diff options
| -rw-r--r-- | var/spack/repos/builtin/packages/r-hdf5r/configure.patch | 98 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/r-hdf5r/package.py | 24 |
2 files changed, 110 insertions, 12 deletions
diff --git a/var/spack/repos/builtin/packages/r-hdf5r/configure.patch b/var/spack/repos/builtin/packages/r-hdf5r/configure.patch new file mode 100644 index 0000000000..3997edd0b2 --- /dev/null +++ b/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 + diff --git a/var/spack/repos/builtin/packages/r-hdf5r/package.py b/var/spack/repos/builtin/packages/r-hdf5r/package.py index 860270bafe..d0bb6ff8d6 100644 --- a/var/spack/repos/builtin/packages/r-hdf5r/package.py +++ b/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:') - - 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 + depends_on('hdf5@1.8.13:+hl') + depends_on('pkgconfig', type='build') + + # 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') |