Merge pull request #811 in HDFFV/hdf5 from hdf5_1_8_20 to 1.8/masterhdf5-1_8_20

* commit '60f76980aab92f0e0730170b99a2363acd3c97fa': (108 commits)
  Update version numbers and remove empty sections in RELEASE.txt.
  Restore line 1154: C2Cppfunction_map.mht to HTML_EXTRA_FILES.
  Update version for 1.8.20 release.
  Fixed documentation warnings
  HDFFV-10329 Correct LINK INTERFACE and VS20013 compile
  Switch default build mode from development to production. Increment version string to pre2.
  Add RELEASE.txt note for HDFFV-10274. (cherry picked from commit f7a7d0a00613cba997212fa8032091629a678797)
  Initialize hid_t variables in test_Attr_bug9. (cherry picked from commit 97bc393449f3fe02c5992872ab2842e12f611ef0)
  Fix HDFFV-10274.  When deleting all (or almost all) of the messages in an object header chunk, where the total amount deleted was greater than 64K, an error would occur due to an off by one error in the code that handled that case.  Fixed this and added a test case. (cherry picked from commit 1b2c2ca9a6a7d7e1fcd5c3302e203f2e2dabf0af)
  Fix linking of libs
  Changed file path to relative.
  iAdd NAG to supported compilers in RELEASE.txt.
  Add description to RELEASE.txt for HDFFV-10323
  Correct issue number
  Set version to 1.8.20-pre1
  Update supported and tested platforms in RELEASE.txt.
  HDFFV-10321 Merge from 1.8
  Incremented lib file .so numbers: revision for all except c++ for code change; current incremented, revision and age set to 0 for c++ due to symbols added and removed.
  updated issues related to Fortran
  Incremented lib file .so numbers: revision for all except c++ for dcode change; current incremented, revision and age set to 0 for c++ due to symbols added and removed.
  ...

1 files changed, 151 insertions, 163 deletions

diff --git a/tools/h5repack/h5repack_refs.c b/tools/h5repack/h5repack_refs.c
index 89d0f76..59b652c 100644
--- a/tools/h5repack/h5repack_refs.c
+++ b/tools/h5repack/h5repack_refs.c
@@ -30,15 +30,10 @@ static herr_t update_ref_value(hid_t obj_id, H5R_type_t ref_type, void *ref_in,
 /*-------------------------------------------------------------------------
  * Function: do_copy_refobjs
  *
- * Purpose: duplicate all referenced HDF5 objects in the file
- *  and create hard links
- *
- * Return: 0, ok, -1 no
- *
- * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
- *
- * Date: December, 10, 2003
+ * Purpose:  duplicate all referenced HDF5 objects in the file
+ *           and create hard links
  *
+ * Return:   0, ok, -1 no
  *-------------------------------------------------------------------------
  */
 
@@ -47,41 +42,39 @@ int do_copy_refobjs(hid_t fidin,
                     trav_table_t *travt,
                     pack_opt_t *options) /* repack options */
 {
-    int       ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
-    hid_t     grp_in = (-1);          /* read group ID */
-    hid_t     grp_out = (-1);         /* write group ID */
-    hid_t     dset_in = (-1);         /* read dataset ID */
-    hid_t     dset_out = (-1);        /* write dataset ID */
-    hid_t     type_in = (-1);         /* named type ID */
-    hid_t     dcpl_id = (-1);         /* dataset creation property list ID */
-    hid_t     space_id = (-1);        /* space ID */
-    hid_t     ftype_id = (-1);        /* file data type ID */
-    hid_t     mtype_id = (-1);        /* memory data type ID */
+    int       ret_value = 0;          /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
+    hid_t     grp_in = -1;            /* read group ID */
+    hid_t     grp_out = -1;           /* write group ID */
+    hid_t     dset_in = -1;           /* read dataset ID */
+    hid_t     dset_out = -1;          /* write dataset ID */
+    hid_t     type_in = -1;           /* named type ID */
+    hid_t     dcpl_id = -1;           /* dataset creation property list ID */
+    hid_t     space_id = -1;          /* space ID */
+    hid_t     ftype_id = -1;          /* file data type ID */
+    hid_t     mtype_id = -1;          /* memory data type ID */
     size_t    msize;                  /* memory size of memory type */
     hsize_t   nelmts;                 /* number of elements in dataset */
     int       rank;                   /* rank of dataset */
     hsize_t   dims[H5S_MAX_RANK];     /* dimensions of dataset */
     unsigned int i, j;
     int       k;
-    named_dt_t *named_dt_head=NULL;   /* Pointer to the stack of named datatypes
-                                         copied */
+    named_dt_t *named_dt_head = NULL; /* Pointer to the stack of named datatypes copied */
 
     /*-------------------------------------------------------------------------
     * browse
     *-------------------------------------------------------------------------
     */
     for(i = 0; i < travt->nobjs; i++) {
-        switch(travt->objs[i].type)
-        {
+        switch(travt->objs[i].type) {
             /*-------------------------------------------------------------------------
-            * H5TRAV_TYPE_GROUP
-            *-------------------------------------------------------------------------
-            */
+             * H5TRAV_TYPE_GROUP
+             *-------------------------------------------------------------------------
+             */
             case H5TRAV_TYPE_GROUP:
                 /*-------------------------------------------------------------------------
-                * copy referenced objects in attributes
-                *-------------------------------------------------------------------------
-                */
+                 * copy referenced objects in attributes
+                 *-------------------------------------------------------------------------
+                 */
                 if((grp_out = H5Gopen2(fidout, travt->objs[i].name, H5P_DEFAULT)) < 0)
                     HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gopen2 failed");
 
@@ -97,18 +90,18 @@ int do_copy_refobjs(hid_t fidin,
                     HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gclose failed");
 
                 /*-------------------------------------------------------------------------
-                * check for hard links
-                *-------------------------------------------------------------------------
-                */
+                 * check for hard links
+                 *-------------------------------------------------------------------------
+                 */
                 if(travt->objs[i].nlinks)
                     for(j = 0; j < travt->objs[i].nlinks; j++)
                         H5Lcreate_hard(fidout, travt->objs[i].name, H5L_SAME_LOC, travt->objs[i].links[j].new_name, H5P_DEFAULT, H5P_DEFAULT);
                 break;
 
             /*-------------------------------------------------------------------------
-            * H5TRAV_TYPE_DATASET
-            *-------------------------------------------------------------------------
-            */
+             * H5TRAV_TYPE_DATASET
+             *-------------------------------------------------------------------------
+             */
             case H5TRAV_TYPE_DATASET:
                 if((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
                     HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed");
@@ -141,27 +134,27 @@ int do_copy_refobjs(hid_t fidin,
                  */
                 if(h5tools_canreadf(NULL, dcpl_id) == 1) {
                     /*-------------------------------------------------------------------------
-                    * test for a valid output dataset
-                    *-------------------------------------------------------------------------
-                    */
+                     * test for a valid output dataset
+                     *-------------------------------------------------------------------------
+                     */
                     dset_out = FAIL;
 
                     /*-------------------------------------------------------------------------
-                    * object references are a special case
-                    * we cannot just copy the buffers, but instead we recreate the reference
-                    *-------------------------------------------------------------------------
-                    */
+                     * object references are a special case
+                     * we cannot just copy the buffers, but instead we recreate the reference
+                     *-------------------------------------------------------------------------
+                     */
                     if(H5Tequal(mtype_id, H5T_STD_REF_OBJ)) {
-                        hid_t            refobj_id;
+                        hid_t            refobj_id = -1;
                         hobj_ref_t       *refbuf = NULL; /* buffer for object references */
                         hobj_ref_t       *buf = NULL;
                         const char*      refname;
                         unsigned         u;
 
                         /*-------------------------------------------------------------------------
-                        * read to memory
-                        *-------------------------------------------------------------------------
-                        */
+                         * read to memory
+                         *-------------------------------------------------------------------------
+                         */
                         if(nelmts) {
                             buf = (hobj_ref_t *)HDmalloc((unsigned)(nelmts * msize));
                             if(buf==NULL) {
@@ -189,22 +182,22 @@ int do_copy_refobjs(hid_t fidin,
                                     /* create the reference, -1 parameter for objects */
                                     if(H5Rcreate(&refbuf[u], fidout, refname, H5R_OBJECT, (hid_t)-1) < 0)
                                         HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Rcreate failed");
-                                    if(options->verbose)
-                                    {
+                                    if(options->verbose) {
                                         printf(FORMAT_OBJ,"dset",travt->objs[i].name );
                                         printf("object <%s> object reference created to <%s>\n",
                                             travt->objs[i].name,
                                             refname);
                                     }
                                 } /*refname*/
-                                H5Oclose(refobj_id);
+                                if (H5Oclose(refobj_id) < 0)
+                                    H5TOOLS_INFO(H5E_tools_min_id_g, "H5Oclose refob failed");
                             } /* u */
                         } /*nelmts*/
 
                         /*-------------------------------------------------------------------------
-                        * create/write dataset/close
-                        *-------------------------------------------------------------------------
-                        */
+                         * create/write dataset/close
+                         *-------------------------------------------------------------------------
+                         */
                         if((dset_out = H5Dcreate2(fidout, travt->objs[i].name, mtype_id, space_id, H5P_DEFAULT, dcpl_id, H5P_DEFAULT)) < 0)
                             HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dcreate2 failed");
                         if(nelmts)
@@ -224,21 +217,20 @@ int do_copy_refobjs(hid_t fidin,
                     } /*H5T_STD_REF_OBJ*/
 
                     /*-------------------------------------------------------------------------
-                    * dataset region references
-                    *-------------------------------------------------------------------------
-                    */
-                    else if(H5Tequal(mtype_id, H5T_STD_REF_DSETREG))
-                    {
-                        hid_t            refobj_id;
+                     * dataset region references
+                     *-------------------------------------------------------------------------
+                     */
+                    else if(H5Tequal(mtype_id, H5T_STD_REF_DSETREG)) {
+                        hid_t            refobj_id = -1;
                         hdset_reg_ref_t  *refbuf = NULL; /* input buffer for region references */
                         hdset_reg_ref_t  *buf = NULL;    /* output buffer */
                         const char*      refname;
                         unsigned         u;
 
                         /*-------------------------------------------------------------------------
-                        * read input to memory
-                        *-------------------------------------------------------------------------
-                        */
+                         * read input to memory
+                         *-------------------------------------------------------------------------
+                         */
                         if(nelmts) {
                             buf = (hdset_reg_ref_t *)HDmalloc((unsigned)(nelmts * msize));
                             if(buf == NULL) {
@@ -249,9 +241,9 @@ int do_copy_refobjs(hid_t fidin,
                                 HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dread failed");
 
                             /*-------------------------------------------------------------------------
-                            * create output
-                            *-------------------------------------------------------------------------
-                            */
+                             * create output
+                             *-------------------------------------------------------------------------
+                             */
                             refbuf = (hdset_reg_ref_t *)HDcalloc(sizeof(hdset_reg_ref_t), (size_t)nelmts); /*init to zero */
                             if(refbuf == NULL) {
                                 printf("cannot allocate memory\n");
@@ -268,7 +260,7 @@ int do_copy_refobjs(hid_t fidin,
                                  * in the second traversal of the file
                                  */
                                 if((refname = MapIdToName(refobj_id, travt)) != NULL) {
-                                    hid_t region_id;    /* region id of the referenced dataset */
+                                    hid_t region_id = -1;    /* region id of the referenced dataset */
 
                                     if((region_id = H5Rget_region(dset_in, H5R_DATASET_REGION, &buf[u])) < 0)
                                         HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Rget_region failed");
@@ -278,22 +270,22 @@ int do_copy_refobjs(hid_t fidin,
                                         HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Rcreate failed");
                                     if(H5Sclose(region_id) < 0)
                                         HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sclose failed");
-                                    if(options->verbose)
-                                    {
+                                    if(options->verbose) {
                                         printf(FORMAT_OBJ,"dset",travt->objs[i].name );
                                         printf("object <%s> region reference created to <%s>\n",
                                             travt->objs[i].name,
                                             refname);
                                     }
                                 } /*refname*/
-                                H5Oclose(refobj_id);
+                                if (H5Oclose(refobj_id) < 0)
+                                    H5TOOLS_INFO(H5E_tools_min_id_g, "H5Oclose refobj_id failed");
                             } /* u */
                         } /*nelmts*/
 
                         /*-------------------------------------------------------------------------
-                        * create/write dataset/close
-                        *-------------------------------------------------------------------------
-                        */
+                         * create/write dataset/close
+                         *-------------------------------------------------------------------------
+                         */
                         if((dset_out = H5Dcreate2(fidout, travt->objs[i].name, mtype_id, space_id, H5P_DEFAULT, dcpl_id, H5P_DEFAULT)) < 0)
                             HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dcreate2 failed");
                         if(nelmts)
@@ -312,27 +304,25 @@ int do_copy_refobjs(hid_t fidin,
                             HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_attr failed");
                     } /* H5T_STD_REF_DSETREG */
                     /*-------------------------------------------------------------------------
-                    * not references, open previously created object in 1st traversal
-                    *-------------------------------------------------------------------------
-                    */
+                     * not references, open previously created object in 1st traversal
+                     *-------------------------------------------------------------------------
+                     */
                     else {
                         if((dset_out = H5Dopen2(fidout, travt->objs[i].name, H5P_DEFAULT)) < 0)
                             HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed");
                     } /* end else */
 
-                    HDassert(dset_out != FAIL);
-
                     /*-------------------------------------------------------------------------
-                    * copy referenced objects in attributes
-                    *-------------------------------------------------------------------------
-                    */
+                     * copy referenced objects in attributes
+                     *-------------------------------------------------------------------------
+                     */
                     if(copy_refs_attr(dset_in, dset_out, options, travt, fidout) < 0)
                         HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_refs_attr failed");
 
                     /*-------------------------------------------------------------------------
-                    * check for hard links
-                    *-------------------------------------------------------------------------
-                    */
+                     * check for hard links
+                     *-------------------------------------------------------------------------
+                     */
                     if(travt->objs[i].nlinks)
                         for(j = 0; j < travt->objs[i].nlinks; j++)
                             H5Lcreate_hard(fidout, travt->objs[i].name, H5L_SAME_LOC, travt->objs[i].links[j].new_name, H5P_DEFAULT, H5P_DEFAULT);
@@ -342,9 +332,9 @@ int do_copy_refobjs(hid_t fidin,
                 } /*can_read*/
 
                 /*-------------------------------------------------------------------------
-                * close
-                *-------------------------------------------------------------------------
-                */
+                 * close
+                 *-------------------------------------------------------------------------
+                 */
                 if(H5Tclose(ftype_id) < 0)
                     HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed");
                 if(H5Tclose(mtype_id) < 0)
@@ -358,9 +348,9 @@ int do_copy_refobjs(hid_t fidin,
                 break;
 
             /*-------------------------------------------------------------------------
-            * H5TRAV_TYPE_NAMED_DATATYPE
-            *-------------------------------------------------------------------------
-            */
+             * H5TRAV_TYPE_NAMED_DATATYPE
+             *-------------------------------------------------------------------------
+             */
             case H5TRAV_TYPE_NAMED_DATATYPE:
                 if((type_in = H5Topen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
                     HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Topen2 failed");
@@ -369,9 +359,9 @@ int do_copy_refobjs(hid_t fidin,
                 break;
 
             /*-------------------------------------------------------------------------
-            * H5TRAV_TYPE_LINK
-            *-------------------------------------------------------------------------
-            */
+             * H5TRAV_TYPE_LINK
+             *-------------------------------------------------------------------------
+             */
             case H5TRAV_TYPE_LINK:
                 /*nothing to do */
                 break;
@@ -389,7 +379,8 @@ int do_copy_refobjs(hid_t fidin,
      * This function is paired with copy_named_datatype() which is called
      * in copy_attr(), so need to free.
      */
-    named_datatype_free(&named_dt_head, 0);
+    if (named_datatype_free(&named_dt_head, 0) < 0)
+        H5TOOLS_INFO(H5E_tools_min_id_g, "named_datatype_free failed");
 
     return ret_value;
 
@@ -404,7 +395,7 @@ done:
         H5Tclose(ftype_id);
         H5Tclose(mtype_id);
         H5Tclose(type_in);
-        named_datatype_free(&named_dt_head, 0);
+        named_datatype_free(&named_dt_head, 1);
     } H5E_END_TRY;
 
     return ret_value;
@@ -414,27 +405,22 @@ done:
 /*-------------------------------------------------------------------------
  * Function: copy_refs_attr
  *
- * Purpose: duplicate all referenced HDF5 located in attributes
- *  relative to LOC_IN, which is obtained either from
- * loc_id = H5Gopen2(fid, name, H5P_DEFAULT);
- * loc_id = H5Dopen2(fid, name, H5P_DEFAULT);
- * loc_id = H5Topen2(fid, name, H5P_DEFAULT);
- *
- * Return: 0, ok, -1 no
+ * Purpose:  duplicate all referenced HDF5 located in attributes
+ *           relative to LOC_IN, which is obtained either from
+ *           loc_id = H5Gopen2(fid, name, H5P_DEFAULT);
+ *           loc_id = H5Dopen2(fid, name, H5P_DEFAULT);
+ *           loc_id = H5Topen2(fid, name, H5P_DEFAULT);
  *
- * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
+ * Return:   0, ok, -1 no
  *
- * Modifier: xcao@hdfgroup.org, 9/12/2011
- *              Update values of references(object and region) for the following types:
+ * Modified:
+ *           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.
- *
- * Date: October, 28, 2003
- *
+ *           This function does not handle references in other complicated structures,
+ *           such as references in nested compound datatypes.
  *-------------------------------------------------------------------------
  */
 
@@ -442,30 +428,32 @@ static int copy_refs_attr(hid_t loc_in,
                           hid_t loc_out,
                           pack_opt_t *options,
                           trav_table_t *travt,
-                          hid_t fidout         /* for saving references */
-                          )
+                          hid_t fidout)         /* for saving references */
 {
-    int        ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
-    hid_t      attr_id = -1;      /* attr ID */
-    hid_t      attr_out = -1;     /* attr ID */
-    hid_t      space_id = -1;     /* space ID */
-    hid_t      ftype_id = -1;     /* file data type ID */
-    hid_t      mtype_id = -1;     /* memory data type ID */
-    size_t     msize;             /* memory size of type */
-    hsize_t    nelmts;            /* number of elements in dataset */
-    hsize_t    dims[H5S_MAX_RANK];/* dimensions of dataset */
-    char       name[255];
-    H5O_info_t oinfo;           /* Object info */
-    unsigned   u, i, j;
-    int        rank;
+    int         ret_value = 0;     /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
+    hid_t       attr_id = -1;      /* attr ID */
+    hid_t       attr_out = -1;     /* attr ID */
+    hid_t       space_id = -1;     /* space ID */
+    hid_t       ftype_id = -1;     /* file data type ID */
+    hid_t       mtype_id = -1;     /* memory data type ID */
+    size_t      msize;             /* memory size of type */
+    hsize_t     nelmts;            /* number of elements in dataset */
+    hsize_t     dims[H5S_MAX_RANK];/* dimensions of dataset */
+    char        name[255];
+    H5O_info_t  oinfo;             /* Object info */
+    unsigned    u, i, j;
+    int         rank;
     H5T_class_t type_class = -1;
-    hbool_t    is_ref=0, is_ref_vlen=0, is_ref_array=0, is_ref_comp=0;
-    void  *refbuf = NULL;
-    void  *buf = NULL;
-    const char* refname = NULL;
-    unsigned *ref_comp_index = NULL;
-    size_t *ref_comp_size = NULL;
-    int    ref_comp_field_n = 0;
+    hbool_t     is_ref = 0,
+                is_ref_vlen = 0,
+                is_ref_array = 0,
+                is_ref_comp = 0;
+    void       *refbuf = NULL;
+    void       *buf = NULL;
+    const char *refname = NULL;
+    unsigned   *ref_comp_index = NULL;
+    size_t     *ref_comp_size = NULL;
+    int         ref_comp_field_n = 0;
 
 
     if(H5Oget_info(loc_in, &oinfo) < 0)
@@ -493,20 +481,20 @@ static int copy_refs_attr(hid_t loc_in,
         is_ref = (type_class == H5T_REFERENCE);
 
         if(type_class == H5T_VLEN ) {
-            hid_t base_type;
+            hid_t base_type = H5Tget_super(ftype_id);
 
-            base_type = H5Tget_super(ftype_id);
-            is_ref_vlen = (H5Tget_class(base_type)==H5T_REFERENCE);
+            is_ref_vlen = (H5Tget_class(base_type) == H5T_REFERENCE);
             msize = H5Tget_size(base_type);
-            H5Tclose(base_type);
+            if (H5Tclose(base_type) < 0)
+                H5TOOLS_INFO(H5E_tools_min_id_g, "H5Tclose base_type failed");
         }
         else if(type_class == H5T_ARRAY ) {
-            hid_t base_type;
+            hid_t base_type = H5Tget_super(ftype_id);
 
-            base_type = H5Tget_super(ftype_id);
-            is_ref_array = (H5Tget_class(base_type)==H5T_REFERENCE);
+            is_ref_array = (H5Tget_class(base_type) == H5T_REFERENCE);
             msize = H5Tget_size(base_type);
-            H5Tclose(base_type);
+            if (H5Tclose(base_type) < 0)
+                H5TOOLS_INFO(H5E_tools_min_id_g, "H5Tclose base_type failed");
         }
         else if(type_class == H5T_COMPOUND) {
             int nmembers = H5Tget_nmembers(ftype_id) ;
@@ -519,14 +507,15 @@ static int copy_refs_attr(hid_t loc_in,
             ref_comp_field_n = 0;
 
             for (i=0; i<(unsigned)nmembers; i++) {
-                hid_t mtid = H5Tget_member_type( ftype_id, i );
+                hid_t mtid = H5Tget_member_type(ftype_id, i);
 
-                if ((H5Tget_class(mtid)==H5T_REFERENCE)) {
+                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 (H5Tclose(mtid) < 0)
+                    H5TOOLS_INFO(H5E_tools_min_id_g, "H5Tclose mtid failed");
             }
 
             /* if compound don't contain reference type member, free the above
@@ -548,9 +537,12 @@ 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);
+            if (H5Tclose(mtype_id) < 0)
+                H5TOOLS_INFO(H5E_tools_min_id_g, "H5Tclose mtype_id failed");
+            if (H5Tclose(ftype_id) < 0)
+                H5TOOLS_INFO(H5E_tools_min_id_g, "H5Tclose ftype_id failed");
+            if (H5Aclose(attr_id) < 0)
+                H5TOOLS_INFO(H5E_tools_min_id_g, "H5Aclose attr_id failed");
             continue;
         }
 
@@ -579,11 +571,11 @@ static int copy_refs_attr(hid_t loc_in,
             unsigned  array_rank = 0;
             hsize_t   array_size = 1;
             hsize_t array_dims[H5S_MAX_RANK];
-            hid_t base_type;
+            hid_t base_type = H5Tget_super(ftype_id);
 
-            base_type = H5Tget_super(ftype_id);
             msize = H5Tget_size(base_type);
-            H5Tclose(base_type);
+            if (H5Tclose(base_type) < 0)
+                H5TOOLS_INFO(H5E_tools_min_id_g, "H5Tclose base_type failed");
 
             array_rank = (unsigned)H5Tget_array_ndims(mtype_id);
             H5Tget_array_dims2(mtype_id, array_dims);
@@ -631,9 +623,9 @@ static int copy_refs_attr(hid_t loc_in,
                     HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aread failed");
 
                 /*-------------------------------------------------------------------------
-                * create output
-                *-------------------------------------------------------------------------
-                */
+                 * create output
+                 *-------------------------------------------------------------------------
+                 */
                 refbuf = (hdset_reg_ref_t *)HDcalloc(sizeof(hdset_reg_ref_t), (size_t)nelmts); /*init to zero */
                 if(refbuf == NULL) {
                     printf( "cannot allocate memory\n" );
@@ -673,7 +665,8 @@ static int copy_refs_attr(hid_t loc_in,
                             HDmemcpy(&(ptr[j]), &ref_out, msize);
                         }
                     }  /* for (i=0; i<nelems; i++) */
-                } else if (H5R_DSET_REG_REF_BUF_SIZE == msize) {
+                }
+                else if (H5R_DSET_REG_REF_BUF_SIZE == msize) {
                     hdset_reg_ref_t ref_out;
 
                     for (i=0; i<(unsigned)nelmts; i++) {
@@ -693,8 +686,7 @@ static int copy_refs_attr(hid_t loc_in,
                 buf = HDmalloc((unsigned)(nelmts * msize));
                 refbuf = buf; /* reuse the read buffer for write */
 
-                if(buf == NULL)
-                {
+                if(buf == NULL) {
                     printf( "cannot read into memory\n" );
                     HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDmalloc failed");
                 } /* end if */
@@ -771,8 +763,6 @@ static int copy_refs_attr(hid_t loc_in,
             HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aclose failed");
     } /* for(u = 0; u < (unsigned)oinfo.num_attrs; u++) */
 
-    return ret_value;
-
 done:
     if(refbuf)
         HDfree(refbuf);
@@ -799,7 +789,7 @@ done:
 /*-------------------------------------------------------------------------
  * Function:    MapIdToName
  *
- * Purpose:    map a ID from a reference to a dataset name
+ * Purpose:     map a ID from a reference to a dataset name
  *
  *-------------------------------------------------------------------------
  */
@@ -807,7 +797,7 @@ static const char*
 MapIdToName(hid_t refobj_id, trav_table_t *travt)
 {
     unsigned int u;
-    const char* ret = NULL;
+    const char   *ret = NULL;
 
     /* linear search */
     for(u = 0; u < travt->nobjs; u++) {
@@ -834,18 +824,16 @@ out:
 /*-------------------------------------------------------------------------
  * Function:    Update_Ref_value
  *
- * Purpose:    Update a reference value
- *
- * Programmer: xcao@hdfgroup.org 9/12/2011
- *
+ * Purpose:     Update a reference value
  *-------------------------------------------------------------------------
  */
 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)
 {
-    int    ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
-    const char* ref_obj_name;
-    hid_t space_id=-1, ref_obj_id=-1;
+    int         ret_value = 0;   /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
+    const char *ref_obj_name;
+    hid_t       space_id = -1;
+    hid_t       ref_obj_id = -1;
 
     ref_obj_id = H5Rdereference(obj_id, ref_type, ref_in);
     if (ref_obj_id < 0)