Prll build fix, sanbox violation fix, #326185, LDFLAGS respected, thanks to Xarthisius providing again an exelent patch set to fix science stuff!

(Portage version: 2.2_rc67/cvs/Linux x86_64)

5 files changed, 473 insertions, 19 deletions

diff --git a/sci-chemistry/psi/ChangeLog b/sci-chemistry/psi/ChangeLog
index e470b737ad35..23732f018d8b 100644
--- a/sci-chemistry/psi/ChangeLog
+++ b/sci-chemistry/psi/ChangeLog
@@ -1,6 +1,14 @@
 # ChangeLog for sci-chemistry/psi
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/psi/ChangeLog,v 1.12 2010/06/24 21:08:01 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/psi/ChangeLog,v 1.13 2010/07/06 11:36:22 jlec Exp $
+
+*psi-3.4.0-r1 (06 Jul 2010)
+
+  06 Jul 2010; Justin Lecher <jlec@gentoo.org> +files/3.4.0-ldflags.patch,
+  -psi-3.4.0.ebuild, +files/3.4.0-man_paths.patch,
+  +files/3.4.0-parallel_fix.patch, +psi-3.4.0-r1.ebuild:
+  Prll build fix, sanbox violation fix, #326185, LDFLAGS respected, thanks
+  to Xarthisius providing the patches
 
 *psi-3.4.0 (24 Jun 2010)
 
diff --git a/sci-chemistry/psi/files/3.4.0-ldflags.patch b/sci-chemistry/psi/files/3.4.0-ldflags.patch
new file mode 100644
index 000000000000..9d7f2767e8ec
--- /dev/null
+++ b/sci-chemistry/psi/files/3.4.0-ldflags.patch
@@ -0,0 +1,21 @@
+Respect LDFLAGS
+
+--- configure.ac
++++ configure.ac
+@@ -288,15 +288,13 @@
+ )
+ AC_SUBST(LDLIBS)
+ 
+-LDFLAGS=
+ LIBDIRS=
+ AC_ARG_WITH(libdirs,
+ [  --with-libdirs          Specifies library directories (-Ldir1 -Ldir2).],
+ LIBDIRS=$withval
+-LDFLAGS=$withval
+ AC_MSG_RESULT([Using extra library directories: $withval])
+ )
+-AC_SUBST(LDFLAGS)
++AC_SUBST(LIBDIRS)
+ 
+ AC_CHECK_PROGS(PERL,perl,perl) AC_SUBST(PERL)
+ 
diff --git a/sci-chemistry/psi/files/3.4.0-man_paths.patch b/sci-chemistry/psi/files/3.4.0-man_paths.patch
new file mode 100644
index 000000000000..02cced160847
--- /dev/null
+++ b/sci-chemistry/psi/files/3.4.0-man_paths.patch
@@ -0,0 +1,25 @@
+Fix man paths
+
+http://bugs.gentoo.org/show_bug.cgi?id=326185
+
+--- src/bin/nonbonded/Makefile.in
++++ src/bin/nonbonded/Makefile.in
+@@ -19,5 +19,5 @@
+ endif
+ 
+ install_man:: nonbonded.1
+-	$(MKDIRS) $(mandir)/man1
+-	$(INSTALL_INCLUDE) $^ $(mandir)/man1
++	$(MKDIRS) $(DESTDIR)$(mandir)/man1
++	$(INSTALL_INCLUDE) $^ $(DESTDIR)$(mandir)/man1
+--- src/bin/intder/Makefile.in
++++ src/bin/intder/Makefile.in
+@@ -21,6 +21,6 @@
+ endif
+ 
+ install_man:: intder.1
+-	$(MKDIRS) $(mandir)/man1
+-	$(INSTALL_INCLUDE) $^ $(mandir)/man1
++	$(MKDIRS) $(DESTDIR)$(mandir)/man1
++	$(INSTALL_INCLUDE) $^ $(DESTDIR)$(mandir)/man1
+ 
diff --git a/sci-chemistry/psi/files/3.4.0-parallel_fix.patch b/sci-chemistry/psi/files/3.4.0-parallel_fix.patch
new file mode 100644
index 000000000000..65234fb40dcb
--- /dev/null
+++ b/sci-chemistry/psi/files/3.4.0-parallel_fix.patch
@@ -0,0 +1,400 @@
+--- Makefile.in
++++ Makefile.in
+@@ -17,62 +17,19 @@
+ INSTALL = @INSTALL@
+ INSTALL_PROGRAM = @INSTALL_PROGRAM@
+ 
+-all:
+-	for dir in $(subdirs); \
+-          do \
+-            (cd $${dir} && echo Making in $${dir} && $(MAKE) all) || exit 1; \
+-          done
+-
+-install: install_host
+-	for dir in $(subdirs); \
+-          do \
+-            (cd $${dir} && echo Making install in $${dir} && $(MAKE) install) || exit 1; \
+-          done
+-
+-install_inc:
+-	for dir in $(subdirs); \
+-          do \
+-            (cd $${dir} && echo Making install in $${dir} && $(MAKE) install_inc) || exit 1; \
+-          done
+-
+-install_man:
+-	for dir in $(subdirs); \
+-          do \
+-            (cd $${dir} && echo Making install in $${dir} && $(MAKE) install_man) || exit 1; \
+-          done
+-
+-depend:
+-	for dir in $(subdirs); \
+-          do \
+-            (cd $${dir} && echo Making depend in $${dir} && $(MAKE) depend) || exit 1; \
+-          done
+-
+-clean:
+-	for dir in $(subdirs); \
+-          do \
+-            (cd $${dir} && echo Making clean in $${dir} && $(MAKE) clean) || exit 1; \
+-          done
+-
+-dclean:
+-	for dir in $(subdirs); \
+-          do \
+-            (cd $${dir} && echo Making dclean in $${dir} && $(MAKE) dclean) || exit 1; \
+-          done
+-
+-targetclean:
+-	for dir in $(subdirs) tests doc; \
+-          do \
+-            (cd $${dir} && echo Making clean in $${dir} && $(MAKE) targetclean) || exit 1; \
+-          done
++all clean install install_inc install_man depend dclean targetclean:
++	for dir in $(subdirs); do \
++		$(MAKE) -C $$dir $@; \
++	done
+ 
+ tests:
+-	(cd tests && echo Running test suite... && $(MAKE)) || exit 1;
++	$(MAKE) -C tests
+ 
+ testsclean:
+-	(cd tests && echo Cleaning test suite... && $(MAKE) clean) || exit 1;
++	$(MAKE) -C tests clean
+ 
+ doc:
+-	(cd doc && echo Building documentation... && $(MAKE)) || exit 1;
++	$(MAKE) -C doc
+ 
+ $(top_srcdir)/configure: $(top_srcdir)/configure.ac $(top_srcdir)/aclocal.m4
+ 	cd $(top_srcdir) && autoconf
+--- lib/Makefile.in
++++ lib/Makefile.in
+@@ -31,7 +31,7 @@
+ 	$(INSTALL_DATA) $(srcdir)/psi.dat $(DESTDIR)$(pkgdatadir)
+ 	for dir in $(subdirs); \
+           do \
+-            (cd $${dir}; echo Making in $${dir}; $(MAKE) install) || exit 1; \
++            $(MAKE) -C $$dir install; \
+           done
+ 
+ install_man: macro.psi
+--- src/Makefile.in
++++ src/Makefile.in
+@@ -6,53 +6,10 @@
+ 
+ default: all
+ 
+-all:
+-	for dir in $(subdirs); \
+-          do \
+-            (cd $${dir} && echo Making in $${dir} && $(MAKE) all) || exit 1; \
+-          done
+-
+-install:
+-	for dir in $(subdirs); \
+-          do \
+-            (cd $${dir} && echo Making install in $${dir} && $(MAKE) install) || exit 1; \
+-          done
+-
+-install_inc:
+-	for dir in $(subdirs); \
+-          do \
+-            (cd $${dir} && echo Making install in $${dir} && $(MAKE) install_inc) || exit 1; \
+-          done
+-
+-install_man:
+-	for dir in $(subdirs); \
+-          do \
+-            (cd $${dir} && echo Making install in $${dir} && $(MAKE) install_man) || exit 1; \
+-          done
+-
+-depend:
+-	for dir in $(subdirs); \
+-          do \
+-            (cd $${dir} && echo Making depend in $${dir} && $(MAKE) depend) || exit 1; \
+-          done
+-
+-clean:
+-	for dir in $(subdirs); \
+-          do \
+-            (cd $${dir} && echo Making clean in $${dir} && $(MAKE) clean) || exit 1; \
+-          done
+-
+-dclean:
+-	for dir in $(subdirs); \
+-          do \
+-            (cd $${dir} && echo Making dclean in $${dir} && $(MAKE) dclean) || exit 1; \
+-          done
+-
+-targetclean:
+-	for dir in $(subdirs); \
+-          do \
+-            (cd $${dir} && echo Making clean in $${dir} && $(MAKE) targetclean) || exit 1; \
+-          done
++all clean install depend dclean targetclean:
++	for dir in $(subdirs); do \
++		$(MAKE) -C $$dir $@; \
++	done
+ 
+ top_srcdir = @top_srcdir@
+ srcdir = @srcdir@
+--- src/lib/Makefile.in
++++ src/lib/Makefile.in
+@@ -4,56 +4,10 @@
+ subdirs = libipv1 libciomr libchkpt libqt libpsio libiwl libdpd libutil \
+           liboptions libmoinfo libbasis libmints
+ 
+-all: default
+-
+-default:
+-	for dir in $(subdirs); \
+-          do \
+-            (cd $${dir} && echo ... Making in $${dir} ... && $(MAKE) default) || exit 1; \
+-          done
+-
+-install:
+-	for dir in $(subdirs); \
+-          do \
+-            (cd $${dir} && echo ... Making install in $${dir} ... && $(MAKE) install) || exit 1; \
+-          done
+-
+-install_inc:
+-	for dir in $(subdirs); \
+-          do \
+-            (cd $${dir} && echo ... Making install in $${dir} ... && $(MAKE) install_inc) || exit 1; \
+-          done
+-
+-install_man:
+-	for dir in $(subdirs); \
+-          do \
+-            (cd $${dir} && echo ... Making install in $${dir} ... && $(MAKE) install_man) || exit 1; \
+-          done
+-
+-depend:
+-	for dir in $(subdirs); \
+-          do \
+-            (cd $${dir} && echo ... Making depend in $${dir} ... && $(MAKE) depend) || exit 1; \
+-          done
+-
+-clean:
+-	for dir in $(subdirs); \
+-          do \
+-            (cd $${dir} && echo ... Making clean in $${dir} ... && $(MAKE) clean) || exit 1; \
+-          done
+-
+-dclean:
+-	for dir in $(subdirs); \
+-          do \
+-            (cd $${dir} && echo ... Making dclean in $${dir} ... && $(MAKE) dclean) || exit 1; \
+-          done
+-
+-targetclean:
+-	for dir in $(subdirs); \
+-          do \
+-            (cd $${dir} && echo ... Making clean in $${dir} ... && $(MAKE) targetclean) || exit 1; \
+-          done
+-
++all clean install install_inc install_man depend dclean targetclean:
++	for dir in $(subdirs); do \
++		$(MAKE) -C $$dir $@; \
++	done
+ 
+ #
+ # keep the configuration information and makefile up-to-date
+--- src/bin/Makefile.in
++++ src/bin/Makefile.in
+@@ -13,55 +13,10 @@
+ subdirs += psirb
+ endif
+ 
+-all: default
+-
+-default:
+-	for dir in $(subdirs); \
+-          do \
+-            (cd $${dir} && echo ... Making in $${dir} ... && $(MAKE) default) || exit 1; \
+-          done
+-
+-install:
+-	for dir in $(subdirs); \
+-          do \
+-            (cd $${dir} && echo ... Making install in $${dir} ... && $(MAKE) install) || exit 1; \
+-          done
+-
+-install_inc:
+-	for dir in $(subdirs); \
+-          do \
+-            (cd $${dir} && echo ... Making install in $${dir} ... && $(MAKE) install_inc) || exit 1; \
+-          done
+-
+-install_man:
+-	for dir in $(subdirs); \
+-          do \
+-            (cd $${dir} && echo ... Making install in $${dir} ... && $(MAKE) install_man) || exit 1; \
+-          done
+-
+-depend:
+-	for dir in $(subdirs); \
+-          do \
+-            (cd $${dir} && echo ... Making depend in $${dir} ... && $(MAKE) depend) || exit 1; \
+-          done
+-
+-clean:
+-	for dir in $(subdirs); \
+-          do \
+-            (cd $${dir} && echo ... Making clean in $${dir} ... && $(MAKE) clean) || exit 1; \
+-          done
+-
+-dclean:
+-	for dir in $(subdirs); \
+-          do \
+-            (cd $${dir} && echo ... Making dclean in $${dir} ... && $(MAKE) dclean) || exit 1; \
+-          done
+-
+-targetclean:
+-	for dir in $(subdirs); \
+-          do \
+-            (cd $${dir} && echo ... Making clean in $${dir} ... && $(MAKE) targetclean) || exit 1; \
+-          done
++all install depend clean dclean targetclean:
++	for dir in $(subdirs); do \
++		$(MAKE) -C $$dir $@; \
++	done
+ 
+ top_srcdir = @top_srcdir@
+ srcdir = @srcdir@
+--- src/samples/Makefile.in
++++ src/samples/Makefile.in
+@@ -5,55 +5,10 @@
+ 
+ subdirs = mints
+ 
+-all: default
+-
+-default:
+-	for dir in $(subdirs); \
+-          do \
+-            (cd $${dir} && echo ... Making in $${dir} ... && $(MAKE) default) || exit 1; \
+-          done
+-
+-install:
+-	for dir in $(subdirs); \
+-          do \
+-            (cd $${dir} && echo ... Making install in $${dir} ... && $(MAKE) install) || exit 1; \
+-          done
+-
+-install_inc:
+-	for dir in $(subdirs); \
+-          do \
+-            (cd $${dir} && echo ... Making install in $${dir} ... && $(MAKE) install_inc) || exit 1; \
+-          done
+-
+-install_man:
+-	for dir in $(subdirs); \
+-          do \
+-            (cd $${dir} && echo ... Making install in $${dir} ... && $(MAKE) install_man) || exit 1; \
+-          done
+-
+-depend:
+-	for dir in $(subdirs); \
+-          do \
+-            (cd $${dir} && echo ... Making depend in $${dir} ... && $(MAKE) depend) || exit 1; \
+-          done
+-
+-clean:
+-	for dir in $(subdirs); \
+-          do \
+-            (cd $${dir} && echo ... Making clean in $${dir} ... && $(MAKE) clean) || exit 1; \
+-          done
+-
+-dclean:
+-	for dir in $(subdirs); \
+-          do \
+-            (cd $${dir} && echo ... Making dclean in $${dir} ... && $(MAKE) dclean) || exit 1; \
+-          done
+-
+-targetclean:
+-	for dir in $(subdirs); \
+-          do \
+-            (cd $${dir} && echo ... Making clean in $${dir} ... && $(MAKE) targetclean) || exit 1; \
+-          done
++all install depend clean dclean targetclean:
++	for dir in $(subdirs); do \
++		$(MAKE) -C $$dir $@; \
++	done
+ 
+ top_srcdir = @top_srcdir@
+ srcdir = @srcdir@
+--- src/util/Makefile.in
++++ src/util/Makefile.in
+@@ -3,55 +3,10 @@
+ 
+ subdirs = tocprint psi2molden
+ 
+-all: default
+-
+-default:
+-	for dir in $(subdirs); \
+-          do \
+-            (cd $${dir} && echo ... Making in $${dir} ... && $(MAKE) default) || exit 1; \
+-          done
+-
+-install:
+-	for dir in $(subdirs); \
+-          do \
+-            (cd $${dir} && echo ... Making install in $${dir} ... && $(MAKE) install) || exit 1; \
+-          done
+-
+-install_inc:
+-	for dir in $(subdirs); \
+-          do \
+-            (cd $${dir} && echo ... Making install in $${dir} ... && $(MAKE) install_inc) || exit 1; \
+-          done
+-
+-install_man:
+-	for dir in $(subdirs); \
+-          do \
+-            (cd $${dir} && echo ... Making install in $${dir} ... && $(MAKE) install_man) || exit 1; \
+-          done
+-
+-depend:
+-	for dir in $(subdirs); \
+-          do \
+-            (cd $${dir} && echo ... Making depend in $${dir} ... && $(MAKE) depend) || exit 1; \
+-          done
+-
+-clean:
+-	for dir in $(subdirs); \
+-          do \
+-            (cd $${dir} && echo ... Making clean in $${dir} ... && $(MAKE) clean) || exit 1; \
+-          done
+-
+-dclean:
+-	for dir in $(subdirs); \
+-          do \
+-            (cd $${dir} && echo ... Making dclean in $${dir} ... && $(MAKE) dclean) || exit 1; \
+-          done
+-
+-targetclean:
+-	for dir in $(subdirs); \
+-          do \
+-            (cd $${dir} && echo ... Making clean in $${dir} ... && $(MAKE) targetclean) || exit 1; \
+-          done
++all install depend clean dclean targetclean:
++	for dir in $(subdirs); do \
++		$(MAKE) -C $$dir $@; \
++	done
+ 
+ top_srcdir = @top_srcdir@
+ srcdir = @srcdir@
+--- src/lib/libipv1/Makefile.in
++++ src/lib/libipv1/Makefile.in
+@@ -58,4 +58,4 @@
+ # in case DODEPEND is no
+ #
+ 
+-ip_read.o: y.tab.h
++ip_read.o: y.tab.c y.tab.h
diff --git a/sci-chemistry/psi/psi-3.4.0.ebuild b/sci-chemistry/psi/psi-3.4.0-r1.ebuild
index 1d80d075dc69..55785e8a3be9 100644
--- a/sci-chemistry/psi/psi-3.4.0.ebuild
+++ b/sci-chemistry/psi/psi-3.4.0-r1.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2010 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/psi/psi-3.4.0.ebuild,v 1.1 2010/06/24 21:08:01 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/psi/psi-3.4.0-r1.ebuild,v 1.1 2010/07/06 11:36:22 jlec Exp $
 
 EAPI="3"
 
@@ -27,17 +27,24 @@ DEPEND="${RDEPEND}
 S="${WORKDIR}/${PN}${PV:0:1}"
 
 src_prepare() {
-	epatch "${FILESDIR}"/${PV}-dont-build-libint.patch
-	epatch "${FILESDIR}"/use-external-libint.patch
-	epatch "${FILESDIR}"/${PV}-gcc-4.3.patch
-	epatch "${FILESDIR}"/${PV}-destdir.patch
-	epatch "${FILESDIR}"/${P}-parallel-make.patch
-	sed "s:^LDFLAGS=:LDFLAGS=${LDFLAGS}:g" -i configure.ac || die
+	epatch "${FILESDIR}"/${PV}-dont-build-libint.patch \
+		"${FILESDIR}"/use-external-libint.patch \
+		"${FILESDIR}"/${PV}-gcc-4.3.patch \
+		"${FILESDIR}"/${PV}-destdir.patch \
+		"${FILESDIR}"/${P}-parallel-make.patch \
+		"${FILESDIR}"/${PV}-man_paths.patch \
+		"${FILESDIR}"/${PV}-ldflags.patch \
+		"${FILESDIR}"/${PV}-parallel_fix.patch
+
 	# Broken test
 	sed \
 		-e 's:scf-mvd-opt ::g' \
 		-e 's:scf-mvd-opt-puream ::g' \
 		-i tests/Makefile.in || die
+
+	sed \
+		-e "/LIBPATTERNS/d" \
+		-i src/{bin,util,samples}/MakeVars.in || die
 	eautoreconf
 }
 
@@ -46,26 +53,19 @@ src_configure() {
 	unset CLIBS
 
 	econf \
-		--with-opt="${CFLAGS}" \
+		--with-opt="${CXXFLAGS}" \
 		--datadir="${EPREFIX}"/usr/share/${PN} \
 		--with-blas="$(pkg-config blas --libs)"
 }
 
 src_compile() {
-	emake -j1 \
-		SCRATCH="${WORKDIR}/libint" \
-		|| die "make failed"
+	emake SCRATCH="${WORKDIR}/libint" DODEPEND="no" || die
 }
 
 src_test() {
-	emake \
-		EXECDIR="${S}"/bin \
-		TESTFLAGS="" \
-		-j1 tests || die
+	emake EXECDIR="${S}"/bin TESTFLAGS="" -j1 tests || die
 }
 
 src_install() {
-	emake -j1 \
-		DESTDIR="${D}" \
-		install || die "install failed"
+	emake DESTDIR="${D}" DODEPEND="no" install || die
 }