Add fortkit dependency for H5Rff.F90 and fix for a libtool sed hack (#…

…4506)

* Add H5fortkit dependecy for H5Rff.F90 (#4482)

* Fix/revert a libtool sed hack (#4501)

* Revert "Remove Autotools sed hack (#3848)"

This reverts commit 8b3ffde.

* Fix libtool sed cleanup on MacOS

Convert sed -i line to sed > libtool.bak && mv libtool.bak libtool
to avoid non-portable -i option.

* Commit changes to configure and fortran/src/Makefile.in from running
autogen.sh after latest code changes.

README.md

@@ -1,4 +1,4 @@
-HDF5 version 1.14.4-3 released on 2024-05-14
+HDF5 version 1.14.4-3 released on 2024-05-20
 
 ![HDF5 Logo](doxygen/img/HDF5.png)
 

configure

@@ -40647,6 +40647,13 @@ if test "X$HDF_FORTRAN" = "Xyes"; then
   esac
 fi
 
+## HDF5 configure code created by autotools with gcc 4.9.2 is adding problematic
+## linker flags:  -l with no library name; -l <libname>, specifically gfortran or m.
+## This sed script corrects "-l <libname>" first and then "-l " with no library name.
+## If the order is not preserved, all instances of "-l " will be removed.
+sed -e '/^postdeps/ s/-l \(a-zA-Z\)/-l\1/g' -e '/^postdeps/ s/-l //g' libtool > libtool.bak
+mv -- libtool.bak libtool
+
 ## show the configure settings
 cat src/libhdf5.settings
 

configure.ac

@@ -4635,5 +4635,12 @@ if test "X$HDF_FORTRAN" = "Xyes"; then
   esac
 fi
 
+## HDF5 configure code created by autotools with gcc 4.9.2 is adding problematic
+## linker flags:  -l with no library name; -l <libname>, specifically gfortran or m.
+## This sed script corrects "-l <libname>" first and then "-l " with no library name.
+## If the order is not preserved, all instances of "-l " will be removed.
+sed -e '/^postdeps/ s/-l \([a-zA-Z]\)/-l\1/g' -e '/^postdeps/ s/-l //g' libtool > libtool.bak
+mv -- libtool.bak libtool
+
 ## show the configure settings
 cat src/libhdf5.settings

fortran/src/Makefile.am

@@ -155,7 +155,7 @@ H5Iff.lo:            $(srcdir)/H5Iff.F90 H5f90global.lo
 H5Lff.lo:            $(srcdir)/H5Lff.F90 H5f90global.lo
 H5Off.lo:            $(srcdir)/H5Off.F90 H5f90global.lo
 H5Pff.lo:            $(srcdir)/H5Pff.F90 H5f90global.lo H5fortkit.lo
-H5Rff.lo:            $(srcdir)/H5Rff.F90 H5f90global.lo
+H5Rff.lo:            $(srcdir)/H5Rff.F90 H5f90global.lo H5fortkit.lo
 H5Sff.lo:            $(srcdir)/H5Sff.F90 H5f90global.lo
 H5Tff.lo:            $(srcdir)/H5Tff.F90 H5f90global.lo
 H5VLff.lo:           $(srcdir)/H5VLff.F90 H5f90global.lo H5fortkit.lo

fortran/src/Makefile.in

@@ -1622,7 +1622,7 @@ H5Iff.lo:            $(srcdir)/H5Iff.F90 H5f90global.lo
 H5Lff.lo:            $(srcdir)/H5Lff.F90 H5f90global.lo
 H5Off.lo:            $(srcdir)/H5Off.F90 H5f90global.lo
 H5Pff.lo:            $(srcdir)/H5Pff.F90 H5f90global.lo H5fortkit.lo
-H5Rff.lo:            $(srcdir)/H5Rff.F90 H5f90global.lo
+H5Rff.lo:            $(srcdir)/H5Rff.F90 H5f90global.lo H5fortkit.lo
 H5Sff.lo:            $(srcdir)/H5Sff.F90 H5f90global.lo
 H5Tff.lo:            $(srcdir)/H5Tff.F90 H5f90global.lo
 H5VLff.lo:           $(srcdir)/H5VLff.F90 H5f90global.lo H5fortkit.lo

release_docs/NEWSLETTER.txt

@@ -1,4 +1,4 @@
-HDF5 version 1.14.4-3 released on 2024-05-14
+HDF5 version 1.14.4-3 released on 2024-05-20
 
 This is a maintenance release with a few changes and updates:
 ----------------------------------------------------------------------------

release_docs/RELEASE.txt

@@ -1,4 +1,4 @@
-HDF5 version 1.14.4-3 released on 2024-05-14
+HDF5 version 1.14.4-3 released on 2024-05-20
 ================================================================================
 
 
@@ -1014,6 +1014,40 @@ Bug Fixes since HDF5-1.14.3 release
 
     Configuration
     -------------
+    - Fixed/reverted an Autotools configure hack that causes problems on MacOS
+
+      A sed line in configure.ac was added in the past to paper over some
+      problems with older versions of the Autotools that would add incorrect
+      linker flags. This used the -i option in a way that caused silent
+      errors on MacOS that did not break the build.
+
+      The original fix for this problem (in 1.14.4) removed the sed line
+      entirely, but it turns out that the sed cleanup is still necessary
+      on some systems, where empty -l options will be added to the libtool
+      script.
+
+      This sed line has been restored and reworked to not use -i.
+
+      Fixes GitHub issues #3843 and #4448
+
+    - Fixed a list index out of range issue in the runTest.cmake file
+
+      Fixed an issue in config/cmake/runTest.cmake where the CMake logic
+      would try to access an invalid list index if the number of lines in
+      a test's output and reference files don't match
+
+    - Fix Autotools -Werror cleanup
+
+      The Autotools temporarily scrub -Werror(=whatever) from CFLAGS, etc.
+      so configure checks don't trip over warnings generated by configure
+      check programs. The sed line originally only scrubbed -Werror but not
+      -Werror=something, which would cause errors when the '=something' was
+      left behind in CFLAGS.
+
+      The sed line has been updated to handle -Werror=something lines.
+
+      Fixes one issue raised in #3872
+
     - Changed default of 'Error on HDF5 doxygen warnings' DOXYGEN_WARN_AS_ERROR option.
 
       The default setting of DOXYGEN_WARN_AS_ERROR to 'FAIL_ON_WARNINGS' has been changed
@@ -1023,16 +1057,6 @@ Bug Fixes since HDF5-1.14.3 release
         * HDF5_ENABLE_DOXY_WARNINGS: ON/OFF (Default: OFF)
         * --enable-doxygen-errors: enable/disable (Default: disable)
 
-    - Removed an Autotools configure hack that causes problems on MacOS
-
-      A sed line in configure.ac was added in the past to paper over some
-      problems with older versions of the Autotools that would add incorrect
-      linker flags. This hack is not needed with recent versions of the
-      Autotools and the sed line errors on MacOS (though this was a silent
-      error that didn't break the build) so the hack has been removed.
-
-      Fixes GitHub issue #3843
-
     - Fixed an issue where the h5tools_test_utils test program was being
       installed on the system for Autotools builds of HDF5