Merge pull request #593 in HDFFV/hdf5 from hdf5_1_8_19 to 1.8/masterhdf5-1_8_19

* commit 'c15238a38fdb3692466bc1218de4c5aeb420fdcc': (153 commits)
  Commit changes to release version strings in README.txt and RELEASE.txt from release.
  Put back link targets for dynamically loaded libraries in Makefile.ams that avoid linking with libhdf5 dependencies.  Some configurations failed unnecessarily to find and link with lz and lsz when these targets were removed.
  Update URL for obtaining source inINSTALL file.
  Disable building of libdynlib* dynamically loaded plugin test libraries on CYGWIN. Added known problem entry to RELEASE.txt. Set version for 1.8.19 release. Barbara updated contents of README.txt file.
  Moved libdynlib* plugin test libraries to noist_LT_LIBRARIES with added flag '-rpath /nowhere' to stop them being installed while keeping them from linking with libhdf5, etc. Incremented version to 1.8.19-pre1 and ran bin/release to create tar and zip files for testing.
  HDF5 1.8.19-pre1 released.
  Add RELEASE.txt entry for H5Dget_chunk_size.
  Remove test entries
  Ran bin/reconfigure after so number change.
  Update hl lib .so numbers:  new function was added. Update RELEASE.txt:  move H5DOread_chunks entry to new features, clarify entry for HDFFV-10051.
  Updated notes for test fixes and added bug fix for h5diff help text.
  Update h5vers and release scripts for 1.8.19 branch, set version to 1.8.19-pre1.
  Make script name consistent across product versions
  Update version to 1.8.19-pre1.
  Propagate .so number changes to Makefile.ins with bin/reconfigure.
  Add toolset option
  Update so version numbers according to the interface compatibility report.
  Update supported Platforms section. Remove empty sub-sections of New Features and Bugs Fixed sections.
  Add entries for HDFFV-10051 and HDFFV-9934 to RELEASE.txt.
  Correct spelling
  ...

1 files changed, 27 insertions, 29 deletions

diff --git a/tools/h5repack/h5repack_refs.c b/tools/h5repack/h5repack_refs.c
index fbaeada..89d0f76 100644
--- a/tools/h5repack/h5repack_refs.c
+++ b/tools/h5repack/h5repack_refs.c
@@ -5,12 +5,10 @@
  *                                                                           *
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *
  * terms governing use, modification, and redistribution, is contained in    *
- * the files COPYING and Copyright.html.  COPYING can be found at the root   *
- * of the source code distribution tree; Copyright.html can be found at the  *
- * root level of an installed copy of the electronic HDF5 document set and   *
- * is linked from the top-level documents page.  It can also be found at     *
- * http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have          *
- * access to either file, you may request a copy from help@hdfgroup.org.     *
+ * the COPYING file, which can be found at the root of the source code       *
+ * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.  *
+ * If you do not have access to either file, you may request a copy from     *
+ * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
 #include "h5repack.h"
@@ -27,7 +25,7 @@ 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
@@ -128,8 +126,8 @@ int do_copy_refobjs(hid_t fidin,
                 for(k = 0; k < rank; k++)
                     nelmts *= dims[k];
 
-                if((mtype_id = h5tools_get_native_type(ftype_id)) < 0)
-                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "h5tools_get_native_type failed");
+                if((mtype_id = H5Tget_native_type(ftype_id, H5T_DIR_DEFAULT)) < 0)
+                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_native_type failed");
 
                 if((msize = H5Tget_size(mtype_id)) == 0)
                     HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_size failed");
@@ -427,13 +425,13 @@ done:
  * 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
  *
@@ -474,7 +472,7 @@ static int copy_refs_attr(hid_t loc_in,
         HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Oget_info failed");
 
     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)
@@ -486,8 +484,8 @@ static int copy_refs_attr(hid_t loc_in,
 
         type_class = H5Tget_class(ftype_id);
 
-        if((mtype_id = h5tools_get_native_type(ftype_id)) < 0)
-            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "h5tools_get_native_type failed");
+        if((mtype_id = H5Tget_native_type(ftype_id, H5T_DIR_DEFAULT)) < 0)
+            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_native_type failed");
 
         if((msize = H5Tget_size(mtype_id)) == 0)
             HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_size failed");
@@ -530,9 +528,9 @@ static int copy_refs_attr(hid_t loc_in,
                 }
                 H5Tclose(mtid);
             }
-            
-            /* if compound don't contain reference type member, free the above 
-             * mallocs. Otherwise there can be memory leaks by the 'continue' 
+
+            /* if compound don't contain reference type member, free the above
+             * mallocs. Otherwise there can be memory leaks by the 'continue'
              * statement below. */
             if (!ref_comp_field_n) {
                 if (ref_comp_index) {
@@ -541,7 +539,7 @@ static int copy_refs_attr(hid_t loc_in,
                 }
 
                 if (ref_comp_size) {
-            	    HDfree(ref_comp_size);
+                    HDfree(ref_comp_size);
                     ref_comp_size = NULL;
                 }
             }
@@ -590,7 +588,7 @@ static int copy_refs_attr(hid_t loc_in,
             array_rank = (unsigned)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;
         }
 
@@ -650,7 +648,7 @@ static int copy_refs_attr(hid_t loc_in,
                 }
             } /* 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 */
@@ -690,7 +688,7 @@ static int copy_refs_attr(hid_t loc_in,
                 }
             } /* 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 */
@@ -730,7 +728,7 @@ static int copy_refs_attr(hid_t loc_in,
                 HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Awrite failed");
 
             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)
@@ -782,10 +780,10 @@ done:
         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);
@@ -799,9 +797,9 @@ done:
 }
 
 /*-------------------------------------------------------------------------
- * 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
  *
  *-------------------------------------------------------------------------
  */
@@ -834,16 +832,16 @@ 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)
 {
     int    ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
     const char* ref_obj_name;