[svn-r27794] Reintegration merge of features/autotools_rework branch with trunk

NOTES:

- Developers will have to run autogen.sh before building with the autotools.

- autogen.sh takes the -p option to mimic the old bin/reconfigure behavior.

- The generated error, overflow and version headers have been left in place.

- The generated H5LT parser code has also been left in place.

- There are no changes for CMake users at this time.

Tested on: h5committest

16 files changed, 64 insertions, 15228 deletions

diff --git a/hl/Makefile.in b/hl/Makefile.in
deleted file mode 100644
index b2309d8..0000000
--- a/hl/Makefile.in
+++ /dev/null
@@ -1,1395 +0,0 @@
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-	    echo "    export HDF5_PARAPREFIX";                                \
-	    echo "    make check";                                            \
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diff --git a/hl/c++/src/Makefile.in b/hl/c++/src/Makefile.in
index 385b720..1cf08ef 100644
--- a/hl/c++/src/Makefile.in
+++ b/hl/c++/src/Makefile.in
@@ -99,9 +99,8 @@ host_triplet = @host@
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+	$(include_HEADERS) $(top_srcdir)/bin/test-driver
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+mkinstalldirs = $(install_sh) -d
 CONFIG_HEADER = $(top_builddir)/src/H5config.h \
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 CONFIG_CLEAN_FILES =
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diff --git a/hl/c++/test/Makefile.in b/hl/c++/test/Makefile.in
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-	list='$(DISTFILES)'; \
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-	      -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
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-	    cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
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-	    test -f "$(distdir)/$$file" \
-	    || cp -p $$d/$$file "$(distdir)/$$file" \
-	    || exit 1; \
-	  fi; \
-	done
-check-am: all-am
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-	  $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
-	    install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
-	      install; \
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-	  $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
-	    install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
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-	fi
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-	-test -z "$(TEST_LOGS)" || rm -f $(TEST_LOGS)
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-
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-
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-	-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
-	-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
-
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-	@echo "it deletes files that may require special tools to rebuild."
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-
-clean-am: clean-generic clean-libtool mostlyclean-am
-
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-dvi-am:
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-html-am:
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-	install-exec install-exec-am install-html install-html-am \
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-	pdf-am ps ps-am recheck tags-am uninstall uninstall-am \
-	uninstall-local
-
-
-# List all build rules defined by HDF5 Makefiles as "PHONY" targets here.
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-# commands that should be executed even if a file with the same name already
-# exists.
-.PHONY: build-check-clean build-check-p build-check-s build-lib build-progs \
-        build-tests check-clean check-install check-p check-s check-vfd \
-        install-doc lib progs tests uninstall-doc _exec_check-s _test help
-
-help:
-	@$(top_srcdir)/bin/makehelp
-
-# Tell automake how to build examples using h5fc
-@BUILD_PARALLEL_CONDITIONAL_TRUE@$(EXTRA_PROG): $(H5FC_PP)
-@BUILD_PARALLEL_CONDITIONAL_TRUE@	$(H5FC_PP) $(H5CCFLAGS) $(FCFLAGS) -o $@ $(srcdir)/$@.f90;
-@BUILD_PARALLEL_CONDITIONAL_FALSE@$(EXTRA_PROG): $(H5FC)
-@BUILD_PARALLEL_CONDITIONAL_FALSE@	$(H5FC) $(H5CCFLAGS) $(FCFLAGS) -o $@ $(srcdir)/$@.f90;
-
-# How to create EXAMPLEDIR if it doesn't already exist
-$(EXAMPLEDIR):
-	-$(top_srcdir)/bin/mkdirs $@
-$(EXAMPLETOPDIR):
-	-$(top_srcdir)/bin/mkdirs $@
-
-# Install and uninstall rules.  We install the source files, not the
-# example programs themselves.
-install-data-local:
-	@$(MAKE) $(AM_MAKEFLAGS) install-examples
-uninstall-local:
-	@$(MAKE) $(AM_MAKEFLAGS) uninstall-examples
-
-install-examples: $(EXAMPLEDIR) $(INSTALL_FILES) 
-	@for f in X $(INSTALL_FILES); do                                     \
-	  if test $$f != X; then                                             \
-	    (set -x; $(INSTALL) $(srcdir)/$$f $(EXAMPLEDIR)/. || exit 1);    \
-            chmod a-x $(EXAMPLEDIR)/$$f;                                     \
-	  fi;                                                                \
-	done
-	@for f in X $(INSTALL_SCRIPT_FILES); do                                   \
-	  if test $$f != X; then                                             \
-	    (set -x; $(INSTALL) $$f $(EXAMPLEDIR)/. || exit 1);\
-	  fi;                                                                \
-	done
-	@for f in X $(INSTALL_TOP_FILES); do                       \
-	  if test $$f != X; then                                             \
-	    (set -x; $(INSTALL) $(srcdir)/$$f $(EXAMPLETOPDIR)/. || exit 1); \
-            chmod a-x $(EXAMPLETOPDIR)/$$f;\
-	  fi;                                                                \
-	done
-	@for f in X $(INSTALL_TOP_SCRIPT_FILES); do                       \
-	  if test $$f != X; then                                             \
-	    (set -x; $(INSTALL) $(srcdir)/$$f $(EXAMPLETOPDIR)/. || exit 1); \
-	  fi;                                                                \
-	done
-
-uninstall-examples:
-	@if test -n "$(INSTALL_FILES)" -a -d $(EXAMPLEDIR); then             \
-	  set -x; cd $(EXAMPLEDIR) && $(RM) $(INSTALL_FILES);                \
-	fi
-	@if test -n "$(INSTALL_SCRIPT_FILES)" -a -d $(EXAMPLEDIR); then           \
-	  set -x; cd $(EXAMPLEDIR) && $(RM) $(INSTALL_SCRIPT_FILES);              \
-	fi
-	@if test -n "$(INSTALL_TOP_FILES)" -a -d $(EXAMPLETOPDIR); then    \
-	  set -x; cd $(EXAMPLETOPDIR) && $(RM) $(INSTALL_TOP_FILES);       \
-	fi
-	@if test -n "$(INSTALL_TOP_SCRIPT_FILES)" -a -d $(EXAMPLETOPDIR); then    \
-	  set -x; cd $(EXAMPLETOPDIR) && $(RM) $(INSTALL_TOP_SCRIPT_FILES);       \
-	fi
-
-installcheck-local:
-	@if test "$(STATIC_SHARED)" = "static, shared"; then               \
-	  H5CCFLAGS="-shlib" $(MAKE) $(AM_MAKEFLAGS) check;                \
-	  $(MAKE) $(AM_MAKEFLAGS) clean;                                   \
-	  H5CCFLAGS="" $(MAKE) $(AM_MAKEFLAGS) check;                      \
-	elif test "$(STATIC_SHARED)" = "shared"; then                     \
-	  H5CCFLAGS="-shlib" $(MAKE) $(AM_MAKEFLAGS) check;                \
-	else                                                              \
-	  $(MAKE) $(AM_MAKEFLAGS) check;                                   \
-	fi 
-	@if test "$(INSTALL_FILES)" -a $(TEST_EXAMPLES_SCRIPT) -a -d $(EXAMPLEDIR); then \
-	    echo "============================";                                         \
-	    echo "Testing $(TEST_EXAMPLES_SCRIPT)";                                      \
-	    echo "============================";                                         \
-	    (cd $(EXAMPLEDIR);                                                           \
-	     /bin/sh ./$(TEST_EXAMPLES_SCRIPT);)                                                   \
-	fi
-
-# Treat all .f90 and .F90 files as preprocessed Fortran.
-.f90.o:
-	$(PPFCCOMPILE) -c -o $@ $(FCFLAGS) $<
-.F90.o:
-	$(PPFCCOMPILE) -c -o $@ $(FCFLAGS) $<
-
-# lib/progs/tests targets recurse into subdirectories. build-* targets
-# build files in this directory.
-build-lib: $(LIB)
-build-progs: $(LIB) $(PROGS)
-build-tests: $(LIB) $(PROGS) $(chk_TESTS)
-
-# General rule for recursive building targets.
-# BUILT_SOURCES contain targets that need to be built before anything else
-# in the directory (e.g., for Fortran type detection)
-lib progs tests check-s check-p :: $(BUILT_SOURCES)
-	@$(MAKE) $(AM_MAKEFLAGS) build-$@ || exit 1;
-	@for d in X $(SUBDIRS); do                                             \
-	    if test $$d != X && test $$d != .; then                           \
-	        (set -x; cd $$d && $(MAKE) $(AM_MAKEFLAGS) $@) || exit 1;     \
-	    fi;                                                               \
-	done
-
-# General rule for recursive cleaning targets.  Like the rule above,
-# but doesn't require building BUILT_SOURCES.
-check-clean ::
-	@$(MAKE) $(AM_MAKEFLAGS) build-$@ || exit 1;
-	@for d in X $(SUBDIRS); do                                             \
-	    if test $$d != X && test $$d != .; then                           \
-	        (set -x; cd $$d && $(MAKE) $(AM_MAKEFLAGS) $@) || exit 1;     \
-	    fi;                                                               \
-	done
-
-# Tell Automake to build tests when the user types `make all' (this is
-# not its default behavior).  Also build EXTRA_LIB and EXTRA_PROG since
-# Automake won't build them automatically, either.
-all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(chk_TESTS)
-
-# make install-doc doesn't do anything outside of doc directory, but
-# Makefiles should recognize it.
-# UPDATE: docs no longer reside in this build tree, so this target
-# is depreciated.
-install-doc uninstall-doc:
-	@echo "Nothing to be done."
-
-# clean up files generated by tests so they can be re-run.
-build-check-clean:
-	$(RM) -rf $(CHECK_CLEANFILES)
-
-# run check-clean whenever mostlyclean is run
-mostlyclean-local: build-check-clean
-
-# check-install is just a synonym for installcheck
-check-install: installcheck
-
-# Run each test in order, passing $(TEST_FLAGS) to the program.
-# Since tests are done in a shell loop, "make -i" does apply inside it.
-# Set HDF5_Make_Ignore to a non-blank string to ignore errors inside the loop.
-# The timestamps give a rough idea how much time the tests use.
-#
-# Note that targets in chk_TESTS (defined above) will be built when the user
-# types 'make tests' or 'make check', but only programs in TEST_PROG,
-# TEST_PROG_PARA, or TEST_SCRIPT will actually be executed.
-check-TESTS: test
-
-test _test:
-	@$(MAKE) build-check-s
-	@$(MAKE) build-check-p
-
-# Actual execution of check-s.
-build-check-s: $(LIB) $(PROGS) $(chk_TESTS)
-	@if test -n "$(TEST_PROG)$(TEST_SCRIPT)"; then      \
-	   echo "===Serial tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
-	fi
-	@$(MAKE) $(AM_MAKEFLAGS) _exec_check-s
-	@if test -n "$(TEST_PROG)$(TEST_SCRIPT)"; then      \
-	    echo "===Serial tests in `echo ${PWD} | sed -e s:.*/::` ended `date`===";\
-	fi
-
-_exec_check-s: $(TEST_PROG_CHKEXE) $(TEST_SCRIPT_CHKSH)
-
-# The dummy.chkexe here prevents the target from being
-# empty if there are no tests in the current directory.
-# $${log} is the log file.
-# $${tname} is the name of test.
-$(TEST_PROG_CHKEXE) $(TEST_PROG_PARA_CHKEXE) dummy.chkexe_:
-	@if test "X$@" != "X.chkexe_" && test "X$@" != "Xdummy.chkexe_"; then \
-	   tname=$(@:.chkexe_=)$(EXEEXT);\
-	   log=$(@:.chkexe_=.chklog); \
-	   echo "============================"; \
-	   if $(top_srcdir)/bin/newer $(@:.chkexe_=.chkexe) $${tname}; then \
-	      echo "No need to test $${tname} again."; \
-	   else \
-	      echo "============================" > $${log}; \
-	      if test "X$(FORTRAN_API)" = "Xyes"; then \
-	         echo "Fortran API: Testing $(HDF5_DRIVER) $${tname} $(TEST_FLAGS)"; \
-	         echo "Fortran API: $(HDF5_DRIVER) $${tname} $(TEST_FLAGS) Test Log" >> $${log}; \
-	      elif test "X$(CXX_API)" = "Xyes"; then \
-	         echo "C++ API: Testing $(HDF5_DRIVER) $${tname} $(TEST_FLAGS)"; \
-	         echo "C++ API: $(HDF5_DRIVER) $${tname} $(TEST_FLAGS) Test Log" >> $${log};\
-	      else \
-	         echo "Testing $(HDF5_DRIVER) $${tname} $(TEST_FLAGS)"; \
-	         echo "$(HDF5_DRIVER) $${tname} $(TEST_FLAGS) Test Log" >> $${log}; \
-	      fi; \
-	      echo "============================" >> $${log}; \
-	      srcdir="$(srcdir)" \
-	         $(TIME) $(RUNEXEC) ./$${tname} $(TEST_FLAGS) >> $${log} 2>&1 \
-	         && touch $(@:.chkexe_=.chkexe) || \
-	         (test $$HDF5_Make_Ignore && echo "*** Error ignored") || \
-	         (cat $${log} && false) || exit 1; \
-	      echo "" >> $${log}; \
-	      echo "Finished testing $${tname} $(TEST_FLAGS)" >> $${log}; \
-	      echo "============================" >> $${log}; \
-	      echo "Finished testing $${tname} $(TEST_FLAGS)"; \
-	      cat $${log}; \
-	   fi; \
-	fi
-
-# The dummysh.chkexe here prevents the target from being
-# empty if there are no tests in the current directory.
-# $${log} is the log file.
-# $${tname} is the name of test.
-$(TEST_SCRIPT_CHKSH) $(TEST_SCRIPT_PARA_CHKSH) dummysh.chkexe_:
-	@if test "X$@" != "X.chkexe_" && test "X$@" != "Xdummysh.chkexe_"; then \
-	   cmd=$(@:.chkexe_=);\
-	   tname=`basename $$cmd`;\
-	   chkname=`basename $(@:.chkexe_=.chkexe)`;\
-	   log=`basename $(@:.chkexe_=.chklog)`; \
-	   echo "============================"; \
-	   if $(top_srcdir)/bin/newer $${chkname} $$cmd $(SCRIPT_DEPEND); then \
-	      echo "No need to test $${tname} again."; \
-	   else \
-	      echo "============================" > $${log}; \
-	      if test "X$(FORTRAN_API)" = "Xyes"; then \
-	         echo "Fortran API: Testing $${tname} $(TEST_FLAGS)"; \
-	         echo "Fortran API: $${tname} $(TEST_FLAGS) Test Log" >> $${log}; \
-	      elif test "X$(CXX_API)" = "Xyes"; then \
-	         echo "C++ API: Testing $${tname} $(TEST_FLAGS)"; \
-	         echo "C++ API: $${tname} $(TEST_FLAGS) Test Log" >> $${log}; \
-	      else \
-	         echo "Testing $${tname} $(TEST_FLAGS)"; \
-	         echo "$${tname} $(TEST_FLAGS) Test Log" >> $${log}; \
-	      fi; \
-	      echo "============================" >> $${log}; \
-	      RUNSERIAL="$(RUNSERIAL)" RUNPARALLEL="$(RUNPARALLEL)"           \
-	      srcdir="$(srcdir)" \
-	         $(TIME) $(SHELL) $$cmd $(TEST_FLAGS) >> $${log} 2>&1 \
-	         && touch $${chkname} || \
-	         (test $$HDF5_Make_Ignore && echo "*** Error ignored") || \
-	         (cat $${log} && false) || exit 1; \
-	      echo "" >> $${log}; \
-	      echo "Finished testing $${tname} $(TEST_FLAGS)" >> $${log}; \
-	      echo "============================" >> $${log}; \
-	      echo "Finished testing $${tname} $(TEST_FLAGS)"; \
-	      cat $${log}; \
-	   fi; \
-	   echo "============================"; \
-	fi
-
-# Actual execution of check-p.
-build-check-p: $(LIB) $(PROGS) $(chk_TESTS)
-	@if test -n "$(TEST_PROG_PARA)$(TEST_SCRIPT_PARA)"; then      \
-	   echo "===Parallel tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
-	fi
-	@if test -n "$(TEST_PROG_PARA)"; then                                \
-	    echo "**** Hint ****";                                            \
-	    echo "Parallel test files reside in the current directory"        \
-	         "by default.";                                               \
-	    echo "Set HDF5_PARAPREFIX to use another directory. E.g.,";       \
-	    echo "    HDF5_PARAPREFIX=/PFS/user/me";                          \
-	    echo "    export HDF5_PARAPREFIX";                                \
-	    echo "    make check";                                            \
-	    echo "**** end of Hint ****";                                     \
-	fi
-	@for test in $(TEST_PROG_PARA) dummy; do                             \
-	   if test $$test != dummy; then                                      \
-	      $(MAKE) $(AM_MAKEFLAGS) $$test.chkexe_ \
-	      RUNEXEC="$(RUNPARALLEL)" || exit 1; \
-	   fi;                                                                \
-	done
-	@for test in $(TEST_SCRIPT_PARA) dummy; do                           \
-	  if test $$test != dummy; then                                      \
-	    $(MAKE) $(AM_MAKEFLAGS) $$test.chkexe_ || exit 1; \
-	  fi;                                                                 \
-	done
-	@if test -n "$(TEST_PROG_PARA)$(TEST_SCRIPT_PARA)"; then      \
-	    echo "===Parallel tests in `echo ${PWD} | sed -e s:.*/::` ended `date`===";\
-	fi
-
-# Run test with different Virtual File Driver
-check-vfd: $(LIB) $(PROGS) $(chk_TESTS)
-	@for vfd in $(VFD_LIST) dummy; do                                     \
-	    if test $$vfd != dummy; then                                      \
-	        echo "============================";                          \
-	        echo "Testing Virtual File Driver $$vfd";                     \
-	        echo "============================";                          \
-	        $(MAKE) $(AM_MAKEFLAGS) check-clean || exit 1;                \
-	        HDF5_DRIVER=$$vfd $(MAKE) $(AM_MAKEFLAGS) check || exit 1;    \
-	    fi;                                                               \
-	done
-
-# List dependencies for each example.  Normally, automake would take
-# care of this for us, but if we tell automake about the programs it
-# will try to build them with the normal C compiler, not h5cc.  This is
-# an inelegant way of solving the problem.
-# All programs share the same build rule and a dependency on the main hdf5
-# and fortran libraries above.
-
-# Tell versions [3.59,3.63) of GNU make to not export all variables.
-# Otherwise a system limit (for SysV at least) may be exceeded.
-.NOEXPORT:
diff --git a/hl/fortran/src/CMakeLists.txt b/hl/fortran/src/CMakeLists.txt
index ead21be..83a205f 100644
--- a/hl/fortran/src/CMakeLists.txt
+++ b/hl/fortran/src/CMakeLists.txt
@@ -48,6 +48,11 @@ if (WIN32)
 else (WIN32)
   set (MOD_BUILD_DIR ${CMAKE_Fortran_MODULE_DIRECTORY}/static)
 endif (WIN32)
+if (WIN32)
+  set (MOD_BUILD_DIR ${CMAKE_Fortran_MODULE_DIRECTORY}/static/\${BUILD_TYPE})
+else (WIN32)
+  set (MOD_BUILD_DIR ${CMAKE_Fortran_MODULE_DIRECTORY}/static)
+endif (WIN32)
 
 #-----------------------------------------------------------------------------
 # Setup include Directories
diff --git a/hl/fortran/src/Makefile.in b/hl/fortran/src/Makefile.in
index 4fada70..4f0496c 100644
--- a/hl/fortran/src/Makefile.in
+++ b/hl/fortran/src/Makefile.in
@@ -104,8 +104,8 @@ DIST_COMMON = $(top_srcdir)/config/commence.am \
 	$(top_srcdir)/config/lt_vers.am \
 	$(top_srcdir)/config/conclude_fc.am \
 	$(top_srcdir)/config/conclude.am $(srcdir)/Makefile.in \
-	$(srcdir)/Makefile.am $(top_srcdir)/bin/mkinstalldirs \
-	$(top_srcdir)/bin/depcomp $(top_srcdir)/bin/test-driver
+	$(srcdir)/Makefile.am $(top_srcdir)/bin/depcomp \
+	$(top_srcdir)/bin/test-driver
 
 # 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,
@@ -119,7 +119,7 @@ am__aclocal_m4_deps = $(top_srcdir)/m4/aclocal_cxx.m4 \
 	$(top_srcdir)/m4/aclocal_fc.m4 $(top_srcdir)/configure.ac
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
-mkinstalldirs = $(SHELL) $(top_srcdir)/bin/mkinstalldirs
+mkinstalldirs = $(install_sh) -d
 CONFIG_HEADER = $(top_builddir)/src/H5config.h \
 	$(top_builddir)/fortran/src/H5config_f.inc
 CONFIG_CLEAN_FILES =
@@ -435,7 +435,6 @@ AM_DEFAULT_VERBOSITY = @AM_DEFAULT_VERBOSITY@
 AM_FCFLAGS = @AM_FCFLAGS@ @H5_FCFLAGS@ -I$(top_builddir)/fortran/src \
 	$(F9XMODFLAG)$(top_builddir)/fortran/src
 AM_LDFLAGS = @AM_LDFLAGS@ @H5_LDFLAGS@ $(am__append_1)
-AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 AUTOCONF = @AUTOCONF@
 AUTOHEADER = @AUTOHEADER@
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deleted file mode 100644
index 117faf2..0000000
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-	         | $(am__list_recheck_tests)` || exit 1; \
-	log_list=`for i in $$bases; do echo $$i.log; done`; \
-	log_list=`echo $$log_list`; \
-	$(MAKE) $(AM_MAKEFLAGS) $(TEST_SUITE_LOG) \
-	        am__force_recheck=am--force-recheck \
-	        TEST_LOGS="$$log_list"; \
-	exit $$?
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-	@p='tstds$(EXEEXT)'; \
-	b='tstds'; \
-	$(am__check_pre) $(LOG_DRIVER) --test-name "$$f" \
-	--log-file $$b.log --trs-file $$b.trs \
-	$(am__common_driver_flags) $(AM_LOG_DRIVER_FLAGS) $(LOG_DRIVER_FLAGS) -- $(LOG_COMPILE) \
-	"$$tst" $(AM_TESTS_FD_REDIRECT)
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-	$(am__check_pre) $(LOG_DRIVER) --test-name "$$f" \
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-	$(am__set_b); \
-	$(am__check_pre) $(SH_LOG_DRIVER) --test-name "$$f" \
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-	  fi; \
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-check-am: all-am
-	$(MAKE) $(AM_MAKEFLAGS) $(check_PROGRAMS)
-	$(MAKE) $(AM_MAKEFLAGS) check-TESTS
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-	@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
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-	  $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
-	    install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
-	      install; \
-	else \
-	  $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
-	    install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
-	    "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'" install; \
-	fi
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-	-test -z "$(TEST_LOGS)" || rm -f $(TEST_LOGS)
-	-test -z "$(TEST_LOGS:.log=.trs)" || rm -f $(TEST_LOGS:.log=.trs)
-	-test -z "$(TEST_SUITE_LOG)" || rm -f $(TEST_SUITE_LOG)
-
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-	-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
-
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-clean: clean-am
-
-clean-am: clean-checkPROGRAMS clean-generic clean-libtool \
-	mostlyclean-am
-
-distclean: distclean-am
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-	distclean-tags
-
-dvi: dvi-am
-
-dvi-am:
-
-html: html-am
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-html-am:
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-install-dvi-am:
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-install-ps: install-ps-am
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-install-ps-am:
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-installcheck-am:
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-maintainer-clean: maintainer-clean-am
-	-rm -f Makefile
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-
-mostlyclean: mostlyclean-am
-
-mostlyclean-am: mostlyclean-compile mostlyclean-generic \
-	mostlyclean-libtool mostlyclean-local
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-.MAKE: check-am install-am install-strip
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-.PHONY: CTAGS GTAGS TAGS all all-am all-local check check-TESTS \
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-	cscopelist-am ctags ctags-am distclean distclean-compile \
-	distclean-generic distclean-libtool distclean-tags distdir dvi \
-	dvi-am html html-am info info-am install install-am \
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-	install-exec install-exec-am install-html install-html-am \
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-
-
-# List all build rules defined by HDF5 Makefiles as "PHONY" targets here.
-# This tells the Makefiles that these targets are not files to be built but
-# commands that should be executed even if a file with the same name already
-# exists.
-.PHONY: build-check-clean build-check-p build-check-s build-lib build-progs \
-        build-tests check-clean check-install check-p check-s check-vfd \
-        install-doc lib progs tests uninstall-doc _exec_check-s _test help
-
-help:
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-
-# Treat all .f90 and .F90 files as preprocessed Fortran.
-.f90.o:
-	$(PPFCCOMPILE) -c -o $@ $(FCFLAGS) $<
-.F90.o:
-	$(PPFCCOMPILE) -c -o $@ $(FCFLAGS) $<
-
-# lib/progs/tests targets recurse into subdirectories. build-* targets
-# build files in this directory.
-build-lib: $(LIB)
-build-progs: $(LIB) $(PROGS)
-build-tests: $(LIB) $(PROGS) $(chk_TESTS)
-
-# General rule for recursive building targets.
-# BUILT_SOURCES contain targets that need to be built before anything else
-# in the directory (e.g., for Fortran type detection)
-lib progs tests check-s check-p :: $(BUILT_SOURCES)
-	@$(MAKE) $(AM_MAKEFLAGS) build-$@ || exit 1;
-	@for d in X $(SUBDIRS); do                                             \
-	    if test $$d != X && test $$d != .; then                           \
-	        (set -x; cd $$d && $(MAKE) $(AM_MAKEFLAGS) $@) || exit 1;     \
-	    fi;                                                               \
-	done
-
-# General rule for recursive cleaning targets.  Like the rule above,
-# but doesn't require building BUILT_SOURCES.
-check-clean ::
-	@$(MAKE) $(AM_MAKEFLAGS) build-$@ || exit 1;
-	@for d in X $(SUBDIRS); do                                             \
-	    if test $$d != X && test $$d != .; then                           \
-	        (set -x; cd $$d && $(MAKE) $(AM_MAKEFLAGS) $@) || exit 1;     \
-	    fi;                                                               \
-	done
-
-# Tell Automake to build tests when the user types `make all' (this is
-# not its default behavior).  Also build EXTRA_LIB and EXTRA_PROG since
-# Automake won't build them automatically, either.
-all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(chk_TESTS)
-
-# make install-doc doesn't do anything outside of doc directory, but
-# Makefiles should recognize it.
-# UPDATE: docs no longer reside in this build tree, so this target
-# is depreciated.
-install-doc uninstall-doc:
-	@echo "Nothing to be done."
-
-# clean up files generated by tests so they can be re-run.
-build-check-clean:
-	$(RM) -rf $(CHECK_CLEANFILES)
-
-# run check-clean whenever mostlyclean is run
-mostlyclean-local: build-check-clean
-
-# check-install is just a synonym for installcheck
-check-install: installcheck
-
-# Run each test in order, passing $(TEST_FLAGS) to the program.
-# Since tests are done in a shell loop, "make -i" does apply inside it.
-# Set HDF5_Make_Ignore to a non-blank string to ignore errors inside the loop.
-# The timestamps give a rough idea how much time the tests use.
-#
-# Note that targets in chk_TESTS (defined above) will be built when the user
-# types 'make tests' or 'make check', but only programs in TEST_PROG,
-# TEST_PROG_PARA, or TEST_SCRIPT will actually be executed.
-check-TESTS: test
-
-test _test:
-	@$(MAKE) build-check-s
-	@$(MAKE) build-check-p
-
-# Actual execution of check-s.
-build-check-s: $(LIB) $(PROGS) $(chk_TESTS)
-	@if test -n "$(TEST_PROG)$(TEST_SCRIPT)"; then      \
-	   echo "===Serial tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
-	fi
-	@$(MAKE) $(AM_MAKEFLAGS) _exec_check-s
-	@if test -n "$(TEST_PROG)$(TEST_SCRIPT)"; then      \
-	    echo "===Serial tests in `echo ${PWD} | sed -e s:.*/::` ended `date`===";\
-	fi
-
-_exec_check-s: $(TEST_PROG_CHKEXE) $(TEST_SCRIPT_CHKSH)
-
-# The dummy.chkexe here prevents the target from being
-# empty if there are no tests in the current directory.
-# $${log} is the log file.
-# $${tname} is the name of test.
-$(TEST_PROG_CHKEXE) $(TEST_PROG_PARA_CHKEXE) dummy.chkexe_:
-	@if test "X$@" != "X.chkexe_" && test "X$@" != "Xdummy.chkexe_"; then \
-	   tname=$(@:.chkexe_=)$(EXEEXT);\
-	   log=$(@:.chkexe_=.chklog); \
-	   echo "============================"; \
-	   if $(top_srcdir)/bin/newer $(@:.chkexe_=.chkexe) $${tname}; then \
-	      echo "No need to test $${tname} again."; \
-	   else \
-	      echo "============================" > $${log}; \
-	      if test "X$(FORTRAN_API)" = "Xyes"; then \
-	         echo "Fortran API: Testing $(HDF5_DRIVER) $${tname} $(TEST_FLAGS)"; \
-	         echo "Fortran API: $(HDF5_DRIVER) $${tname} $(TEST_FLAGS) Test Log" >> $${log}; \
-	      elif test "X$(CXX_API)" = "Xyes"; then \
-	         echo "C++ API: Testing $(HDF5_DRIVER) $${tname} $(TEST_FLAGS)"; \
-	         echo "C++ API: $(HDF5_DRIVER) $${tname} $(TEST_FLAGS) Test Log" >> $${log};\
-	      else \
-	         echo "Testing $(HDF5_DRIVER) $${tname} $(TEST_FLAGS)"; \
-	         echo "$(HDF5_DRIVER) $${tname} $(TEST_FLAGS) Test Log" >> $${log}; \
-	      fi; \
-	      echo "============================" >> $${log}; \
-	      srcdir="$(srcdir)" \
-	         $(TIME) $(RUNEXEC) ./$${tname} $(TEST_FLAGS) >> $${log} 2>&1 \
-	         && touch $(@:.chkexe_=.chkexe) || \
-	         (test $$HDF5_Make_Ignore && echo "*** Error ignored") || \
-	         (cat $${log} && false) || exit 1; \
-	      echo "" >> $${log}; \
-	      echo "Finished testing $${tname} $(TEST_FLAGS)" >> $${log}; \
-	      echo "============================" >> $${log}; \
-	      echo "Finished testing $${tname} $(TEST_FLAGS)"; \
-	      cat $${log}; \
-	   fi; \
-	fi
-
-# The dummysh.chkexe here prevents the target from being
-# empty if there are no tests in the current directory.
-# $${log} is the log file.
-# $${tname} is the name of test.
-$(TEST_SCRIPT_CHKSH) $(TEST_SCRIPT_PARA_CHKSH) dummysh.chkexe_:
-	@if test "X$@" != "X.chkexe_" && test "X$@" != "Xdummysh.chkexe_"; then \
-	   cmd=$(@:.chkexe_=);\
-	   tname=`basename $$cmd`;\
-	   chkname=`basename $(@:.chkexe_=.chkexe)`;\
-	   log=`basename $(@:.chkexe_=.chklog)`; \
-	   echo "============================"; \
-	   if $(top_srcdir)/bin/newer $${chkname} $$cmd $(SCRIPT_DEPEND); then \
-	      echo "No need to test $${tname} again."; \
-	   else \
-	      echo "============================" > $${log}; \
-	      if test "X$(FORTRAN_API)" = "Xyes"; then \
-	         echo "Fortran API: Testing $${tname} $(TEST_FLAGS)"; \
-	         echo "Fortran API: $${tname} $(TEST_FLAGS) Test Log" >> $${log}; \
-	      elif test "X$(CXX_API)" = "Xyes"; then \
-	         echo "C++ API: Testing $${tname} $(TEST_FLAGS)"; \
-	         echo "C++ API: $${tname} $(TEST_FLAGS) Test Log" >> $${log}; \
-	      else \
-	         echo "Testing $${tname} $(TEST_FLAGS)"; \
-	         echo "$${tname} $(TEST_FLAGS) Test Log" >> $${log}; \
-	      fi; \
-	      echo "============================" >> $${log}; \
-	      RUNSERIAL="$(RUNSERIAL)" RUNPARALLEL="$(RUNPARALLEL)"           \
-	      srcdir="$(srcdir)" \
-	         $(TIME) $(SHELL) $$cmd $(TEST_FLAGS) >> $${log} 2>&1 \
-	         && touch $${chkname} || \
-	         (test $$HDF5_Make_Ignore && echo "*** Error ignored") || \
-	         (cat $${log} && false) || exit 1; \
-	      echo "" >> $${log}; \
-	      echo "Finished testing $${tname} $(TEST_FLAGS)" >> $${log}; \
-	      echo "============================" >> $${log}; \
-	      echo "Finished testing $${tname} $(TEST_FLAGS)"; \
-	      cat $${log}; \
-	   fi; \
-	   echo "============================"; \
-	fi
-
-# Actual execution of check-p.
-build-check-p: $(LIB) $(PROGS) $(chk_TESTS)
-	@if test -n "$(TEST_PROG_PARA)$(TEST_SCRIPT_PARA)"; then      \
-	   echo "===Parallel tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
-	fi
-	@if test -n "$(TEST_PROG_PARA)"; then                                \
-	    echo "**** Hint ****";                                            \
-	    echo "Parallel test files reside in the current directory"        \
-	         "by default.";                                               \
-	    echo "Set HDF5_PARAPREFIX to use another directory. E.g.,";       \
-	    echo "    HDF5_PARAPREFIX=/PFS/user/me";                          \
-	    echo "    export HDF5_PARAPREFIX";                                \
-	    echo "    make check";                                            \
-	    echo "**** end of Hint ****";                                     \
-	fi
-	@for test in $(TEST_PROG_PARA) dummy; do                             \
-	   if test $$test != dummy; then                                      \
-	      $(MAKE) $(AM_MAKEFLAGS) $$test.chkexe_ \
-	      RUNEXEC="$(RUNPARALLEL)" || exit 1; \
-	   fi;                                                                \
-	done
-	@for test in $(TEST_SCRIPT_PARA) dummy; do                           \
-	  if test $$test != dummy; then                                      \
-	    $(MAKE) $(AM_MAKEFLAGS) $$test.chkexe_ || exit 1; \
-	  fi;                                                                 \
-	done
-	@if test -n "$(TEST_PROG_PARA)$(TEST_SCRIPT_PARA)"; then      \
-	    echo "===Parallel tests in `echo ${PWD} | sed -e s:.*/::` ended `date`===";\
-	fi
-
-# Run test with different Virtual File Driver
-check-vfd: $(LIB) $(PROGS) $(chk_TESTS)
-	@for vfd in $(VFD_LIST) dummy; do                                     \
-	    if test $$vfd != dummy; then                                      \
-	        echo "============================";                          \
-	        echo "Testing Virtual File Driver $$vfd";                     \
-	        echo "============================";                          \
-	        $(MAKE) $(AM_MAKEFLAGS) check-clean || exit 1;                \
-	        HDF5_DRIVER=$$vfd $(MAKE) $(AM_MAKEFLAGS) check || exit 1;    \
-	    fi;                                                               \
-	done
-
-# Tell versions [3.59,3.63) of GNU make to not export all variables.
-# Otherwise a system limit (for SysV at least) may be exceeded.
-.NOEXPORT:
diff --git a/hl/src/CMakeLists.txt b/hl/src/CMakeLists.txt
index 23943f9..8d1a37f 100644
--- a/hl/src/CMakeLists.txt
+++ b/hl/src/CMakeLists.txt
@@ -1,26 +1,71 @@
 cmake_minimum_required (VERSION 3.1.0)
 PROJECT (HDF5_HL_SRC)
 
+if (HDF5_GENERATE_HEADERS)
+  find_package (BISON)
+  if (BISON_FOUND)
+    find_package (FLEX)
+    if (FLEX_FOUND)
+      BISON_TARGET (H5LT_PARSER H5LTparse.y ${CMAKE_CURRENT_BINARY_DIR}/H5LTparse.c COMPILE_FLAGS "-d -pH5LTyy")
+      if (WIN32)
+        FLEX_TARGET (H5LT_SCANNER H5LTanalyze.l ${CMAKE_CURRENT_BINARY_DIR}/H5LTanalyze.c COMPILE_FLAGS "--wincompat --nounistd -PH5LTyy")
+      else (WIN32)
+        FLEX_TARGET (H5LT_SCANNER H5LTanalyze.l ${CMAKE_CURRENT_BINARY_DIR}/H5LTanalyze.c COMPILE_FLAGS "--nounistd -PH5LTyy")
+      endif (WIN32)
+      ADD_FLEX_BISON_DEPENDENCY(H5LT_SCANNER H5LT_PARSER)
+
+      if (BISON_H5LT_PARSER_DEFINED AND FLEX_H5LT_SCANNER_DEFINED)
+        include_directories(${CMAKE_CURRENT_BINARY_DIR})
+        set (HL_SRCS
+            ${CMAKE_CURRENT_BINARY_DIR}/H5LTanalyze.c
+            ${CMAKE_CURRENT_BINARY_DIR}/H5LTparse.c
+        )
+        set (HL_HEADERS
+            ${CMAKE_CURRENT_BINARY_DIR}/H5LTparse.h
+        )
+        set_source_files_properties (${CMAKE_CURRENT_BINARY_DIR}/H5LTanalyze.c GENERATED)
+        set_source_files_properties (${CMAKE_CURRENT_BINARY_DIR}/H5LTparse.c GENERATED)
+        set_source_files_properties (${CMAKE_CURRENT_BINARY_DIR}/H5LTparse.h GENERATED)
+      else (BISON_H5LT_PARSER_DEFINED AND FLEX_H5LT_SCANNER_DEFINED)
+        message (STATUS "Error during generate of files")
+      endif (BISON_H5LT_PARSER_DEFINED AND FLEX_H5LT_SCANNER_DEFINED)
+    else (FLEX_FOUND)
+      message (STATUS "Cannot generate files - flex not found")
+    endif (FLEX_FOUND)
+  else (BISON_FOUND)
+    message (STATUS "Cannot generate files - bison not found")
+  endif (BISON_FOUND)
+else (HDF5_GENERATE_HEADERS)
+  set (HL_SRCS
+      ${HDF5_HL_SRC_SOURCE_DIR}/H5LTanalyze.c
+      ${HDF5_HL_SRC_SOURCE_DIR}/H5LTparse.c
+  )
+  set (HL_HEADERS
+      ${HDF5_HL_SRC_SOURCE_DIR}/H5LTparse.h
+  )
+endif (HDF5_GENERATE_HEADERS)
 
 #-----------------------------------------------------------------------------
 # List Source files
 #-----------------------------------------------------------------------------
 set (HL_SRCS
+    ${HL_SRCS}
     ${HDF5_HL_SRC_SOURCE_DIR}/H5DO.c
     ${HDF5_HL_SRC_SOURCE_DIR}/H5DS.c
     ${HDF5_HL_SRC_SOURCE_DIR}/H5IM.c
     ${HDF5_HL_SRC_SOURCE_DIR}/H5LT.c
-    ${HDF5_HL_SRC_SOURCE_DIR}/H5LTanalyze.c
-    ${HDF5_HL_SRC_SOURCE_DIR}/H5LTparse.c
+    #${HDF5_HL_SRC_SOURCE_DIR}/H5LTanalyze.c
+    #${HDF5_HL_SRC_SOURCE_DIR}/H5LTparse.c
     ${HDF5_HL_SRC_SOURCE_DIR}/H5PT.c
     ${HDF5_HL_SRC_SOURCE_DIR}/H5TB.c
 )
 
 set (HL_HEADERS
+    ${HL_HEADERS}
     ${HDF5_HL_SRC_SOURCE_DIR}/H5DOpublic.h
     ${HDF5_HL_SRC_SOURCE_DIR}/H5DSpublic.h
     ${HDF5_HL_SRC_SOURCE_DIR}/H5IMpublic.h
-    ${HDF5_HL_SRC_SOURCE_DIR}/H5LTparse.h
+    #${HDF5_HL_SRC_SOURCE_DIR}/H5LTparse.h
     ${HDF5_HL_SRC_SOURCE_DIR}/H5LTpublic.h
     ${HDF5_HL_SRC_SOURCE_DIR}/H5PTpublic.h
     ${HDF5_HL_SRC_SOURCE_DIR}/H5TBpublic.h
@@ -54,7 +99,7 @@ if (BUILD_SHARED_LIBS)
 endif (BUILD_SHARED_LIBS)
 
 #-----------------------------------------------------------------------------
-# Add file(s) to CMake Install 
+# Add file(s) to CMake Install
 #-----------------------------------------------------------------------------
 install (
     FILES
@@ -72,7 +117,7 @@ if (HDF5_EXPORTED_TARGETS)
   if (BUILD_SHARED_LIBS)
     INSTALL_TARGET_PDB (${HDF5_HL_LIBSH_TARGET} ${HDF5_INSTALL_BIN_DIR} hllibraries)
   endif (BUILD_SHARED_LIBS)
-  
+
   install (
       TARGETS
           ${install_targets}
diff --git a/hl/src/Makefile.in b/hl/src/Makefile.in
index 32e9f20..c219736 100644
--- a/hl/src/Makefile.in
+++ b/hl/src/Makefile.in
@@ -99,9 +99,8 @@ host_triplet = @host@
 DIST_COMMON = $(top_srcdir)/config/commence.am \
 	$(top_srcdir)/config/lt_vers.am \
 	$(top_srcdir)/config/conclude.am $(srcdir)/Makefile.in \
-	$(srcdir)/Makefile.am $(top_srcdir)/bin/mkinstalldirs \
-	$(top_srcdir)/bin/depcomp $(include_HEADERS) \
-	$(top_srcdir)/bin/test-driver COPYING
+	$(srcdir)/Makefile.am $(top_srcdir)/bin/depcomp \
+	$(include_HEADERS) $(top_srcdir)/bin/test-driver COPYING
 TESTS =
 subdir = hl/src
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
@@ -109,7 +108,7 @@ am__aclocal_m4_deps = $(top_srcdir)/m4/aclocal_cxx.m4 \
 	$(top_srcdir)/m4/aclocal_fc.m4 $(top_srcdir)/configure.ac
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
-mkinstalldirs = $(SHELL) $(top_srcdir)/bin/mkinstalldirs
+mkinstalldirs = $(install_sh) -d
 CONFIG_HEADER = $(top_builddir)/src/H5config.h \
 	$(top_builddir)/fortran/src/H5config_f.inc
 CONFIG_CLEAN_FILES =
@@ -406,7 +405,6 @@ AM_CXXFLAGS = @AM_CXXFLAGS@ @H5_CXXFLAGS@
 AM_DEFAULT_VERBOSITY = @AM_DEFAULT_VERBOSITY@
 AM_FCFLAGS = @AM_FCFLAGS@ @H5_FCFLAGS@
 AM_LDFLAGS = @AM_LDFLAGS@ @H5_LDFLAGS@
-AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 AUTOCONF = @AUTOCONF@
 AUTOHEADER = @AUTOHEADER@
diff --git a/hl/test/Makefile.in b/hl/test/Makefile.in
deleted file mode 100644
index 325a426..0000000
--- a/hl/test/Makefile.in
+++ /dev/null
@@ -1,1496 +0,0 @@
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-
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-
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