[svn-r17645] Purpose:

    Merge from Trunk

Description:

    Merging all of my CFLAGS-related changes from trunk to 1.8

    This includes revision #s: 17616, 17625, 17627, 17639, and 17643.

Tested:

    h5committest and some additional checks on our FreeBSD as well 
    as NCSA's machines.

21 files changed, 243 insertions, 142 deletions

diff --git a/hl/Makefile.in b/hl/Makefile.in
index 07dbefc..addfd5a 100755
--- a/hl/Makefile.in
+++ b/hl/Makefile.in
@@ -114,6 +114,16 @@ am__relativize = \
 ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
+
+# H5_CFLAGS holds flags that should be used when building hdf5,
+# but which should not be exported to h5cc for building other programs.
+# AM_CFLAGS is an automake construct which should be used by Makefiles 
+# instead of CFLAGS, as CFLAGS is reserved solely for the user to define.
+AM_CFLAGS = @AM_CFLAGS@ @H5_CFLAGS@
+AM_CPPFLAGS = @AM_CPPFLAGS@ @H5_CPPFLAGS@
+AM_CXXFLAGS = @AM_CXXFLAGS@ @H5_CXXFLAGS@
+AM_FCFLAGS = @AM_FCFLAGS@ @H5_FCFLAGS@
+AM_LDFLAGS = @AM_LDFLAGS@
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 
@@ -127,21 +137,18 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-
-# H5_CFLAGS holds flags that should be used as CFLAGS when building hdf5,
-# but which shouldn't be exported to h5cc for building other programs.
-CFLAGS = @CFLAGS@ @H5_CFLAGS@
+CFLAGS = @CFLAGS@
 CLEARFILEBUF = @CLEARFILEBUF@
 CODESTACK = @CODESTACK@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@
 CYGPATH_W = @CYGPATH_W@
 DEBUG_PKG = @DEBUG_PKG@
 DEFAULT_API_VERSION = @DEFAULT_API_VERSION@
@@ -164,7 +171,7 @@ F9XMODEXT = @F9XMODEXT@
 F9XMODFLAG = @F9XMODFLAG@
 F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
-FCFLAGS = @FCFLAGS@ @H5_FCFLAGS@
+FCFLAGS = @FCFLAGS@
 FCFLAGS_f90 = @FCFLAGS_f90@
 FCLIBS = @FCLIBS@
 FGREP = @FGREP@
diff --git a/hl/c++/Makefile.in b/hl/c++/Makefile.in
index a2535cd..87a582c 100644
--- a/hl/c++/Makefile.in
+++ b/hl/c++/Makefile.in
@@ -110,6 +110,16 @@ am__relativize = \
 ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
+
+# H5_CFLAGS holds flags that should be used when building hdf5,
+# but which should not be exported to h5cc for building other programs.
+# AM_CFLAGS is an automake construct which should be used by Makefiles 
+# instead of CFLAGS, as CFLAGS is reserved solely for the user to define.
+AM_CFLAGS = @AM_CFLAGS@ @H5_CFLAGS@
+AM_CPPFLAGS = @AM_CPPFLAGS@ @H5_CPPFLAGS@
+AM_CXXFLAGS = @AM_CXXFLAGS@ @H5_CXXFLAGS@
+AM_FCFLAGS = @AM_FCFLAGS@ @H5_FCFLAGS@
+AM_LDFLAGS = @AM_LDFLAGS@
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 
@@ -123,21 +133,18 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-
-# H5_CFLAGS holds flags that should be used as CFLAGS when building hdf5,
-# but which shouldn't be exported to h5cc for building other programs.
-CFLAGS = @CFLAGS@ @H5_CFLAGS@
+CFLAGS = @CFLAGS@
 CLEARFILEBUF = @CLEARFILEBUF@
 CODESTACK = @CODESTACK@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@
 CYGPATH_W = @CYGPATH_W@
 DEBUG_PKG = @DEBUG_PKG@
 DEFAULT_API_VERSION = @DEFAULT_API_VERSION@
@@ -160,7 +167,7 @@ F9XMODEXT = @F9XMODEXT@
 F9XMODFLAG = @F9XMODFLAG@
 F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
-FCFLAGS = @FCFLAGS@ @H5_FCFLAGS@
+FCFLAGS = @FCFLAGS@
 FCFLAGS_f90 = @FCFLAGS_f90@
 FCLIBS = @FCLIBS@
 FGREP = @FGREP@
diff --git a/hl/c++/examples/Makefile.in b/hl/c++/examples/Makefile.in
index 27e1585..4b11346 100644
--- a/hl/c++/examples/Makefile.in
+++ b/hl/c++/examples/Makefile.in
@@ -76,6 +76,16 @@ DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
 ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
+
+# H5_CFLAGS holds flags that should be used when building hdf5,
+# but which should not be exported to h5cc for building other programs.
+# AM_CFLAGS is an automake construct which should be used by Makefiles 
+# instead of CFLAGS, as CFLAGS is reserved solely for the user to define.
+AM_CFLAGS = @AM_CFLAGS@ @H5_CFLAGS@
+AM_CPPFLAGS = @AM_CPPFLAGS@ @H5_CPPFLAGS@
+AM_CXXFLAGS = @AM_CXXFLAGS@ @H5_CXXFLAGS@
+AM_FCFLAGS = @AM_FCFLAGS@ @H5_FCFLAGS@
+AM_LDFLAGS = @AM_LDFLAGS@
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 
@@ -89,21 +99,18 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-
-# H5_CFLAGS holds flags that should be used as CFLAGS when building hdf5,
-# but which shouldn't be exported to h5cc for building other programs.
-CFLAGS = @CFLAGS@ @H5_CFLAGS@
+CFLAGS = @CFLAGS@
 CLEARFILEBUF = @CLEARFILEBUF@
 CODESTACK = @CODESTACK@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@
 CYGPATH_W = @CYGPATH_W@
 DEBUG_PKG = @DEBUG_PKG@
 DEFAULT_API_VERSION = @DEFAULT_API_VERSION@
@@ -126,7 +133,7 @@ F9XMODEXT = @F9XMODEXT@
 F9XMODFLAG = @F9XMODFLAG@
 F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
-FCFLAGS = @FCFLAGS@ @H5_FCFLAGS@
+FCFLAGS = @FCFLAGS@
 FCFLAGS_f90 = @FCFLAGS_f90@
 FCLIBS = @FCLIBS@
 FGREP = @FGREP@
diff --git a/hl/c++/src/Makefile.am b/hl/c++/src/Makefile.am
index 1ff24be..15986d6 100644
--- a/hl/c++/src/Makefile.am
+++ b/hl/c++/src/Makefile.am
@@ -28,12 +28,12 @@ INCLUDES=-I$(top_srcdir)/src -I$(top_srcdir)/hl/src
 lib_LTLIBRARIES=libhdf5_hl_cpp.la
 
 # Add libtool numbers to the HDF5 HL C++ library (from config/lt_vers.am)
-libhdf5_hl_cpp_la_LDFLAGS= -version-info $(LT_VERS_INTERFACE):$(LT_VERS_REVISION):$(LT_VERS_AGE)
+libhdf5_hl_cpp_la_LDFLAGS= -version-info $(LT_VERS_INTERFACE):$(LT_VERS_REVISION):$(LT_VERS_AGE) $(AM_LDFLAGS)
 
 # Shared C++ libraries aren't universally supported.
 if CXX_SHARED_CONDITIONAL
 else
-  AM_LDFLAGS=-static
+  AM_LDFLAGS+=-static
 endif
 
 # Source files for the library
diff --git a/hl/c++/src/Makefile.in b/hl/c++/src/Makefile.in
index c0539e0..ed55ae4 100644
--- a/hl/c++/src/Makefile.in
+++ b/hl/c++/src/Makefile.in
@@ -56,6 +56,9 @@ DIST_COMMON = $(include_HEADERS) $(srcdir)/Makefile.am \
 	$(srcdir)/Makefile.in $(top_srcdir)/config/commence.am \
 	$(top_srcdir)/config/conclude.am \
 	$(top_srcdir)/config/lt_vers.am
+
+# Shared C++ libraries aren't universally supported.
+@CXX_SHARED_CONDITIONAL_FALSE@am__append_1 = -static
 TESTS =
 subdir = hl/c++/src
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
@@ -119,6 +122,16 @@ DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
 ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
+
+# H5_CFLAGS holds flags that should be used when building hdf5,
+# but which should not be exported to h5cc for building other programs.
+# AM_CFLAGS is an automake construct which should be used by Makefiles 
+# instead of CFLAGS, as CFLAGS is reserved solely for the user to define.
+AM_CFLAGS = @AM_CFLAGS@ @H5_CFLAGS@
+AM_CPPFLAGS = @AM_CPPFLAGS@ @H5_CPPFLAGS@
+AM_CXXFLAGS = @AM_CXXFLAGS@ @H5_CXXFLAGS@
+AM_FCFLAGS = @AM_FCFLAGS@ @H5_FCFLAGS@
+AM_LDFLAGS = @AM_LDFLAGS@ $(am__append_1)
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 
@@ -132,21 +145,18 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-
-# H5_CFLAGS holds flags that should be used as CFLAGS when building hdf5,
-# but which shouldn't be exported to h5cc for building other programs.
-CFLAGS = @CFLAGS@ @H5_CFLAGS@
+CFLAGS = @CFLAGS@
 CLEARFILEBUF = @CLEARFILEBUF@
 CODESTACK = @CODESTACK@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@
 CYGPATH_W = @CYGPATH_W@
 DEBUG_PKG = @DEBUG_PKG@
 DEFAULT_API_VERSION = @DEFAULT_API_VERSION@
@@ -169,7 +179,7 @@ F9XMODEXT = @F9XMODEXT@
 F9XMODFLAG = @F9XMODFLAG@
 F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
-FCFLAGS = @FCFLAGS@ @H5_FCFLAGS@
+FCFLAGS = @FCFLAGS@
 FCFLAGS_f90 = @FCFLAGS_f90@
 FCLIBS = @FCLIBS@
 FGREP = @FGREP@
@@ -380,10 +390,7 @@ INCLUDES = -I$(top_srcdir)/src -I$(top_srcdir)/hl/src
 lib_LTLIBRARIES = libhdf5_hl_cpp.la
 
 # Add libtool numbers to the HDF5 HL C++ library (from config/lt_vers.am)
-libhdf5_hl_cpp_la_LDFLAGS = -version-info $(LT_VERS_INTERFACE):$(LT_VERS_REVISION):$(LT_VERS_AGE)
-
-# Shared C++ libraries aren't universally supported.
-@CXX_SHARED_CONDITIONAL_FALSE@AM_LDFLAGS = -static
+libhdf5_hl_cpp_la_LDFLAGS = -version-info $(LT_VERS_INTERFACE):$(LT_VERS_REVISION):$(LT_VERS_AGE) $(AM_LDFLAGS)
 
 # Source files for the library
 # At the moment, only the H5PT Packet Table has a C++ API.
diff --git a/hl/c++/test/Makefile.am b/hl/c++/test/Makefile.am
index beebc33..6dcea1c 100644
--- a/hl/c++/test/Makefile.am
+++ b/hl/c++/test/Makefile.am
@@ -26,7 +26,7 @@ INCLUDES=-I$(top_srcdir)/src -I$(top_srcdir)/c++/src -I$(top_srcdir)/hl/src -I$(
 # Shared C++ libraries aren't universally supported.
 if CXX_SHARED_CONDITIONAL
 else
-  AM_LDFLAGS=-static
+  AM_LDFLAGS+=-static
 endif
 
 # These are our main targets.  They should be listed in the order to be
diff --git a/hl/c++/test/Makefile.in b/hl/c++/test/Makefile.in
index c2de2e7..6bb1a99 100644
--- a/hl/c++/test/Makefile.in
+++ b/hl/c++/test/Makefile.in
@@ -53,6 +53,9 @@ host_triplet = @host@
 DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
 	$(top_srcdir)/config/commence.am \
 	$(top_srcdir)/config/conclude.am
+
+# Shared C++ libraries aren't universally supported.
+@CXX_SHARED_CONDITIONAL_FALSE@am__append_1 = -static
 check_PROGRAMS = $(am__EXEEXT_1)
 TESTS = $(check_PROGRAMS)
 subdir = hl/c++/test
@@ -93,6 +96,16 @@ DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
 ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
+
+# H5_CFLAGS holds flags that should be used when building hdf5,
+# but which should not be exported to h5cc for building other programs.
+# AM_CFLAGS is an automake construct which should be used by Makefiles 
+# instead of CFLAGS, as CFLAGS is reserved solely for the user to define.
+AM_CFLAGS = @AM_CFLAGS@ @H5_CFLAGS@
+AM_CPPFLAGS = @AM_CPPFLAGS@ @H5_CPPFLAGS@
+AM_CXXFLAGS = @AM_CXXFLAGS@ @H5_CXXFLAGS@
+AM_FCFLAGS = @AM_FCFLAGS@ @H5_FCFLAGS@
+AM_LDFLAGS = @AM_LDFLAGS@ $(am__append_1)
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 
@@ -106,21 +119,18 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-
-# H5_CFLAGS holds flags that should be used as CFLAGS when building hdf5,
-# but which shouldn't be exported to h5cc for building other programs.
-CFLAGS = @CFLAGS@ @H5_CFLAGS@
+CFLAGS = @CFLAGS@
 CLEARFILEBUF = @CLEARFILEBUF@
 CODESTACK = @CODESTACK@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@
 CYGPATH_W = @CYGPATH_W@
 DEBUG_PKG = @DEBUG_PKG@
 DEFAULT_API_VERSION = @DEFAULT_API_VERSION@
@@ -143,7 +153,7 @@ F9XMODEXT = @F9XMODEXT@
 F9XMODFLAG = @F9XMODFLAG@
 F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
-FCFLAGS = @FCFLAGS@ @H5_FCFLAGS@
+FCFLAGS = @FCFLAGS@
 FCFLAGS_f90 = @FCFLAGS_f90@
 FCLIBS = @FCLIBS@
 FGREP = @FGREP@
@@ -344,9 +354,6 @@ CHECK_CLEANFILES = *.chkexe *.chklog *.clog
 # Include directories
 INCLUDES = -I$(top_srcdir)/src -I$(top_srcdir)/c++/src -I$(top_srcdir)/hl/src -I$(top_srcdir)/hl/c++/src -I$(top_srcdir)/test -I$(top_builddir)/hl/test -I$(top_srcdir)/hl/test
 
-# Shared C++ libraries aren't universally supported.
-@CXX_SHARED_CONDITIONAL_FALSE@AM_LDFLAGS = -static
-
 # These are our main targets.  They should be listed in the order to be
 # executed, generally most specific tests to least specific tests.
 TEST_PROG = ptableTest
diff --git a/hl/examples/Makefile.in b/hl/examples/Makefile.in
index 0a2ec12..0380eaf 100644
--- a/hl/examples/Makefile.in
+++ b/hl/examples/Makefile.in
@@ -76,6 +76,16 @@ DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
 ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
+
+# H5_CFLAGS holds flags that should be used when building hdf5,
+# but which should not be exported to h5cc for building other programs.
+# AM_CFLAGS is an automake construct which should be used by Makefiles 
+# instead of CFLAGS, as CFLAGS is reserved solely for the user to define.
+AM_CFLAGS = @AM_CFLAGS@ @H5_CFLAGS@
+AM_CPPFLAGS = @AM_CPPFLAGS@ @H5_CPPFLAGS@
+AM_CXXFLAGS = @AM_CXXFLAGS@ @H5_CXXFLAGS@
+AM_FCFLAGS = @AM_FCFLAGS@ @H5_FCFLAGS@
+AM_LDFLAGS = @AM_LDFLAGS@
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 
@@ -89,21 +99,18 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-
-# H5_CFLAGS holds flags that should be used as CFLAGS when building hdf5,
-# but which shouldn't be exported to h5cc for building other programs.
-CFLAGS = @CFLAGS@ @H5_CFLAGS@
+CFLAGS = @CFLAGS@
 CLEARFILEBUF = @CLEARFILEBUF@
 CODESTACK = @CODESTACK@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@
 CYGPATH_W = @CYGPATH_W@
 DEBUG_PKG = @DEBUG_PKG@
 DEFAULT_API_VERSION = @DEFAULT_API_VERSION@
@@ -126,7 +133,7 @@ F9XMODEXT = @F9XMODEXT@
 F9XMODFLAG = @F9XMODFLAG@
 F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
-FCFLAGS = @FCFLAGS@ @H5_FCFLAGS@
+FCFLAGS = @FCFLAGS@
 FCFLAGS_f90 = @FCFLAGS_f90@
 FCLIBS = @FCLIBS@
 FGREP = @FGREP@
diff --git a/hl/fortran/Makefile.in b/hl/fortran/Makefile.in
index 9daf03a..79e0ce5 100644
--- a/hl/fortran/Makefile.in
+++ b/hl/fortran/Makefile.in
@@ -114,6 +114,16 @@ am__relativize = \
 ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
+
+# H5_CFLAGS holds flags that should be used when building hdf5,
+# but which should not be exported to h5cc for building other programs.
+# AM_CFLAGS is an automake construct which should be used by Makefiles 
+# instead of CFLAGS, as CFLAGS is reserved solely for the user to define.
+AM_CFLAGS = @AM_CFLAGS@ @H5_CFLAGS@
+AM_CPPFLAGS = @AM_CPPFLAGS@ @H5_CPPFLAGS@
+AM_CXXFLAGS = @AM_CXXFLAGS@ @H5_CXXFLAGS@
+AM_FCFLAGS = @AM_FCFLAGS@ @H5_FCFLAGS@
+AM_LDFLAGS = @AM_LDFLAGS@
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 
@@ -127,21 +137,18 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-
-# H5_CFLAGS holds flags that should be used as CFLAGS when building hdf5,
-# but which shouldn't be exported to h5cc for building other programs.
-CFLAGS = @CFLAGS@ @H5_CFLAGS@
+CFLAGS = @CFLAGS@
 CLEARFILEBUF = @CLEARFILEBUF@
 CODESTACK = @CODESTACK@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@
 CYGPATH_W = @CYGPATH_W@
 DEBUG_PKG = @DEBUG_PKG@
 DEFAULT_API_VERSION = @DEFAULT_API_VERSION@
@@ -164,7 +171,7 @@ F9XMODEXT = @F9XMODEXT@
 F9XMODFLAG = @F9XMODFLAG@
 F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
-FCFLAGS = @FCFLAGS@ @H5_FCFLAGS@
+FCFLAGS = @FCFLAGS@
 FCFLAGS_f90 = @FCFLAGS_f90@
 FCLIBS = @FCLIBS@
 FGREP = @FGREP@
diff --git a/hl/fortran/examples/Makefile.in b/hl/fortran/examples/Makefile.in
index 07b916e..90bdc90 100644
--- a/hl/fortran/examples/Makefile.in
+++ b/hl/fortran/examples/Makefile.in
@@ -76,6 +76,16 @@ DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
 ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
+
+# H5_CFLAGS holds flags that should be used when building hdf5,
+# but which should not be exported to h5cc for building other programs.
+# AM_CFLAGS is an automake construct which should be used by Makefiles 
+# instead of CFLAGS, as CFLAGS is reserved solely for the user to define.
+AM_CFLAGS = @AM_CFLAGS@ @H5_CFLAGS@
+AM_CPPFLAGS = @AM_CPPFLAGS@ @H5_CPPFLAGS@
+AM_CXXFLAGS = @AM_CXXFLAGS@ @H5_CXXFLAGS@
+AM_FCFLAGS = @AM_FCFLAGS@ @H5_FCFLAGS@
+AM_LDFLAGS = @AM_LDFLAGS@
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 
@@ -89,21 +99,18 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-
-# H5_CFLAGS holds flags that should be used as CFLAGS when building hdf5,
-# but which shouldn't be exported to h5cc for building other programs.
-CFLAGS = @CFLAGS@ @H5_CFLAGS@
+CFLAGS = @CFLAGS@
 CLEARFILEBUF = @CLEARFILEBUF@
 CODESTACK = @CODESTACK@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@
 CYGPATH_W = @CYGPATH_W@
 DEBUG_PKG = @DEBUG_PKG@
 DEFAULT_API_VERSION = @DEFAULT_API_VERSION@
@@ -126,7 +133,7 @@ F9XMODEXT = @F9XMODEXT@
 F9XMODFLAG = @F9XMODFLAG@
 F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
-FCFLAGS = @FCFLAGS@ @H5_FCFLAGS@
+FCFLAGS = @FCFLAGS@
 FCFLAGS_f90 = @FCFLAGS_f90@
 FCLIBS = @FCLIBS@
 FGREP = @FGREP@
diff --git a/hl/fortran/src/Makefile.am b/hl/fortran/src/Makefile.am
index fbc3908..d4fec65 100644
--- a/hl/fortran/src/Makefile.am
+++ b/hl/fortran/src/Makefile.am
@@ -24,20 +24,20 @@ include $(top_srcdir)/config/lt_vers.am
 
 INCLUDES=-I$(top_srcdir)/src -I$(top_srcdir)/hl/src -I$(top_builddir)/hl/src \
          -I$(top_srcdir)/fortran/src -I$(top_builddir)/fortran/src
-AM_FCFLAGS=-I$(top_builddir)/fortran/src $(F9XMODFLAG)$(top_builddir)/fortran/src
+AM_FCFLAGS+=-I$(top_builddir)/fortran/src $(F9XMODFLAG)$(top_builddir)/fortran/src
 
 # Our main target, the high-level fortran library
 lib_LTLIBRARIES=libhdf5hl_fortran.la
 
 # Add libtool numbers to the HDF5 HL Fortran library (from config/lt_vers.am)
-libhdf5hl_fortran_la_LDFLAGS= -version-info $(LT_VERS_INTERFACE):$(LT_VERS_REVISION):$(LT_VERS_AGE)
+libhdf5hl_fortran_la_LDFLAGS= -version-info $(LT_VERS_INTERFACE):$(LT_VERS_REVISION):$(LT_VERS_AGE) $(AM_LDFLAGS)
 
 # Some Fortran compilers can't build shared libraries, so sometimes we
 # want to build a shared C library and a static Fortran library.  If so,
 # pass the -static flag to the library linker.
 if FORTRAN_SHARED_CONDITIONAL
 else
-   AM_LDFLAGS=-static
+   AM_LDFLAGS+=-static
 endif
 
 # Source files for the library
diff --git a/hl/fortran/src/Makefile.in b/hl/fortran/src/Makefile.in
index a24ffb0..870858e 100644
--- a/hl/fortran/src/Makefile.in
+++ b/hl/fortran/src/Makefile.in
@@ -55,6 +55,11 @@ DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
 	$(top_srcdir)/config/commence.am \
 	$(top_srcdir)/config/conclude.am \
 	$(top_srcdir)/config/lt_vers.am
+
+# Some Fortran compilers can't build shared libraries, so sometimes we
+# want to build a shared C library and a static Fortran library.  If so,
+# pass the -static flag to the library linker.
+@FORTRAN_SHARED_CONDITIONAL_FALSE@am__append_1 = -static
 TESTS =
 subdir = hl/fortran/src
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
@@ -125,6 +130,17 @@ DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
 ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
+
+# H5_CFLAGS holds flags that should be used when building hdf5,
+# but which should not be exported to h5cc for building other programs.
+# AM_CFLAGS is an automake construct which should be used by Makefiles 
+# instead of CFLAGS, as CFLAGS is reserved solely for the user to define.
+AM_CFLAGS = @AM_CFLAGS@ @H5_CFLAGS@
+AM_CPPFLAGS = @AM_CPPFLAGS@ @H5_CPPFLAGS@
+AM_CXXFLAGS = @AM_CXXFLAGS@ @H5_CXXFLAGS@
+AM_FCFLAGS = @AM_FCFLAGS@ @H5_FCFLAGS@ -I$(top_builddir)/fortran/src \
+	$(F9XMODFLAG)$(top_builddir)/fortran/src
+AM_LDFLAGS = @AM_LDFLAGS@ $(am__append_1)
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 
@@ -138,21 +154,18 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-
-# H5_CFLAGS holds flags that should be used as CFLAGS when building hdf5,
-# but which shouldn't be exported to h5cc for building other programs.
-CFLAGS = @CFLAGS@ @H5_CFLAGS@
+CFLAGS = @CFLAGS@
 CLEARFILEBUF = @CLEARFILEBUF@
 CODESTACK = @CODESTACK@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@
 CYGPATH_W = @CYGPATH_W@
 DEBUG_PKG = @DEBUG_PKG@
 DEFAULT_API_VERSION = @DEFAULT_API_VERSION@
@@ -175,7 +188,7 @@ F9XMODEXT = @F9XMODEXT@
 F9XMODFLAG = @F9XMODFLAG@
 F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
-FCFLAGS = @FCFLAGS@ @H5_FCFLAGS@
+FCFLAGS = @FCFLAGS@
 FCFLAGS_f90 = @FCFLAGS_f90@
 FCLIBS = @FCLIBS@
 FGREP = @FGREP@
@@ -381,18 +394,12 @@ LT_VERS_AGE = 0
 INCLUDES = -I$(top_srcdir)/src -I$(top_srcdir)/hl/src -I$(top_builddir)/hl/src \
          -I$(top_srcdir)/fortran/src -I$(top_builddir)/fortran/src
 
-AM_FCFLAGS = -I$(top_builddir)/fortran/src $(F9XMODFLAG)$(top_builddir)/fortran/src
 
 # Our main target, the high-level fortran library
 lib_LTLIBRARIES = libhdf5hl_fortran.la
 
 # Add libtool numbers to the HDF5 HL Fortran library (from config/lt_vers.am)
-libhdf5hl_fortran_la_LDFLAGS = -version-info $(LT_VERS_INTERFACE):$(LT_VERS_REVISION):$(LT_VERS_AGE)
-
-# Some Fortran compilers can't build shared libraries, so sometimes we
-# want to build a shared C library and a static Fortran library.  If so,
-# pass the -static flag to the library linker.
-@FORTRAN_SHARED_CONDITIONAL_FALSE@AM_LDFLAGS = -static
+libhdf5hl_fortran_la_LDFLAGS = -version-info $(LT_VERS_INTERFACE):$(LT_VERS_REVISION):$(LT_VERS_AGE) $(AM_LDFLAGS)
 
 # Source files for the library
 #if BUILD_PARALLEL_CONDITIONAL
diff --git a/hl/fortran/test/Makefile.am b/hl/fortran/test/Makefile.am
index 70645b9..83081e3 100644
--- a/hl/fortran/test/Makefile.am
+++ b/hl/fortran/test/Makefile.am
@@ -21,15 +21,15 @@
 
 include $(top_srcdir)/config/commence.am
 
-AM_CPPFLAGS=-I$(top_srcdir)/src -I$(top_builddir)/src -I$(top_srcdir)/hl/src
-AM_FCFLAGS=-I$(top_builddir)/fortran/src -I$(top_builddir)/hl/fortran/src $(F9XMODFLAG)$(top_builddir)/fortran/src $(F9XMODFLAG)$(top_builddir)/hl/fortran/src
+AM_CPPFLAGS+=-I$(top_srcdir)/src -I$(top_builddir)/src -I$(top_srcdir)/hl/src
+AM_FCFLAGS+=-I$(top_builddir)/fortran/src -I$(top_builddir)/hl/fortran/src $(F9XMODFLAG)$(top_builddir)/fortran/src $(F9XMODFLAG)$(top_builddir)/hl/fortran/src
 
 # Some Fortran compilers can't build shared libraries, so sometimes we
 # need to make sure the Fortran programs link against the static version
 # of the HDF5 library.  We do this by passing the -static flag to the linker.
 if FORTRAN_SHARED_CONDITIONAL
 else
-   AM_LDFLAGS=-static
+   AM_LDFLAGS+=-static
 endif
 
 # Our main target, the test programs
diff --git a/hl/fortran/test/Makefile.in b/hl/fortran/test/Makefile.in
index 4bf9413..0581c5f 100644
--- a/hl/fortran/test/Makefile.in
+++ b/hl/fortran/test/Makefile.in
@@ -53,6 +53,11 @@ host_triplet = @host@
 DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
 	$(top_srcdir)/config/commence.am \
 	$(top_srcdir)/config/conclude.am
+
+# Some Fortran compilers can't build shared libraries, so sometimes we
+# need to make sure the Fortran programs link against the static version
+# of the HDF5 library.  We do this by passing the -static flag to the linker.
+@FORTRAN_SHARED_CONDITIONAL_FALSE@am__append_1 = -static
 check_PROGRAMS = $(am__EXEEXT_1)
 TESTS = $(check_PROGRAMS)
 subdir = hl/fortran/test
@@ -96,6 +101,20 @@ DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
 ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
+
+# H5_CFLAGS holds flags that should be used when building hdf5,
+# but which should not be exported to h5cc for building other programs.
+# AM_CFLAGS is an automake construct which should be used by Makefiles 
+# instead of CFLAGS, as CFLAGS is reserved solely for the user to define.
+AM_CFLAGS = @AM_CFLAGS@ @H5_CFLAGS@
+AM_CPPFLAGS = @AM_CPPFLAGS@ @H5_CPPFLAGS@ -I$(top_srcdir)/src \
+	-I$(top_builddir)/src -I$(top_srcdir)/hl/src
+AM_CXXFLAGS = @AM_CXXFLAGS@ @H5_CXXFLAGS@
+AM_FCFLAGS = @AM_FCFLAGS@ @H5_FCFLAGS@ -I$(top_builddir)/fortran/src \
+	-I$(top_builddir)/hl/fortran/src \
+	$(F9XMODFLAG)$(top_builddir)/fortran/src \
+	$(F9XMODFLAG)$(top_builddir)/hl/fortran/src
+AM_LDFLAGS = @AM_LDFLAGS@ $(am__append_1)
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 
@@ -109,21 +128,18 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-
-# H5_CFLAGS holds flags that should be used as CFLAGS when building hdf5,
-# but which shouldn't be exported to h5cc for building other programs.
-CFLAGS = @CFLAGS@ @H5_CFLAGS@
+CFLAGS = @CFLAGS@
 CLEARFILEBUF = @CLEARFILEBUF@
 CODESTACK = @CODESTACK@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@
 CYGPATH_W = @CYGPATH_W@
 DEBUG_PKG = @DEBUG_PKG@
 DEFAULT_API_VERSION = @DEFAULT_API_VERSION@
@@ -146,7 +162,7 @@ F9XMODEXT = @F9XMODEXT@
 F9XMODFLAG = @F9XMODFLAG@
 F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
-FCFLAGS = @FCFLAGS@ @H5_FCFLAGS@
+FCFLAGS = @FCFLAGS@
 FCFLAGS_f90 = @FCFLAGS_f90@
 FCLIBS = @FCLIBS@
 FGREP = @FGREP@
@@ -346,13 +362,6 @@ TRACE = perl $(top_srcdir)/bin/trace
 # Temporary files.
 CHECK_CLEANFILES = *.chkexe *.chklog *.clog dsetf[1-4].h5 f1img.h5 \
 	f1tab.h5
-AM_CPPFLAGS = -I$(top_srcdir)/src -I$(top_builddir)/src -I$(top_srcdir)/hl/src
-AM_FCFLAGS = -I$(top_builddir)/fortran/src -I$(top_builddir)/hl/fortran/src $(F9XMODFLAG)$(top_builddir)/fortran/src $(F9XMODFLAG)$(top_builddir)/hl/fortran/src
-
-# Some Fortran compilers can't build shared libraries, so sometimes we
-# need to make sure the Fortran programs link against the static version
-# of the HDF5 library.  We do this by passing the -static flag to the linker.
-@FORTRAN_SHARED_CONDITIONAL_FALSE@AM_LDFLAGS = -static
 
 # Our main target, the test programs
 TEST_PROG = tstlite tstimage tsttable
diff --git a/hl/src/Makefile.am b/hl/src/Makefile.am
index 27371c0..0a95422 100644
--- a/hl/src/Makefile.am
+++ b/hl/src/Makefile.am
@@ -22,13 +22,13 @@ include $(top_srcdir)/config/commence.am
 include $(top_srcdir)/config/lt_vers.am
 
 # Add include directories to the C preprocessor flags
-AM_CPPFLAGS=-I$(top_srcdir)/src
+AM_CPPFLAGS+=-I$(top_srcdir)/src
 
 # This library is our main target.
 lib_LTLIBRARIES=libhdf5_hl.la
 
 # Add libtool numbers to the HDF5 HL library (from config/lt_vers.am)
-libhdf5_hl_la_LDFLAGS= -version-info $(LT_VERS_INTERFACE):$(LT_VERS_REVISION):$(LT_VERS_AGE)
+libhdf5_hl_la_LDFLAGS= -version-info $(LT_VERS_INTERFACE):$(LT_VERS_REVISION):$(LT_VERS_AGE) $(AM_LDFLAGS)
 
 libhdf5_hl_la_SOURCES=H5DS.c H5IM.c H5LT.c H5LTanalyze.c H5LTparse.c H5PT.c H5TB.c
 
diff --git a/hl/src/Makefile.in b/hl/src/Makefile.in
index 4a51fce..ce35439 100644
--- a/hl/src/Makefile.in
+++ b/hl/src/Makefile.in
@@ -120,6 +120,18 @@ DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
 ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
+
+# H5_CFLAGS holds flags that should be used when building hdf5,
+# but which should not be exported to h5cc for building other programs.
+# AM_CFLAGS is an automake construct which should be used by Makefiles 
+# instead of CFLAGS, as CFLAGS is reserved solely for the user to define.
+AM_CFLAGS = @AM_CFLAGS@ @H5_CFLAGS@
+
+# Add include directories to the C preprocessor flags
+AM_CPPFLAGS = @AM_CPPFLAGS@ @H5_CPPFLAGS@ -I$(top_srcdir)/src
+AM_CXXFLAGS = @AM_CXXFLAGS@ @H5_CXXFLAGS@
+AM_FCFLAGS = @AM_FCFLAGS@ @H5_FCFLAGS@
+AM_LDFLAGS = @AM_LDFLAGS@
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 
@@ -133,21 +145,18 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-
-# H5_CFLAGS holds flags that should be used as CFLAGS when building hdf5,
-# but which shouldn't be exported to h5cc for building other programs.
-CFLAGS = @CFLAGS@ @H5_CFLAGS@
+CFLAGS = @CFLAGS@
 CLEARFILEBUF = @CLEARFILEBUF@
 CODESTACK = @CODESTACK@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@
 CYGPATH_W = @CYGPATH_W@
 DEBUG_PKG = @DEBUG_PKG@
 DEFAULT_API_VERSION = @DEFAULT_API_VERSION@
@@ -170,7 +179,7 @@ F9XMODEXT = @F9XMODEXT@
 F9XMODFLAG = @F9XMODFLAG@
 F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
-FCFLAGS = @FCFLAGS@ @H5_FCFLAGS@
+FCFLAGS = @FCFLAGS@
 FCFLAGS_f90 = @FCFLAGS_f90@
 FCLIBS = @FCLIBS@
 FGREP = @FGREP@
@@ -374,14 +383,11 @@ LT_VERS_INTERFACE = 6
 LT_VERS_REVISION = 2
 LT_VERS_AGE = 0
 
-# Add include directories to the C preprocessor flags
-AM_CPPFLAGS = -I$(top_srcdir)/src
-
 # This library is our main target.
 lib_LTLIBRARIES = libhdf5_hl.la
 
 # Add libtool numbers to the HDF5 HL library (from config/lt_vers.am)
-libhdf5_hl_la_LDFLAGS = -version-info $(LT_VERS_INTERFACE):$(LT_VERS_REVISION):$(LT_VERS_AGE)
+libhdf5_hl_la_LDFLAGS = -version-info $(LT_VERS_INTERFACE):$(LT_VERS_REVISION):$(LT_VERS_AGE) $(AM_LDFLAGS)
 libhdf5_hl_la_SOURCES = H5DS.c H5IM.c H5LT.c H5LTanalyze.c H5LTparse.c H5PT.c H5TB.c
 
 # Public header files (to be installed)
diff --git a/hl/test/Makefile.am b/hl/test/Makefile.am
index d20b7d3..fc6e969 100644
--- a/hl/test/Makefile.am
+++ b/hl/test/Makefile.am
@@ -22,7 +22,7 @@
 include $(top_srcdir)/config/commence.am
 
 # Add include directories to C preprocessor flags
-AM_CPPFLAGS=-I. -I$(srcdir) -I$(top_builddir)/src -I$(top_srcdir)/src -I$(top_builddir)/test -I$(top_srcdir)/test -I$(top_srcdir)/hl/src
+AM_CPPFLAGS+=-I. -I$(srcdir) -I$(top_builddir)/src -I$(top_srcdir)/src -I$(top_builddir)/test -I$(top_srcdir)/test -I$(top_srcdir)/hl/src
 
 # The tests depend on the hdf5, hdf5 test,  and hdf5_hl libraries
 LDADD=$(LIBH5_HL) $(LIBH5TEST) $(LIBHDF5)
diff --git a/hl/test/Makefile.in b/hl/test/Makefile.in
index 29cfb11..4a5aa5b 100644
--- a/hl/test/Makefile.in
+++ b/hl/test/Makefile.in
@@ -121,6 +121,21 @@ DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
 ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
+
+# H5_CFLAGS holds flags that should be used when building hdf5,
+# but which should not be exported to h5cc for building other programs.
+# AM_CFLAGS is an automake construct which should be used by Makefiles 
+# instead of CFLAGS, as CFLAGS is reserved solely for the user to define.
+AM_CFLAGS = @AM_CFLAGS@ @H5_CFLAGS@
+
+# Add include directories to C preprocessor flags
+AM_CPPFLAGS = @AM_CPPFLAGS@ @H5_CPPFLAGS@ -I. -I$(srcdir) \
+	-I$(top_builddir)/src -I$(top_srcdir)/src \
+	-I$(top_builddir)/test -I$(top_srcdir)/test \
+	-I$(top_srcdir)/hl/src
+AM_CXXFLAGS = @AM_CXXFLAGS@ @H5_CXXFLAGS@
+AM_FCFLAGS = @AM_FCFLAGS@ @H5_FCFLAGS@
+AM_LDFLAGS = @AM_LDFLAGS@
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 
@@ -134,21 +149,18 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-
-# H5_CFLAGS holds flags that should be used as CFLAGS when building hdf5,
-# but which shouldn't be exported to h5cc for building other programs.
-CFLAGS = @CFLAGS@ @H5_CFLAGS@
+CFLAGS = @CFLAGS@
 CLEARFILEBUF = @CLEARFILEBUF@
 CODESTACK = @CODESTACK@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@
 CYGPATH_W = @CYGPATH_W@
 DEBUG_PKG = @DEBUG_PKG@
 DEFAULT_API_VERSION = @DEFAULT_API_VERSION@
@@ -171,7 +183,7 @@ F9XMODEXT = @F9XMODEXT@
 F9XMODFLAG = @F9XMODFLAG@
 F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
-FCFLAGS = @FCFLAGS@ @H5_FCFLAGS@
+FCFLAGS = @FCFLAGS@
 FCFLAGS_f90 = @FCFLAGS_f90@
 FCLIBS = @FCLIBS@
 FGREP = @FGREP@
@@ -373,9 +385,6 @@ CHECK_CLEANFILES = *.chkexe *.chklog *.clog combine_tables[1-2].h5 \
 	test_ds[1-9].h5 test_image[1-3].h5 test_lite[1-2].h5 \
 	test_table.h5 test_packet_table.h5 test_packet_compress.h5
 
-# Add include directories to C preprocessor flags
-AM_CPPFLAGS = -I. -I$(srcdir) -I$(top_builddir)/src -I$(top_srcdir)/src -I$(top_builddir)/test -I$(top_srcdir)/test -I$(top_srcdir)/hl/src
-
 # The tests depend on the hdf5, hdf5 test,  and hdf5_hl libraries
 LDADD = $(LIBH5_HL) $(LIBH5TEST) $(LIBHDF5)
 
diff --git a/hl/tools/Makefile.in b/hl/tools/Makefile.in
index df2337a..855d60b 100644
--- a/hl/tools/Makefile.in
+++ b/hl/tools/Makefile.in
@@ -111,6 +111,16 @@ am__relativize = \
 ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
+
+# H5_CFLAGS holds flags that should be used when building hdf5,
+# but which should not be exported to h5cc for building other programs.
+# AM_CFLAGS is an automake construct which should be used by Makefiles 
+# instead of CFLAGS, as CFLAGS is reserved solely for the user to define.
+AM_CFLAGS = @AM_CFLAGS@ @H5_CFLAGS@
+AM_CPPFLAGS = @AM_CPPFLAGS@ @H5_CPPFLAGS@
+AM_CXXFLAGS = @AM_CXXFLAGS@ @H5_CXXFLAGS@
+AM_FCFLAGS = @AM_FCFLAGS@ @H5_FCFLAGS@
+AM_LDFLAGS = @AM_LDFLAGS@
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 
@@ -124,21 +134,18 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-
-# H5_CFLAGS holds flags that should be used as CFLAGS when building hdf5,
-# but which shouldn't be exported to h5cc for building other programs.
-CFLAGS = @CFLAGS@ @H5_CFLAGS@
+CFLAGS = @CFLAGS@
 CLEARFILEBUF = @CLEARFILEBUF@
 CODESTACK = @CODESTACK@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@
 CYGPATH_W = @CYGPATH_W@
 DEBUG_PKG = @DEBUG_PKG@
 DEFAULT_API_VERSION = @DEFAULT_API_VERSION@
@@ -161,7 +168,7 @@ F9XMODEXT = @F9XMODEXT@
 F9XMODFLAG = @F9XMODFLAG@
 F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
-FCFLAGS = @FCFLAGS@ @H5_FCFLAGS@
+FCFLAGS = @FCFLAGS@
 FCFLAGS_f90 = @FCFLAGS_f90@
 FCLIBS = @FCLIBS@
 FGREP = @FGREP@
diff --git a/hl/tools/gif2h5/Makefile.am b/hl/tools/gif2h5/Makefile.am
index f1cec06..895c75f 100644
--- a/hl/tools/gif2h5/Makefile.am
+++ b/hl/tools/gif2h5/Makefile.am
@@ -32,8 +32,8 @@ bin_PROGRAMS=gif2h5 h52gif
 noinst_PROGRAMS=h52gifgentst
 
 # Add h52gif and gif2h5 specific linker flags here
-h52gif_LDFLAGS = $(LT_STATIC_EXEC)
-gif2h5_LDFLAGS = $(LT_STATIC_EXEC)
+h52gif_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
+gif2h5_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
 
 gif2h5_SOURCES=gif2hdf.c gif2mem.c decompress.c gifread.c writehdf.c 
 
diff --git a/hl/tools/gif2h5/Makefile.in b/hl/tools/gif2h5/Makefile.in
index 71a16c4..e43dd07 100644
--- a/hl/tools/gif2h5/Makefile.in
+++ b/hl/tools/gif2h5/Makefile.in
@@ -111,6 +111,16 @@ DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
 ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
+
+# H5_CFLAGS holds flags that should be used when building hdf5,
+# but which should not be exported to h5cc for building other programs.
+# AM_CFLAGS is an automake construct which should be used by Makefiles 
+# instead of CFLAGS, as CFLAGS is reserved solely for the user to define.
+AM_CFLAGS = @AM_CFLAGS@ @H5_CFLAGS@
+AM_CPPFLAGS = @AM_CPPFLAGS@ @H5_CPPFLAGS@
+AM_CXXFLAGS = @AM_CXXFLAGS@ @H5_CXXFLAGS@
+AM_FCFLAGS = @AM_FCFLAGS@ @H5_FCFLAGS@
+AM_LDFLAGS = @AM_LDFLAGS@
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 
@@ -124,21 +134,18 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-
-# H5_CFLAGS holds flags that should be used as CFLAGS when building hdf5,
-# but which shouldn't be exported to h5cc for building other programs.
-CFLAGS = @CFLAGS@ @H5_CFLAGS@
+CFLAGS = @CFLAGS@
 CLEARFILEBUF = @CLEARFILEBUF@
 CODESTACK = @CODESTACK@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@
 CYGPATH_W = @CYGPATH_W@
 DEBUG_PKG = @DEBUG_PKG@
 DEFAULT_API_VERSION = @DEFAULT_API_VERSION@
@@ -161,7 +168,7 @@ F9XMODEXT = @F9XMODEXT@
 F9XMODFLAG = @F9XMODFLAG@
 F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
-FCFLAGS = @FCFLAGS@ @H5_FCFLAGS@
+FCFLAGS = @FCFLAGS@
 FCFLAGS_f90 = @FCFLAGS_f90@
 FCLIBS = @FCLIBS@
 FGREP = @FGREP@
@@ -367,8 +374,8 @@ TEST_SCRIPT = $(srcdir)/h52giftest.sh
 check_SCRIPTS = $(TEST_SCRIPT)
 
 # Add h52gif and gif2h5 specific linker flags here
-h52gif_LDFLAGS = $(LT_STATIC_EXEC)
-gif2h5_LDFLAGS = $(LT_STATIC_EXEC)
+h52gif_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
+gif2h5_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
 gif2h5_SOURCES = gif2hdf.c gif2mem.c decompress.c gifread.c writehdf.c 
 h52gif_SOURCES = hdf2gif.c hdfgifwr.c 
 h52gifgentst_SOURCES = h52gifgentst.c