r-hdf5r: use pkg-config to find hdf5 (#27847)

* r-hdf5r: use pkg-config to find hdf5

Since hdf5 was switched from autotools to cmake, the hdf5 compiler
wrappers can not be used to find and configure hdf5. This PR switches to
using pkg-config for configuration.

* Add comment about configure patch

var/spack/repos/builtin/packages/r-hdf5r/configure.patch

@@ -0,0 +1,98 @@
+diff -ru a/configure b/configure
+--- a/configure	2021-11-15 13:13:34.000000000 -0600
++++ b/configure	2021-12-07 15:08:23.118115118 -0600
+@@ -3673,43 +3673,15 @@
+         with_hdf5="no"
+         with_hdf5_fortran="no"
+     else
+-                HDF5_SHOW=$(eval $H5CC -show)
+ 
+-                HDF5_CC=$(eval $H5CC -show | $AWK '{print $1}')
+-        if test "$HDF5_CC" = "ccache"; then
+-            HDF5_CC=$(eval $H5CC -show | $AWK '{print $2}')
+-        fi
+-
+-
+-                HDF5_VERSION=$(eval $H5CC -showconfig | $GREP 'HDF5 Version:' \
+-            | $AWK '{print $3}')
++                HDF5_VERSION=$(eval pkg-config --modversion hdf5)
+         HDF5_MAJOR_VERSION=$(echo $HDF5_VERSION | $AWK -F \. '{print $1}')
+         HDF5_MINOR_VERSION=$(echo $HDF5_VERSION | $AWK -F \. {'print $2'})
+         HDF5_REVISION_VERSION=$(echo $HDF5_VERSION | $AWK -F \. {'print $3'})
+ 
+-                                                                                HDF5_tmp_flags=$(eval $H5CC -showconfig \
+-            | $GREP 'FLAGS\|Extra libraries:' \
+-            | $AWK -F: '{printf("%s "), $2}' )
+-
+-                HDF5_tmp_inst=$(eval $H5CC -showconfig \
+-            | $GREP 'Installation point:' \
+-            | $AWK '{print $NF}' )
+-
+-                HDF5_CPPFLAGS="-I${HDF5_tmp_inst}/include"
+-
+-                for arg in $HDF5_SHOW $HDF5_tmp_flags ; do
+-          case "$arg" in
+-            -I*) echo $HDF5_CPPFLAGS | $GREP -e "$arg" 2>&1 >/dev/null \
+-                  || HDF5_CPPFLAGS="$arg $HDF5_CPPFLAGS"
+-              ;;
+-            -L*) echo $HDF5_LDFLAGS | $GREP -e "$arg" 2>&1 >/dev/null \
+-                  || HDF5_LDFLAGS="$arg $HDF5_LDFLAGS"
+-              ;;
+-            -l*) echo $HDF5_LIBS | $GREP -e "$arg" 2>&1 >/dev/null \
+-                  || HDF5_LIBS="$arg $HDF5_LIBS"
+-              ;;
+-          esac
+-        done
++
++                HDF5_CPPFLAGS=$(eval pkg-config --cflags hdf5)
++                HDF5_LDFLAGS=$(eval pkg-config --libs hdf5)
+ 
+         HDF5_LIBS="$HDF5_LIBS -lhdf5"
+         { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes (version $HDF5_VERSION)" >&5
+@@ -3725,7 +3697,6 @@
+         ax_lib_hdf5_save_CPPFLAGS=$CPPFLAGS
+         ax_lib_hdf5_save_LIBS=$LIBS
+         ax_lib_hdf5_save_LDFLAGS=$LDFLAGS
+-        CC=$HDF5_CC
+         CPPFLAGS=$HDF5_CPPFLAGS
+         LIBS=$HDF5_LIBS
+         LDFLAGS=$HDF5_LDFLAGS
+@@ -3893,20 +3864,6 @@
+             with_hdf5_fortran="yes"
+ 
+ 
+-                        for arg in `$H5FC -show`
+-            do
+-              case "$arg" in #(
+-                -I*) echo $HDF5_FFLAGS | $GREP -e "$arg" >/dev/null \
+-                      || HDF5_FFLAGS="$arg $HDF5_FFLAGS"
+-                  ;;#(
+-                -L*) echo $HDF5_FFLAGS | $GREP -e "$arg" >/dev/null \
+-                      || HDF5_FFLAGS="$arg $HDF5_FFLAGS"
+-                                                               echo $HDF5_FFLAGS | $GREP -e "-I${arg#-L}" >/dev/null \
+-                      || HDF5_FFLAGS="-I${arg#-L} $HDF5_FFLAGS"
+-                  ;;
+-              esac
+-            done
+-
+                         for arg in $HDF5_LIBS
+             do
+               case "$arg" in #(
+@@ -4384,8 +4341,6 @@
+     as_fn_error $? "${GREP} does not support option -o" "$LINENO" 5
+   fi
+ 
+-  LIBS=`${H5CC} -show | ${GREP} -o " \-[lL][^[:space:]]\+" | tr "\n" " "`
+-
+ 
+     HDF5R_LIBS="${LIBS} -L. -lhdf5_hl -lhdf5 -lz -lm"
+ 
+@@ -4447,8 +4402,6 @@
+ 
+ 
+ 
+-  HDF5R_CPPFLAGS=`${H5CC} -show -c myconftest.c | ${GREP} -o "\-I[^[:space:]]\+" | tr "\n" " "`
+-
+   rm -f myconftest.c
+ fi
+ 

var/spack/repos/builtin/packages/r-hdf5r/package.py

@@ -20,21 +20,21 @@ class RHdf5r(RPackage):
     url      = "https://cloud.r-project.org/src/contrib/hdf5r_1.2.0.tar.gz"
     list_url = "https://cloud.r-project.org/src/contrib/Archive/hdf5r"
 
+    version('1.3.5',
+            sha256='87b75173ab226a9fbaa5b28289349f3c56b638629560a172994b8f9323c1622f')
     version('1.3.3', sha256='a0f83cbf21563e81dbd1a1bd8379623ed0c9c4df4e094c75013abfd7a5271545')
     version('1.2.0', sha256='58813e334fd3f9040038345a7186e5cb02090898883ac192477a76a5b8b4fe81')
 
     depends_on('r@3.2.2:', type=('build', 'run'))
     depends_on('r-r6', type=('build', 'run'))
     depends_on('r-bit64', type=('build', 'run'))
-    depends_on('hdf5@1.8.13:')
+    depends_on('hdf5@1.8.13:+hl')
+    depends_on('pkgconfig', type='build')
 
-    def configure_args(self):
-        if 'mpi' in self.spec:
-            args = [
-                '--with-hdf5={0}/h5pcc'.format(self.spec['hdf5'].prefix.bin),
-            ]
-        else:
-            args = [
-                '--with-hdf5={0}/h5cc'.format(self.spec['hdf5'].prefix.bin),
-            ]
-        return args
+    # The configure script in the package uses the hdf5 h5cc compiler wrapper
+    # in the PATH to configure hdf5. That works fine if hdf5 was built with
+    # autotools but the hdf5 package in Spack is built with cmake. The compiler
+    # wrapper built with cmake does not support the '-show' or '-showconfig'
+    # flags. The following patch replaces those commands in the configure
+    # script with pkg-config commands.
+    patch('configure.patch')