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
  ...

14 files changed, 195 insertions, 223 deletions

diff --git a/tools/misc/CMakeLists.txt b/tools/misc/CMakeLists.txt
index 12d5a52..da1af42 100644
--- a/tools/misc/CMakeLists.txt
+++ b/tools/misc/CMakeLists.txt
@@ -1,4 +1,4 @@
-cmake_minimum_required (VERSION 3.1.0)
+cmake_minimum_required (VERSION 3.2.2)
 PROJECT (HDF5_TOOLS_MISC)
 
 #-----------------------------------------------------------------------------
@@ -42,7 +42,7 @@ set (H5_DEP_EXECUTABLES
 #-----------------------------------------------------------------------------
 #if (NOT WIN32)
 #  configure_file (${HDF5_TOOLS_MISC_SOURCE_DIR}/h5cc.in ${HDF5_BINARY_DIR}/h5cc @ONLY)
-#endif (NOT WIN32)
+#endif ()
 
 if (BUILD_TESTING)
   # --------------------------------------------------------------------
@@ -55,7 +55,7 @@ if (BUILD_TESTING)
     target_link_libraries (h5repart_gentest ${HDF5_LIB_TARGET} ${HDF5_TOOLS_LIB_TARGET})
     set_target_properties (h5repart_gentest PROPERTIES FOLDER generator/tools)
     #add_test (NAME h5repart_gentest COMMAND $<TARGET_FILE:h5repart_gentest>)
-  endif (HDF5_BUILD_GENERATORS)
+  endif ()
 
   add_executable (h5repart_test ${HDF5_TOOLS_MISC_SOURCE_DIR}/repart_test.c)
   TARGET_NAMING (h5repart_test STATIC)
@@ -64,7 +64,7 @@ if (BUILD_TESTING)
   set_target_properties (h5repart_test PROPERTIES FOLDER tools)
 
   include (CMakeTests.cmake)
-endif (BUILD_TESTING)
+endif ()
 
 ##############################################################################
 ##############################################################################
@@ -75,15 +75,16 @@ endif (BUILD_TESTING)
 #-----------------------------------------------------------------------------
 # Rules for Installation of tools using make Install target
 #-----------------------------------------------------------------------------
+if (HDF5_EXPORTED_TARGETS)
+  INSTALL_PROGRAM_PDB (h5debug ${HDF5_INSTALL_BIN_DIR} toolsapplications)
+  INSTALL_PROGRAM_PDB (h5repart ${HDF5_INSTALL_BIN_DIR} toolsapplications)
+  INSTALL_PROGRAM_PDB (h5mkgrp ${HDF5_INSTALL_BIN_DIR} toolsapplications)
 
-#INSTALL_PROGRAM_PDB (h5debug ${HDF5_INSTALL_BIN_DIR} toolsapplications)
-#INSTALL_PROGRAM_PDB (h5repart ${HDF5_INSTALL_BIN_DIR} toolsapplications)
-#INSTALL_PROGRAM_PDB (h5mkgrp ${HDF5_INSTALL_BIN_DIR} toolsapplications)
-
-install (
-    TARGETS
-        h5debug h5repart h5mkgrp
-    EXPORT
-        ${HDF5_EXPORTED_TARGETS}
-    RUNTIME DESTINATION ${HDF5_INSTALL_BIN_DIR} COMPONENT toolsapplications
-)
+  install (
+      TARGETS
+          h5debug h5repart h5mkgrp
+      EXPORT
+          ${HDF5_EXPORTED_TARGETS}
+      RUNTIME DESTINATION ${HDF5_INSTALL_BIN_DIR} COMPONENT toolsapplications
+  )
+endif ()
diff --git a/tools/misc/CMakeTests.cmake b/tools/misc/CMakeTests.cmake
index 6822be5..afc760b 100644
--- a/tools/misc/CMakeTests.cmake
+++ b/tools/misc/CMakeTests.cmake
@@ -1,3 +1,14 @@
+#
+# Copyright by The HDF Group.
+# All rights reserved.
+#
+# This file is part of HDF5.  The full HDF5 copyright notice, including
+# terms governing use, modification, and redistribution, is contained in
+# 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.
+
 
 ##############################################################################
 ##############################################################################
@@ -31,7 +42,7 @@
 
   foreach (h5_file ${HDF5_REFERENCE_TEST_FILES})
     HDFTEST_COPY_FILE("${HDF5_TOOLS_SRC_DIR}/testfiles/${h5_file}" "${PROJECT_BINARY_DIR}/${h5_file}" "h5repart_files")
-  endforeach (h5_file ${HDF5_REFERENCE_TEST_FILES})
+  endforeach ()
   add_custom_target(h5repart_files ALL COMMENT "Copying files needed by h5repart tests" DEPENDS ${h5repart_files_list})
 
   set (HDF5_MKGRP_TEST_FILES
@@ -56,7 +67,7 @@
 
   foreach (h5_mkgrp_file ${HDF5_MKGRP_TEST_FILES})
     HDFTEST_COPY_FILE("${HDF5_TOOLS_SRC_DIR}/testfiles/${h5_mkgrp_file}" "${PROJECT_BINARY_DIR}/testfiles/${h5_mkgrp_file}" "h5mkgrp_files")
-  endforeach (h5_mkgrp_file ${HDF5_MKGRP_TEST_FILES})
+  endforeach ()
 
   HDFTEST_COPY_FILE("${PROJECT_SOURCE_DIR}/testfiles/h5mkgrp_help.txt" "${PROJECT_BINARY_DIR}/testfiles/h5mkgrp_help.txt" "h5mkgrp_files")
   add_custom_target(h5mkgrp_files ALL COMMENT "Copying files needed by h5mkgrp tests" DEPENDS ${h5mkgrp_files_list})
@@ -69,18 +80,16 @@
 ##############################################################################
 ##############################################################################
 
-  MACRO (ADD_H5_TEST resultfile resultcode resultoption)
+  macro (ADD_H5_TEST resultfile resultcode resultoption)
     if (NOT HDF5_ENABLE_USING_MEMCHECKER)
       add_test (
           NAME H5MKGRP-${resultfile}-clear-objects
           COMMAND    ${CMAKE_COMMAND}
               -E remove
                   ${resultfile}.h5
-                  ${resultfile}.out
-                  ${resultfile}.out.err
       )
       set_tests_properties (H5MKGRP-${resultfile}-clear-objects PROPERTIES WORKING_DIRECTORY "${PROJECT_BINARY_DIR}/testfiles")
-    endif (NOT HDF5_ENABLE_USING_MEMCHECKER)
+    endif ()
 
     add_test (
         NAME H5MKGRP-${resultfile}
@@ -90,8 +99,8 @@
     if (HDF5_ENABLE_USING_MEMCHECKER)
       if (NOT "${last_test}" STREQUAL "")
         set_tests_properties (H5MKGRP-${resultfile} PROPERTIES DEPENDS ${last_test})
-      endif (NOT "${last_test}" STREQUAL "")
-    else (HDF5_ENABLE_USING_MEMCHECKER)
+      endif ()
+    else ()
       set_tests_properties (H5MKGRP-${resultfile} PROPERTIES DEPENDS H5MKGRP-${resultfile}-clear-objects)
       add_test (
           NAME H5MKGRP-${resultfile}-h5ls
@@ -106,20 +115,18 @@
               -P "${HDF_RESOURCES_EXT_DIR}/runTest.cmake"
       )
       set_tests_properties (H5MKGRP-${resultfile}-h5ls PROPERTIES DEPENDS H5MKGRP-${resultfile})
-    endif (HDF5_ENABLE_USING_MEMCHECKER)
-  ENDMACRO (ADD_H5_TEST resultfile resultcode resultoption)
+    endif ()
+  endmacro ()
 
-  MACRO (ADD_H5_CMP resultfile resultcode)
+  macro (ADD_H5_CMP resultfile resultcode)
     if (HDF5_ENABLE_USING_MEMCHECKER)
       add_test (NAME H5MKGRP_CMP-${resultfile} COMMAND $<TARGET_FILE:h5mkgrp> ${ARGN})
-    else (HDF5_ENABLE_USING_MEMCHECKER)
+    else ()
       add_test (
           NAME H5MKGRP_CMP-${resultfile}-clear-objects
           COMMAND    ${CMAKE_COMMAND}
               -E remove
                   ${resultfile}.h5
-                  ${resultfile}.out
-                  ${resultfile}.out.err
       )
       set_tests_properties (H5MKGRP_CMP-${resultfile}-clear-objects PROPERTIES WORKING_DIRECTORY "${PROJECT_BINARY_DIR}/testfiles")
       add_test (
@@ -134,8 +141,8 @@
               -P "${HDF_RESOURCES_EXT_DIR}/runTest.cmake"
       )
       set_tests_properties (H5MKGRP_CMP-${resultfile} PROPERTIES DEPENDS H5MKGRP_CMP-${resultfile}-clear-objects)
-    endif (HDF5_ENABLE_USING_MEMCHECKER)
-  ENDMACRO (ADD_H5_CMP resultfile resultcode)
+    endif ()
+  endmacro ()
 
 ##############################################################################
 ##############################################################################
@@ -158,7 +165,7 @@
   )
   if (NOT "${last_test}" STREQUAL "")
     set_tests_properties (H5REPART-clearall-objects PROPERTIES DEPENDS ${last_test})
-  endif (NOT "${last_test}" STREQUAL "")
+  endif ()
   set (last_test "H5REPART-clearall-objects")
 
   # repartition family member size to 20,000 bytes.
@@ -230,9 +237,9 @@
     set_tests_properties (H5MKGRP-clearall-objects PROPERTIES WORKING_DIRECTORY "${PROJECT_BINARY_DIR}/testfiles")
     if (NOT "${last_test}" STREQUAL "")
       set_tests_properties (H5MKGRP-clearall-objects PROPERTIES DEPENDS ${last_test})
-    endif (NOT "${last_test}" STREQUAL "")
+    endif ()
     set (last_test "H5MKGRP-clearall-objects")
-  endif (HDF5_ENABLE_USING_MEMCHECKER)
+  endif ()
 
   # Check that help & version is displayed properly
   ADD_H5_CMP (h5mkgrp_help 0 "-h")
diff --git a/tools/misc/Makefile.am b/tools/misc/Makefile.am
index 882f8f2..91a045e 100644
--- a/tools/misc/Makefile.am
+++ b/tools/misc/Makefile.am
@@ -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.
 ##
 ## Makefile.am
 ## Run automake to generate a Makefile.in from this file.
diff --git a/tools/misc/Makefile.in b/tools/misc/Makefile.in
index dfbdc2a..6a54bd8 100644
--- a/tools/misc/Makefile.in
+++ b/tools/misc/Makefile.in
@@ -21,12 +21,10 @@
 #
 # 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.
 #
 # HDF5 Library Makefile(.in)
 #
@@ -583,6 +581,7 @@ THREADSAFE = @THREADSAFE@
 TIME = @TIME@
 TR = @TR@
 TRACE_API = @TRACE_API@
+UNAME_CYGWIN = @UNAME_CYGWIN@
 UNAME_INFO = @UNAME_INFO@
 USE_FILTER_DEFLATE = @USE_FILTER_DEFLATE@
 USE_FILTER_SZIP = @USE_FILTER_SZIP@
@@ -732,7 +731,7 @@ LDADD = $(LIBH5TOOLS) $(LIBHDF5)
 # named h5pcc if hdf5 is being built in parallel mode.
 @BUILD_PARALLEL_CONDITIONAL_TRUE@H5CC_NAME = h5pcc
 
-# Automake needs to be taught how to build lib, progs, and tests targets.
+# Automake needs to be taught how to build lib, dyn, progs, and tests targets.
 # These will be filled in automatically for the most part (e.g.,
 # lib_LIBRARIES are built for lib target), but EXTRA_LIB, EXTRA_PROG, and
 # EXTRA_TEST variables are supplied to allow the user to force targets to
diff --git a/tools/misc/h5cc.in b/tools/misc/h5cc.in
index 1645855..9c4e3ca 100644
--- a/tools/misc/h5cc.in
+++ b/tools/misc/h5cc.in
@@ -6,12 +6,10 @@
 #
 # 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.
 ##
 
 # This tool is adapted from the mpicc command of the MPICH Software.
diff --git a/tools/misc/h5debug.c b/tools/misc/h5debug.c
index 9c9153a..f758b1f 100644
--- a/tools/misc/h5debug.c
+++ b/tools/misc/h5debug.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.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
 /*-------------------------------------------------------------------------
@@ -57,15 +55,15 @@
 /*-------------------------------------------------------------------------
  * Function:    get_H5B2_class
  *
- * Purpose:	Determine the v2 B-tree class from the buffer read in.
+ * Purpose:  Determine the v2 B-tree class from the buffer read in.
  *              B-trees are debugged through the B-tree subclass.  The subclass
  *              identifier is two bytes after the B-tree signature.
  *
- * Return:	Non-NULL on success/NULL on failure
+ * Return:  Non-NULL on success/NULL on failure
  *
- * Programmer:	Quincey Koziol
- *		koziol@hdfgroup.org
- *		Sep 11 2008
+ * Programmer:  Quincey Koziol
+ *    koziol@hdfgroup.org
+ *    Sep 11 2008
  *
  *-------------------------------------------------------------------------
  */
@@ -143,16 +141,18 @@ get_H5B2_class(const uint8_t *sig)
 int
 main(int argc, char *argv[])
 {
-    hid_t	fid, fapl, dxpl;
+    hid_t  fid, fapl, dxpl;
     H5F_t       *f;
     haddr_t     addr = 0, extra = 0, extra2 = 0, extra3 = 0, extra4 = 0;
     uint8_t     sig[H5F_SIGNATURE_LEN];
     size_t      u;
+    H5E_auto2_t func;
+    void 	*edata;
     herr_t      status = SUCCEED;
 
     if(argc == 1) {
-  		HDfprintf(stderr, "Usage: %s filename [signature-addr [extra]]\n", argv[0]);
-  		HDexit(1);
+  	HDfprintf(stderr, "Usage: %s filename [signature-addr [extra]]\n", argv[0]);
+  	HDexit(1);
     } /* end if */
 
     /* Initialize the library */
@@ -161,6 +161,10 @@ main(int argc, char *argv[])
         HDexit(1);
     } /* end if */
 
+    /* Disable error reporting */
+    H5Eget_auto2(H5E_DEFAULT, &func, &edata);
+    H5Eset_auto2(H5E_DEFAULT, NULL, NULL);
+
     /*
      * Open the file and get the file descriptor.
      */
@@ -448,6 +452,8 @@ main(int argc, char *argv[])
     H5Pclose(fapl);
     H5Fclose(fid);
 
+    H5Eset_auto2(H5E_DEFAULT, func, edata);
+
     return 0;
 } /* main() */
 
diff --git a/tools/misc/h5mkgrp.c b/tools/misc/h5mkgrp.c
index 8dee706..597b6b3 100644
--- a/tools/misc/h5mkgrp.c
+++ b/tools/misc/h5mkgrp.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.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
 
@@ -63,7 +61,7 @@ param_t params;             /* Command line parameter settings */
 static void
 leave(int ret)
 {
-    int curr_group;
+    size_t curr_group;
 
     if (params.fname)
         HDfree (params.fname);
@@ -180,8 +178,8 @@ parse_command_line(int argc, const char *argv[], param_t *parms)
     } /* end if */
 
     /* Allocate space for the group name pointers */
-    parms->ngroups = (argc - opt_ind);
-    parms->groups = HDmalloc(parms->ngroups * sizeof(char *));
+    parms->ngroups = (size_t)(argc - opt_ind);
+    parms->groups = (char **)HDmalloc(parms->ngroups * sizeof(char *));
 
     /* Retrieve the group names */
     curr_group = 0;
@@ -328,9 +326,6 @@ main(int argc, const char *argv[])
         leave(EXIT_FAILURE);
     } /* end if */
 
-    /* Shut down h5tools lib */
-    h5tools_close();
-
     leave(EXIT_SUCCESS);
 } /* end main() */
 
diff --git a/tools/misc/h5redeploy.in b/tools/misc/h5redeploy.in
index 6b6ef87..242459a 100644
--- a/tools/misc/h5redeploy.in
+++ b/tools/misc/h5redeploy.in
@@ -6,12 +6,10 @@
 #
 # 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.
 #
 
 ## Update HDF5 compiler tools after the HDF5 software has been installed  ##
diff --git a/tools/misc/h5repart.c b/tools/misc/h5repart.c
index ffd52e8..911e0c6 100644
--- a/tools/misc/h5repart.c
+++ b/tools/misc/h5repart.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.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
 /*
@@ -194,27 +192,25 @@ main (int argc, char *argv[])
     int		src, dst=-1;		/*source & destination files	*/
     int		need_seek=FALSE;	/*destination needs to seek?	*/
     int		need_write;		/*data needs to be written?	*/
-    /*struct stat	sb;			temporary file stat buffer	*/
-	/*struct _stati64 sb;*/
-	h5_stat_t sb;
+    h5_stat_t sb;                       /*temporary file stat buffer	*/
 
     int		verbose=FALSE;		/*display file names?		*/
 
-    const char	*src_gen_name;		/*general source name		*/
-    char	src_name[NAMELEN];	/*source member name		*/
+    const char	*src_gen_name;  /*general source name		*/
+    char	*src_name=NULL;	    /*source member name		*/
 
     int		src_is_family;		/*is source name a family name?	*/
     int		src_membno=0;		/*source member number		*/
 
-    const char	*dst_gen_name;		/*general destination name	*/
-    char	dst_name[NAMELEN];	/*destination member name	*/
+    const char	*dst_gen_name;	/*general destination name	*/
+    char	*dst_name=NULL;	    /*destination member name	*/
     int		dst_is_family;		/*is dst name a family name?	*/
     int		dst_membno=0;		/*destination member number	*/
 
     off_t	left_overs=0;		/*amount of zeros left over	*/
     off_t	src_offset=0;		/*offset in source member	*/
     off_t	dst_offset=0;		/*offset in destination member	*/
-    off_t	src_size;		/*source logical member size	*/
+    off_t	src_size;           /*source logical member size	*/
     off_t	src_act_size;		/*source actual member size	*/
     off_t	dst_size=1 GB;		/*destination logical memb size	*/
     hid_t       fapl;                   /*file access property list     */
@@ -232,24 +228,30 @@ main (int argc, char *argv[])
      * Parse switches.
      */
     while (argno<argc && '-'==argv[argno][0]) {
-	if (!strcmp (argv[argno], "-v")) {
-	    verbose = TRUE;
-	    argno++;
-	} else if (!strcmp(argv[argno], "-V")) {
-	    printf("This is %s version %u.%u release %u\n",
-		   prog_name, H5_VERS_MAJOR, H5_VERS_MINOR, H5_VERS_RELEASE);
-	    exit(EXIT_SUCCESS);
+        if (!strcmp (argv[argno], "-v")) {
+            verbose = TRUE;
+            argno++;
+        } else if (!strcmp(argv[argno], "-V")) {
+            printf("This is %s version %u.%u release %u\n",
+                prog_name, H5_VERS_MAJOR, H5_VERS_MINOR, H5_VERS_RELEASE);
+            exit(EXIT_SUCCESS);
         } else if (!strcmp (argv[argno], "-family_to_sec2")) {
-	    family_to_sec2 = TRUE;
-	    argno++;
-	} else if ('b'==argv[argno][1]) {
-	    blk_size = get_size (prog_name, &argno, argc, argv);
-	} else if ('m'==argv[argno][1]) {
-	    dst_size = get_size (prog_name, &argno, argc, argv);
-	} else {
-	    usage (prog_name);
-	}
-    }
+            family_to_sec2 = TRUE;
+            argno++;
+        } else if ('b'==argv[argno][1]) {
+            blk_size = (size_t)get_size (prog_name, &argno, argc, argv);
+        } else if ('m'==argv[argno][1]) {
+            dst_size = get_size (prog_name, &argno, argc, argv);
+        } else {
+            usage (prog_name);
+        } /* end if */
+    } /* end while */
+
+    /* allocate names */
+    if(NULL == (src_name = (char *)HDcalloc((size_t)NAMELEN, sizeof(char))))
+        exit(EXIT_FAILURE);
+    if(NULL == (dst_name = (char *)HDcalloc((size_t)NAMELEN, sizeof(char))))
+        exit(EXIT_FAILURE);
 
     /*
      * Get the name for the source file and open the first member.  The size
@@ -261,13 +263,13 @@ main (int argc, char *argv[])
     src_is_family = strcmp (src_name, src_gen_name);
 
     if ((src=HDopen(src_name, O_RDONLY,0))<0) {
-	perror (src_name);
-	exit (EXIT_FAILURE);
+        perror (src_name);
+        exit (EXIT_FAILURE);
     }
 
     if (HDfstat(src, &sb)<0) {
-	perror ("fstat");
-	exit (EXIT_FAILURE);
+        perror ("fstat");
+        exit (EXIT_FAILURE);
     }
     src_size = src_act_size = sb.st_size;
     if (verbose) fprintf (stderr, "< %s\n", src_name);
@@ -290,7 +292,7 @@ main (int argc, char *argv[])
     if (argno<argc) usage (prog_name);
 
     /* Now the real work, split the file */
-    buf = HDmalloc (blk_size);
+    buf = (char *)HDmalloc(blk_size);
     while (src_offset<src_size) {
 
 	/* Read a block.  The amount to read is the minimum of:
@@ -302,7 +304,7 @@ main (int argc, char *argv[])
 	if (dst_is_family) n = (size_t)MIN((off_t)n, dst_size-dst_offset);
 	if (left_overs) {
 	    n = (size_t)MIN ((off_t)n, left_overs);
-	    left_overs -= n;
+	    left_overs = left_overs - (off_t)n;
 	    need_write = FALSE;
 	} else if (src_offset<src_act_size) {
 	    n = (size_t)MIN ((off_t)n, src_act_size-src_offset);
@@ -353,16 +355,16 @@ main (int argc, char *argv[])
 	 * loop.   The destination offset must be updated so we can fix
 	 * trailing holes.
 	 */
-	src_offset += n;
+	src_offset = src_offset + (off_t)n;
 	if (src_offset==src_act_size) {
 	    HDclose (src);
 	    if (!src_is_family) {
-		dst_offset += n;
+                dst_offset = dst_offset + (off_t)n;
 		break;
 	    }
 	    sprintf (src_name, src_gen_name, ++src_membno);
 	    if ((src=HDopen (src_name, O_RDONLY,0))<0 && ENOENT==errno) {
-		dst_offset += n;
+                dst_offset = dst_offset + (off_t)n;
 		break;
 	    } else if (src<0) {
 		perror (src_name);
@@ -386,7 +388,7 @@ main (int argc, char *argv[])
 	 * needed. The first member is extended to the logical member size
 	 * but other members might be smaller if they end with a hole.
 	 */
-	dst_offset += n;
+        dst_offset = dst_offset + (off_t)n;
 	if (dst_is_family && dst_offset==dst_size) {
 	    if (0==dst_membno) {
 		if (HDlseek (dst, dst_size-1, SEEK_SET)<0) {
@@ -468,7 +470,7 @@ main (int argc, char *argv[])
         }
 
         /* Set the property of the new member size as hsize_t */
-        hdsize = dst_size;
+        hdsize = (hsize_t)dst_size;
         if(H5Pset(fapl, H5F_ACS_FAMILY_NEWSIZE_NAME, &hdsize) < 0) {
             perror ("H5Pset");
             exit (EXIT_FAILURE);
@@ -485,19 +487,22 @@ main (int argc, char *argv[])
     H5E_BEGIN_TRY {
         file=H5Fopen(dst_gen_name, H5F_ACC_RDWR, fapl);
     } H5E_END_TRY;
+
     if(file>=0) {
         if(H5Fclose(file)<0) {
             perror ("H5Fclose");
             exit (EXIT_FAILURE);
-        }
-    }
+        } /* end if */
+    } /* end if */
 
     if(H5Pclose(fapl)<0) {
         perror ("H5Pclose");
         exit (EXIT_FAILURE);
-    }
+    } /* end if */
 
     /* Free resources and return */
-    HDfree (buf);
+    HDfree(src_name);
+    HDfree(dst_name);
+    HDfree(buf);
     return EXIT_SUCCESS;
-}
+} /* end main */
diff --git a/tools/misc/h5repart_gentest.c b/tools/misc/h5repart_gentest.c
index f7d9a73..5c1ff87 100644
--- a/tools/misc/h5repart_gentest.c
+++ b/tools/misc/h5repart_gentest.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.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
 /*
@@ -27,12 +25,13 @@
 #define FAMILY_SIZE     1024
 #define FILENAME        "family_file%05d.h5"
 
+static int buf[FAMILY_NUMBER][FAMILY_SIZE];
+
 int main(void)
 {
     hid_t       file=(-1), fapl, space=(-1), dset=(-1);
     char        dname[]="dataset";
     int         i, j;
-    int         buf[FAMILY_NUMBER][FAMILY_SIZE];
     hsize_t     dims[2]={FAMILY_NUMBER, FAMILY_SIZE};
 
     /* Set property list and file name for FAMILY driver */
diff --git a/tools/misc/repart_test.c b/tools/misc/repart_test.c
index e6da779..372f46a 100644
--- a/tools/misc/repart_test.c
+++ b/tools/misc/repart_test.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.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
 /*
diff --git a/tools/misc/talign.c b/tools/misc/talign.c
index 2d0a9d1..83bb92a 100644
--- a/tools/misc/talign.c
+++ b/tools/misc/talign.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.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
 /*
@@ -19,7 +17,7 @@
  */
 #include <string.h>
 #include <stdlib.h>
-/*#include <unistd.h>	*//* Required for unlink() */
+/*#include <unistd.h>    *//* Required for unlink() */
 
 #include "hdf5.h"
 #include "H5private.h"
@@ -37,11 +35,11 @@ const char *setname = "align";
 
 int main(void)
 {
-    hid_t fil,spc,set;
-    hid_t cs6, cmp, fix;
-    hid_t cmp1, cmp2, cmp3;
-    hid_t plist;
-    hid_t array_dt;
+    hid_t fil=-1, spc=-1, set=-1;
+    hid_t cs6=-1, cmp=-1, fix=-1;
+    hid_t cmp1=-1, cmp2=-1, cmp3=-1;
+    hid_t plist=-1;
+    hid_t array_dt=-1;
 
     hsize_t dim[2];
     hsize_t cdim[4];
@@ -49,7 +47,7 @@ int main(void)
     char string5[5];
     float fok[2] = {1234.0f, 2341.0f};
     float fnok[2] = {5678.0f, 6785.0f};
-    float *fptr;
+    float *fptr = NULL;
 
     char *data = NULL;
 
@@ -88,8 +86,7 @@ int main(void)
     H5Tinsert(cmp, "Not Ok", sizeof(fok) + sizeof(string5), array_dt);
     H5Tclose(array_dt);
 
-    fix = h5tools_get_native_type(cmp);
-
+    fix = H5Tget_native_type(cmp, H5T_DIR_DEFAULT);
     cmp1 = H5Tcreate(H5T_COMPOUND, sizeof(fok));
 
     cdim[0] = sizeof(fok) / sizeof(float);
@@ -108,7 +105,7 @@ int main(void)
     H5Tclose(array_dt);
 
     plist = H5Pcreate(H5P_DATASET_XFER);
-    if((error = H5Pset_preserve(plist, 1)) < 0) 
+    if((error = H5Pset_preserve(plist, 1)) < 0)
         goto out;
 
     /*
@@ -137,6 +134,7 @@ int main(void)
 
     H5Dread(set, fix, spc, H5S_ALL, H5P_DEFAULT, data);
     fptr = (float *)(data + H5Tget_member_offset(fix, 1));
+    H5Dclose(set);
 
 out:
     if(error < 0) {
@@ -194,7 +192,9 @@ out:
     if(data)
         HDfree(data);
     H5Sclose(spc);
+    H5Tclose(cs6);
     H5Tclose(cmp);
+    H5Tclose(fix);
     H5Tclose(cmp1);
     H5Tclose(cmp2);
     H5Tclose(cmp3);
@@ -205,35 +205,3 @@ out:
     return result;
 }
 
-/*-------------------------------------------------------------------------
- * Function: h5tools_get_native_type
- *
- * Purpose: Wrapper around H5Tget_native_type() to work around
- *  Problems with bitfields.
- *
- * Return: Success:    datatype ID
- *
- *  Failure:    FAIL
- *
- * Programmer: Quincey Koziol
- *              Tuesday, October  5, 2004
- *
- * Modifications:
- *
- *-------------------------------------------------------------------------
- */
-hid_t
-h5tools_get_native_type(hid_t type)
-{
-    hid_t p_type;
-    H5T_class_t type_class;
-
-    type_class = H5Tget_class(type);
-    if(type_class==H5T_BITFIELD)
-        p_type=H5Tcopy(type);
-    else
-        p_type = H5Tget_native_type(type,H5T_DIR_DEFAULT);
-
-    return(p_type);
-}
-
diff --git a/tools/misc/testh5mkgrp.sh.in b/tools/misc/testh5mkgrp.sh.in
index 190e824..2d2e5f7 100644
--- a/tools/misc/testh5mkgrp.sh.in
+++ b/tools/misc/testh5mkgrp.sh.in
@@ -6,12 +6,10 @@
 #
 # 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.
 #
 # Tests for the h5mkgrp tool
 #
@@ -103,7 +101,7 @@ COPY_TESTFILES_TO_TESTDIR()
                 $CP -f $tstfile $TESTDIR
                 if [ $? -ne 0 ]; then
                     echo "Error: FAILED to copy $tstfile ."
-                
+
                     # Comment out this to CREATE expected file
                     exit $EXIT_FAILURE
                 fi
@@ -117,7 +115,7 @@ CLEAN_TESTFILES_AND_TESTDIR()
     # skip rm if srcdir is same as destdir
     # this occurs when build/test performed in source dir and
     # make cp fail
-    SDIR=`$DIRNAME $tstfile`
+    SDIR=$SRC_H5MKGRP_TESTFILES
     INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'`
     INODE_DDIR=`$LS -i -d $TESTDIR | $AWK -F' ' '{print $1}'`
     if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then
@@ -127,7 +125,7 @@ CLEAN_TESTFILES_AND_TESTDIR()
 
 # Print a line-line message left justified in a field of 70 characters
 # beginning with the word "Testing".
-TESTING() 
+TESTING()
 {
     SPACES="                                                               "
     echo "Testing $* $SPACES" |cut -c1-70 |tr -d '\012'
@@ -139,7 +137,7 @@ TESTING()
 # Print a line-line message left justified in a field of 70 characters
 # beginning with the word "Verifying".
 #
-VERIFY_H5LS() 
+VERIFY_H5LS()
 {
     SPACES="                                                               "
     echo "Verifying h5ls file structure $* $SPACES" | cut -c1-70 | tr -d '\012'
@@ -151,7 +149,7 @@ VERIFY_H5LS()
 # Assumed arguments:
 # $* arguments for h5mkgrp.
 
-TOOLTEST() 
+TOOLTEST()
 {
     TESTING $H5MKGRP $@
     (
@@ -176,7 +174,7 @@ TOOLTEST()
 
 # Call the h5ls tool to verify the correct output data in the destination file
 #
-H5LSTEST() 
+H5LSTEST()
 {
     expect="$TESTDIR/`basename $1 .h5`.ls"
     actual="$TESTDIR/`basename $1 .h5`.out"
@@ -196,9 +194,11 @@ H5LSTEST()
     STDERR_FILTER $actual
 
    if [ ! -f $expect ]; then
-    # Create the expect file if it doesn't yet exist.
-    echo " CREATED"
-    cp $actual $expect
+      # Create the expect file if it doesn't yet exist.
+      echo " CREATED"
+      cp $actual $expect
+      echo "    Expected result (*.ls) missing"
+      nerrors="`expr $nerrors + 1`"
    elif $CMP $expect $actual; then
       echo " PASSED"
    else
@@ -220,7 +220,7 @@ H5LSTEST()
 # $1 is test file name
 # $2 is h5mkgrp options
 # $* are groups to create
-RUNTEST() 
+RUNTEST()
 {
     FILEOUT=$1
     shift
@@ -249,7 +249,7 @@ RUNTEST()
 # $1 is test expected output file
 # $2 is h5mkgrp options
 # $* are groups to create
-CMPTEST() 
+CMPTEST()
 {
     FILEOUT=$1
     expect="$TESTDIR/`basename $1 .h5`.txt"
@@ -265,11 +265,13 @@ CMPTEST()
     $RUNSERIAL $H5MKGRP_BIN $@
     ) >$actual 2>$actual_err
     cat $actual_err >> $actual
-    
+
    if [ ! -f $expect ]; then
     # Create the expect file if it doesn't yet exist.
-    echo " CREATED"
-    cp $actual $expect
+      echo " CREATED"
+      cp $actual $expect
+      echo "    Expected result (*.txt) missing"
+      nerrors="`expr $nerrors + 1`"
    elif $CMP $expect $actual; then
       echo " PASSED"
    else
@@ -307,7 +309,7 @@ RUNTEST h5mkgrp_several_v.h5 "-v" one two
 RUNTEST h5mkgrp_several_p.h5 "-p" one two
 RUNTEST h5mkgrp_several_l.h5 "-l" one two
 
-# Create various nested groups 
+# Create various nested groups
 RUNTEST h5mkgrp_nested_p.h5 "-p" /one/two
 RUNTEST h5mkgrp_nested_lp.h5 "-lp" /one/two
 RUNTEST h5mkgrp_nested_mult_p.h5 "-p" /one/two /three/four
diff --git a/tools/misc/testh5repart.sh.in b/tools/misc/testh5repart.sh.in
index fc33e0e..e33a905 100644
--- a/tools/misc/testh5repart.sh.in
+++ b/tools/misc/testh5repart.sh.in
@@ -6,12 +6,10 @@
 #
 # 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.
 #
 # Tests for the h5repart tool
 
@@ -80,13 +78,13 @@ OUTPUTTEST() {
 
 # Print a "SKIP" message
 SKIP() {
-	 TESTING $REPART $@
-	  echo  " -SKIP-"
+    TESTING $REPART $@
+    echo  " -SKIP-"
 }
 
 ##############################################################################
 ##############################################################################
-###			  T H E   T E S T S                                ###
+###              T H E   T E S T S                                ###
 ##############################################################################
 ##############################################################################