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.
  ...

7 files changed, 60 insertions, 43 deletions

diff --git a/tools/h5jam/CMakeTests.cmake b/tools/h5jam/CMakeTests.cmake
index 47276eb..646ae06 100644
--- a/tools/h5jam/CMakeTests.cmake
+++ b/tools/h5jam/CMakeTests.cmake
@@ -60,6 +60,13 @@
       endif ()
     else ()
       add_test (
+          NAME H5JAM-${expectfile}-clear-objects
+          COMMAND    ${CMAKE_COMMAND}
+              -E remove
+              ${expectfile}.out
+              ${expectfile}.out.err
+      )
+      add_test (
           NAME H5JAM-${expectfile}
           COMMAND "${CMAKE_COMMAND}"
               -D "TEST_PROGRAM=$<TARGET_FILE:h5jam>"
@@ -70,6 +77,7 @@
               -D "TEST_REFERENCE=testfiles/${expectfile}.txt"
               -P "${HDF_RESOURCES_EXT_DIR}/runTest.cmake"
       )
+      set_tests_properties (H5JAM-${expectfile} PROPERTIES DEPENDS "H5JAM-${expectfile}-clear-objects")
     endif ()
   endmacro ()
 
@@ -86,6 +94,13 @@
       endif ()
     else ()
       add_test (
+          NAME H5JAM-UNJAM-${expectfile}-clear-objects
+          COMMAND    ${CMAKE_COMMAND}
+              -E remove
+              ${expectfile}.out
+              ${expectfile}.out.err
+      )
+      add_test (
           NAME H5JAM-UNJAM-${expectfile}
           COMMAND "${CMAKE_COMMAND}"
               -D "TEST_PROGRAM=$<TARGET_FILE:h5unjam>"
@@ -96,6 +111,7 @@
               -D "TEST_REFERENCE=testfiles/${expectfile}.txt"
               -P "${HDF_RESOURCES_EXT_DIR}/runTest.cmake"
       )
+      set_tests_properties (H5JAM-UNJAM-${expectfile} PROPERTIES DEPENDS "H5JAM-UNJAM-${expectfile}-clear-objects")
     endif ()
   endmacro ()
 
@@ -103,6 +119,16 @@
     # If using memchecker add tests without using scripts
     if (NOT HDF5_ENABLE_USING_MEMCHECKER)
       add_test (
+          NAME H5JAM-${testname}-CHECKFILE-clear-objects
+          COMMAND    ${CMAKE_COMMAND}
+              -E remove
+              ${actual}.new
+              ${actual}.new.err
+              ${actual}.out
+              ${actual}.out.err
+      )
+      set_tests_properties (H5JAM-${testname}-CHECKFILE-clear-objects PROPERTIES DEPENDS ${testdepends})
+      add_test (
           NAME H5JAM-${testname}-CHECKFILE-H5DMP
           COMMAND "${CMAKE_COMMAND}"
               -D "TEST_PROGRAM=$<TARGET_FILE:h5dump>"
@@ -114,7 +140,7 @@
               -D "TEST_SKIP_COMPARE=TRUE"
               -P "${HDF_RESOURCES_EXT_DIR}/runTest.cmake"
       )
-      set_tests_properties (H5JAM-${testname}-CHECKFILE-H5DMP PROPERTIES DEPENDS ${testdepends})
+      set_tests_properties (H5JAM-${testname}-CHECKFILE-H5DMP PROPERTIES DEPENDS H5JAM-${testname}-CHECKFILE-clear-objects)
       add_test (
           NAME H5JAM-${testname}-CHECKFILE-H5DMP_CMP
           COMMAND "${CMAKE_COMMAND}"
diff --git a/tools/h5jam/Makefile.in b/tools/h5jam/Makefile.in
index 5613fa0..0939991 100644
--- a/tools/h5jam/Makefile.in
+++ b/tools/h5jam/Makefile.in
@@ -603,6 +603,7 @@ dvidir = @dvidir@
 enable_shared = @enable_shared@
 enable_static = @enable_static@
 exec_prefix = @exec_prefix@
+fortran_linux_linker_option = @fortran_linux_linker_option@
 host = @host@
 host_alias = @host_alias@
 host_cpu = @host_cpu@
diff --git a/tools/h5jam/h5jam.c b/tools/h5jam/h5jam.c
index b15a18f..269ca89 100644
--- a/tools/h5jam/h5jam.c
+++ b/tools/h5jam/h5jam.c
@@ -76,13 +76,13 @@ usage (const char *prog)
     HDfprintf (stdout,
     "Adds user block to front of an HDF5 file and creates a new concatenated file.\n");
     HDfprintf (stdout, "\n");
-    HDfprintf (stdout, 
+    HDfprintf (stdout,
     "OPTIONS\n");
-    HDfprintf (stdout, 
+    HDfprintf (stdout,
     "  -i in_file.h5    Specifies the input HDF5 file.\n");
-    HDfprintf (stdout, 
+    HDfprintf (stdout,
     "  -u in_user_file  Specifies the file to be inserted into the user block.\n");
-    HDfprintf (stdout, 
+    HDfprintf (stdout,
     "                   Can be any file format except an HDF5 format.\n");
     HDfprintf (stdout,
     "  -o out_file.h5   Specifies the output HDF5 file.\n");
@@ -389,7 +389,7 @@ main (int argc, const char *argv[])
         HDfree (input_file);
     if(output_file)
         HDfree (output_file);
-    
+
     if(ufid >= 0)
         HDclose (ufid);
     if(h5fid >= 0)
diff --git a/tools/h5jam/h5jamgentest.c b/tools/h5jam/h5jamgentest.c
index fa8bd4e..12ea6b8 100644
--- a/tools/h5jam/h5jamgentest.c
+++ b/tools/h5jam/h5jamgentest.c
@@ -20,8 +20,6 @@
  * trying it on a new platform, ...), you need to verify the correctness
  * of the expected output and update the corresponding *.ddl files.
  */
-#include <assert.h>
-#include <limits.h>
 
 #include "hdf5.h"
 #include "H5private.h"
diff --git a/tools/h5jam/h5unjam.c b/tools/h5jam/h5unjam.c
index 8f6b686..9c83740 100644
--- a/tools/h5jam/h5unjam.c
+++ b/tools/h5jam/h5unjam.c
@@ -135,28 +135,28 @@ static int
 parse_command_line(int argc, const char *argv[])
 {
     int opt = FALSE;
-	
+
    /* parse command line options */
     while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) {
         switch((char)opt) {
             case 'o':
                 output_file = HDstrdup(opt_arg);
-				if (output_file)
-				    h5tools_set_data_output_file(output_file, 1);
-	            break;
+                if (output_file)
+                    h5tools_set_data_output_file(output_file, 1);
+                break;
 
             case 'i':
                 input_file = HDstrdup(opt_arg);
-				if (input_file)
-   				    h5tools_set_input_file(input_file, 1);
-	            break;;
+                if (input_file)
+                    h5tools_set_input_file(input_file, 1);
+                break;;
 
             case 'u':
                 ub_file = HDstrdup(opt_arg);
-				if (ub_file)
-				    h5tools_set_output_file(ub_file, 1);
-				else 
-				    rawoutstream = stdout;			
+                if (ub_file)
+                    h5tools_set_output_file(ub_file, 1);
+                else
+                    rawoutstream = stdout;
                 break;
 
             case 'd':
@@ -182,7 +182,7 @@ parse_command_line(int argc, const char *argv[])
     }
 
     return EXIT_SUCCESS;
-    
+
 done:
     if(input_file)
         HDfree(input_file);
@@ -242,7 +242,7 @@ main(int argc, const char *argv[])
         h5tools_setstatus(EXIT_FAILURE);
         goto done;
     }
-  
+
     testval = H5Fis_hdf5(input_file);
 
     if (testval <= 0) {
@@ -274,10 +274,8 @@ main(int argc, const char *argv[])
         goto done;
     }
 
-    status = H5Pclose(plist);
-    HDassert(status >= 0);
-    status = H5Fclose(ifile);
-    HDassert(status >= 0);
+    H5Pclose(plist);
+    H5Fclose(ifile);
 
     if (usize == 0) {
   /* no user block to remove: message? */
@@ -305,7 +303,7 @@ main(int argc, const char *argv[])
             error_msg("unable to open output HDF5 file \"%s\"\n", input_file);
             h5tools_setstatus(EXIT_FAILURE);
             goto done;
-    } 
+    }
 
     /* copy from 0 to 'usize - 1' into ufid  */
     if (!do_delete) {
@@ -323,18 +321,18 @@ main(int argc, const char *argv[])
         h5tools_setstatus(EXIT_FAILURE);
         goto done;
     }
- 
+
 done:
     if(input_file)
         HDfree(input_file);
-		
+
     if(output_file)
         HDfree(output_file);
-		
+
     if(ub_file) {
         HDfree(ub_file);
     }
-	   
+
     h5tools_close();
 
     return h5tools_getstatus();
@@ -374,7 +372,7 @@ copy_to_file( FILE *infid, FILE *ofid, ssize_t _where, ssize_t how_much )
         else
             bytes_in = how_much;
 
-			/* Seek to correct position in input file */
+            /* Seek to correct position in input file */
         HDfseek(infid, from, SEEK_SET);
 
         /* Read data to buffer */
@@ -396,11 +394,11 @@ copy_to_file( FILE *infid, FILE *ofid, ssize_t _where, ssize_t how_much )
         to += bytes_read;
 
        /* Write nchars bytes to output file */
-		bytes_wrote = HDfwrite(buf, (size_t)1, bytes_read, ofid);
-		if(bytes_wrote != bytes_read || (0 == bytes_wrote && HDferror(ofid))) { /* error */
-			ret_value = -1;
-			goto done;
-		} /* end if */
+        bytes_wrote = HDfwrite(buf, (size_t)1, bytes_read, ofid);
+        if(bytes_wrote != bytes_read || (0 == bytes_wrote && HDferror(ofid))) { /* error */
+            ret_value = -1;
+            goto done;
+        } /* end if */
     } /* end while */
 
 done:
diff --git a/tools/h5jam/tellub.c b/tools/h5jam/tellub.c
index fad14b7..8e4b3ac 100644
--- a/tools/h5jam/tellub.c
+++ b/tools/h5jam/tellub.c
@@ -11,12 +11,6 @@
  * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
-#include <stdio.h>
-
-#ifdef H5_HAVE_UNISTD_H
-#include <unistd.h>
-#endif
-
 #include "hdf5.h"
 #include "H5private.h"
 #include "h5tools.h"
diff --git a/tools/h5jam/testh5jam.sh.in b/tools/h5jam/testh5jam.sh.in
index d28db72..187054b 100644
--- a/tools/h5jam/testh5jam.sh.in
+++ b/tools/h5jam/testh5jam.sh.in
@@ -603,7 +603,7 @@ CLEANUP taz3.h5
 JAMTEST $TESTDIR/u512.txt $TESTDIR/twithub.h5 --clobber taz4.h5
 CHECKFILE $TESTDIR/tall.h5 taz4.h5
 CLEANUP taz4.h5
-JAMTEST $TESTDIR/u513.txt $TESTDIR/twithub.h5 --clobber taz5.h5 
+JAMTEST $TESTDIR/u513.txt $TESTDIR/twithub.h5 --clobber taz5.h5
 CHECKFILE $TESTDIR/tall.h5 taz5.h5
 CLEANUP taz5.h5