[svn-r25497] Description:

    Merge changes that correspond to the 64-bit ID changes (without the actual
switch to 64-bit IDs) to the 1.8 release branch.  (Plus a few minor cleanups
and alignments with the trunk that aren't on the branch)

Tested on:
    Mac OSX/64 10.9.4 (amazon) w/C++ & FORTRAN
    (h5committested on branch already for a week)

18 files changed, 159 insertions, 159 deletions

diff --git a/tools/h5copy/h5copygentest.c b/tools/h5copy/h5copygentest.c
index e45d24a..49204f5 100644
--- a/tools/h5copy/h5copygentest.c
+++ b/tools/h5copy/h5copygentest.c
@@ -237,10 +237,10 @@ static void gent_named_vl(hid_t loc_id)
 
     /* allocate and initialize VL dataset to write */
     buf[0].len = 1;
-    buf[0].p = malloc( 1 * sizeof(int));
+    buf[0].p = HDmalloc( 1 * sizeof(int));
     ((int *)buf[0].p)[0]=1;
     buf[1].len = 2;
-    buf[1].p = malloc( 2 * sizeof(int));
+    buf[1].p = HDmalloc( 2 * sizeof(int));
     ((int *)buf[1].p)[0]=2;
     ((int *)buf[1].p)[1]=3;
 
@@ -283,16 +283,16 @@ static void gent_nested_vl(hid_t loc_id)
 
     /* allocate and initialize VL dataset to write */
     buf[0].len = 1;
-    buf[0].p = malloc( 1 * sizeof(hvl_t));
+    buf[0].p = HDmalloc( 1 * sizeof(hvl_t));
     tvl = (hvl_t *)buf[0].p;
-    tvl->p = malloc( 1 * sizeof(int) );
+    tvl->p = HDmalloc( 1 * sizeof(int) );
     tvl->len = 1;
     ((int *)tvl->p)[0]=1;
 
     buf[1].len = 1;
-    buf[1].p = malloc( 1 * sizeof(hvl_t));
+    buf[1].p = HDmalloc( 1 * sizeof(hvl_t));
     tvl = (hvl_t *)buf[1].p;
-    tvl->p = malloc( 2 * sizeof(int) );
+    tvl->p = HDmalloc( 2 * sizeof(int) );
     tvl->len = 2;
     ((int *)tvl->p)[0]=2;
     ((int *)tvl->p)[1]=3;
@@ -454,23 +454,23 @@ static herr_t gen_obj_ref(hid_t loc_id)
 
     /*--------------
      * add group  */
-     oid = H5Gcreate2 (loc_id, OBJ_REF_GRP, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+    oid = H5Gcreate2 (loc_id, OBJ_REF_GRP, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
     if (oid < 0)
     {
         fprintf(stderr, "Error: %s %d> H5Gcreate2 failed.\n", FUNC, __LINE__);
         ret = FAIL;
         goto out;
     }
-     H5Gclose(oid);
+    H5Gclose(oid);
 
-    status = H5Rcreate (&or_data[0], loc_id, OBJ_REF_DS, H5R_OBJECT, -1);
+    status = H5Rcreate (&or_data[0], loc_id, OBJ_REF_DS, H5R_OBJECT, (hid_t)-1);
     if (status < 0)
     {
         fprintf(stderr, "Error: %s %d> H5Rcreate failed.\n", FUNC, __LINE__);
         ret = FAIL;
         goto out;
     }
-    status = H5Rcreate (&or_data[1], loc_id, OBJ_REF_GRP, H5R_OBJECT, -1);
+    status = H5Rcreate (&or_data[1], loc_id, OBJ_REF_GRP, H5R_OBJECT, (hid_t)-1);
     if (status < 0)
     {
         fprintf(stderr, "Error: %s %d> H5Rcreate failed.\n", FUNC, __LINE__);
diff --git a/tools/h5diff/h5diffgentest.c b/tools/h5diff/h5diffgentest.c
index d554abd..80405e9 100644
--- a/tools/h5diff/h5diffgentest.c
+++ b/tools/h5diff/h5diffgentest.c
@@ -978,8 +978,8 @@ int test_attributes(const char *file,
     */
 
     write_attr_in(did,"dset",fid,make_diffs);
-    write_attr_in(gid,NULL,0,make_diffs);
-    write_attr_in(root_id,NULL,0,make_diffs);
+    write_attr_in(gid,NULL,(hid_t)0,make_diffs);
+    write_attr_in(root_id,NULL,(hid_t)0,make_diffs);
 
 
     /* Close */
@@ -4127,9 +4127,9 @@ static int test_comp_vlen_strings(const char *fname1, const char *grp_name, int
     did_comp = H5Dcreate2(gid, "Compound_dset9", tid9_comp, sid_comp, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
 
     /* obj references */
-    status=H5Rcreate(&(comp9_buf.objref1),gid,"Compound_dset2",H5R_OBJECT,-1);
-    status=H5Rcreate(&(comp9_buf.objref2),gid,"Compound_dset3",H5R_OBJECT,-1);
-    status=H5Rcreate(&(comp9_buf.objref3),gid,"Compound_dset4",H5R_OBJECT,-1);
+    status=H5Rcreate(&(comp9_buf.objref1),gid,"Compound_dset2",H5R_OBJECT,(hid_t)-1);
+    status=H5Rcreate(&(comp9_buf.objref2),gid,"Compound_dset3",H5R_OBJECT,(hid_t)-1);
+    status=H5Rcreate(&(comp9_buf.objref3),gid,"Compound_dset4",H5R_OBJECT,(hid_t)-1);
 
     status = H5Dwrite(did_comp, tid9_comp, H5S_ALL, H5S_ALL, H5P_DEFAULT, &comp9_buf);
     if (status < 0)
@@ -5416,8 +5416,8 @@ void write_attr_in(hid_t loc_id,
     /* Create references to dataset */
     if (dset_name)
     {
-        status=H5Rcreate(&buf4[0],fid,dset_name,H5R_OBJECT,-1);
-        status=H5Rcreate(&buf4[1],fid,dset_name,H5R_OBJECT,-1);
+        status=H5Rcreate(&buf4[0],fid,dset_name,H5R_OBJECT,(hid_t)-1);
+        status=H5Rcreate(&buf4[1],fid,dset_name,H5R_OBJECT,(hid_t)-1);
         write_attr(loc_id,1,dims,"reference",H5T_STD_REF_OBJ,buf4);
     }
 
@@ -5698,7 +5698,7 @@ void write_attr_in(hid_t loc_id,
     {
         for (i = 0; i < 3; i++) {
             for (j = 0; j < 2; j++) {
-                status=H5Rcreate(&buf42[i][j],fid,dset_name,H5R_OBJECT,-1);
+                status=H5Rcreate(&buf42[i][j],fid,dset_name,H5R_OBJECT,(hid_t)-1);
             }
         }
         write_attr(loc_id,2,dims2,"reference2D",H5T_STD_REF_OBJ,buf42);
@@ -6094,7 +6094,7 @@ void write_attr_in(hid_t loc_id,
         for (i = 0; i < 4; i++) {
             for (j = 0; j < 3; j++) {
                 for (k = 0; k < 2; k++)
-                    status=H5Rcreate(&buf43[i][j][k],fid,dset_name,H5R_OBJECT,-1);
+                    status=H5Rcreate(&buf43[i][j][k],fid,dset_name,H5R_OBJECT,(hid_t)-1);
             }
         }
         write_attr(loc_id,3,dims3,"reference3D",H5T_STD_REF_OBJ,buf43);
@@ -6460,8 +6460,8 @@ void write_dset_in(hid_t loc_id,
     /* Create references to dataset */
     if (dset_name)
     {
-        status=H5Rcreate(&buf4[0],fid,dset_name,H5R_OBJECT,-1);
-        status=H5Rcreate(&buf4[1],fid,dset_name,H5R_OBJECT,-1);
+        status=H5Rcreate(&buf4[0],fid,dset_name,H5R_OBJECT,(hid_t)-1);
+        status=H5Rcreate(&buf4[1],fid,dset_name,H5R_OBJECT,(hid_t)-1);
         write_dset(loc_id,1,dims,"reference",H5T_STD_REF_OBJ,buf4);
     }
 
@@ -6675,7 +6675,7 @@ void write_dset_in(hid_t loc_id,
     {
         for (i = 0; i < 3; i++) {
             for (j = 0; j < 2; j++) {
-                status=H5Rcreate(&buf42[i][j],fid,dset_name,H5R_OBJECT,-1);
+                status=H5Rcreate(&buf42[i][j],fid,dset_name,H5R_OBJECT,(hid_t)-1);
             }
         }
         write_dset(loc_id,2,dims2,"reference2D",H5T_STD_REF_OBJ,buf42);
@@ -6886,7 +6886,7 @@ void write_dset_in(hid_t loc_id,
         for (i = 0; i < 4; i++) {
             for (j = 0; j < 3; j++) {
                 for (k = 0; k < 2; k++)
-                    status=H5Rcreate(&buf43[i][j][k],fid,dset_name,H5R_OBJECT,-1);
+                    status=H5Rcreate(&buf43[i][j][k],fid,dset_name,H5R_OBJECT,(hid_t)-1);
             }
         }
         write_dset(loc_id,3,dims3,"reference3D",H5T_STD_REF_OBJ,buf43);
diff --git a/tools/h5dump/h5dump_xml.c b/tools/h5dump/h5dump_xml.c
index c081ee0..64667cb 100644
--- a/tools/h5dump/h5dump_xml.c
+++ b/tools/h5dump/h5dump_xml.c
@@ -1937,7 +1937,7 @@ xml_dump_data(hid_t obj_id, int obj_data, struct subset_t UNUSED * sset, int UNU
             datactx.need_prefix = TRUE;
             datactx.indent_level = ctx.indent_level;
             datactx.cur_column = ctx.cur_column;
-            status = h5tools_dump_dset(rawoutstream, outputformat, &datactx, obj_id, -1, NULL);
+            status = h5tools_dump_dset(rawoutstream, outputformat, &datactx, obj_id, NULL);
         }
     } 
     else {
diff --git a/tools/h5dump/h5dumpgentest.c b/tools/h5dump/h5dumpgentest.c
index 884670e..046c5e1 100644
--- a/tools/h5dump/h5dumpgentest.c
+++ b/tools/h5dump/h5dumpgentest.c
@@ -2043,16 +2043,16 @@ static void gent_objref(void)
     dataset = H5Dcreate2(fid1, "Dataset3", H5T_STD_REF_OBJ, sid1, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
 
     /* Create reference to dataset */
-    H5Rcreate(&wbuf[0], fid1, "/Group1/Dataset1", H5R_OBJECT, -1);
+    H5Rcreate(&wbuf[0], fid1, "/Group1/Dataset1", H5R_OBJECT, (hid_t)-1);
 
     /* Create reference to dataset */
-    H5Rcreate(&wbuf[1], fid1, "/Group1/Dataset2", H5R_OBJECT, -1);
+    H5Rcreate(&wbuf[1], fid1, "/Group1/Dataset2", H5R_OBJECT, (hid_t)-1);
 
     /* Create reference to group */
-    H5Rcreate(&wbuf[2], fid1, "/Group1", H5R_OBJECT, -1);
+    H5Rcreate(&wbuf[2], fid1, "/Group1", H5R_OBJECT, (hid_t)-1);
 
     /* Create reference to named datatype */
-    H5Rcreate(&wbuf[3], fid1, "/Group1/Datatype1", H5R_OBJECT, -1);
+    H5Rcreate(&wbuf[3], fid1, "/Group1/Datatype1", H5R_OBJECT, (hid_t)-1);
 
     /* Write selection to disk */
     H5Dwrite(dataset, H5T_STD_REF_OBJ, H5S_ALL, H5S_ALL, H5P_DEFAULT, wbuf);
@@ -3913,8 +3913,8 @@ static void write_attr_in(hid_t loc_id,
     /* Create references to dataset */
     if(dset_name)
     {
-        status=H5Rcreate(&buf4[0],fid,dset_name,H5R_OBJECT,-1);
-        status=H5Rcreate(&buf4[1],fid,dset_name,H5R_OBJECT,-1);
+        status=H5Rcreate(&buf4[0],fid,dset_name,H5R_OBJECT,(hid_t)-1);
+        status=H5Rcreate(&buf4[1],fid,dset_name,H5R_OBJECT,(hid_t)-1);
         write_attr(loc_id,1,dims,"reference",H5T_STD_REF_OBJ,buf4);
     }
 
@@ -4020,7 +4020,7 @@ static void write_attr_in(hid_t loc_id,
     {
         for(i = 0; i < 3; i++) {
             for(j = 0; j < 2; j++) {
-                status=H5Rcreate(&buf42[i][j],fid,dset_name,H5R_OBJECT,-1);
+                status=H5Rcreate(&buf42[i][j],fid,dset_name,H5R_OBJECT,(hid_t)-1);
             }
         }
         write_attr(loc_id,2,dims2,"reference2D",H5T_STD_REF_OBJ,buf42);
@@ -4151,7 +4151,7 @@ static void write_attr_in(hid_t loc_id,
         for(i = 0; i < 4; i++) {
             for(j = 0; j < 3; j++) {
                 for(k = 0; k < 2; k++)
-                    status=H5Rcreate(&buf43[i][j][k],fid,dset_name,H5R_OBJECT,-1);
+                    status=H5Rcreate(&buf43[i][j][k],fid,dset_name,H5R_OBJECT,(hid_t)-1);
             }
         }
         write_attr(loc_id,3,dims3,"reference3D",H5T_STD_REF_OBJ,buf43);
@@ -4355,8 +4355,8 @@ static void write_dset_in(hid_t loc_id,
     /* Create references to dataset */
     if(dset_name)
     {
-        status=H5Rcreate(&buf4[0],fid,dset_name,H5R_OBJECT,-1);
-        status=H5Rcreate(&buf4[1],fid,dset_name,H5R_OBJECT,-1);
+        status=H5Rcreate(&buf4[0],fid,dset_name,H5R_OBJECT,(hid_t)-1);
+        status=H5Rcreate(&buf4[1],fid,dset_name,H5R_OBJECT,(hid_t)-1);
         write_dset(loc_id,1,dims,"reference",H5T_STD_REF_OBJ,buf4);
     }
 
@@ -4462,7 +4462,7 @@ static void write_dset_in(hid_t loc_id,
     {
         for(i = 0; i < 3; i++) {
             for(j = 0; j < 2; j++) {
-                status=H5Rcreate(&buf42[i][j],fid,dset_name,H5R_OBJECT,-1);
+                status=H5Rcreate(&buf42[i][j],fid,dset_name,H5R_OBJECT,(hid_t)-1);
             }
         }
         write_dset(loc_id,2,dims2,"reference2D",H5T_STD_REF_OBJ,buf42);
@@ -4605,7 +4605,7 @@ static void write_dset_in(hid_t loc_id,
         for(i = 0; i < 4; i++) {
             for(j = 0; j < 3; j++) {
                 for(k = 0; k < 2; k++)
-                    status=H5Rcreate(&buf43[i][j][k],fid,dset_name,H5R_OBJECT,-1);
+                    status=H5Rcreate(&buf43[i][j][k],fid,dset_name,H5R_OBJECT,(hid_t)-1);
             }
         }
         write_dset(loc_id,3,dims3,"reference3D",H5T_STD_REF_OBJ,buf43);
@@ -4730,8 +4730,8 @@ static void gent_attr_all(void)
      */
 
     write_attr_in(did,"dset",fid);
-    write_attr_in(group_id,NULL,0);
-    write_attr_in(root_id,NULL,0);
+    write_attr_in(group_id,NULL,(hid_t)0);
+    write_attr_in(root_id,NULL,(hid_t)0);
 
     /*-------------------------------------------------------------------------
      * write a series of datasets on group 2
diff --git a/tools/h5jam/getub.c b/tools/h5jam/getub.c
index afb0da6..776eaeb 100644
--- a/tools/h5jam/getub.c
+++ b/tools/h5jam/getub.c
@@ -162,7 +162,7 @@ main (int argc, const char *argv[])
   if (res < (long)size)
     {
       if (buf)
-  free (buf);
+  HDfree (buf);
       HDclose (fd);
       exit (EXIT_FAILURE);
     }
@@ -170,7 +170,7 @@ main (int argc, const char *argv[])
   HDwrite (1, buf, (unsigned)size);
 
   if (buf)
-    free (buf);
+    HDfree (buf);
   HDclose (fd);
   return (EXIT_SUCCESS);
 }
diff --git a/tools/h5ls/h5ls.c b/tools/h5ls/h5ls.c
index d8768fb..4b8a50b 100644
--- a/tools/h5ls/h5ls.c
+++ b/tools/h5ls/h5ls.c
@@ -1464,7 +1464,7 @@ dump_dataset_values(hid_t dset)
     h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, (hsize_t)0, (hsize_t)0);
     ctx.need_prefix = TRUE;
     ctx.cur_column = (size_t)curr_pos;
-    if (h5tools_dump_dset(rawoutstream, info, &ctx, dset, -1, NULL) < 0) {
+    if (h5tools_dump_dset(rawoutstream, info, &ctx, dset, NULL) < 0) {
         h5tools_str_reset(&buffer);
         h5tools_str_append(&buffer, "        Unable to print data.");
         h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, (hsize_t)0, (hsize_t)0);
diff --git a/tools/h5repack/h5repack_copy.c b/tools/h5repack/h5repack_copy.c
index 63b5373..a25e789 100644
--- a/tools/h5repack/h5repack_copy.c
+++ b/tools/h5repack/h5repack_copy.c
@@ -39,7 +39,7 @@
 #define CHECK_H5DRW_ERROR(_fun, _did, _mtid, _msid, _fsid, _pid, _buf)  {  \
     H5E_BEGIN_TRY {  \
         if(_fun(_did, _mtid, _msid, _fsid, _pid, _buf) < 0) {  \
-            int _err_num = 0; \
+            hid_t _err_num = 0; \
             char _msg[80]; \
             H5Ewalk2(H5E_DEFAULT, H5E_WALK_DOWNWARD, walk_error_callback, &_err_num); \
             H5Eget_msg(_err_num, NULL, _msg, (size_t)80); \
diff --git a/tools/h5repack/h5repack_main.c b/tools/h5repack/h5repack_main.c
index c25b7ea..3d4de6f 100644
--- a/tools/h5repack/h5repack_main.c
+++ b/tools/h5repack/h5repack_main.c
@@ -21,6 +21,8 @@
 #define PROGRAMNAME "h5repack"
 
 static int parse_command_line(int argc, const char **argv, pack_opt_t* options);
+static void leave(int ret);
+
 
 /* module-scoped variables */
 static int has_i_o = 0;
@@ -520,7 +522,6 @@ done:
 int main(int argc, const char **argv) {
 
 	pack_opt_t options; /*the global options */
-	int ret = -1;
 
 	h5tools_setprogname(PROGRAMNAME);
 	h5tools_setstatus(EXIT_SUCCESS);
diff --git a/tools/h5repack/h5repack_refs.c b/tools/h5repack/h5repack_refs.c
index b844280..2b39249 100644
--- a/tools/h5repack/h5repack_refs.c
+++ b/tools/h5repack/h5repack_refs.c
@@ -189,7 +189,7 @@ int do_copy_refobjs(hid_t fidin,
                                  */
                                 if((refname = MapIdToName(refobj_id, travt)) != NULL) {
                                     /* create the reference, -1 parameter for objects */
-                                    if(H5Rcreate(&refbuf[u], fidout, refname, H5R_OBJECT, -1) < 0)
+                                    if(H5Rcreate(&refbuf[u], fidout, refname, H5R_OBJECT, (hid_t)-1) < 0)
                                         goto error;
                                     if(options->verbose)
                                     {
diff --git a/tools/h5repack/h5repacktst.c b/tools/h5repack/h5repacktst.c
index 4510bd5..a32f33a 100644
--- a/tools/h5repack/h5repacktst.c
+++ b/tools/h5repack/h5repacktst.c
@@ -2271,7 +2271,7 @@ int make_deflate(hid_t loc_id)
 
     /* create a reference to the dataset, test second seeep of file for references */
 
-    if (H5Rcreate(&bufref[0],loc_id,"dset_deflate",H5R_OBJECT,-1) < 0)
+    if (H5Rcreate(&bufref[0],loc_id,"dset_deflate",H5R_OBJECT,(hid_t)-1) < 0)
         goto out;
     if (write_dset(loc_id,1,dims1r,"ref",H5T_STD_REF_OBJ,bufref) < 0)
         goto out;
@@ -3322,7 +3322,7 @@ int make_big(hid_t loc_id)
         goto out;
 
     /* initialize buffer to 0  */
-    buf=(signed  char *) calloc( nelmts, size);
+    buf=(signed  char *) HDcalloc( nelmts, size);
 
     if (H5Sselect_hyperslab (f_sid,H5S_SELECT_SET,hs_start,NULL,hs_size, NULL) < 0)
         goto out;
@@ -3769,7 +3769,7 @@ int write_dset_in(hid_t loc_id,
     buf4[1]=0;
     if (dset_name)
     {
-        if (H5Rcreate(&buf4[0],file_id,dset_name,H5R_OBJECT,-1) < 0)
+        if (H5Rcreate(&buf4[0],file_id,dset_name,H5R_OBJECT,(hid_t)-1) < 0)
             goto out;
         if (write_dset(loc_id,1,dims1r,"refobj",H5T_STD_REF_OBJ,buf4) < 0)
             goto out;
@@ -3803,10 +3803,10 @@ int write_dset_in(hid_t loc_id,
     /* Allocate and initialize VL dataset to write */
 
     buf5[0].len = 1;
-    buf5[0].p = malloc( 1 * sizeof(int));
+    buf5[0].p = HDmalloc( 1 * sizeof(int));
     ((int *)buf5[0].p)[0]=1;
     buf5[1].len = 2;
-    buf5[1].p = malloc( 2 * sizeof(int));
+    buf5[1].p = HDmalloc( 2 * sizeof(int));
     ((int *)buf5[1].p)[0] = 2;
     ((int *)buf5[1].p)[1] = 3;
 
@@ -3865,7 +3865,7 @@ int write_dset_in(hid_t loc_id,
 
         /* allocate and initialize array data to write */
         size = ( TEST_BUFSIZE / sizeof(double) + 1 ) * sizeof(double);
-        dbuf = (double*)malloc( size );
+        dbuf = (double*)HDmalloc( size );
         if (NULL == dbuf)
         {
             printf ("\nError: Cannot allocate memory for \"arrayd\" data buffer size %dMB.\n", (int) size / 1000000 );
@@ -4004,7 +4004,7 @@ int write_dset_in(hid_t loc_id,
     /* Create references to dataset */
     if (dset_name)
     {
-        if (H5Rcreate(&buf42[0][0], file_id, dset_name, H5R_OBJECT, -1) < 0)
+        if (H5Rcreate(&buf42[0][0], file_id, dset_name, H5R_OBJECT, (hid_t)-1) < 0)
             goto out;
         if (write_dset(loc_id, 2, dims2r, "refobj2D", H5T_STD_REF_OBJ, buf42) < 0)
             goto out;
@@ -4039,7 +4039,7 @@ int write_dset_in(hid_t loc_id,
         {
             int l;
 
-            buf52[i][j].p = malloc((i + 1) * sizeof(int));
+            buf52[i][j].p = HDmalloc((i + 1) * sizeof(int));
             buf52[i][j].len = (size_t)(i + 1);
             for(l = 0; l < i + 1; l++)
             {
@@ -4223,7 +4223,7 @@ int write_dset_in(hid_t loc_id,
     /* Create references to dataset */
     if (dset_name)
     {
-        if (H5Rcreate(&buf43[0][0][0], file_id, dset_name, H5R_OBJECT, -1) < 0)
+        if (H5Rcreate(&buf43[0][0][0], file_id, dset_name, H5R_OBJECT, (hid_t)-1) < 0)
             goto out;
         if (write_dset(loc_id, 3, dims3r, "refobj3D", H5T_STD_REF_OBJ, buf43) < 0)
             goto out;
@@ -4260,7 +4260,7 @@ int write_dset_in(hid_t loc_id,
             {
                 int l;
 
-                buf53[i][j][k].p = malloc((i + 1) * sizeof(int));
+                buf53[i][j][k].p = HDmalloc((i + 1) * sizeof(int));
                 buf53[i][j][k].len = (size_t)(i + 1);
                 for(l = 0; l < i + 1; l++)
                 {
@@ -4390,8 +4390,8 @@ int make_dset_reg_ref(hid_t loc_id)
     int             retval = -1;  /* return value */
 
     /* Allocate write & read buffers */
-    wbuf = (hdset_reg_ref_t *)calloc(sizeof(hdset_reg_ref_t), (size_t)SPACE1_DIM1);
-    dwbuf = (int *)malloc(sizeof(int) * SPACE2_DIM1 * SPACE2_DIM2);
+    wbuf = (hdset_reg_ref_t *)HDcalloc(sizeof(hdset_reg_ref_t), (size_t)SPACE1_DIM1);
+    dwbuf = (int *)HDmalloc(sizeof(int) * SPACE2_DIM1 * SPACE2_DIM2);
 
     /* Create dataspace for datasets */
     if ((sid2 = H5Screate_simple(SPACE2_RANK, dims2, NULL)) < 0)
@@ -4681,9 +4681,9 @@ int write_attr_in(hid_t loc_id,
     /* object references ( H5R_OBJECT  */
     if (dset_name)
     {
-        if (H5Rcreate(&buf4[0],fid,dset_name,H5R_OBJECT,-1) < 0)
+        if (H5Rcreate(&buf4[0],fid,dset_name,H5R_OBJECT,(hid_t)-1) < 0)
             goto out;
-        if (H5Rcreate(&buf4[1],fid,dset_name,H5R_OBJECT,-1) < 0)
+        if (H5Rcreate(&buf4[1],fid,dset_name,H5R_OBJECT,(hid_t)-1) < 0)
             goto out;
         if (make_attr(loc_id,1,dims,"reference",H5T_STD_REF_OBJ,buf4) < 0)
             goto out;
@@ -4731,10 +4731,10 @@ int write_attr_in(hid_t loc_id,
     /* Allocate and initialize VL dataset to write */
 
     buf5[0].len = 1;
-    buf5[0].p = malloc( 1 * sizeof(int));
+    buf5[0].p = HDmalloc( 1 * sizeof(int));
     ((int *)buf5[0].p)[0]=1;
     buf5[1].len = 2;
-    buf5[1].p = malloc(2 * sizeof(int));
+    buf5[1].p = HDmalloc(2 * sizeof(int));
     ((int *)buf5[1].p)[0] = 2;
     ((int *)buf5[1].p)[1] = 3;
 
@@ -4995,7 +4995,7 @@ int write_attr_in(hid_t loc_id,
         {
             for (j = 0; j < 2; j++)
             {
-                if (H5Rcreate(&buf42[i][j],fid,dset_name,H5R_OBJECT,-1) < 0)
+                if (H5Rcreate(&buf42[i][j],fid,dset_name,H5R_OBJECT,(hid_t)-1) < 0)
                     goto out;
             }
         }
@@ -5051,7 +5051,7 @@ int write_attr_in(hid_t loc_id,
         for (j = 0; j < 2; j++)
         {
             int l;
-            buf52[i][j].p = malloc((i + 1) * sizeof(int));
+            buf52[i][j].p = HDmalloc((i + 1) * sizeof(int));
             buf52[i][j].len = (size_t)(i + 1);
             for (l = 0; l < i + 1; l++)
                 if (make_diffs)((int *)buf52[i][j].p)[l] = 0;
@@ -5430,7 +5430,7 @@ int write_attr_in(hid_t loc_id,
             for (j = 0; j < 3; j++)
             {
                 for (k = 0; k < 2; k++)
-                    if (H5Rcreate(&buf43[i][j][k],fid,dset_name,H5R_OBJECT,-1) < 0)
+                    if (H5Rcreate(&buf43[i][j][k],fid,dset_name,H5R_OBJECT,(hid_t)-1) < 0)
                         goto out;
             }
         }
@@ -5517,7 +5517,7 @@ int write_attr_in(hid_t loc_id,
             for (k = 0; k < 2; k++)
             {
                 int l;
-                buf53[i][j][k].p = malloc((i + 1) * sizeof(int));
+                buf53[i][j][k].p = HDmalloc((i + 1) * sizeof(int));
                 buf53[i][j][k].len = (size_t)i + 1;
                 for (l = 0; l < i + 1; l++)
                     if (make_diffs)
@@ -5939,7 +5939,7 @@ static herr_t add_attr_with_objref(hid_t file_id, hid_t obj_id)
      * add attribute with obj ref type
      */    
     /* ref to dset */
-    status = H5Rcreate(&data_attr_objref[0],file_id,NAME_OBJ_DS1,H5R_OBJECT,-1);
+    status = H5Rcreate(&data_attr_objref[0],file_id,NAME_OBJ_DS1,H5R_OBJECT,(hid_t)-1);
     if (status < 0)
     {
         fprintf(stderr, "Error: %s %d> H5Rcreate failed.\n", FUNC, __LINE__);
@@ -5948,7 +5948,7 @@ static herr_t add_attr_with_objref(hid_t file_id, hid_t obj_id)
     }
 
     /* ref to group */
-    status = H5Rcreate(&data_attr_objref[1],file_id,NAME_OBJ_GRP,H5R_OBJECT,-1);
+    status = H5Rcreate(&data_attr_objref[1],file_id,NAME_OBJ_GRP,H5R_OBJECT,(hid_t)-1);
     if (status < 0)
     {
         fprintf(stderr, "Error: %s %d> H5Rcreate failed.\n", FUNC, __LINE__);
@@ -5957,7 +5957,7 @@ static herr_t add_attr_with_objref(hid_t file_id, hid_t obj_id)
     }
 
     /* ref to datatype */
-    status = H5Rcreate(&data_attr_objref[2],file_id,NAME_OBJ_NDTYPE,H5R_OBJECT,-1);
+    status = H5Rcreate(&data_attr_objref[2],file_id,NAME_OBJ_NDTYPE,H5R_OBJECT,(hid_t)-1);
     if (status < 0)
     {
         fprintf(stderr, "Error: %s %d> H5Rcreate failed.\n", FUNC, __LINE__);
@@ -6210,7 +6210,7 @@ static herr_t gen_obj_ref(hid_t loc_id)
      * Passing -1 as reference is an object.*/
 
     /* obj ref to dataset */
-    status = H5Rcreate (&objref_buf[0], loc_id, NAME_OBJ_DS1, H5R_OBJECT, -1);
+    status = H5Rcreate (&objref_buf[0], loc_id, NAME_OBJ_DS1, H5R_OBJECT, (hid_t)-1);
     if (status < 0)
     {
         fprintf(stderr, "Error: %s %d> H5Rcreate failed.\n", FUNC, __LINE__);
@@ -6219,7 +6219,7 @@ static herr_t gen_obj_ref(hid_t loc_id)
     }
 
     /* obj ref to group */
-    status = H5Rcreate (&objref_buf[1], loc_id, NAME_OBJ_GRP, H5R_OBJECT, -1);
+    status = H5Rcreate (&objref_buf[1], loc_id, NAME_OBJ_GRP, H5R_OBJECT, (hid_t)-1);
     if (status < 0)
     {
         fprintf(stderr, "Error: %s %d> H5Rcreate failed.\n", FUNC, __LINE__);
@@ -6228,7 +6228,7 @@ static herr_t gen_obj_ref(hid_t loc_id)
     }
 
     /* obj ref to named-datatype */
-    status = H5Rcreate (&objref_buf[2], loc_id, NAME_OBJ_NDTYPE, H5R_OBJECT, -1);
+    status = H5Rcreate (&objref_buf[2], loc_id, NAME_OBJ_NDTYPE, H5R_OBJECT, (hid_t)-1);
     if (status < 0)
     {
         fprintf(stderr, "Error: %s %d> H5Rcreate failed.\n", FUNC, __LINE__);
@@ -6650,7 +6650,7 @@ static herr_t make_complex_attr_references(hid_t loc_id)
      * Create the object references into compound type
      */
      /* references to dataset */
-    status = H5Rcreate (&(comp_objref_data[0].val_objref), loc_id, NAME_OBJ_DS1, H5R_OBJECT,-1);
+    status = H5Rcreate (&(comp_objref_data[0].val_objref), loc_id, NAME_OBJ_DS1, H5R_OBJECT,(hid_t)-1);
     if (status < 0)
     {
         fprintf(stderr, "Error: %s %d> H5Rcreate failed.\n", FUNC, __LINE__);
@@ -6660,7 +6660,7 @@ static herr_t make_complex_attr_references(hid_t loc_id)
     comp_objref_data[0].val_int = 0;
 
      /* references to group */
-    status = H5Rcreate (&(comp_objref_data[1].val_objref), loc_id, NAME_OBJ_GRP, H5R_OBJECT,-1);
+    status = H5Rcreate (&(comp_objref_data[1].val_objref), loc_id, NAME_OBJ_GRP, H5R_OBJECT,(hid_t)-1);
     if (status < 0)
     {
         fprintf(stderr, "Error: %s %d> H5Rcreate failed.\n", FUNC, __LINE__);
@@ -6670,7 +6670,7 @@ static herr_t make_complex_attr_references(hid_t loc_id)
     comp_objref_data[1].val_int = 10;
 
      /* references to datatype */
-    status = H5Rcreate (&(comp_objref_data[2].val_objref), loc_id, NAME_OBJ_NDTYPE, H5R_OBJECT,-1);
+    status = H5Rcreate (&(comp_objref_data[2].val_objref), loc_id, NAME_OBJ_NDTYPE, H5R_OBJECT,(hid_t)-1);
     if (status < 0)
     {
         fprintf(stderr, "Error: %s %d> H5Rcreate failed.\n", FUNC, __LINE__);
@@ -6743,17 +6743,17 @@ static herr_t make_complex_attr_references(hid_t loc_id)
      * prepare vlen data
      */
      vlen_objref_data[0].len = LEN0_VLEN_OBJREF;
-     vlen_objref_data[0].p = malloc (vlen_objref_data[0].len * sizeof(hobj_ref_t));
+     vlen_objref_data[0].p = HDmalloc (vlen_objref_data[0].len * sizeof(hobj_ref_t));
      vlen_objref_data[1].len = LEN1_VLEN_OBJREF;
-     vlen_objref_data[1].p = malloc (vlen_objref_data[1].len * sizeof(hobj_ref_t));
+     vlen_objref_data[1].p = HDmalloc (vlen_objref_data[1].len * sizeof(hobj_ref_t));
      vlen_objref_data[2].len = LEN2_VLEN_OBJREF;
-     vlen_objref_data[2].p = malloc (vlen_objref_data[2].len * sizeof(hobj_ref_t));
+     vlen_objref_data[2].p = HDmalloc (vlen_objref_data[2].len * sizeof(hobj_ref_t));
 
      /* 
       * create obj references 
       */
      /* reference to dataset */
-     status = H5Rcreate (&((hobj_ref_t*)vlen_objref_data[0].p)[0], loc_id, NAME_OBJ_DS1, H5R_OBJECT, -1);
+     status = H5Rcreate (&((hobj_ref_t*)vlen_objref_data[0].p)[0], loc_id, NAME_OBJ_DS1, H5R_OBJECT, (hid_t)-1);
     if (status < 0)
     {
         fprintf(stderr, "Error: %s %d> H5Rcreate failed.\n", FUNC, __LINE__);
@@ -6761,7 +6761,7 @@ static herr_t make_complex_attr_references(hid_t loc_id)
         goto out;
     }
      /* reference to group */
-     status = H5Rcreate (&((hobj_ref_t*)vlen_objref_data[1].p)[0], loc_id, NAME_OBJ_GRP, H5R_OBJECT, -1); 
+     status = H5Rcreate (&((hobj_ref_t*)vlen_objref_data[1].p)[0], loc_id, NAME_OBJ_GRP, H5R_OBJECT, (hid_t)-1); 
     if (status < 0)
     {
         fprintf(stderr, "Error: %s %d> H5Rcreate failed.\n", FUNC, __LINE__);
@@ -6769,7 +6769,7 @@ static herr_t make_complex_attr_references(hid_t loc_id)
         goto out;
     }
      /* reference to datatype */
-     status = H5Rcreate (&((hobj_ref_t*)vlen_objref_data[2].p)[0], loc_id, NAME_OBJ_NDTYPE, H5R_OBJECT, -1);
+     status = H5Rcreate (&((hobj_ref_t*)vlen_objref_data[2].p)[0], loc_id, NAME_OBJ_NDTYPE, H5R_OBJECT, (hid_t)-1);
     if (status < 0)
     {
         fprintf(stderr, "Error: %s %d> H5Rcreate failed.\n", FUNC, __LINE__);
@@ -6812,7 +6812,7 @@ static herr_t make_complex_attr_references(hid_t loc_id)
      * prepare vlen data
      */
     vlen_regref_data[0].len = LEN0_VLEN_REGREF;
-    vlen_regref_data[0].p = malloc (vlen_regref_data[0].len * sizeof(hdset_reg_ref_t));
+    vlen_regref_data[0].p = HDmalloc (vlen_regref_data[0].len * sizeof(hdset_reg_ref_t));
 
     /*
      * create region reference 
diff --git a/tools/h5stat/h5stat.c b/tools/h5stat/h5stat.c
index de36c19..a3a0d13 100644
--- a/tools/h5stat/h5stat.c
+++ b/tools/h5stat/h5stat.c
@@ -32,9 +32,9 @@
 #define DEF_SIZE_SMALL_DSETS        	10
 #define DEF_SIZE_SMALL_ATTRS  		10
 
-#define  H5_NFILTERS_IMPL        	8     /* Number of currently implemented filters + one to
-                                          	 accommodate for user-define filters + one
-						 to accomodate datasets whithout any filters */
+#define  H5_NFILTERS_IMPL        8     /* Number of currently implemented filters + one to
+                                          accommodate for user-define filters + one
+                                          to accomodate datasets whithout any filters */
 
 
 
@@ -855,7 +855,7 @@ parse_command_line(int argc, const char *argv[], struct handler_t **hand_ret)
 			error_msg("Invalid threshold for small datasets\n");
 			goto error;
 		    }
-		} else 
+		} else
 		    error_msg("Missing threshold for small datasets\n");
 
                 break;
@@ -878,7 +878,7 @@ parse_command_line(int argc, const char *argv[], struct handler_t **hand_ret)
 			goto error;
 		    }
 		} else
-		    error_msg("Missing threshold for small # of attributes\n");
+                    error_msg("Missing threshold for small # of attributes\n");
 
                 break;
 
@@ -1592,9 +1592,9 @@ main(int argc, const char *argv[])
             iter.SM_heap_storage_size = finfo.sohm.msgs_info.heap_size;
         } /* end else */
 
-	iter.num_small_groups = (unsigned long *)calloc((size_t)sgroups_threshold, sizeof(unsigned long));
-	iter.num_small_attrs = (unsigned long *)calloc((size_t)(sattrs_threshold+1), sizeof(unsigned long));
-	iter.small_dset_dims = (unsigned long *)calloc((size_t)sdsets_threshold, sizeof(unsigned long));
+	iter.num_small_groups = (unsigned long *)HDcalloc((size_t)sgroups_threshold, sizeof(unsigned long));
+	iter.num_small_attrs = (unsigned long *)HDcalloc((size_t)(sattrs_threshold+1), sizeof(unsigned long));
+	iter.small_dset_dims = (unsigned long *)HDcalloc((size_t)sdsets_threshold, sizeof(unsigned long));
 
 	if(iter.num_small_groups == NULL || iter.num_small_attrs == NULL || iter.small_dset_dims == NULL) {
 	    error_msg("Unable to allocate memory for tracking small groups/datasets/attributes\n");
diff --git a/tools/lib/h5tools.c b/tools/lib/h5tools.c
index fb12408..a7b0e5e 100644
--- a/tools/lib/h5tools.c
+++ b/tools/lib/h5tools.c
@@ -844,18 +844,18 @@ h5tools_simple_prefix(FILE *stream, const h5tool_format_t *info,
        the prefix is printed one indentation level before */
     if (info->pindex) {
         for (i = 0; i < indentlevel - 1; i++) {
-            PUTSTREAM(h5tools_str_fmt(&str, 0, info->line_indent), stream);
+            PUTSTREAM(h5tools_str_fmt(&str, (size_t)0, info->line_indent), stream);
         }
     }
 
     if (elmtno == 0 && secnum == 0 && info->line_1st) {
-        PUTSTREAM(h5tools_str_fmt(&prefix, 0, info->line_1st), stream);
+        PUTSTREAM(h5tools_str_fmt(&prefix, (size_t)0, info->line_1st), stream);
     }
     else if (secnum && info->line_cont) {
-        PUTSTREAM(h5tools_str_fmt(&prefix, 0, info->line_cont), stream);
+        PUTSTREAM(h5tools_str_fmt(&prefix, (size_t)0, info->line_cont), stream);
     }
     else {
-        PUTSTREAM(h5tools_str_fmt(&prefix, 0, info->line_pre), stream);
+        PUTSTREAM(h5tools_str_fmt(&prefix, (size_t)0, info->line_pre), stream);
     }
 
     templength = h5tools_str_len(&prefix);
@@ -863,7 +863,7 @@ h5tools_simple_prefix(FILE *stream, const h5tool_format_t *info,
     for (i = 0; i < indentlevel; i++) {
         /*we already made the indent for the array indices case */
         if (!info->pindex) {
-            PUTSTREAM(h5tools_str_fmt(&prefix, 0, info->line_indent), stream);
+            PUTSTREAM(h5tools_str_fmt(&prefix, (size_t)0, info->line_indent), stream);
             templength += h5tools_str_len(&prefix);
         }
         else {
@@ -937,22 +937,22 @@ h5tools_region_simple_prefix(FILE *stream, const h5tool_format_t *info,
        the prefix is printed one indentation level before */
     if (info->pindex)
         for (i = 0; i < indentlevel - 1; i++) {
-            PUTSTREAM(h5tools_str_fmt(&str, 0, info->line_indent), stream);
+            PUTSTREAM(h5tools_str_fmt(&str, (size_t)0, info->line_indent), stream);
         }
 
     if (elmtno == 0 && secnum == 0 && info->line_1st) {
-        PUTSTREAM(h5tools_str_fmt(&prefix, 0, info->line_1st), stream);
+        PUTSTREAM(h5tools_str_fmt(&prefix, (size_t)0, info->line_1st), stream);
     } else if (secnum && info->line_cont) {
-        PUTSTREAM(h5tools_str_fmt(&prefix, 0, info->line_cont), stream);
+        PUTSTREAM(h5tools_str_fmt(&prefix, (size_t)0, info->line_cont), stream);
     } else
-        PUTSTREAM(h5tools_str_fmt(&prefix, 0, info->line_pre), stream);
+        PUTSTREAM(h5tools_str_fmt(&prefix, (size_t)0, info->line_pre), stream);
 
     templength = h5tools_str_len(&prefix);
 
     for (i = 0; i < indentlevel; i++) {
         /*we already made the indent for the array indices case */
         if (!info->pindex) {
-            PUTSTREAM(h5tools_str_fmt(&prefix, 0, info->line_indent), stream);
+            PUTSTREAM(h5tools_str_fmt(&prefix, (size_t)0, info->line_indent), stream);
             templength += h5tools_str_len(&prefix);
         }
         else {
@@ -1009,7 +1009,7 @@ h5tools_render_element(FILE *stream, const h5tool_format_t *info,
     if (stream == NULL)
         return dimension_break;
 
-    s = h5tools_str_fmt(buffer, 0, "%s");
+    s = h5tools_str_fmt(buffer, (size_t)0, "%s");
 
     /*
      * If the element would split on multiple lines if printed at our
@@ -1163,7 +1163,7 @@ h5tools_render_region_element(FILE *stream, const h5tool_format_t *info,
     int      secnum; /*section sequence number */
     int      multiline; /*datum was multiline  */
 
-    s = h5tools_str_fmt(buffer, 0, "%s");
+    s = h5tools_str_fmt(buffer, (size_t)0, "%s");
 
     /*
      * If the element would split on multiple lines if printed at our
diff --git a/tools/lib/h5tools_dump.c b/tools/lib/h5tools_dump.c
index f11065c..5ab066e 100644
--- a/tools/lib/h5tools_dump.c
+++ b/tools/lib/h5tools_dump.c
@@ -1748,11 +1748,11 @@ CATCH
  */
 int
 h5tools_dump_dset(FILE *stream, const h5tool_format_t *info, h5tools_context_t *ctx, 
-        hid_t dset, hid_t _p_type, struct subset_t *sset)
+        hid_t dset, struct subset_t *sset)
 {
-    hid_t     f_space;
-    hid_t     p_type = _p_type;
-    hid_t     f_type;
+    hid_t     f_space = -1;
+    hid_t     p_type = -1;
+    hid_t     f_type = -1;
     H5S_class_t space_type;
     int       status = FAIL;
     h5tool_format_t info_dflt;
@@ -1765,26 +1765,26 @@ h5tools_dump_dset(FILE *stream, const h5tool_format_t *info, h5tools_context_t *
         info = &info_dflt;
     }
 
-    if (p_type < 0) {
-        f_type = H5Dget_type(dset);
-
-        if (info->raw || bin_form == 1)
-            p_type = H5Tcopy(f_type);
-        else if (bin_form == 2)
-            p_type = h5tools_get_little_endian_type(f_type);
-        else if (bin_form == 3)
-            p_type = h5tools_get_big_endian_type(f_type);
-        else
-            p_type = h5tools_get_native_type(f_type);
+    f_type = H5Dget_type(dset);
+    if (f_type < 0)
+        goto done;
 
-        H5Tclose(f_type);
+    if (info->raw || bin_form == 1)
+        p_type = H5Tcopy(f_type);
+    else if (bin_form == 2)
+        p_type = h5tools_get_little_endian_type(f_type);
+    else if (bin_form == 3)
+        p_type = h5tools_get_big_endian_type(f_type);
+    else
+        p_type = h5tools_get_native_type(f_type);
 
-        if (p_type < 0)
-            goto done;
-    }
+    if (p_type < 0)
+        goto done;
 
     /* Check the data space */
     f_space = H5Dget_space(dset);
+    if (f_space < 0)
+        goto done;
 
     space_type = H5Sget_simple_extent_type(f_space);
 
@@ -1799,12 +1799,13 @@ h5tools_dump_dset(FILE *stream, const h5tool_format_t *info, h5tools_context_t *
         /* space is H5S_NULL */
         status = SUCCEED;
 
-    /* Close the dataspace */
-    H5Sclose(f_space);
-
 done:
-    if (p_type != _p_type)
+    if (f_type > 0)
+        H5Tclose(f_type);
+    if (p_type > 0)
         H5Tclose(p_type);
+    if (f_space > 0)
+        H5Sclose(f_space);
 
     return status;
 }
@@ -3859,7 +3860,7 @@ h5tools_dump_data(FILE *stream, const h5tool_format_t *info,
         }
         else
             datactx.need_prefix = TRUE;
-        status = h5tools_dump_dset(stream, info, &datactx, obj_id, -1, sset);
+        status = h5tools_dump_dset(stream, info, &datactx, obj_id, sset);
         if((display_char && H5Tget_size(f_type) == 1) && (H5Tget_class(f_type) == H5T_INTEGER)) {
             h5tools_str_reset(&buffer);
             h5tools_str_append(&buffer, "\"");
diff --git a/tools/lib/h5tools_dump.h b/tools/lib/h5tools_dump.h
index 061a3db..b05f226 100644
--- a/tools/lib/h5tools_dump.h
+++ b/tools/lib/h5tools_dump.h
@@ -40,7 +40,7 @@ H5TOOLS_DLL void    h5tools_dump_init(void);
 
 H5TOOLS_DLL int     h5tools_dump_dset(FILE *stream, const h5tool_format_t *info,
                             h5tools_context_t *ctx/*in,out*/, hid_t dset,
-                            hid_t p_typ, struct subset_t *sset);
+                            struct subset_t *sset);
 H5TOOLS_DLL int     h5tools_dump_mem(FILE *stream, const h5tool_format_t *info,
                             h5tools_context_t *ctx/*in,out*/, hid_t obj_id,
                             hid_t type, hid_t space, void *mem);
diff --git a/tools/lib/h5tools_str.c b/tools/lib/h5tools_str.c
index d43fc33..ac191d6 100644
--- a/tools/lib/h5tools_str.c
+++ b/tools/lib/h5tools_str.c
@@ -352,7 +352,7 @@ h5tools_str_prefix(h5tools_str_t *str/*in,out*/, const h5tool_format_t *info,
     }
 
     /* Add prefix and suffix to the index */
-    return h5tools_str_fmt(str, 0, OPT(info->idx_fmt, "%s: "));
+    return h5tools_str_fmt(str, (size_t)0, OPT(info->idx_fmt, "%s: "));
 }
 
 /*-------------------------------------------------------------------------
@@ -412,7 +412,7 @@ h5tools_str_region_prefix(h5tools_str_t *str, const h5tool_format_t *info,
     }
 
     /* Add prefix and suffix to the index */
-    return h5tools_str_fmt(str, 0, OPT(info->idx_fmt, "%s: "));
+    return h5tools_str_fmt(str, (size_t)0, OPT(info->idx_fmt, "%s: "));
 }
 
 /*-------------------------------------------------------------------------
diff --git a/tools/misc/h5debug.c b/tools/misc/h5debug.c
index 6b043ba..9c9153a 100644
--- a/tools/misc/h5debug.c
+++ b/tools/misc/h5debug.c
@@ -21,33 +21,31 @@
  *
  * Purpose:             Debugs an existing HDF5 file at a low level.
  *
- * Modifications:
- *
  *-------------------------------------------------------------------------
  */
-#define H5A_PACKAGE	/*suppress error about including H5Apkg  */
-#define H5B2_PACKAGE	/*suppress error about including H5B2pkg  */
-#define H5B2_TESTING	/*suppress warning about H5B2 testing funcs*/
+#define H5A_PACKAGE     /*suppress error about including H5Apkg  */
+#define H5B2_PACKAGE    /*suppress error about including H5B2pkg */
+#define H5B2_TESTING    /*suppress warning about H5B2 testing funcs*/
 #define H5D_PACKAGE     /*suppress error about including H5Dpkg  */
-#define H5F_PACKAGE	/*suppress error about including H5Fpkg	  */
-#define H5G_PACKAGE	/*suppress error about including H5Gpkg	  */
-#define H5HF_PACKAGE	/*suppress error about including H5HFpkg  */
-#define H5O_PACKAGE	/*suppress error about including H5Opkg	  */
-#define H5SM_PACKAGE	/*suppress error about including H5SMpkg  */
-
-#include "H5private.h"	/* Generic Functions			*/
-#include "H5Apkg.h"	/* Attributes				*/
-#include "H5B2pkg.h"	/* v2 B-trees				*/
-#include "H5Dpkg.h"     /* Datasets             		*/
-#include "H5Eprivate.h"	/* Error handling		  	*/
-#include "H5Fpkg.h"     /* File access				*/
-#include "H5FSprivate.h" /* Free space manager			*/
-#include "H5Gpkg.h"	/* Groups				*/
-#include "H5HFpkg.h"	/* Fractal heaps			*/
-#include "H5HGprivate.h" /* Global Heaps			*/
-#include "H5Iprivate.h"	/* IDs			  		*/
-#include "H5Opkg.h"     /* Object headers			*/
-#include "H5SMpkg.h"	/* Implicitly shared messages		*/
+#define H5F_PACKAGE     /*suppress error about including H5Fpkg  */
+#define H5G_PACKAGE     /*suppress error about including H5Gpkg  */
+#define H5HF_PACKAGE    /*suppress error about including H5HFpkg */
+#define H5O_PACKAGE     /*suppress error about including H5Opkg  */
+#define H5SM_PACKAGE    /*suppress error about including H5SMpkg */
+
+#include "H5private.h"  /* Generic Functions    */
+#include "H5Apkg.h"     /* Attributes           */
+#include "H5B2pkg.h"    /* v2 B-trees           */
+#include "H5Dpkg.h"     /* Datasets             */
+#include "H5Eprivate.h" /* Error handling       */
+#include "H5Fpkg.h"     /* File access          */
+#include "H5FSprivate.h" /* Free space manager  */
+#include "H5Gpkg.h"     /* Groups               */
+#include "H5HFpkg.h"    /* Fractal heaps        */
+#include "H5HGprivate.h" /* Global Heaps        */
+#include "H5Iprivate.h" /* IDs                  */
+#include "H5Opkg.h"     /* Object headers       */
+#include "H5SMpkg.h"    /* Implicitly shared messages    */
 
 /* File drivers */
 #include "H5FDfamily.h"
@@ -192,13 +190,13 @@ main(int argc, char *argv[])
      * Parse command arguments.
      */
     if(argc > 2)
-        addr = HDstrtoll(argv[2], NULL, 0);
+        addr = (haddr_t)HDstrtoll(argv[2], NULL, 0);
     if(argc > 3)
-        extra = HDstrtoll(argv[3], NULL, 0);
+        extra = (haddr_t)HDstrtoll(argv[3], NULL, 0);
     if(argc > 4)
-        extra2 = HDstrtoll(argv[4], NULL, 0);
+        extra2 = (haddr_t)HDstrtoll(argv[4], NULL, 0);
     if(argc > 5)
-        extra3 = HDstrtoll(argv[5], NULL, 0);
+        extra3 = (haddr_t)HDstrtoll(argv[5], NULL, 0);
     if(argc > 6)
         extra4 = (haddr_t)HDstrtoll(argv[6], NULL, 0);
 
diff --git a/tools/misc/h5repart.c b/tools/misc/h5repart.c
index 07f6bfd..ffd52e8 100644
--- a/tools/misc/h5repart.c
+++ b/tools/misc/h5repart.c
@@ -290,7 +290,7 @@ main (int argc, char *argv[])
     if (argno<argc) usage (prog_name);
 
     /* Now the real work, split the file */
-    buf = malloc (blk_size);
+    buf = HDmalloc (blk_size);
     while (src_offset<src_size) {
 
 	/* Read a block.  The amount to read is the minimum of:
@@ -498,6 +498,6 @@ main (int argc, char *argv[])
     }
 
     /* Free resources and return */
-    free (buf);
+    HDfree (buf);
     return EXIT_SUCCESS;
 }
diff --git a/tools/misc/talign.c b/tools/misc/talign.c
index 3fd1694..2d0a9d1 100644
--- a/tools/misc/talign.c
+++ b/tools/misc/talign.c
@@ -126,7 +126,7 @@ int main(void)
     H5Dclose(set);
 
     /* Now open the set, and read it back in */
-    data = (char *)malloc(H5Tget_size(fix));
+    data = (char *)HDmalloc(H5Tget_size(fix));
 
     if(!data) {
         perror("malloc() failed");
@@ -192,7 +192,7 @@ out:
     }
 
     if(data)
-        free(data);
+        HDfree(data);
     H5Sclose(spc);
     H5Tclose(cmp);
     H5Tclose(cmp1);