sys-cluster/parallel-netcdf: restrict tests, respect flags

Closes: https://bugs.gentoo.org/835036
Closes: https://bugs.gentoo.org/815742
Closes: https://bugs.gentoo.org/815739
Signed-off-by: Alessandro Barbieri <lssndrbarbieri@gmail.com>

sys-cluster/parallel-netcdf/files/parallel-netcdf-1.12.2-no-DESTDIR-for-info-clarity.patch

@@ -0,0 +1,55 @@
+--- a/Makefile.am
++++ b/Makefile.am
+@@ -65,40 +65,40 @@
+ 	@echo '+----------------------------------------------------------------------------+'
+ 	@echo '|'
+ 	@echo '|  PnetCDF has been successfully installed under'
+-	@echo '|          $(DESTDIR)$(prefix)'
++	@echo '|          $(prefix)'
+ 	@echo '|'
+ 	@echo '|  * PnetCDF header files have been installed in'
+-	@echo '|          $(DESTDIR)$(prefix)/include'
++	@echo '|          $(prefix)/include'
+ 	@echo '|  * PnetCDF library files have been installed in'
+-	@echo '|          $(DESTDIR)$(exec_prefix)/lib'
++	@echo '|          $(exec_prefix)/lib'
+ 	@echo '|  * PnetCDF utility programs have been installed in'
+-	@echo '|          $(DESTDIR)$(exec_prefix)/bin'
++	@echo '|          $(exec_prefix)/bin'
+ 	@echo '|  * PnetCDF man pages have been installed in'
+-	@echo '|          $(DESTDIR)$(prefix)/share/man'
++	@echo '|          $(prefix)/share/man'
+ 	@echo '|'
+ 	@echo '|  To compile your PnetCDF programs, please add the following to the command'
+ 	@echo '|  line, so the compiler can find the PnetCDF header files:'
+-	@echo '|      -I$(DESTDIR)$(prefix)/include'
++	@echo '|      -I$(prefix)/include'
+ 	@echo '|'
+ 	@if test "x$(has_fortran)" = xyes -a 'x$(FC_MODINC)' != 'x-I' ; then \
+ 	 echo '|  Add the following line to compile your Fortran programs' ; \
+-	 echo '|      $(FC_MODINC)$(DESTDIR)$(prefix)/include' ; \
++	 echo '|      $(FC_MODINC)$(prefix)/include' ; \
+ 	 echo '|' ; \
+ 	fi
+ 	@echo '|  Add the following line to link your program to PnetCDF library:'
+-	@echo '|      -L$(DESTDIR)$(exec_prefix)/lib -lpnetcdf'
++	@echo '|      -L$(exec_prefix)/lib -lpnetcdf'
+ 	@echo '|'
+ 	@if test "x$(enable_shared)" = xyes ; then \
+ 	 echo '|  Add the following to your run-time environment variable LD_LIBRARY_PATH,' ; \
+ 	 echo '|  when linking your executable with the PnetCDF shared libraries.' ; \
+          if test "x$(enable_netcdf4)" = xyes -a "x$(enable_adios)" = xyes ; then \
+-         echo '|      $(DESTDIR)$(exec_prefix)/lib:$(netcdf4_libdir):$(adios_libdir)' ; \
++         echo '|      $(exec_prefix)/lib:$(netcdf4_libdir):$(adios_libdir)' ; \
+          elif test "x$(enable_netcdf4)" = xyes ; then \
+-         echo '|      $(DESTDIR)$(exec_prefix)/lib:$(netcdf4_libdir)' ; \
++         echo '|      $(exec_prefix)/lib:$(netcdf4_libdir)' ; \
+          elif test "x$(enable_adios)" = xyes ; then \
+-         echo '|      $(DESTDIR)$(exec_prefix)/lib:$(adios_libdir)' ; \
++         echo '|      $(exec_prefix)/lib:$(adios_libdir)' ; \
+          else \
+-	 echo '|      $(DESTDIR)$(exec_prefix)/lib' ; \
++	 echo '|      $(exec_prefix)/lib' ; \
+ 	 fi ; \
+ 	 echo '|' ; \
+ 	fi

sys-cluster/parallel-netcdf/files/parallel-netcdf-1.12.2-respect-flags.patch

@@ -0,0 +1,44 @@
+--- a/src/utils/ncmpidiff/Makefile.am
++++ b/src/utils/ncmpidiff/Makefile.am
+@@ -18,7 +18,7 @@
+ cdfdiff_SOURCES = cdfdiff.c
+ 
+ cdfdiff$(EXEEXT): cdfdiff.c Makefile
+-	$(SEQ_CC) -I$(top_srcdir)/src/utils/ncvalidator -o $@ $<
++	$(SEQ_CC) $(CFLAGS) $(LDFLAGS) -PIE -I$(top_srcdir)/src/utils/ncvalidator -o $@ $<
+ 
+ $(top_builddir)/src/libs/libpnetcdf.la:
+ 	set -e; cd $(top_builddir)/src/libs && $(MAKE) $(MFLAGS)
+--- a/src/utils/ncoffsets/Makefile.am
++++ b/src/utils/ncoffsets/Makefile.am
+@@ -10,7 +10,7 @@
+ EXTRA_DIST = ncoffsets.c
+ 
+ ncoffsets$(EXEEXT): ncoffsets.c
+-	$(SEQ_CC) -o $@ $<
++	$(SEQ_CC) $(CFLAGS) $(LDFLAGS) -PIE -o $@ $<
+ 
+ dist_man_MANS = ncoffsets.1
+ 
+--- a/src/utils/ncvalidator/Makefile.am
++++ b/src/utils/ncvalidator/Makefile.am
+@@ -76,7 +76,7 @@
+ TST_HDF5_FILES = pad_superblock.h5
+ 
+ ncvalidator$(EXEEXT): ncvalidator.c Makefile
+-	$(SEQ_CC) -o $@ $<
++	$(SEQ_CC) $(CFLAGS) $(LDFLAGS) -PIE -o $@ $<
+ 
+ # autimake 1.11.3 has not yet implemented AM_TESTS_ENVIRONMENT
+ # For newer versions, we can use AM_TESTS_ENVIRONMENT instead
+--- a/src/utils/pnetcdf_version/Makefile.am
++++ b/src/utils/pnetcdf_version/Makefile.am
+@@ -22,7 +22,7 @@
+ endif
+ 
+ pnetcdf_version$(EXEEXT): pnetcdf_version.c
+-	$(SEQ_CC) $(XDEFS) -o $@ $<
++	$(SEQ_CC) $(CFLAGS) $(LDFLAGS) -PIE $(XDEFS) -o $@ $<
+ 
+ dist_man_MANS = pnetcdf_version.1
+ 

sys-cluster/parallel-netcdf/parallel-netcdf-1.12.2.ebuild

@@ -36,6 +36,12 @@ BDEPEND="
 	)
 "
 
+RESTRICT="test" # tests require MPI set up
+PATCHES=(
+	"${FILESDIR}/${P}-no-DESTDIR-for-info-clarity.patch"
+	"${FILESDIR}/${P}-respect-flags.patch"
+)
+
 pkg_setup() {
 	fortran-2_pkg_setup
 }