465,7 @@ main (int argc, const char *argv[])
 
     /* free link info path */
     if (linkinfo.trg_path)
-        HDfree(linkinfo.trg_path);
+        HDfree((char*)linkinfo.trg_path);
 
     /* close propertis */
     if(H5Pclose(ocpl_id)<0)
@@ -497,7 +497,7 @@ error:
 
     /* free link info path */
     if (linkinfo.trg_path)
-        HDfree(linkinfo.trg_path);
+        HDfree((char*)linkinfo.trg_path);
 
  H5E_BEGIN_TRY {
     H5Pclose(ocpl_id);
diff --git a/tools/h5diff/h5diff_common.c b/tools/h5diff/h5diff_common.c
index f7532f2..b8e46f3 100644
--- a/tools/h5diff/h5diff_common.c
+++ b/tools/h5diff/h5diff_common.c
@@ -17,6 +17,7 @@
 #include <string.h>
 #include "h5diff.h"
 #include "h5diff_common.h"
+#include "h5tools.h"
 #include "h5tools_utils.h"
 
 static int check_n_input( const char* );
@@ -53,7 +54,7 @@ static struct long_options l_opts[] = {
  *
  *-------------------------------------------------------------------------
  */
-static check_options(diff_opt_t* options)
+static void check_options(diff_opt_t* options)
 {
     /*--------------------------------------------------------------
      * check for mutually exclusive options 
@@ -179,7 +180,7 @@ void parse_command_line(int argc,
             }
 
             /* init */
-            exclude_node->obj_path = opt_arg;
+            exclude_node->obj_path = (char*)opt_arg;
             exclude_node->obj_type = H5TRAV_TYPE_UNKNOWN;
             exclude_prev = exclude_head;
             
diff --git a/tools/h5diff/h5diff_main.c b/tools/h5diff/h5diff_main.c
index 51a49c2..607d58e 100644
--- a/tools/h5diff/h5diff_main.c
+++ b/tools/h5diff/h5diff_main.c
@@ -18,6 +18,7 @@
 #include <memory.h>
 #include "h5diff.h"
 #include "h5diff_common.h"
+#include "h5tools.h"
 #include "h5tools_utils.h"
 
 
diff --git a/tools/h5diff/ph5diff_main.c b/tools/h5diff/ph5diff_main.c
index 5bd5567..1fc563b 100644
--- a/tools/h5diff/ph5diff_main.c
+++ b/tools/h5diff/ph5diff_main.c
@@ -19,6 +19,7 @@
 #include <string.h>
 #include <assert.h>
 #include "h5diff_common.h"
+#include "h5tools.h"
 #include "h5tools_utils.h"
 
 /* Name of tool */
diff --git a/tools/h5import/h5import.c b/tools/h5import/h5import.c
index 89701bd..56dc5ab 100755
--- a/tools/h5import/h5import.c
+++ b/tools/h5import/h5import.c
@@ -20,6 +20,7 @@
 #include <string.h>
 #include <ctype.h>
 #include "h5import.h"
+#include "h5tools.h"
 #include "h5tools_utils.h"
 
 /* Name of tool */
@@ -1361,7 +1362,7 @@ static int processConfigurationFile(char *infile, struct Input *in)
             break;
 
         case 12: /* EXTERNAL-STORAGE */
-            if (in->configOptionVector[EXTERNAL] == 1) {
+            if (in->configOptionVector[EXTERNALSTORE] == 1) {
                 (void) HDfprintf(stderr, err15a, infile);
                 HDfclose(strm);
                 return (-1);
@@ -1372,7 +1373,7 @@ static int processConfigurationFile(char *infile, struct Input *in)
                 HDfclose(strm);
                 return (-1);
             }
-            in->configOptionVector[EXTERNAL] = 1;
+            in->configOptionVector[EXTERNALSTORE] = 1;
             break;
 
         case 13: /* MAXIMUM-DIMENSIONS */
@@ -1435,7 +1436,7 @@ static int validateConfigurationParameters(struct Input *in)
         return (-1);
     }
 
-    if (in->configOptionVector[EXTERNAL] == 1) {
+    if (in->configOptionVector[EXTERNALSTORE] == 1) {
         if ((in->configOptionVector[COMPRESS] == 1) || (in->configOptionVector[CHUNK] == 1) || (in->configOptionVector[EXTEND] == 1)) {
             (void) HDfprintf(stderr, "%s", err2);
             return (-1);
@@ -2360,7 +2361,7 @@ static int process(struct Options *opt)
                 H5Pset_deflate(proplist, (unsigned) in->compressionParam);
             }
 
-            if (in->configOptionVector[EXTERNAL] == 1) {
+            if (in->configOptionVector[EXTERNALSTORE] == 1) {
                 /* creating the external file if it doesnt exist */
                 if ((extfile = HDfopen(in->externFilename, "ab")) == NULL) {
                     (void) HDfprintf(stderr, "%s", err4);
diff --git a/tools/h5import/h5import.h b/tools/h5import/h5import.h
index 05de476..dbc6844 100755
--- a/tools/h5import/h5import.h
+++ b/tools/h5import/h5import.h
@@ -47,7 +47,7 @@
 #define CHUNK            0
 #define COMPRESS         1
 #define EXTEND           2
-#define EXTERNAL         3
+#define EXTERNALSTORE    3
 #define DIM              4
 #define RANK             5
 #define PATH             6
diff --git a/tools/h5jam/getub.c b/tools/h5jam/getub.c
index 39a78ae..f536605 100644
--- a/tools/h5jam/getub.c
+++ b/tools/h5jam/getub.c
@@ -21,6 +21,7 @@
 #endif
 
 #include "H5private.h"
+#include "h5tools.h"
 #include "h5tools_utils.h"
 
 void parse_command_line (int argc, const char *argv[]);
diff --git a/tools/h5jam/h5jam.c b/tools/h5jam/h5jam.c
index 923bc5a..981eead 100644
--- a/tools/h5jam/h5jam.c
+++ b/tools/h5jam/h5jam.c
@@ -15,6 +15,7 @@
 
 #include "hdf5.h"
 #include "H5private.h"
+#include "h5tools.h"
 #include "h5tools_utils.h"
 
 /* Name of tool */
diff --git a/tools/h5jam/h5unjam.c b/tools/h5jam/h5unjam.c
index 1dfdfc7..4751dad 100644
--- a/tools/h5jam/h5unjam.c
+++ b/tools/h5jam/h5unjam.c
@@ -15,6 +15,7 @@
 
 #include "hdf5.h"
 #include "H5private.h"
+#include "h5tools.h"
 #include "h5tools_utils.h"
 
 /* Name of tool */
diff --git a/tools/h5jam/tellub.c b/tools/h5jam/tellub.c
index 2ffcbda..0169d71 100644
--- a/tools/h5jam/tellub.c
+++ b/tools/h5jam/tellub.c
@@ -21,6 +21,7 @@
 
 #include "hdf5.h"
 #include "H5private.h"
+#include "h5tools.h"
 #include "h5tools_utils.h"
 
 #define TRUE 1
diff --git a/tools/h5ls/h5ls.c b/tools/h5ls/h5ls.c
index 3e335e9..7315796 100644
--- a/tools/h5ls/h5ls.c
+++ b/tools/h5ls/h5ls.c
@@ -3127,7 +3127,7 @@ list_lnk(const char *name, const H5L_info_t *linfo, void *_iter)
             ret = H5tools_get_symlink_info(iter->fid, name, &lnk_info, follow_symlink_g);
             /* lnk_info.trg_path is malloced in H5tools_get_symlink_info()
              * so it will be freed via buf later */
-            buf = lnk_info.trg_path;
+            buf = (char*)lnk_info.trg_path;
             /* error */
             if (ret < 0)
                 goto done;
@@ -3185,7 +3185,7 @@ list_lnk(const char *name, const H5L_info_t *linfo, void *_iter)
             ret = H5tools_get_symlink_info(iter->fid, name, &lnk_info, follow_link);
             /* lnk_info.trg_path is malloced in H5tools_get_symlink_info()
              * so it will be freed via buf later */
-            buf = lnk_info.trg_path;
+            buf = (char*)lnk_info.trg_path;
             /* error */
             if (ret < 0)
                 goto done;
diff --git a/tools/h5repack/h5repack.c b/tools/h5repack/h5repack.c
index b36eb37..28d66c5 100644
--- a/tools/h5repack/h5repack.c
+++ b/tools/h5repack/h5repack.c
@@ -493,24 +493,24 @@ int copy_attr(hid_t loc_in,
         type_class = H5Tget_class(wtype_id);
         is_ref = (type_class == H5T_REFERENCE);
         if (type_class == H5T_VLEN ||type_class == H5T_ARRAY ) {
-          hid_t base_type = -1;
-          base_type = H5Tget_super(ftype_id);
-          is_ref = (is_ref || (H5Tget_class(base_type)==H5T_REFERENCE));
-          H5Tclose(base_type);
+        	hid_t base_type = -1;
+        	base_type = H5Tget_super(ftype_id);
+        	is_ref = (is_ref || (H5Tget_class(base_type)==H5T_REFERENCE));
+        	H5Tclose(base_type);
         }
 
         if (type_class == H5T_COMPOUND) {
-          int nmembers = H5Tget_nmembers(wtype_id) ;
-          for (j=0; j<nmembers; j++) {
-            hid_t mtid = H5Tget_member_type( wtype_id, j );
-            H5T_class_t mtclass = H5Tget_class(mtid);
-            H5Tclose(mtid);
-
-            if (mtclass==H5T_REFERENCE) {
-              is_ref = 1;
-              break;
-            }
-          } /* for (j=0; i<nmembers; j++) */
+        	int nmembers = H5Tget_nmembers(wtype_id) ;
+        	for (j=0; j<nmembers; j++) {
+        		hid_t mtid = H5Tget_member_type( wtype_id, j );
+        		H5T_class_t mtclass = H5Tget_class(mtid);
+        		H5Tclose(mtid);
+
+        		if (mtclass==H5T_REFERENCE) {
+        			is_ref = 1;
+        			break;
+        		}
+        	} /* for (j=0; i<nmembers; j++) */
         } /* if (type_class == H5T_COMPOUND) */
 
         if(is_ref) {
diff --git a/tools/h5repack/h5repack_main.c b/tools/h5repack/h5repack_main.c
index 15b57b0..720e8d6 100644
--- a/tools/h5repack/h5repack_main.c
+++ b/tools/h5repack/h5repack_main.c
@@ -13,6 +13,7 @@
  * access to either file, you may request a copy from help@hdfgroup.org.     *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
+#include "h5tools.h"
 #include "h5tools_utils.h"
 #include "h5repack.h"
 
diff --git a/tools/h5repack/h5repack_opttable.c b/tools/h5repack/h5repack_opttable.c
index b1a3469..d0fcff3 100644
--- a/tools/h5repack/h5repack_opttable.c
+++ b/tools/h5repack/h5repack_opttable.c
@@ -14,6 +14,7 @@
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
 #include "h5repack.h"
+#include "h5tools.h"
 #include "h5tools_utils.h"
 
 /*-------------------------------------------------------------------------
diff --git a/tools/h5repack/h5repack_parse.c b/tools/h5repack/h5repack_parse.c
index 910b182..70eadd2 100644
--- a/tools/h5repack/h5repack_parse.c
+++ b/tools/h5repack/h5repack_parse.c
@@ -14,6 +14,7 @@
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
 #include "h5repack.h"
+#include "h5tools.h"
 #include "h5tools_utils.h"
 
 /*-------------------------------------------------------------------------
diff --git a/tools/h5repack/h5repack_refs.c b/tools/h5repack/h5repack_refs.c
index 915b0e9..7108491 100644
--- a/tools/h5repack/h5repack_refs.c
+++ b/tools/h5repack/h5repack_refs.c
@@ -28,7 +28,7 @@ static const char* MapIdToName(hid_t refobj_id,trav_table_t *travt);
 static int copy_refs_attr(hid_t loc_in, hid_t loc_out, pack_opt_t *options,
                           trav_table_t *travt, hid_t fidout);
 static herr_t update_ref_value(hid_t obj_id, H5R_type_t ref_type, void *ref_in,
-    hid_t fid_out, void *ref_out, trav_table_t *travt);
+		hid_t fid_out, void *ref_out, trav_table_t *travt);
 
 /*-------------------------------------------------------------------------
  * Function: do_copy_refobjs
@@ -432,13 +432,13 @@ error:
  * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
  *
  * Modifier: xcao@hdfgroup.org, 9/12/2011
- *            Update values of references(object and region) for the following types:
+ * 	         Update values of references(object and region) for the following types:
  *               1) References,
  *               2) ARRAY of reference,
  *               3) VLEN of references.
  *               4) COMPOUND of references.
  *          This function does not handle references in other complicated structures,
- *        such as references in nested compound datatypes.
+ *		    such as references in nested compound datatypes.
  *
  * Date: October, 28, 2003
  *
@@ -479,7 +479,7 @@ static int copy_refs_attr(hid_t loc_in,
 
     for(u = 0; u < (unsigned)oinfo.num_attrs; u++)
     {
-      is_ref = is_ref_vlen = is_ref_array = is_ref_comp = 0;
+    	is_ref = is_ref_vlen = is_ref_array = is_ref_comp = 0;
 
         /* open attribute */
         if((attr_id = H5Aopen_by_idx(loc_in, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC, (hsize_t)u, H5P_DEFAULT, H5P_DEFAULT)) < 0)
@@ -500,39 +500,39 @@ static int copy_refs_attr(hid_t loc_in,
         is_ref = (type_class == H5T_REFERENCE);
 
         if (type_class == H5T_VLEN ) {
-          hid_t base_type = -1;
-          base_type = H5Tget_super(ftype_id);
-          is_ref_vlen = (H5Tget_class(base_type)==H5T_REFERENCE);
-          msize = H5Tget_size(base_type);
-          H5Tclose(base_type);
+        	hid_t base_type = -1;
+        	base_type = H5Tget_super(ftype_id);
+        	is_ref_vlen = (H5Tget_class(base_type)==H5T_REFERENCE);
+        	msize = H5Tget_size(base_type);
+        	H5Tclose(base_type);
         }
 
         if (type_class == H5T_ARRAY ) {
-          hid_t base_type = -1;
-          base_type = H5Tget_super(ftype_id);
-          is_ref_array = (H5Tget_class(base_type)==H5T_REFERENCE);
-          msize = H5Tget_size(base_type);
-          H5Tclose(base_type);
+        	hid_t base_type = -1;
+        	base_type = H5Tget_super(ftype_id);
+        	is_ref_array = (H5Tget_class(base_type)==H5T_REFERENCE);
+        	msize = H5Tget_size(base_type);
+        	H5Tclose(base_type);
         }
 
         if (type_class == H5T_COMPOUND) {
-          int nmembers = H5Tget_nmembers(ftype_id) ;
-          if (nmembers < 1)
-            goto error;
+        	int nmembers = H5Tget_nmembers(ftype_id) ;
+        	if (nmembers < 1)
+        		goto error;
 
             ref_comp_index = (int *)HDmalloc(nmembers*sizeof (int));
             ref_comp_size = (size_t *)HDmalloc(nmembers*sizeof(ref_comp_size));
             ref_comp_field_n = 0;
 
-          for (i=0; i<(unsigned)nmembers; i++) {
-            hid_t mtid = H5Tget_member_type( ftype_id, i );
-            if ((H5Tget_class(mtid)==H5T_REFERENCE)) {
-              ref_comp_index[ref_comp_field_n] = i;
-              ref_comp_size[ref_comp_field_n] = H5Tget_size(mtid);
-              ref_comp_field_n++;
-            }
-            H5Tclose(mtid);
-          }
+        	for (i=0; i<(unsigned)nmembers; i++) {
+        		hid_t mtid = H5Tget_member_type( ftype_id, i );
+        		if ((H5Tget_class(mtid)==H5T_REFERENCE)) {
+        			ref_comp_index[ref_comp_field_n] = i;
+        			ref_comp_size[ref_comp_field_n] = H5Tget_size(mtid);
+        			ref_comp_field_n++;
+        		}
+        		H5Tclose(mtid);
+        	}
             
             /* if compound don't contain reference type member, free the above 
              * mallocs. Otherwise there can be memory leaks by the 'continue' 
@@ -541,14 +541,14 @@ static int copy_refs_attr(hid_t loc_in,
             {
                 if (ref_comp_index) 
                 {
-                  HDfree(ref_comp_index);
-                  ref_comp_index = NULL;
+                	HDfree(ref_comp_index);
+                	ref_comp_index = NULL;
                 }
 
                 if (ref_comp_size) 
                 {
-                  HDfree(ref_comp_size);
-                  ref_comp_size = NULL;
+            	    HDfree(ref_comp_size);
+        	        ref_comp_size = NULL;
                 }
             }
         }
@@ -556,10 +556,10 @@ static int copy_refs_attr(hid_t loc_in,
         is_ref_comp = (ref_comp_field_n > 0);
 
         if (!(is_ref || is_ref_vlen || is_ref_array || is_ref_comp)) {
-          H5Tclose(mtype_id);
-             H5Tclose(ftype_id);
-          H5Aclose(attr_id);
-          continue;
+        	H5Tclose(mtype_id);
+           	H5Tclose(ftype_id);
+        	H5Aclose(attr_id);
+        	continue;
         }
 
         /* get name */
@@ -584,18 +584,18 @@ static int copy_refs_attr(hid_t loc_in,
             nelmts *= dims[j];
 
         if (is_ref_array) {
-          unsigned        array_rank = 0;
-          hsize_t    array_size = 1;
-          hsize_t array_dims[H5S_MAX_RANK];
-          hid_t base_type = -1;
-          base_type = H5Tget_super(ftype_id);
-          msize = H5Tget_size(base_type);
-             H5Tclose(base_type);
-
-          array_rank = H5Tget_array_ndims(mtype_id);
-          H5Tget_array_dims2(mtype_id, array_dims);
+        	unsigned        array_rank = 0;
+        	hsize_t    array_size = 1;
+        	hsize_t array_dims[H5S_MAX_RANK];
+        	hid_t base_type = -1;
+        	base_type = H5Tget_super(ftype_id);
+        	msize = H5Tget_size(base_type);
+           	H5Tclose(base_type);
+
+        	array_rank = H5Tget_array_ndims(mtype_id);
+        	H5Tget_array_dims2(mtype_id, array_dims);
             for(j = 0; j <array_rank; j++)
-              array_size *= array_dims[j];
+            	array_size *= array_dims[j];
             nelmts *= array_size;
          }
 
@@ -626,7 +626,7 @@ static int copy_refs_attr(hid_t loc_in,
                 for(i = 0; i < (unsigned)nelmts; i++)
                 {
                     if (update_ref_value(attr_id, H5R_OBJECT, &((hobj_ref_t *)buf)[i], fidout, &((hobj_ref_t *)refbuf)[i], travt)<0)
-                    continue;
+                		continue;
                     if(options->verbose)
                         printf("object <%s> reference created to <%s>\n", name, refname);
                 } /* k */
@@ -657,13 +657,13 @@ static int copy_refs_attr(hid_t loc_in,
                 for(i = 0; i < (unsigned)nelmts; i++)
                 {
                     if (update_ref_value(attr_id, H5R_DATASET_REGION, &((hdset_reg_ref_t *)buf)[i], fidout, &((hdset_reg_ref_t *)refbuf)[i], travt)<0)
-                    continue;
+                		continue;
                     if(options->verbose)
                         printf("object <%s> region reference created to <%s>\n", name, refname);
                 }
             } /* H5T_STD_REF_DSETREG */
             else if (is_ref_vlen) {
-              /* handle VLEN of references */
+            	/* handle VLEN of references */
 
                 buf = (hvl_t *)HDmalloc((unsigned)(nelmts * sizeof(hvl_t)));
                 refbuf = buf; /* reuse the read buffer for write */
@@ -677,31 +677,31 @@ static int copy_refs_attr(hid_t loc_in,
                 if(H5Aread(attr_id, mtype_id, buf) < 0)
                     goto error;
 
-         if (H5R_OBJ_REF_BUF_SIZE==msize) {
-          hobj_ref_t ref_out;
-          for (i=0; i<(unsigned)nelmts; i++) {
-            hobj_ref_t *ptr = (hobj_ref_t *)((hvl_t *)buf)[i].p;
-            for (j=0; j<((hvl_t *)buf)[i].len; j++ ) {
-              if (update_ref_value(attr_id, H5R_OBJECT, &(ptr[j]), fidout, &ref_out, travt)<0)
-                continue;
-              HDmemcpy(&(ptr[j]), &ref_out, msize);
-            }
-          }  /* for (i=0; i<nelems; i++) */
-        } else if (H5R_DSET_REG_REF_BUF_SIZE == msize) {
-
-          hdset_reg_ref_t ref_out;
-          for (i=0; i<(unsigned)nelmts; i++) {
-            hdset_reg_ref_t *ptr = (hdset_reg_ref_t *)((hvl_t *)buf)[i].p;
-            for (j=0; j<((hvl_t *)buf)[i].len; j++ ) {
-              if (update_ref_value(attr_id, H5R_DATASET_REGION, &(ptr[j]), fidout, &ref_out, travt)<0)
-                continue;
-              HDmemcpy(&(ptr[j]), &ref_out, msize);
-            }
-          }  /* for (i=0; i<nelems; i++) */
-        }
+ 				if (H5R_OBJ_REF_BUF_SIZE==msize) {
+					hobj_ref_t ref_out;
+					for (i=0; i<(unsigned)nelmts; i++) {
+						hobj_ref_t *ptr = (hobj_ref_t *)((hvl_t *)buf)[i].p;
+						for (j=0; j<((hvl_t *)buf)[i].len; j++ ) {
+							if (update_ref_value(attr_id, H5R_OBJECT, &(ptr[j]), fidout, &ref_out, travt)<0)
+								continue;
+							HDmemcpy(&(ptr[j]), &ref_out, msize);
+						}
+					}  /* for (i=0; i<nelems; i++) */
+				} else if (H5R_DSET_REG_REF_BUF_SIZE == msize) {
+
+					hdset_reg_ref_t ref_out;
+					for (i=0; i<(unsigned)nelmts; i++) {
+						hdset_reg_ref_t *ptr = (hdset_reg_ref_t *)((hvl_t *)buf)[i].p;
+						for (j=0; j<((hvl_t *)buf)[i].len; j++ ) {
+							if (update_ref_value(attr_id, H5R_DATASET_REGION, &(ptr[j]), fidout, &ref_out, travt)<0)
+								continue;
+							HDmemcpy(&(ptr[j]), &ref_out, msize);
+						}
+					}  /* for (i=0; i<nelems; i++) */
+				}
             } /* else if (is_ref_vlen) */
             else if (is_ref_comp) {
-              /* handle ref fields in a compound */
+            	/* handle ref fields in a compound */
 
                 buf = HDmalloc((unsigned)(nelmts * msize));
                 refbuf = buf; /* reuse the read buffer for write */
@@ -716,22 +716,22 @@ static int copy_refs_attr(hid_t loc_in,
                     goto error;
 
                 for (i=0; i<(unsigned)nelmts; i++) {
-                  for (j=0; j<(unsigned)ref_comp_field_n; j++) {
-                    if (ref_comp_size[j] == H5R_OBJ_REF_BUF_SIZE) {
-                      int idx = i*msize+H5Tget_member_offset( mtype_id, (unsigned)ref_comp_index[j]);
-                      hobj_ref_t ref_out;
-                      if (update_ref_value(attr_id, H5R_OBJECT, (hobj_ref_t *)(((char *)buf)+idx), fidout, &ref_out, travt)<0)
-                        continue;
-                      HDmemcpy(((char *)buf)+idx, &ref_out, ref_comp_size[j]);
-                     } /* if */
-                    else if (ref_comp_size[j] == H5R_DSET_REG_REF_BUF_SIZE) {
-                      int idx = i*msize+H5Tget_member_offset( mtype_id, (unsigned)ref_comp_index[j]);
-                      hdset_reg_ref_t ref_out;
-                      if (update_ref_value(attr_id, H5R_DATASET_REGION, (hdset_reg_ref_t *)(((char *)buf)+idx), fidout, &ref_out, travt)<0)
-                        continue;
-                      HDmemcpy(((char *)buf)+idx, &ref_out, ref_comp_size[j]);
-                     } /* else if */
-                  } /* j */
+                	for (j=0; j<(unsigned)ref_comp_field_n; j++) {
+                		if (ref_comp_size[j] == H5R_OBJ_REF_BUF_SIZE) {
+                			int idx = i*msize+H5Tget_member_offset( mtype_id, (unsigned)ref_comp_index[j]);
+                			hobj_ref_t ref_out;
+                			if (update_ref_value(attr_id, H5R_OBJECT, (hobj_ref_t *)(((char *)buf)+idx), fidout, &ref_out, travt)<0)
+                				continue;
+                			HDmemcpy(((char *)buf)+idx, &ref_out, ref_comp_size[j]);
+                 		} /* if */
+                		else if (ref_comp_size[j] == H5R_DSET_REG_REF_BUF_SIZE) {
+                			int idx = i*msize+H5Tget_member_offset( mtype_id, (unsigned)ref_comp_index[j]);
+                			hdset_reg_ref_t ref_out;
+                			if (update_ref_value(attr_id, H5R_DATASET_REGION, (hdset_reg_ref_t *)(((char *)buf)+idx), fidout, &ref_out, travt)<0)
+                				continue;
+                			HDmemcpy(((char *)buf)+idx, &ref_out, ref_comp_size[j]);
+                 		} /* else if */
+                	} /* j */
                 } /* i */
             } /* else if (is_ref_comp) */
 
@@ -739,11 +739,11 @@ static int copy_refs_attr(hid_t loc_in,
                  goto error;
 
             if (is_ref_vlen && buf)
-              H5Dvlen_reclaim (mtype_id, space_id, H5P_DEFAULT, buf);
+            	H5Dvlen_reclaim (mtype_id, space_id, H5P_DEFAULT, buf);
         } /* if (nelmts) */
 
         if (refbuf == buf)
-          refbuf = NULL; /* set it to NULL to avoid double free since buf and refbuf are the same. */
+        	refbuf = NULL; /* set it to NULL to avoid double free since buf and refbuf are the same. */
 
         if(buf) {
             HDfree(buf);
@@ -756,13 +756,13 @@ static int copy_refs_attr(hid_t loc_in,
         }
 
         if (ref_comp_index) {
-          HDfree(ref_comp_index);
-          ref_comp_index = NULL;
+        	HDfree(ref_comp_index);
+        	ref_comp_index = NULL;
         }
 
         if (ref_comp_size) {
-          HDfree(ref_comp_size);
-          ref_comp_size = NULL;
+        	HDfree(ref_comp_size);
+        	ref_comp_size = NULL;
         }
 
         if(H5Aclose(attr_out) < 0)
@@ -785,16 +785,16 @@ static int copy_refs_attr(hid_t loc_in,
     return 0;
 
 error:
-  if(refbuf)
-    HDfree(refbuf);
-  if(buf)
-    HDfree(buf);
+	if(refbuf)
+		HDfree(refbuf);
+	if(buf)
+		HDfree(buf);
 
     if (ref_comp_index)
-      HDfree(ref_comp_index);
+    	HDfree(ref_comp_index);
 
     if (ref_comp_size)
-      HDfree(ref_comp_size);
+    	HDfree(ref_comp_size);
 
     H5E_BEGIN_TRY {
         H5Tclose(ftype_id);
@@ -808,9 +808,9 @@ error:
 }
 
 /*-------------------------------------------------------------------------
- * Function:  MapIdToName
+ * Function:	MapIdToName
  *
- * Purpose:  map a ID from a reference to a dataset name
+ * Purpose:	map a ID from a reference to a dataset name
  *
  *-------------------------------------------------------------------------
  */
@@ -843,41 +843,41 @@ out:
 }
 
 /*-------------------------------------------------------------------------
- * Function:  Update_Ref_value
+ * Function:	Update_Ref_value
  *
- * Purpose:  Update a reference value
+ * Purpose:	Update a reference value
  *
  * Programmer: xcao@hdfgroup.org 9/12/2011
  *
  *-------------------------------------------------------------------------
  */
 static herr_t update_ref_value(hid_t obj_id, H5R_type_t ref_type, void *ref_in,
-    hid_t fid_out, void *ref_out, trav_table_t *travt)
+		hid_t fid_out, void *ref_out, trav_table_t *travt)
 {
-  herr_t ret = -1;
-  const char* ref_obj_name;
-  hid_t space_id=-1, ref_obj_id=-1;
+	herr_t ret = -1;
+	const char* ref_obj_name;
+	hid_t space_id=-1, ref_obj_id=-1;
 
-  ref_obj_id = H5Rdereference2(obj_id, H5P_DEFAULT, ref_type, ref_in);
-  if (ref_obj_id<0)
-    goto done;
+    ref_obj_id = H5Rdereference2(obj_id, H5P_DEFAULT, ref_type, ref_in);
+    if (ref_obj_id<0)
+       goto done;
 
-  ref_obj_name = MapIdToName(ref_obj_id, travt);
-  if (ref_obj_name == NULL)
-    goto done;
+	ref_obj_name = MapIdToName(ref_obj_id, travt);
+	if (ref_obj_name == NULL)
+		goto done;
 
-  if (ref_type == H5R_DATASET_REGION) {
-    space_id = H5Rget_region(obj_id, H5R_DATASET_REGION, ref_in);
-    if (space_id < 0)
-      goto done;
-  }
+	if (ref_type == H5R_DATASET_REGION) {
+		space_id = H5Rget_region(obj_id, H5R_DATASET_REGION, ref_in);
+		if (space_id < 0)
+			goto done;
+	}
 
     ret = H5Rcreate(ref_out, fid_out, ref_obj_name, ref_type, space_id);
 
     if (ret < 0)
-      goto done;
+    	goto done;
 
-  ret = 0;
+	ret = 0;
 
 done:
     H5E_BEGIN_TRY {
@@ -885,6 +885,6 @@ done:
       H5Oclose(ref_obj_id);
     } H5E_END_TRY;
 
-  return ret;
+	return ret;
 }
 
diff --git a/tools/h5repack/h5repack_verify.c b/tools/h5repack/h5repack_verify.c
index b0ab1d1..47cba5b 100644
--- a/tools/h5repack/h5repack_verify.c
+++ b/tools/h5repack/h5repack_verify.c
@@ -14,16 +14,17 @@
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
 #include "h5repack.h"
+#include "h5tools.h"
 #include "h5tools_utils.h"
 
-static int verify_layout(hid_t pid, pack_info_t *obj);
-static int verify_filters(hid_t pid, hid_t tid, int nfilters, filter_info_t *filter);
-
 /* number of members in an array */
 #ifndef NELMTS
-#    define NELMTS(X)		(sizeof(X)/sizeof(X[0]))
+#    define NELMTS(X)    (sizeof(X)/sizeof(X[0]))
 #endif
 
+static int verify_layout(hid_t pid, pack_info_t *obj);
+static int verify_filters(hid_t pid, hid_t tid, int nfilters, filter_info_t *filter);
+
 
 /*-------------------------------------------------------------------------
  * Function: h5repack_verify
@@ -301,9 +302,9 @@ error:
  *
  * Purpose: verify which layout is present in the property list DCPL_ID
  *
- *  H5D_COMPACT	  	= 0
- *  H5D_CONTIGUOUS	= 1
- *  H5D_CHUNKED		= 2
+ *  H5D_COMPACT      = 0
+ *  H5D_CONTIGUOUS  = 1
+ *  H5D_CHUNKED    = 2
  *
  * Return: 1 has, 0 does not, -1 error
  *
diff --git a/tools/h5repack/testh5repack_detect_szip.c b/tools/h5repack/testh5repack_detect_szip.c
index 0a6a77a..e91b2f7 100644
--- a/tools/h5repack/testh5repack_detect_szip.c
+++ b/tools/h5repack/testh5repack_detect_szip.c
@@ -16,6 +16,7 @@
 #include <stdio.h>
 #include "h5repack.h"
 #include "h5tools.h"
+#include "h5tools_utils.h"
 #include "h5test.h"
 
 
diff --git a/tools/lib/h5diff.c b/tools/lib/h5diff.c
index f86e914..bc8acd5 100644
--- a/tools/lib/h5diff.c
+++ b/tools/lib/h5diff.c
@@ -614,7 +614,7 @@ static herr_t trav_grp_symlinks(const char *path, const H5L_info_t *linfo,
 
 done:    
     if (lnk_info.trg_path)
-        HDfree(lnk_info.trg_path);
+        HDfree((char *)lnk_info.trg_path);
     return 0;
 }    
 
@@ -728,25 +728,25 @@ hsize_t h5diff(const char *fname1,
         /* make the given object1 fullpath, start with "/"  */
         if (HDstrncmp(objname1, "/", 1))
         {
-            HDstrcpy(obj1fullname, "/");
-            HDstrcat(obj1fullname, objname1);
+            HDstrcpy((char *)obj1fullname, "/");
+            HDstrcat((char *)obj1fullname, objname1);
         }
         else
-            HDstrcpy(obj1fullname, objname1);
+            HDstrcpy((char *)obj1fullname, objname1);
 
         /* make the given object2 fullpath, start with "/" */
         if (HDstrncmp(objname2, "/", 1))
         {
-            HDstrcpy(obj2fullname, "/");
-            HDstrcat(obj2fullname, objname2);
+            HDstrcpy((char *)obj2fullname, "/");
+            HDstrcat((char *)obj2fullname, objname2);
         }
         else
-            HDstrcpy(obj2fullname, objname2);
+            HDstrcpy((char *)obj2fullname, objname2);
 
         /*----------------------------------------------------------
          * check if obj1 is root, group, single object or symlink
          */
-        if(!HDstrcmp(obj1fullname, "/"))
+        if(!HDstrcmp((char *)obj1fullname, "/"))
         {
             obj1type = H5TRAV_TYPE_GROUP;
         }
@@ -856,9 +856,9 @@ hsize_t h5diff(const char *fname1,
     {
         /* set root group */
         obj1fullname = (char*)HDcalloc(2, sizeof(char));
-        HDstrcat(obj1fullname, "/");
+        HDstrcat((char *)obj1fullname, "/");
         obj2fullname = (char*)HDcalloc(2, sizeof(char));
-        HDstrcat(obj2fullname, "/");
+        HDstrcat((char *)obj2fullname, "/");
     }
 
 
@@ -1045,15 +1045,15 @@ out:
 
     /* free buffers */
     if (obj1fullname)
-        HDfree(obj1fullname);
+        HDfree((char *)obj1fullname);
     if (obj2fullname)
-        HDfree(obj2fullname);
+        HDfree((char *)obj2fullname);
 
     /* free link info buffer */
     if (trg_linfo1.trg_path)
-        HDfree(trg_linfo1.trg_path);
+        HDfree((char *)trg_linfo1.trg_path);
     if (trg_linfo2.trg_path)
-        HDfree(trg_linfo2.trg_path);
+        HDfree((char *)trg_linfo2.trg_path);
 
     /* close */
     H5E_BEGIN_TRY
@@ -1112,9 +1112,9 @@ hsize_t diff_match(hid_t file1_id, const char *grp1, trav_info_t *info1,
      * make full path
      */
     if (HDstrcmp (grp1, "/"))
-        grp1_path = grp1;
+        grp1_path = (char *)grp1;
     if (HDstrcmp (grp2, "/"))
-        grp2_path = grp2;
+        grp2_path = (char *)grp2;
 
     /*-------------------------------------------------------------------------
     * regarding the return value of h5diff (0, no difference in files, 1 difference )
@@ -1769,9 +1769,9 @@ out:
 
     /* free link info buffer */
     if (linkinfo1.trg_path)
-        HDfree(linkinfo1.trg_path);
+        HDfree((char *)linkinfo1.trg_path);
     if (linkinfo2.trg_path)
-        HDfree(linkinfo2.trg_path);
+        HDfree((char *)linkinfo2.trg_path);
 
     return nfound;
 }
@@ -2163,9 +2163,9 @@ hsize_t diff(hid_t file1_id,
 
     /* free link info buffer */
     if (linkinfo1.trg_path)
-        HDfree(linkinfo1.trg_path);
+        HDfree((char *)linkinfo1.trg_path);
     if (linkinfo2.trg_path)
-        HDfree(linkinfo2.trg_path);
+        HDfree((char *)linkinfo2.trg_path);
 
     return nfound;
 
@@ -2206,9 +2206,9 @@ out2:
 
     /* free link info buffer */
     if (linkinfo1.trg_path)
-        HDfree(linkinfo1.trg_path);
+        HDfree((char *)linkinfo1.trg_path);
     if (linkinfo2.trg_path)
-        HDfree(linkinfo2.trg_path);
+        HDfree((char *)linkinfo2.trg_path);
 
     /* close */
     /* disable error reporting */