Brought the scripts in bin/ in line with develop.

15 files changed, 347 insertions, 258 deletions

diff --git a/bin/batch/ctestP.sl.in.cmake b/bin/batch/ctestP.sl.in.cmake
index 6399de7..1069fa9 100644
--- a/bin/batch/ctestP.sl.in.cmake
+++ b/bin/batch/ctestP.sl.in.cmake
@@ -10,5 +10,5 @@
 cd @HDF5_BINARY_DIR@
 ctest . -R MPI_TEST_ -C Release -T test >& ctestP.out
 
-echo "Done running ctestP.sl" 
+echo "Done running ctestP.sl"
 
diff --git a/bin/checkapi b/bin/checkapi
index 6882dea..f5dcacc 100755
--- a/bin/checkapi
+++ b/bin/checkapi
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 #
 # Copyright by The HDF Group.
 # Copyright by the Board of Trustees of the University of Illinois.
@@ -13,6 +13,8 @@
 #
 require 5.003;
 
+use warnings;
+
 # Purpose: insures that API functions aren't called internally.
 # Usage:   checkapi H5*.c
 my $filename = "";
diff --git a/bin/checkposix b/bin/checkposix
index 7ab741c..233d15c 100755
--- a/bin/checkposix
+++ b/bin/checkposix
@@ -1,5 +1,6 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 require 5.003;
+use warnings;
 
 #
 # Copyright by The HDF Group.
@@ -13,101 +14,165 @@ require 5.003;
 # If you do not have access to either file, you may request a copy from
 # help@hdfgroup.org.
 #
-# Robb Matzke, matzke@llnl.gov
-# 30 Aug 1997
+# Dana Robinson
+# Spring 2019
+# (Original by Robb Matzke)
 #
-# Purpose: Given the names of C source files this script will print the
-#	   file name, line number, and function name of any function that
-#	   doesn't begin with the letter `h' or `H' as stipulated by the
-#	   HDF5 programming style guide.
+# Purpose:  Given the names of C source files this script will print the
+#           file name, line number, and function name of any function that
+#           doesn't begin with the letter 'h' or 'H' as stipulated by the
+#           HDF5 programming style guide.
 #
-#	   Emacs users can run this script as the compile command and
-#	   use `next-error' (usually bound to M-`) to find each name
-#	   violation.
-
-if(<>) {
-    if($ARGV =~ /\//) {
-        ($filename) = ($ARGV =~ /^.*\/([A-Za-z0-9_]*)\.c$/);
-    } else {
-        ($filename) = ($ARGV =~ /([A-Za-z0-9_]*)\.c$/);
+#           Emacs users can run this script as the compile command and
+#           use 'next-error' (usually bound to M-`) to find each name
+#           violation.
+
+use File::Basename;
+
+# Loop over all files passed to the function
+foreach $arg (@ARGV) {
+
+    # Get the filename from the path
+    $filename = fileparse($arg);
+
+    # Skip files that don't include H5private.h
+    # H5system. has to be inspected by hand since it wraps POSIX files
+    #
+    # H5detect and H5make_libsettings are created before the library exists
+    # so calls that link to function replacements won't work. We'll ignore
+    # it here.
+    #
+    # If a user specifies one file, process it no matter what so people
+    # can inspect files we normally skip (like H5system.c).
+    if($#ARGV gt 0 and $filename =~ /H5FDmulti|H5FDstdio|H5VLpassthru|H5system|H5detect|H5make_libsettings/) {
+        print "$filename is exempt from using Standard library macro wrappers\n";
+        next;
     }
 
-    if($filename =~ /H5FDmulti|H5FDstdio/) {
-        print "$ARGV is exempt from using Standard library macro wrappers\n";
-    } else {
-        while (<>) {
-
-           # Get rid of comments by removing the inside part.
-           s|/\*.*?\*/||g;
-           if ($in_comment) {
-              if (/\*\//) {
-                 s|.*?\*/||;
-                 $in_comment = 0;
-              } else {
-                 $_="\n";
-              }
-           } elsif (m|/\*|) {
-              s|/\*.*||;
-              $in_comment = 1;
-           }
-
-           # Get rid of string constants if they begin and end on this line.
-           s/([\'\"])([^\1]|\\\1)*?\1/$1$1/g;
-
-           # Get rid of preprocessor directives
-           s/^\#.*//;
-
-           # Skip callbacks invoked as methods in a struct
-           next if $_ =~ /\b(\)?->|\.)\(?([a-z_A-Z]\w*)\s*\(/;
-
-           # Now find all function calls on this line which don't start with 'H'
-           while (($name)=/\b([a-z_A-GI-Z]\w*)\s*\(/) {
-              $_ = $';
+    # Open the file
+    open(my $fh, "<", $arg) or do {
+        warn "NOTE: Unable to open $arg: !$\n";
+        next;
+    };
+
+    # Loop over all lines in the file to find undecorated functions
+    while (<$fh>) {
+
+        # Get rid of comments by removing the inside part.
+        s|/\*.*?\*/||g;
+        if ($in_comment) {
+            if (/\*\//) {
+                s|.*?\*/||;
+                $in_comment = 0;
+            } else {
+                $_="\n";
+            }
+        } elsif (m|/\*|) {
+            s|/\*.*||;
+            $in_comment = 1;
+        }
+
+        # Get rid of string constants if they begin and end on this line.
+        s/([\'\"])([^\1]|\\\1)*?\1/$1$1/g;
+
+        # Get rid of preprocessor directives
+        s/^\#.*//;
+
+        # Skip callbacks invoked as methods in a struct
+        next if $_ =~ /\b(\)?]?->|\.)\(?([a-z_A-Z]\w*)\s*\(/;
+
+        # Now find all function calls on this line which don't start with 'H'
+        while (($name)=/\b([a-z_A-GI-Z]\w*)\s*\(/) {
+            $_ = $';
               
-              # Ignore C statements that look sort of like function
-              # calls.
-              next if $name =~ /^(if|for|offsetof|return|sizeof|switch|while|void)$/;
-
-              # Ignore things that get misdetected because of the simplified
-              # parsing that takes place here.
-              next if $name =~ /^(int|herr_t|_term_interface)$/;
-
-              # These are really HDF5 functions/macros even though they don't
-              # start with `h' or `H'.
-              next if $name =~ /^FUNC_(ENTER|LEAVE)(_(NO)?API|_PACKAGE|_STATIC)?(_NOFS|_NOCLEAR|_NOINIT)?(_NOFUNC|_TAG)?$/;
-              next if $name =~ /^(BEGIN|END)_FUNC$/;
-              next if $name =~ /^U?INT(8|16|32|64)(ENCODE|DECODE)(_VAR)?$/;
-              next if $name =~ /^CI_(PRINT_STATS|INC_SRC|INC_DST)$/;
-              next if $name =~ /^(ABS|ADDR_OVERFLOW|ALL_MEMBERS|BOUND|CONSTR|DETECT_[I|F|M]|DOWN)$/;
-              next if $name =~ /^(MIN3?|MAX3?|NELMTS|POWER_OF_TWO|REGION_OVERFLOW)$/;
-              next if $name =~ /^(UNIQUE_MEMBERS)$/;
-              next if $name =~ /^addr_defined$/;
-
-              # These functions/macros are exempt.
-              next if $name =~ /^(main|[fs]?printf|va_(start|arg|end))$/;
-
-              # These are Windows system calls. Ignore them.
-              next if $name =~ /^(_get_osfhandle|GetFileInformationByHandle|SetFilePointer|GetLastError|SetEndOfFile)$/;
-              next if $name =~ /^(FindNextFile|FindClose|_tzset|Wgettimeofday|GetSystemTimeAsFileTime|Wgetlogin|GetUserName)$/;
-
-              # These are MPI function calls. Ignore them.
-              next if $name =~ /^(MPI_|MPE_)/;
-
-              # These are POSIX threads function calls. Ignore them.
-              next if $name =~ /^pthread_/;
-
-              # These are Windows threads function calls. Ignore them.
-              next if $name =~ /^(_beginthread|(Initialize|Enter|Leave)CriticalSection|TlsAlloc)$/;
-
-              # These are zlib & szlib function calls. Ignore them.
-              next if $name =~ /^(inflate|SZ_)/;
-              next if $name =~ /^compress2$/;
-
-              print "$ARGV:$.: $name\n";
-           }
-
-        } continue {
-           close ARGV if eof;       # reset line number
+            # Ignore C statements that look sort of like function
+            # calls.
+            next if $name =~ /^(if|for|offsetof|return|sizeof|switch|while|void)$/;
+
+            # Ignore things that get misdetected because of the simplified
+            # parsing that takes place here.
+            next if $name =~ /^(int|herr_t|_term_interface|_term_package)$/;
+
+            # These are really HDF5 functions/macros even though they don't
+            # start with `h' or `H'.
+            next if $name =~ /^FUNC_(ENTER|LEAVE)(_(NO)?API|_PACKAGE|_STATIC)?(_NOFS|_NOCLEAR|_NOINIT)?(_NOFUNC|_TAG)?$/;
+            next if $name =~ /^(BEGIN|END)_FUNC$/;
+            next if $name =~ /^U?INT(8|16|32|64)(ENCODE|DECODE)(_VAR)?$/;
+            next if $name =~ /^CI_(PRINT_STATS|INC_SRC|INC_DST)$/;
+            next if $name =~ /^(ABS|ADDR_OVERFLOW|ALL_MEMBERS|BOUND|CONSTR|DETECT_[I|F|M]|DOWN)$/;
+            next if $name =~ /^(MIN3?|MAX3?|NELMTS|POWER_OF_TWO|REGION_OVERFLOW)$/;
+            next if $name =~ /^(UNIQUE_MEMBERS|S_ISDIR)$/;
+            next if $name =~ /^addr_defined$/;
+
+            # These functions/macros are exempt.
+            # op, cb, and OP are often spuriously flagged so ignore them.
+            next if $name =~ /^(main|op|cb|OP)$/;
+
+            # This often appears in preprocessor lines that span multiple lines
+            next if $name =~ /^(defined)$/;
+
+            # These are Windows system calls. Ignore them.
+            next if $name =~ /^(_get_osfhandle|GetFileInformationByHandle|SetFilePointer|GetLastError|SetEndOfFile)$/;
+            next if $name =~ /^(FindNextFile|FindClose|_tzset|Wgettimeofday|GetSystemTimeAsFileTime|Wgetlogin|GetUserName)$/;
+            next if $name =~ /^(DeleteCriticalSection|TlsFree|TlsGetValue|CreateThread)$/;
+            next if $name =~ /^(ExpandEnvironmentStringsA|LockFileEx|UnlockFileEx)$/;
+            next if $name =~ /^(DllMain|LocalAlloc|LocalFree)$/;
+            next if $name =~ /^(FindFirstFileA|FindNextFileA)$/;
+            next if $name =~ /^(_beginthread|(Initialize|Enter|Leave)CriticalSection|TlsAlloc)$/;
+
+            # These are MPI function calls. Ignore them.
+            next if $name =~ /^(MPI_|MPE_)/;
+
+            # These are POSIX threads function calls. Ignore them.
+            next if $name =~ /^pthread_/;
+
+            # These are zlib & szlib function calls. Ignore them.
+            next if $name =~ /^(inflate|SZ_)/;
+            next if $name =~ /^compress2$/;
+
+            # These is an H5Dfill function. Ignore it in this file.
+            if($filename =~ /H5Dfill/) {
+                next if $name =~ /^(alloc_func)$/;
+            }
+
+            # These are H5Zscaleoffset functions. Ignore them in this file.
+            if($filename =~ /H5Zscaleoffset/) {
+                next if $name =~ /^(pow_fun|round_fun|abs_fun|lround_fun|llround_fun)$/;
+            }
+
+            # TESTING (not comprehensive - just noise reduction)
+            
+            # Test macros and functions (testhdf5.h)
+            next if $name =~ /^(AddTest|TestErrPrintf|TestSummary|TestCleanup|TestShutdown)$/;
+            next if $name =~ /^(CHECK|CHECK_PTR|CHECK_PTR_NULL|CHECK_PTR_EQ|CHECK_I)$/;
+            next if $name =~ /^(VERIFY|VERIFY_STR|VERIFY|TYPE|MESSAGE|ERROR)$/;
+
+            # Test macros and functions (h5test.h)
+            next if $name =~ /^(TESTING|PASSED|SKIPPED|FAIL_PUTS_ERROR|FAIL_STACK_ERROR|TEST_ERROR)$/;
+            next if $name =~ /^(GetTestExpress)$/;
+
+            # Ignore functions that start with test_ or check_
+            next if $name =~ /^test_/;
+            next if $name =~ /^check_/;
+
+            # Ignore functions that start with h5_
+            next if $name =~ /^h5_/;
+
+            # Ignore usage functions
+            next if $name =~ /^usage$/;
+
+            print "$filename:$.: $name\n";
         }
+
     }
+
+    # Close the file
+    close($fh);
+}
+
+if($#ARGV gt 0) {
+    print "\n";
+    print "NOTE:\n";
+    print "If any files were skipped due to being exempt, you can inspect them manually\n";
+    print "by using this script on them one at a time, which will always process the file.\n";
 }
diff --git a/bin/debug-ohdr b/bin/debug-ohdr
index 5b0a4b3..1363456 100755
--- a/bin/debug-ohdr
+++ b/bin/debug-ohdr
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 #
 # Copyright by The HDF Group.
 # Copyright by the Board of Trustees of the University of Illinois.
diff --git a/bin/dependencies b/bin/dependencies
index 82247da..367351a 100755
--- a/bin/dependencies
+++ b/bin/dependencies
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 #
 # Copyright by The HDF Group.
 # Copyright by the Board of Trustees of the University of Illinois.
@@ -11,6 +11,8 @@
 # If you do not have access to either file, you may request a copy from
 # help@hdfgroup.org.
 #
+use warnings;
+
 my $depend_file;
 my $new_depend_file;
 my $srcdir;
diff --git a/bin/distdep b/bin/distdep
index 4643700..c20a099 100755
--- a/bin/distdep
+++ b/bin/distdep
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -p
+#!/usr/bin/env perl -p
 #
 # Copyright by The HDF Group.
 # Copyright by the Board of Trustees of the University of Illinois.
diff --git a/bin/errors b/bin/errors
index 3c99fdc..107bb9c 100755
--- a/bin/errors
+++ b/bin/errors
@@ -1,5 +1,6 @@
-#!/usr/local/bin/perl -w
+#!/usr/bin/env perl
 require 5.003;
+use warnings;
 use Text::Tabs;
 
 # NOTE: THE FORMAT OF HRETURN_ERROR AND HGOTO_ERROR MACROS HAS
diff --git a/bin/h5cc.in b/bin/h5cc.in
index 9c4e3ca..62a0884 100644
--- a/bin/h5cc.in
+++ b/bin/h5cc.in
@@ -83,10 +83,10 @@ CLINKERBASE="@CC@"
 # CFLAGS, CPPFLAGS and LDFLAGS are reserved for use by the script user.
 # FLAGS brought from the hdf5 build are put in H5BLD_*FLAGS.
 
-# User's CPPFLAGS and CFLAGS come after their H5BLD counterparts.  User's 
-# LDFLAGS come just before clibpath, user's LIBS come after $link_objs and 
-# before the hdf5 libraries in $link_args, followed by any external library 
-# paths and libraries from AM_LDFLAGS, LDFLAGS, AM_LIBS or LIBS carried in 
+# User's CPPFLAGS and CFLAGS come after their H5BLD counterparts.  User's
+# LDFLAGS come just before clibpath, user's LIBS come after $link_objs and
+# before the hdf5 libraries in $link_args, followed by any external library
+# paths and libraries from AM_LDFLAGS, LDFLAGS, AM_LIBS or LIBS carried in
 # from the hdf5 build. The order of the flags is intended to give precedence
 # to the user's flags.
 H5BLD_CFLAGS="@AM_CFLAGS@ @CFLAGS@"
@@ -102,9 +102,9 @@ LDFLAGS="${HDF5_LDFLAGS:-$LDFLAGSBASE}"
 LIBS="${HDF5_LIBS:-$LIBSBASE}"
 
 # If a static library is available, the default will be to use it.  If the only
-# available library is shared, it will be used by default.  The user can 
+# available library is shared, it will be used by default.  The user can
 # override either default, although choosing an unavailable library will result
-# in link errors.  
+# in link errors.
 STATIC_AVAILABLE="@enable_static@"
 if test "${STATIC_AVAILABLE}" = "yes"; then
   USE_SHARED_LIB="${HDF5_USE_SHLIB:-no}"
@@ -121,13 +121,6 @@ usage() {
   echo "    -echo        Show all the shell commands executed"
   echo "    -prefix=DIR  Prefix directory to find HDF5 lib/ and include/"
   echo "                   subdirectories [default: $prefix]"
-  # A wonderfully informative "usage" message.
-  echo "usage: $prog_name [OPTIONS] <compile line>"
-  echo "  OPTIONS:"
-  echo "    -help        This help message."
-  echo "    -echo        Show all the shell commands executed"
-  echo "    -prefix=DIR  Prefix directory to find HDF5 lib/ and include/"
-  echo "                   subdirectories [default: $prefix]"
   echo "    -show        Show the commands without executing them"
   echo "    -showconfig  Show the HDF5 library configuration summary"
   echo "    -shlib       Compile with shared HDF5 libraries [default for hdf5 built"
@@ -147,7 +140,7 @@ usage() {
   echo "   HDF5_CC                  -  use a different C compiler"
   echo "   HDF5_CLINKER             -  use a different linker"
   echo "   HDF5_USE_SHLIB=[yes|no]  -  use shared or static version of the HDF5 library"
-  echo "                                 [default: no except when built with only" 
+  echo "                                 [default: no except when built with only"
   echo "                                           shared libraries]"
   echo " "
   echo " You can also add or change paths and flags to the compile line using"
@@ -325,7 +318,7 @@ fi
 
 if test "x$do_link" = "xyes"; then
   shared_link=""
-# conditionnaly link with the hl library  
+# conditionnaly link with the hl library
   if test "X$HL" = "Xhl"; then
    libraries=" $libraries -lhdf5_hl -lhdf5 "
   else
@@ -386,10 +379,10 @@ if test "x$do_link" = "xyes"; then
   # module. It's okay if they're included twice in the compile line.
   link_args="$link_args $H5BLD_LDFLAGS $H5BLD_LIBS"
 
-  # User's CPPFLAGS and CFLAGS come after their H5BLD counterparts.  User's 
-  # LDFLAGS come just before clibpath, user's LIBS come after $link_objs and 
-  # before the hdf5 libraries in $link_args, followed by any external library 
-  # paths and libraries from AM_LDFLAGS, LDFLAGS, AM_LIBS or LIBS carried in 
+  # User's CPPFLAGS and CFLAGS come after their H5BLD counterparts.  User's
+  # LDFLAGS come just before clibpath, user's LIBS come after $link_objs and
+  # before the hdf5 libraries in $link_args, followed by any external library
+  # paths and libraries from AM_LDFLAGS, LDFLAGS, AM_LIBS or LIBS carried in
   # from the hdf5 build. The order of the flags is intended to give precedence
   # to the user's flags.
   $SHOW $CLINKER $H5BLD_CPPFLAGS $CPPFLAGS $H5BLD_CFLAGS $CFLAGS $LDFLAGS $clibpath $link_objs $LIBS $link_args $shared_link
diff --git a/bin/iostats b/bin/iostats
index f054b9c..e389992 100755
--- a/bin/iostats
+++ b/bin/iostats
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 #
 # Copyright by The HDF Group.
 # Copyright by the Board of Trustees of the University of Illinois.
diff --git a/bin/make_err b/bin/make_err
index 623c1b6..7f38591 100755
--- a/bin/make_err
+++ b/bin/make_err
@@ -1,6 +1,7 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 require 5.003;
 $indent=4;
+use warnings;
 
 #
 # Copyright by The HDF Group.
diff --git a/bin/make_overflow b/bin/make_overflow
index ccd640e..cee0126 100755
--- a/bin/make_overflow
+++ b/bin/make_overflow
@@ -1,6 +1,7 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 require 5.003;
 use strict;
+use warnings;
 
 # Global settings
 
diff --git a/bin/make_vers b/bin/make_vers
index 4de2dbd..d2dca4e 100755
--- a/bin/make_vers
+++ b/bin/make_vers
@@ -1,5 +1,6 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 require 5.003;
+use warnings;
 
 # Global settings
 # (The max_idx parameter is the only thing that needs to be changed when adding
@@ -89,7 +90,8 @@ sub print_checkoptions ($) {
     my $curr_idx;               # Current API version index
 
     # Print the option checking
-    print $fh "\n/* Issue error if contradicting macros have been defined. */\n";
+    print $fh "\n\n/* Issue error if contradicting macros have been defined. */\n";
+    print $fh "/* (Can't use an older (deprecated) API version if deprecated symbols have been disabled) */\n";
 
     # Print the #ifdef
     print $fh "#if (";
@@ -118,26 +120,40 @@ sub print_checkoptions ($) {
 ##############################################################################
 # Print "global" API version macro settings
 #
-sub print_globalapivers ($) {
+sub print_globalapidefvers ($) {
     my $fh = shift;             # File handle for output file
     my $curr_idx;               # Current API version index
 
     # Print the descriptive comment
-    print $fh "\n\n/* If a particular \"global\" version of the library's interfaces is chosen,\n";
-    print $fh " *      set the versions for the API symbols affected.\n";
+    print $fh "\n\n/* If a particular default \"global\" version of the library's interfaces is\n";
+    print $fh " *      chosen, set the corresponding version macro for API symbols.\n";
     print $fh " *\n";
-    print $fh " * Note: If an application has already chosen a particular version for an\n";
-    print $fh " *      API symbol, the individual API version macro takes priority.\n";
     print $fh " */\n";
 
     for $curr_idx ($min_sup_idx .. ($max_idx - 1)) {
         # Print API version ifdef
-        print $fh "#if defined(H5_USE_1", ($curr_idx * 2), "_API_DEFAULT) && !defined(H5_USE_1", ($curr_idx * 2), "_API)\n";
+        print $fh "\n#if defined(H5_USE_1", ($curr_idx * 2), "_API_DEFAULT) && !defined(H5_USE_1", ($curr_idx * 2), "_API)\n";
         # Print API version definition
         print $fh " " x $indent, "#define H5_USE_1", ($curr_idx * 2), "_API 1\n";
         # Print API version endif
-        print $fh "#endif /* H5_USE_1", ($curr_idx * 2), "_API_DEFAULT && !H5_USE_1", ($curr_idx * 2), "_API */\n\n";
+        print $fh "#endif /* H5_USE_1", ($curr_idx * 2), "_API_DEFAULT && !H5_USE_1", ($curr_idx * 2), "_API */\n";
     }
+}
+
+##############################################################################
+# Print "global" API symbol version macro settings
+#
+sub print_globalapisymbolvers ($) {
+    my $fh = shift;             # File handle for output file
+    my $curr_idx;               # Current API version index
+
+    # Print the descriptive comment
+    print $fh "\n\n/* If a particular \"global\" version of the library's interfaces is chosen,\n";
+    print $fh " *      set the versions for the API symbols affected.\n";
+    print $fh " *\n";
+    print $fh " * Note: If an application has already chosen a particular version for an\n";
+    print $fh " *      API symbol, the individual API version macro takes priority.\n";
+    print $fh " */\n";
 
     # Loop over supported older library APIs and define the appropriate macros
     for $curr_idx ($min_sup_idx .. ($max_idx - 1)) {
@@ -443,8 +459,9 @@ sub create_public ($) {
     print_copyright(*HEADER);
     print_warning(*HEADER);
     print_startprotect(*HEADER, $file);
+    print_globalapidefvers(*HEADER);
     print_checkoptions(*HEADER);
-    print_globalapivers(*HEADER);
+    print_globalapisymbolvers(*HEADER);
     print_defaultapivers(*HEADER);
     print_endprotect(*HEADER, $file);
 
diff --git a/bin/release b/bin/release
index 7a24938..9cf857a 100755
--- a/bin/release
+++ b/bin/release
@@ -39,36 +39,36 @@ USAGE()
 {
 cat << EOF
 Usage: $0 -d <dir> [--docver BRANCHNAME] [-h] [--nocheck] [--private] <methods> ...
-   -d DIR	The name of the directory where the releas(es) should be
-                placed.
+   -d DIR               The name of the directory where the releas(es) should be
+                        placed.
    --docver BRANCHNAME  This is added for 1.8 and beyond to get the correct
                         version of documentation files from the hdf5docs
                         repository.  BRANCHNAME for v1.8 should be hdf5_1_8.
-   -h           print the help page.
-   --nocheck	Ignore errors in MANIFEST file.
-   --private	Make a private release with today's date in version information.
-         
+   -h                   print the help page.
+   --nocheck            Ignore errors in MANIFEST file.
+   --private            Make a private release with today's date in version information.
+
 This must be run at the top level of the source directory.
 The other command-line options are the names of the programs to use
 for compressing the resulting tar archive (if none are given then
 "tar" is assumed):
 
-    tar		-- use tar and don't do any compressing.
-    gzip	-- use gzip with "-9" and append ".gz" to the output name.
+    tar         -- use tar and don't do any compressing.
+    gzip        -- use gzip with "-9" and append ".gz" to the output name.
     bzip2       -- use bzip2 with "-9" and append ".bz2" to the output name.
-    zip		-- convert all text files to DOS style and form a zip file for Windows use.
-    cmake-tgz   -- create a tar file using the gzip default level with a build-unix.sh 
+    zip         -- convert all text files to DOS style and form a zip file for Windows use.
+    cmake-tgz   -- create a tar file using the gzip default level with a build-unix.sh
                    command file and all other CMake files needed to build HDF5 source
                    using CMake on unix machines.
     cmake-zip   -- convert all text files to DOS style and create a zip file inluding cmake
-                   scripts and .bat files to build HDF5 source using CMake on Windows. 
-    hpc-cmake-tgz  
-                -- create a tar file using the gzip default level with a build-unix.sh 
+                   scripts and .bat files to build HDF5 source using CMake on Windows.
+    hpc-cmake-tgz
+                -- create a tar file using the gzip default level with a build-unix.sh
                    command file and all other CMake files needed to build HDF5 source
                    using CMake on unix machines, with HDF5options.cmake files for serial
                    and parallel builds on machines requiring batch jobs to run tests.
                    The default is for parallel build, with serial only build by changing
-                   the HDF5options.cmake symlink to ser-HDF5options.cmake.  More 
+                   the HDF5options.cmake symlink to ser-HDF5options.cmake.  More
                    information is available in the README_HPC file.
     doc         -- produce the latest doc tree in addition to the archive.
 
@@ -122,8 +122,8 @@ EOF
 tar2zip()
 {
     if [ $# -ne 3 ]; then
-	echo "usage: tar2zip <tarfilename> <zipfilename>"
-	return 1
+        echo "usage: tar2zip <tarfilename> <zipfilename>"
+        return 1
     fi
     ztmpdir=/tmp/ztmpdir$$
     mkdir -p $ztmpdir
@@ -135,23 +135,23 @@ tar2zip()
     (cd $ztmpdir; tar xf -) < $tarfile
     # sanity check
     if [ ! -d $ztmpdir/$version ]; then
-	echo "untar did not create $ztmpdir/$version source dir"
-	# cleanup
-	rm -rf $ztmpdir
-	return 1
+        echo "untar did not create $ztmpdir/$version source dir"
+        # cleanup
+        rm -rf $ztmpdir
+        return 1
     fi
     # step 2: convert text files
     # There maybe a simpler way to do this.
     # options used in unix2dos:
-    # -k   Keep the date stamp 
+    # -k   Keep the date stamp
     # -q   quiet mode
     # grep redirect output to /dev/null because -q or -s are not portable.
     find $ztmpdir/$version | \
-	while read inf; do \
-	    if file $inf | grep "$inf\: .*text" > /dev/null 2>&1 ; then \
-		unix2dos -q -k $inf; \
-	    fi\
-	done
+        while read inf; do \
+            if file $inf | grep "$inf\: .*text" > /dev/null 2>&1 ; then \
+            unix2dos -q -k $inf; \
+            fi \
+        done
     # step 3: make zipball
     # -9 maximum compression
     # -y Store symbolic links as such in the zip archive
@@ -202,8 +202,8 @@ tar2zip()
 tar2cmakezip()
 {
     if [ $# -ne 3 ]; then
-	echo "usage: tar2cmakezip <tarfilename> <zipfilename>"
-	return 1
+        echo "usage: tar2cmakezip <tarfilename> <zipfilename>"
+        return 1
     fi
     cmziptmpdir=/tmp/cmziptmpdir$$
     cmziptmpsubdir=$cmziptmpdir/CMake-$HDF5_VERS
@@ -216,10 +216,10 @@ tar2cmakezip()
     (cd $cmziptmpsubdir; tar xf -) < $tarfile
     # sanity check
     if [ ! -d $cmziptmpsubdir/$version ]; then
-	echo "untar did not create $cmziptmpsubdir/$version source dir"
-	# cleanup
-	rm -rf $cmziptmpdir
-	return 1
+        echo "untar did not create $cmziptmpsubdir/$version source dir"
+        # cleanup
+        rm -rf $cmziptmpdir
+        return 1
     fi
 
     # step 2: add batch file for building CMake on window
@@ -241,15 +241,15 @@ tar2cmakezip()
     # step 4: convert text files
     # There maybe a simpler way to do this.
     # options used in unix2dos:
-    # -k   Keep the date stamp 
+    # -k   Keep the date stamp
     # -q   quiet mode
     # grep redirect output to /dev/null because -q or -s are not portable.
     find $cmziptmpsubdir/$version | \
-	while read inf; do \
-	    if file $inf | grep "$inf\: .*text" > /dev/null 2>&1 ; then \
-		unix2dos -q -k $inf; \
-	    fi\
-	done
+        while read inf; do \
+            if file $inf | grep "$inf\: .*text" > /dev/null 2>&1 ; then \
+                unix2dos -q -k $inf; \
+            fi \
+        done
 
     # step 3: make zipball
     # -9 maximum compression
@@ -301,8 +301,8 @@ tar2cmakezip()
 tar2cmaketgz()
 {
     if [ $# -ne 3 ]; then
-	echo "usage: tar2cmaketgz <tarfilename> <tgzfilename>"
-	return 1
+        echo "usage: tar2cmaketgz <tarfilename> <tgzfilename>"
+        return 1
     fi
     cmgztmpdir=/tmp/cmgztmpdir$$
     cmgztmpsubdir=$cmgztmpdir/CMake-$HDF5_VERS
@@ -315,10 +315,10 @@ tar2cmaketgz()
     (cd $cmgztmpsubdir; tar xf -) < $tarfile
     # sanity check
     if [ ! -d $cmgztmpsubdir/$version ]; then
-	echo "untar did not create $cmgztmpsubdir/$version source dir"
-	# cleanup
-	rm -rf $cmgztmpdir
-	return 1
+        echo "untar did not create $cmgztmpsubdir/$version source dir"
+        # cleanup
+        rm -rf $cmgztmpdir
+        return 1
     fi
 
 
@@ -332,8 +332,8 @@ tar2cmaketgz()
     cp $cmgztmpsubdir/$version/config/cmake/scripts/CTestScript.cmake $cmgztmpsubdir
     cp $cmgztmpsubdir/$version/config/cmake/scripts/HDF5config.cmake $cmgztmpsubdir
     cp $cmgztmpsubdir/$version/config/cmake/scripts/HDF5options.cmake $cmgztmpsubdir
-    tar czf $DEST/CMake-$HDF5_VERS.tar.gz -C $cmgztmpdir . || exit 1 
-                 
+    tar czf $DEST/CMake-$HDF5_VERS.tar.gz -C $cmgztmpdir . || exit 1
+
     # cleanup
     rm -rf $cmgztmpdir
 }
@@ -384,8 +384,8 @@ tar2cmaketgz()
 tar2hpccmaketgz()
 {
     if [ $# -ne 3 ]; then
-	echo "usage: tar2hpccmaketgz <tarfilename> <tgzfilename>"
-	return 1
+        echo "usage: tar2hpccmaketgz <tarfilename> <tgzfilename>"
+        return 1
     fi
     cmgztmpdir=/tmp/cmgztmpdir$$
     cmgztmpsubdir=$cmgztmpdir/HPC-CMake-$HDF5_VERS
@@ -398,10 +398,10 @@ tar2hpccmaketgz()
     (cd $cmgztmpsubdir; tar xf -) < $tarfile
     # sanity check
     if [ ! -d $cmgztmpsubdir/$version ]; then
-	echo "untar did not create $cmgztmpsubdir/$version source dir"
-	# cleanup
-	rm -rf $cmgztmpdir
-	return 1
+        echo "untar did not create $cmgztmpsubdir/$version source dir"
+        # cleanup
+        rm -rf $cmgztmpdir
+        return 1
     fi
 
 
@@ -419,8 +419,8 @@ tar2hpccmaketgz()
     cp $cmgztmpsubdir/$version/config/cmake/scripts/HPC/ser-HDF5options.cmake $cmgztmpsubdir
     cp $cmgztmpsubdir/$version/config/cmake/scripts/HPC/par-HDF5options.cmake $cmgztmpsubdir
     (cd $cmgztmpsubdir; ln -s par-HDF5options.cmake HDF5options.cmake)
-    tar czf $DEST/HPC-CMake-$HDF5_VERS.tar.gz -C $cmgztmpdir . || exit 1 
-                 
+    tar czf $DEST/HPC-CMake-$HDF5_VERS.tar.gz -C $cmgztmpdir . || exit 1
+
     # cleanup
     rm -rf $cmgztmpdir
 }
@@ -442,7 +442,7 @@ check=yes
 release_date=`date +%F`
 today=`date +%Y%m%d`
 pmode='no'
-tmpdir="../#release_tmp.$$"	# tmp work directory
+tmpdir="../#release_tmp.$$"    # tmp work directory
 DOC_URL=https://git@bitbucket.hdfgroup.org/scm/hdffv/hdf5doc.git
 CPPLUS_RM_NAME=cpplus_RM
 MAINT_MODE_ENABLED=""
@@ -459,11 +459,11 @@ fi
 RESTORE_VERSION()
 {
     if [ X-${VERS_OLD} != X- ]; then
-	echo restoring version information back to $VERS_OLD
-	rm -f config/lt_vers.am
-	cp $tmpdir/lt_vers.am config/lt_vers.am
-	bin/h5vers -s $VERS_OLD
-	VERS_OLD=
+        echo restoring version information back to $VERS_OLD
+        rm -f config/lt_vers.am
+        cp $tmpdir/lt_vers.am config/lt_vers.am
+        bin/h5vers -s $VERS_OLD
+        VERS_OLD=
     fi
 }
 
@@ -473,32 +473,32 @@ while [ -n "$1" ]; do
     arg=$1
     shift
     case "$arg" in
-	-d)
-	    DEST=$1
-	    shift
-	    ;;
-	--nocheck)
-	    check=no
-	    ;;
-	-h)
-	    USAGE
-	    exit 0
-	    ;;
-	--private)
-	    pmode=yes
-	    ;;
+        -d)
+            DEST=$1
+            shift
+            ;;
+        --nocheck)
+            check=no
+            ;;
+        -h)
+            USAGE
+            exit 0
+            ;;
+        --private)
+            pmode=yes
+            ;;
         --docver)
             DOCVERSION=$1
             shift
             ;;
-	-*)
-	    echo "Unknown switch: $arg" 1>&2
-	    USAGE
-	    exit 1
-	    ;;
-	*)
-	    methods="$methods $arg"
-	    ;;
+        -*)
+            echo "Unknown switch: $arg" 1>&2
+            USAGE
+            exit 1
+            ;;
+        *)
+            methods="$methods $arg"
+            ;;
     esac
 done
 
@@ -548,12 +548,12 @@ if [ "X$fail" = "Xyes" ]; then
         echo ""
         echo "Note!  If you are running bin/release in a development branch"
         echo "later than v 1.8 the MANIFEST check is expected to fail when"
-        echo "autogen.sh has not been run successfully. Either run autogen.sh " 
+        echo "autogen.sh has not been run successfully. Either run autogen.sh "
         echo "with /usr/hdf/bin/AUTOTOOLS at the beginning of PATH or add the"
         echo "--nocheck argument to the bin/release command."
         exit 1
     else
-	echo "Continuing anyway..."
+        echo "Continuing anyway..."
     fi
 fi
 
@@ -587,7 +587,7 @@ test "$verbose" && echo "   Running tar..." 1>&2
 ( \
     cd $tmpdir; \
     tar cf $HDF5_VERS.tar $HDF5_VERS/Makefile \
-	`sed 's/^\.\//hdf5-'$VERS'\//' $MANIFEST` || exit 1 \
+    `sed 's/^\.\//hdf5-'$VERS'\//' $MANIFEST` || exit 1 \
 )
 
 # Compress
@@ -595,61 +595,61 @@ MD5file=$HDF5_VERS.md5
 cp /dev/null $DEST/$MD5file
 for comp in $methods; do
     case $comp in
-	tar)
-	    cp -p $tmpdir/$HDF5_VERS.tar $DEST/$HDF5_VERS.tar
-	    (cd $DEST; md5sum $HDF5_VERS.tar >> $MD5file) 
-	    ;;
-	gzip)
-	    test "$verbose" && echo "   Running gzip..." 1>&2
-	    gzip -9 <$tmpdir/$HDF5_VERS.tar >$DEST/$HDF5_VERS.tar.gz
-	    (cd $DEST; md5sum $HDF5_VERS.tar.gz >> $MD5file) 
-	    ;;
+        tar)
+            cp -p $tmpdir/$HDF5_VERS.tar $DEST/$HDF5_VERS.tar
+            (cd $DEST; md5sum $HDF5_VERS.tar >> $MD5file) 
+            ;;
+        gzip)
+            test "$verbose" && echo "   Running gzip..." 1>&2
+            gzip -9 <$tmpdir/$HDF5_VERS.tar >$DEST/$HDF5_VERS.tar.gz
+            (cd $DEST; md5sum $HDF5_VERS.tar.gz >> $MD5file) 
+            ;;
         cmake-tgz)
-	    test "$verbose" && echo "   Creating CMake tar.gz file..." 1>&2
-	    tar2cmaketgz $HDF5_VERS $tmpdir/$HDF5_VERS.tar $DEST/CMake-$HDF5_VERS.tar.gz 1>&2
-	    (cd $DEST; md5sum CMake-$HDF5_VERS.tar.gz >> $MD5file) 
+            test "$verbose" && echo "   Creating CMake tar.gz file..." 1>&2
+            tar2cmaketgz $HDF5_VERS $tmpdir/$HDF5_VERS.tar $DEST/CMake-$HDF5_VERS.tar.gz 1>&2
+            (cd $DEST; md5sum CMake-$HDF5_VERS.tar.gz >> $MD5file) 
             ;;
         hpc-cmake-tgz)
-	    test "$verbose" && echo "   Creating HPC-CMake tar.gz file..." 1>&2
-	    tar2hpccmaketgz $HDF5_VERS $tmpdir/$HDF5_VERS.tar $DEST/HPC-CMake-$HDF5_VERS.tar.gz 1>&2
-	    (cd $DEST; md5sum HPC-CMake-$HDF5_VERS.tar.gz >> $MD5file) 
+            test "$verbose" && echo "   Creating HPC-CMake tar.gz file..." 1>&2
+            tar2hpccmaketgz $HDF5_VERS $tmpdir/$HDF5_VERS.tar $DEST/HPC-CMake-$HDF5_VERS.tar.gz 1>&2
+            (cd $DEST; md5sum HPC-CMake-$HDF5_VERS.tar.gz >> $MD5file) 
+            ;;
+        bzip2)
+            test "$verbose" && echo "   Running bzip2..." 1>&2
+            bzip2 -9 <$tmpdir/$HDF5_VERS.tar >$DEST/$HDF5_VERS.tar.bz2
+            (cd $DEST; md5sum $HDF5_VERS.tar.bz2 >> $MD5file) 
+            ;;
+        zip)
+            test "$verbose" && echo "   Creating zip ball..." 1>&2
+            tar2zip $HDF5_VERS $tmpdir/$HDF5_VERS.tar $DEST/$HDF5_VERS.zip 1>&2
+            (cd $DEST; md5sum $HDF5_VERS.zip >> $MD5file) 
             ;;
-	bzip2)
-	    test "$verbose" && echo "   Running bzip2..." 1>&2
-	    bzip2 -9 <$tmpdir/$HDF5_VERS.tar >$DEST/$HDF5_VERS.tar.bz2
-	    (cd $DEST; md5sum $HDF5_VERS.tar.bz2 >> $MD5file) 
-	    ;;
-	zip)
-	    test "$verbose" && echo "   Creating zip ball..." 1>&2
-	    tar2zip $HDF5_VERS $tmpdir/$HDF5_VERS.tar $DEST/$HDF5_VERS.zip 1>&2
-	    (cd $DEST; md5sum $HDF5_VERS.zip >> $MD5file) 
-	    ;;
         cmake-zip)
             test "$verbose" && echo "   Creating CMake-zip ball..." 1>&2
             tar2cmakezip $HDF5_VERS $tmpdir/$HDF5_VERS.tar $DEST/CMake-$HDF5_VERS.zip 1>&2
             (cd $DEST; md5sum CMake-$HDF5_VERS.zip >> $MD5file)
             ;;
-	doc)
+        doc)
             if [ "${DOCVERSION}" = "" ]; then
                 DOCVERSION=master
             fi
-	    test "$verbose" && echo "   Creating docs..." 1>&2
-	    # Check out docs from git repo
-	    (cd $tmpdir; git clone -q $DOC_URL ${DOCVERSION} > /dev/null) || exit 1
+            test "$verbose" && echo "   Creating docs..." 1>&2
+            # Check out docs from git repo
+            (cd $tmpdir; git clone -q $DOC_URL ${DOCVERSION} > /dev/null) || exit 1
             # Create doxygen C++ RM
-	    (cd c++/src && doxygen cpp_doc_config > /dev/null ) || exit 1
-	    # Replace version of C++ RM with just-created version
-	    rm -rf $tmpdir/${DOCVERSION}/html/$CPPLUS_RM_NAME || exit 1
-	    mv c++/src/$CPPLUS_RM_NAME $tmpdir/${DOCVERSION}/html/$CPPLUS_RM_NAME || exit 1
+            (cd c++/src && doxygen cpp_doc_config > /dev/null ) || exit 1
+            # Replace version of C++ RM with just-created version
+            rm -rf $tmpdir/${DOCVERSION}/html/$CPPLUS_RM_NAME || exit 1
+            mv c++/src/$CPPLUS_RM_NAME $tmpdir/${DOCVERSION}/html/$CPPLUS_RM_NAME || exit 1
             # Compress the docs and move them to the release area
-	    mv $tmpdir/${DOCVERSION} $tmpdir/${HDF5_VERS}_docs || exit 1
-	    (cd $tmpdir && tar cf ${HDF5_VERS}_docs.tar ${HDF5_VERS}_docs) || exit 1
-	    mv $tmpdir/${HDF5_VERS}_docs.tar $DEST || exit 1
-	    ;;
-	*)
-	    echo "***Error*** Unknown method $comp"
-	    exit 1
-	    ;;
+            mv $tmpdir/${DOCVERSION} $tmpdir/${HDF5_VERS}_docs || exit 1
+            (cd $tmpdir && tar cf ${HDF5_VERS}_docs.tar ${HDF5_VERS}_docs) || exit 1
+            mv $tmpdir/${HDF5_VERS}_docs.tar $DEST || exit 1
+            ;;
+        *)
+            echo "***Error*** Unknown method $comp"
+            exit 1
+            ;;
     esac
 done
 
diff --git a/bin/runbkgprog b/bin/runbkgprog
index 69fa2d0..f04ea89 100644
--- a/bin/runbkgprog
+++ b/bin/runbkgprog
@@ -1,5 +1,6 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 require 5.003;
+use warnings;
 $indent=4;
 
 #
diff --git a/bin/trace b/bin/trace
index d9a2e3b..1a39891 100755
--- a/bin/trace
+++ b/bin/trace
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 ##
 # Copyright by The HDF Group.
 # Copyright by the Board of Trustees of the University of Illinois.
@@ -12,6 +12,7 @@
 # help@hdfgroup.org.
 ##
 require 5.003;
+use warnings;
 $Source = "";
 
 ##############################################################################
@@ -192,6 +193,11 @@ sub argstring ($$$) {
   # certain type qualifiers, and indirection.
   $atype =~ s/^\bconst\b//;
   $atype =~ s/\bH5_ATTR_UNUSED\b//g;
+  $atype =~ s/\bH5_ATTR_DEPRECATED_USED\b//g;
+  $atype =~ s/\bH5_ATTR_NDEBUG_UNUSED\b//g;
+  $atype =~ s/\bH5_ATTR_DEBUG_API_USED\b//g;
+  $atype =~ s/\bH5_ATTR_PARALLEL_UNUSED\b//g;
+  $atype =~ s/\bH5_ATTR_PARALLEL_USED\b//g;
   $atype =~ s/\s+/ /g;
   $ptr = length $1 if  $atype =~ s/(\*+)//;
   $atype =~ s/^\s+//;
@@ -297,7 +303,7 @@ sub rewrite_func ($$$$$) {
     # Ignored due to NO TRACE comment.
   } elsif ($body =~ s/((\n[ \t]*)H5TRACE\d+\s*\(.*?\);)\n/"$2$trace"/es) {
     # Replaced an H5TRACE macro.
-  } elsif ($body=~s/((\n[ \t]*)FUNC_ENTER\w*\s*(\(.*?\))?;??)\n/"$1$2$trace"/es) {
+  } elsif ($body=~s/((\n[ \t]*)FUNC_ENTER\w*[ \t]*(\(.*?\))?;??)\n/"$1$2$trace"/es) {
     # Added an H5TRACE macro after a FUNC_ENTER macro.
   } else {
     errmesg $file, $name, "unable to insert tracing information";