[svn-r1802] Changes since 19991019

----------------------

./MANIFEST
./configure.in
./configure			[REGENERATED]
	Added more checking for `make' features.

./Makefile.in
./doc/Makefile.in
./doc/html/Makefile.in
./doc/html/Tutor/Makefile.in
./examples/Makefile.in
./pablo/Makefile.in
./src/Makefile.in
./test/Makefile.in
./testpar/Makefile.in
./tools/Makefile.in
./config/commence.in
./config/conclude.in
./config/depend.in		[REMOVED]
./config/depend1.in		[NEW]
./config/depend2.in		[NEW]
./config/depend3.in		[NEW]
./config/depend4.in		[NEW]
./config/dependN.in		[NEW]
	The directory search stuff was moved into commence.in, thereby
	shortening the Makefile.in prologues.

./doc/html/Dependencies		[NEW]
./doc/html/Tutor/Dependencies	[NEW]
./examples/Dependencies		[NEW]
./src/Dependencies		[NEW]
./test/Dependencies		[NEW]
./testpar/Dependencies		[NEW]
./tools/Dependencies		[NEW]
	The `.distdep' files were all renamed to `Dependencies' to make them
	more obvious. They are required (but may be empty) in every directory
	that has a Makefile.in that ends with @CONCLUDE@ (you'll get an
	obvious error from make if you forgot to create one).

./bin/trace
./src/H5.c
	Added H5E_major_t and H5E_minor_t although tracing only prints the
	integer value.

./src/H5E.c
./src/H5Epublic.h
	Added tracing information.

./src/H5FDcore.c
./src/H5FDfamily.c
./src/H5FDgass.c
./src/H5FDmpio.c
./src/H5FDsec2.c
./src/H5FDstdio.c
	Fixed places where FUNC_LEAVE() evaluated it's argument more than
	once.

	Added tracing information.

	Wrapped long lines.

./config/gnu-flags
	Fixed a syntax error when we don't have a gnu compiler.

3 files changed, 372 insertions, 4 deletions

diff --git a/tools/Dependencies b/tools/Dependencies
new file mode 100644
index 0000000..4195c30
--- /dev/null
+++ b/tools/Dependencies
@@ -0,0 +1,365 @@
+## This file is machine generated on GNU systems.
+## Only temporary changes may be made here.
+
+h5tools.lo: \
+   h5tools.c \
+   h5tools.h \
+   hdf5.h \
+   H5public.h \
+   H5config.h \
+   H5api_adpt.h \
+   H5Ipublic.h \
+   H5Apublic.h \
+   H5ACpublic.h \
+   H5Bpublic.h \
+   H5Dpublic.h \
+   H5Epublic.h \
+   H5Fpublic.h \
+   H5FDpublic.h \
+   H5Gpublic.h \
+   H5HGpublic.h \
+   H5HLpublic.h \
+   H5MMpublic.h \
+   H5Opublic.h \
+   H5Ppublic.h \
+   H5Zpublic.h \
+   H5Rpublic.h \
+   H5RApublic.h \
+   H5Spublic.h \
+   H5Tpublic.h \
+   H5FDcore.h \
+   H5FDfamily.h \
+   H5FDmpio.h \
+   H5FDsec2.h \
+   H5FDstdio.h \
+   H5FDgass.h \
+   H5FDmulti.h \
+   H5private.h
+h5findshd.lo: \
+   h5findshd.c \
+   hdf5.h \
+   H5public.h \
+   H5config.h \
+   H5api_adpt.h \
+   H5Ipublic.h \
+   H5Apublic.h \
+   H5ACpublic.h \
+   H5Bpublic.h \
+   H5Dpublic.h \
+   H5Epublic.h \
+   H5Fpublic.h \
+   H5FDpublic.h \
+   H5Gpublic.h \
+   H5HGpublic.h \
+   H5HLpublic.h \
+   H5MMpublic.h \
+   H5Opublic.h \
+   H5Ppublic.h \
+   H5Zpublic.h \
+   H5Rpublic.h \
+   H5RApublic.h \
+   H5Spublic.h \
+   H5Tpublic.h \
+   H5FDcore.h \
+   H5FDfamily.h \
+   H5FDmpio.h \
+   H5FDsec2.h \
+   H5FDstdio.h \
+   H5FDgass.h \
+   H5FDmulti.h \
+   H5private.h
+h5debug.lo: \
+   h5debug.c \
+   H5private.h \
+   H5public.h \
+   H5config.h \
+   H5api_adpt.h \
+   H5Iprivate.h \
+   H5Ipublic.h \
+   H5Bprivate.h \
+   H5Bpublic.h \
+   H5Fprivate.h \
+   H5Fpublic.h \
+   H5FDpublic.h \
+   H5MMpublic.h \
+   H5Pprivate.h \
+   H5Ppublic.h \
+   H5Dpublic.h \
+   H5Zpublic.h \
+   H5Gprivate.h \
+   H5Gpublic.h \
+   H5HGprivate.h \
+   H5HGpublic.h \
+   H5HLprivate.h \
+   H5HLpublic.h \
+   H5Oprivate.h \
+   H5Opublic.h \
+   H5Tprivate.h \
+   H5Tpublic.h \
+   H5Rprivate.h \
+   H5Rpublic.h \
+   H5Sprivate.h \
+   H5Spublic.h \
+   H5Zprivate.h
+h5import.lo: \
+   h5import.c \
+   hdf5.h \
+   H5public.h \
+   H5config.h \
+   H5api_adpt.h \
+   H5Ipublic.h \
+   H5Apublic.h \
+   H5ACpublic.h \
+   H5Bpublic.h \
+   H5Dpublic.h \
+   H5Epublic.h \
+   H5Fpublic.h \
+   H5FDpublic.h \
+   H5Gpublic.h \
+   H5HGpublic.h \
+   H5HLpublic.h \
+   H5MMpublic.h \
+   H5Opublic.h \
+   H5Ppublic.h \
+   H5Zpublic.h \
+   H5Rpublic.h \
+   H5RApublic.h \
+   H5Spublic.h \
+   H5Tpublic.h \
+   H5FDcore.h \
+   H5FDfamily.h \
+   H5FDmpio.h \
+   H5FDsec2.h \
+   H5FDstdio.h \
+   H5FDgass.h \
+   H5FDmulti.h
+h5ls.lo: \
+   h5ls.c \
+   H5private.h \
+   H5public.h \
+   H5config.h \
+   H5api_adpt.h \
+   h5tools.h \
+   hdf5.h \
+   H5Ipublic.h \
+   H5Apublic.h \
+   H5ACpublic.h \
+   H5Bpublic.h \
+   H5Dpublic.h \
+   H5Epublic.h \
+   H5Fpublic.h \
+   H5FDpublic.h \
+   H5Gpublic.h \
+   H5HGpublic.h \
+   H5HLpublic.h \
+   H5MMpublic.h \
+   H5Opublic.h \
+   H5Ppublic.h \
+   H5Zpublic.h \
+   H5Rpublic.h \
+   H5RApublic.h \
+   H5Spublic.h \
+   H5Tpublic.h \
+   H5FDcore.h \
+   H5FDfamily.h \
+   H5FDmpio.h \
+   H5FDsec2.h \
+   H5FDstdio.h \
+   H5FDgass.h
+h5repart.lo: \
+   h5repart.c \
+   hdf5.h \
+   H5public.h \
+   H5config.h \
+   H5api_adpt.h \
+   H5Ipublic.h \
+   H5Apublic.h \
+   H5ACpublic.h \
+   H5Bpublic.h \
+   H5Dpublic.h \
+   H5Epublic.h \
+   H5Fpublic.h \
+   H5FDpublic.h \
+   H5Gpublic.h \
+   H5HGpublic.h \
+   H5HLpublic.h \
+   H5MMpublic.h \
+   H5Opublic.h \
+   H5Ppublic.h \
+   H5Zpublic.h \
+   H5Rpublic.h \
+   H5RApublic.h \
+   H5Spublic.h \
+   H5Tpublic.h \
+   H5FDcore.h \
+   H5FDfamily.h \
+   H5FDmpio.h \
+   H5FDsec2.h \
+   H5FDstdio.h \
+   H5FDgass.h \
+   H5FDmulti.h
+h5dump.lo: \
+   h5dump.c \
+   h5dump.h \
+   hdf5.h \
+   H5public.h \
+   H5config.h \
+   H5api_adpt.h \
+   H5Ipublic.h \
+   H5Apublic.h \
+   H5ACpublic.h \
+   H5Bpublic.h \
+   H5Dpublic.h \
+   H5Epublic.h \
+   H5Fpublic.h \
+   H5FDpublic.h \
+   H5Gpublic.h \
+   H5HGpublic.h \
+   H5HLpublic.h \
+   H5MMpublic.h \
+   H5Opublic.h \
+   H5Ppublic.h \
+   H5Zpublic.h \
+   H5Rpublic.h \
+   H5RApublic.h \
+   H5Spublic.h \
+   H5Tpublic.h \
+   H5FDcore.h \
+   H5FDfamily.h \
+   H5FDmpio.h \
+   H5FDsec2.h \
+   H5FDstdio.h \
+   H5FDgass.h \
+   H5FDmulti.h \
+   H5private.h
+h5dumputil.lo: \
+   h5dumputil.c \
+   h5dump.h \
+   hdf5.h \
+   H5public.h \
+   H5config.h \
+   H5api_adpt.h \
+   H5Ipublic.h \
+   H5Apublic.h \
+   H5ACpublic.h \
+   H5Bpublic.h \
+   H5Dpublic.h \
+   H5Epublic.h \
+   H5Fpublic.h \
+   H5FDpublic.h \
+   H5Gpublic.h \
+   H5HGpublic.h \
+   H5HLpublic.h \
+   H5MMpublic.h \
+   H5Opublic.h \
+   H5Ppublic.h \
+   H5Zpublic.h \
+   H5Rpublic.h \
+   H5RApublic.h \
+   H5Spublic.h \
+   H5Tpublic.h \
+   H5FDcore.h \
+   H5FDfamily.h \
+   H5FDmpio.h \
+   H5FDsec2.h \
+   H5FDstdio.h \
+   H5FDgass.h \
+   H5FDmulti.h
+h5toh4.lo: \
+   h5toh4.c \
+   h5toh4.h \
+   hdf5.h \
+   H5public.h \
+   H5config.h \
+   H5api_adpt.h \
+   H5Ipublic.h \
+   H5Apublic.h \
+   H5ACpublic.h \
+   H5Bpublic.h \
+   H5Dpublic.h \
+   H5Epublic.h \
+   H5Fpublic.h \
+   H5FDpublic.h \
+   H5Gpublic.h \
+   H5HGpublic.h \
+   H5HLpublic.h \
+   H5MMpublic.h \
+   H5Opublic.h \
+   H5Ppublic.h \
+   H5Zpublic.h \
+   H5Rpublic.h \
+   H5RApublic.h \
+   H5Spublic.h \
+   H5Tpublic.h \
+   H5FDcore.h \
+   H5FDfamily.h \
+   H5FDmpio.h \
+   H5FDsec2.h \
+   H5FDstdio.h \
+   H5FDgass.h \
+   H5FDmulti.h
+h5dumptst.lo: \
+   h5dumptst.c \
+   hdf5.h \
+   H5public.h \
+   H5config.h \
+   H5api_adpt.h \
+   H5Ipublic.h \
+   H5Apublic.h \
+   H5ACpublic.h \
+   H5Bpublic.h \
+   H5Dpublic.h \
+   H5Epublic.h \
+   H5Fpublic.h \
+   H5FDpublic.h \
+   H5Gpublic.h \
+   H5HGpublic.h \
+   H5HLpublic.h \
+   H5MMpublic.h \
+   H5Opublic.h \
+   H5Ppublic.h \
+   H5Zpublic.h \
+   H5Rpublic.h \
+   H5RApublic.h \
+   H5Spublic.h \
+   H5Tpublic.h \
+   H5FDcore.h \
+   H5FDfamily.h \
+   H5FDmpio.h \
+   H5FDsec2.h \
+   H5FDstdio.h \
+   H5FDgass.h \
+   H5FDmulti.h \
+   H5private.h
+pdb2hdf.lo: \
+   pdb2hdf.c \
+   hdf5.h \
+   H5public.h \
+   H5config.h \
+   H5api_adpt.h \
+   H5Ipublic.h \
+   H5Apublic.h \
+   H5ACpublic.h \
+   H5Bpublic.h \
+   H5Dpublic.h \
+   H5Epublic.h \
+   H5Fpublic.h \
+   H5FDpublic.h \
+   H5Gpublic.h \
+   H5HGpublic.h \
+   H5HLpublic.h \
+   H5MMpublic.h \
+   H5Opublic.h \
+   H5Ppublic.h \
+   H5Zpublic.h \
+   H5Rpublic.h \
+   H5RApublic.h \
+   H5Spublic.h \
+   H5Tpublic.h \
+   H5FDcore.h \
+   H5FDfamily.h \
+   H5FDmpio.h \
+   H5FDsec2.h \
+   H5FDstdio.h \
+   H5FDgass.h \
+   H5FDmulti.h
diff --git a/tools/Makefile.in b/tools/Makefile.in
index 0740ece..6f1b6b1 100644
--- a/tools/Makefile.in
+++ b/tools/Makefile.in
@@ -7,8 +7,6 @@
 top_srcdir=@top_srcdir@
 top_builddir=..
 srcdir=@srcdir@
-VPATH=.:@srcdir@
-.PATH: . @srcdir@
 @COMMENCE@
 
 ## Add include directory to the C preprocessor flags, add -lh5tools and
diff --git a/tools/pdb2hdf.c b/tools/pdb2hdf.c
index 1612392..a28f5b7 100644
--- a/tools/pdb2hdf.c
+++ b/tools/pdb2hdf.c
@@ -220,7 +220,6 @@ fix_type(PDBfile *pdb, const char *s)
 	mpos = nbits - (d->format[5]+msize);
 	H5Tset_fields(type, spos, epos, esize, mpos, msize);
 	H5Tset_ebias(type, d->format[7]);
-	
     }
     return type;
 }
@@ -347,6 +346,7 @@ traverse(PDBfile *pdb, const char *pdb_file_name, hid_t hdf)
 		fprintf(stderr, "cannot traverse out of PDB %s\n", list[i]);
 		goto error;
 	    }
+	    H5Gclose(group);
 	    
 	} else {
 	    /* This is some non-directory PDB object */
@@ -382,6 +382,11 @@ traverse(PDBfile *pdb, const char *pdb_file_name, hid_t hdf)
 	}
 	
     }
+
+    for (i=0; i<nitems; i++) {
+	SC_free(list[i]);
+    }
+    SC_free(list);
     return 0;
 
  error:
@@ -479,7 +484,7 @@ main(int argc, char *argv[])
 		exit(1);
 	    }
 	    H5Pclose(fapl);
-
+	    
 	    /*
 	     * Traverse the PDB file to create the HDF5 file.
 	     */