Version Bump, #279566

Package-Manager: portage-2.2_rc67/cvs/Linux x86_64

6 files changed, 445 insertions, 1 deletions

diff --git a/sci-chemistry/psi/ChangeLog b/sci-chemistry/psi/ChangeLog
index 1d54fe968846..e470b737ad35 100644
--- a/sci-chemistry/psi/ChangeLog
+++ b/sci-chemistry/psi/ChangeLog
@@ -1,6 +1,13 @@
 # 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 1.11 2010/02/26 02:44:04 markusle Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/psi/ChangeLog,v 1.12 2010/06/24 21:08:01 jlec Exp $
+
+*psi-3.4.0 (24 Jun 2010)
+
+  24 Jun 2010; Justin Lecher <jlec@gentoo.org> +files/3.4.0-destdir.patch,
+  +psi-3.4.0.ebuild, +files/psi-3.4.0-parallel-make.patch,
+  +files/3.4.0-dont-build-libint.patch, +files/3.4.0-gcc-4.3.patch:
+  Version Bump, #279566
 
   26 Feb 2010; Markus Dittrich <markusle@gentoo.org> psi-3.2.3.ebuild:
   Fixed some QA issues.
diff --git a/sci-chemistry/psi/files/3.4.0-destdir.patch b/sci-chemistry/psi/files/3.4.0-destdir.patch
new file mode 100644
index 000000000000..45db9529aa4d
--- /dev/null
+++ b/sci-chemistry/psi/files/3.4.0-destdir.patch
@@ -0,0 +1,41 @@
+diff --git a/Makefile.in b/Makefile.in
+index aca5a16..2e49f0a 100644
+--- a/Makefile.in
++++ b/Makefile.in
+@@ -8,6 +8,7 @@ subdirs = lib include src
+ 
+ top_srcdir = @top_srcdir@
+ srcdir = @srcdir@
++datarootdir = @datarootdir@
+ VPATH = @srcdir@
+ top_objdir = .
+ 
+diff --git a/lib/ruby/Makefile.in b/lib/ruby/Makefile.in
+index b31ce7f..e099e1b 100644
+--- a/lib/ruby/Makefile.in
++++ b/lib/ruby/Makefile.in
+@@ -29,10 +29,10 @@ ccenergy.rb    cclambda.rb    chkpt.rb       color.rb       deriv2.rb      frequ
+ cceom.rb       ccsort.rb      cints.rb       cphf.rb        detci.rb       input.rb       optking.rb     psi3.rb        testcases.rb 
+ 
+ install: $(RUBYSRC)
+-	$(MKDIRS) $(rubydatadir)
++	$(MKDIRS) $(DESTDIR)/$(rubydatadir)
+ 	for rbfile in $(RUBYSRC); \
+           do \
+-            ($(INSTALL_DATA) $(srcdir)/$${rbfile} $(rubydatadir)) || exit 1; \
++            ($(INSTALL_DATA) $(srcdir)/$${rbfile} $(DESTDIR)/$(rubydatadir)) || exit 1; \
+           done
+ 
+ install_man: 
+diff --git a/src/bin/Makefile.in b/src/bin/Makefile.in
+index e1abb46..4eddf8d 100644
+--- a/src/bin/Makefile.in
++++ b/src/bin/Makefile.in
+@@ -65,6 +65,7 @@ targetclean:
+ 
+ top_srcdir = @top_srcdir@
+ srcdir = @srcdir@
++datarootdir = @datarootdir@
+ top_objdir = ../..
+ 
+ $(top_srcdir)/configure: $(top_srcdir)/configure.ac $(top_srcdir)/aclocal.m4
diff --git a/sci-chemistry/psi/files/3.4.0-dont-build-libint.patch b/sci-chemistry/psi/files/3.4.0-dont-build-libint.patch
new file mode 100644
index 000000000000..0d65cee8a1a9
--- /dev/null
+++ b/sci-chemistry/psi/files/3.4.0-dont-build-libint.patch
@@ -0,0 +1,13 @@
+diff --git a/src/lib/Makefile.in b/src/lib/Makefile.in
+index 42e025d..b098a36 100644
+--- a/src/lib/Makefile.in
++++ b/src/lib/Makefile.in
+@@ -2,7 +2,7 @@
+ .PHONY:	default all install depend clean dclean targetclean
+ 
+ subdirs = libipv1 libciomr libchkpt libqt libpsio libiwl libdpd libutil \
+-          liboptions libmoinfo libint libderiv libr12 libbasis libmints
++          liboptions libmoinfo libbasis libmints
+ 
+ all: default
+ 
diff --git a/sci-chemistry/psi/files/3.4.0-gcc-4.3.patch b/sci-chemistry/psi/files/3.4.0-gcc-4.3.patch
new file mode 100644
index 000000000000..8283e6d8d8ea
--- /dev/null
+++ b/sci-chemistry/psi/files/3.4.0-gcc-4.3.patch
@@ -0,0 +1,293 @@
+diff --git a/src/bin/mcscf/block_matrix.cc b/src/bin/mcscf/block_matrix.cc
+index fe1e131..3ad0bcd 100644
+--- a/src/bin/mcscf/block_matrix.cc
++++ b/src/bin/mcscf/block_matrix.cc
+@@ -1,6 +1,7 @@
+ #include "block_matrix.h"
+ #include "matrix_base.h"
+ #include "memory_manager.h"
++#include <cstdio>
+ 
+ extern FILE* outfile;
+ 
+diff --git a/src/bin/mcscf/block_vector.cc b/src/bin/mcscf/block_vector.cc
+index fb383c7..36f55d4 100644
+--- a/src/bin/mcscf/block_vector.cc
++++ b/src/bin/mcscf/block_vector.cc
+@@ -1,6 +1,7 @@
+ #include "block_vector.h"
+ #include "vector_base.h"
+ #include "memory_manager.h"
++#include <cstdio>
+ 
+ extern FILE* outfile;
+ 
+diff --git a/src/bin/mcscf/sblock_matrix.cc b/src/bin/mcscf/sblock_matrix.cc
+index 61aa7cc..4da4263 100644
+--- a/src/bin/mcscf/sblock_matrix.cc
++++ b/src/bin/mcscf/sblock_matrix.cc
+@@ -1,4 +1,5 @@
+ #include <cstdlib>
++#include <cstdio>
+ #include <psifiles.h>
+ #include "sblock_matrix.h"
+ 
+@@ -103,4 +104,4 @@ void SBlockMatrix::check(const char* cstr)
+   }
+ }
+ 
+-}}
+\ No newline at end of file
++}}
+diff --git a/src/bin/mcscf/sblock_vector.cc b/src/bin/mcscf/sblock_vector.cc
+index 63c3926..f24fc5b 100644
+--- a/src/bin/mcscf/sblock_vector.cc
++++ b/src/bin/mcscf/sblock_vector.cc
+@@ -1,4 +1,5 @@
+ #include <cstdlib>
++#include <cstdio>
+ #include <psifiles.h>
+ 
+ #include "sblock_vector.h"
+@@ -58,4 +59,4 @@ void SBlockVector::check(const char* cstr)
+   }
+ }
+ 
+-}}
+\ No newline at end of file
++}}
+diff --git a/src/bin/mcscf/scf.cc b/src/bin/mcscf/scf.cc
+index 77318fd..7d1e17f 100644
+--- a/src/bin/mcscf/scf.cc
++++ b/src/bin/mcscf/scf.cc
+@@ -5,6 +5,7 @@
+ 
+ #include <iostream>
+ #include <cmath>
++#include <cstdio>
+ 
+ extern FILE* outfile;
+ 
+diff --git a/src/bin/mcscf/scf_Feff.cc b/src/bin/mcscf/scf_Feff.cc
+index 584aa83..8a99c3b 100644
+--- a/src/bin/mcscf/scf_Feff.cc
++++ b/src/bin/mcscf/scf_Feff.cc
+@@ -1,4 +1,5 @@
+ #include <liboptions/liboptions.h>
++#include <cstdio>
+ 
+ #include "scf.h"
+ 
+diff --git a/src/bin/mcscf/scf_canonicalize_MO.cc b/src/bin/mcscf/scf_canonicalize_MO.cc
+index a2b3915..96bb6cc 100644
+--- a/src/bin/mcscf/scf_canonicalize_MO.cc
++++ b/src/bin/mcscf/scf_canonicalize_MO.cc
+@@ -1,6 +1,7 @@
+ #include "scf.h"
+ 
+ #include <liboptions/liboptions.h>
++#include <cstdio>
+ 
+ namespace psi{ namespace mcscf{
+ 
+diff --git a/src/bin/mcscf/scf_check_orthonormality.cc b/src/bin/mcscf/scf_check_orthonormality.cc
+index 63fbbbb..a13436c 100644
+--- a/src/bin/mcscf/scf_check_orthonormality.cc
++++ b/src/bin/mcscf/scf_check_orthonormality.cc
+@@ -1,5 +1,6 @@
+ #include <iostream>
+ #include <cmath>
++#include <cstdio>
+ 
+ #include "scf.h"
+ 
+diff --git a/src/bin/mcscf/scf_compute_energy.cc b/src/bin/mcscf/scf_compute_energy.cc
+index fe7ee6d..20194eb 100644
+--- a/src/bin/mcscf/scf_compute_energy.cc
++++ b/src/bin/mcscf/scf_compute_energy.cc
+@@ -1,4 +1,5 @@
+ #include <iostream>
++#include <cstdio>
+ 
+ #include "scf.h"
+ 
+diff --git a/src/bin/mcscf/scf_diis.cc b/src/bin/mcscf/scf_diis.cc
+index 9bcde15..261492a 100644
+--- a/src/bin/mcscf/scf_diis.cc
++++ b/src/bin/mcscf/scf_diis.cc
+@@ -1,4 +1,5 @@
+ #include <iostream>
++#include <cstdio>
+ 
+ #include <liboptions/liboptions.h>
+ 
+diff --git a/src/bin/mcscf/scf_iterate_scf_equations.cc b/src/bin/mcscf/scf_iterate_scf_equations.cc
+index 9e96360..3a3acc3 100644
+--- a/src/bin/mcscf/scf_iterate_scf_equations.cc
++++ b/src/bin/mcscf/scf_iterate_scf_equations.cc
+@@ -1,6 +1,7 @@
+ #include <cstdlib>
+ #include <iostream>
+ #include <cmath>
++#include <cstdio>
+ 
+ #include <liboptions/liboptions.h>
+ 
+diff --git a/src/bin/mcscf/scf_pairs.cc b/src/bin/mcscf/scf_pairs.cc
+index b0a8c9d..af5fc35 100644
+--- a/src/bin/mcscf/scf_pairs.cc
++++ b/src/bin/mcscf/scf_pairs.cc
+@@ -1,4 +1,5 @@
+ #include <iostream>
++#include <cstdio>
+ 
+ #include <libmoinfo/libmoinfo.h>
+ 
+diff --git a/src/bin/mcscf/scf_print_eigenvectors_and_MO.cc b/src/bin/mcscf/scf_print_eigenvectors_and_MO.cc
+index 3aac92a..e28e9e3 100644
+--- a/src/bin/mcscf/scf_print_eigenvectors_and_MO.cc
++++ b/src/bin/mcscf/scf_print_eigenvectors_and_MO.cc
+@@ -3,6 +3,7 @@
+ #include <string>
+ #include <utility>
+ #include <algorithm>
++#include <cstdio>
+ 
+ #include <libmoinfo/libmoinfo.h>
+ 
+diff --git a/src/bin/psimrcc/blas_algorithms.cc b/src/bin/psimrcc/blas_algorithms.cc
+index bb36025..0a5a3e2 100644
+--- a/src/bin/psimrcc/blas_algorithms.cc
++++ b/src/bin/psimrcc/blas_algorithms.cc
+@@ -1,5 +1,6 @@
+ #include <libmoinfo/libmoinfo.h>
+ #include <libutil/libutil.h>
++#include <cstdio>
+ 
+ #include "blas.h"
+ #include "memory_manager.h"
+diff --git a/src/bin/psimrcc/blas_compatibile.cc b/src/bin/psimrcc/blas_compatibile.cc
+index 8de6d73..7caf4f3 100644
+--- a/src/bin/psimrcc/blas_compatibile.cc
++++ b/src/bin/psimrcc/blas_compatibile.cc
+@@ -1,6 +1,7 @@
+ #include "blas.h"
+ #include <libutil/libutil.h>
+ #include <cstdlib>
++#include <cstdio>
+ 
+ extern FILE *infile, *outfile;
+ 
+diff --git a/src/bin/psimrcc/blas_parser.cc b/src/bin/psimrcc/blas_parser.cc
+index d211a24..78fe60a 100644
+--- a/src/bin/psimrcc/blas_parser.cc
++++ b/src/bin/psimrcc/blas_parser.cc
+@@ -3,6 +3,7 @@
+ #include "debugging.h"
+ #include <libutil/libutil.h>
+ #include <algorithm>
++#include <cstdio>
+ 
+ namespace psi{ namespace psimrcc{
+ 
+diff --git a/src/bin/psimrcc/blas_solve.cc b/src/bin/psimrcc/blas_solve.cc
+index b138a5b..f5dcdfc 100644
+--- a/src/bin/psimrcc/blas_solve.cc
++++ b/src/bin/psimrcc/blas_solve.cc
+@@ -1,6 +1,7 @@
+ #include "blas.h"
+ #include "debugging.h"
+ #include <libmoinfo/libmoinfo.h>
++#include <cstdio>
+ 
+ namespace psi{ namespace psimrcc{
+ 
+diff --git a/src/bin/psimrcc/index.cc b/src/bin/psimrcc/index.cc
+index 3465d88..68c2b77 100644
+--- a/src/bin/psimrcc/index.cc
++++ b/src/bin/psimrcc/index.cc
+@@ -5,6 +5,7 @@
+  ***************************************************************************/
+ #include <iostream>
+ #include <algorithm>
++#include <cstdio>
+ 
+ #include <libmoinfo/libmoinfo.h>
+ 
+diff --git a/src/bin/psimrcc/operation.cc b/src/bin/psimrcc/operation.cc
+index edbaed5..f4e881f 100644
+--- a/src/bin/psimrcc/operation.cc
++++ b/src/bin/psimrcc/operation.cc
+@@ -7,6 +7,7 @@
+ #include "debugging.h"
+ #include "blas.h"
+ #include <libutil/libutil.h>
++#include <cstdio>
+ 
+ namespace psi{ namespace psimrcc{
+ 
+diff --git a/src/bin/psimrcc/operation_compute.cc b/src/bin/psimrcc/operation_compute.cc
+index 7d2553c..72a1b39 100644
+--- a/src/bin/psimrcc/operation_compute.cc
++++ b/src/bin/psimrcc/operation_compute.cc
+@@ -11,6 +11,7 @@
+ #include "algebra_interface.h"
+ #include <libmoinfo/libmoinfo.h>
+ #include <cstdlib>
++#include <cstdio>
+ 
+ extern FILE *infile, *outfile;
+ 
+diff --git a/src/bin/psimrcc/sort_out_of_core.cc b/src/bin/psimrcc/sort_out_of_core.cc
+index 3f255c9..8fa31a3 100644
+--- a/src/bin/psimrcc/sort_out_of_core.cc
++++ b/src/bin/psimrcc/sort_out_of_core.cc
+@@ -8,6 +8,7 @@
+ #include "sort.h"
+ #include "matrix.h"
+ #include <libmoinfo/libmoinfo.h>
++#include <cstdio>
+ 
+ extern FILE* outfile;
+ 
+diff --git a/src/lib/libmoinfo/moinfo_model_space.cc b/src/lib/libmoinfo/moinfo_model_space.cc
+index 3bf2030..0a63cde 100644
+--- a/src/lib/libmoinfo/moinfo_model_space.cc
++++ b/src/lib/libmoinfo/moinfo_model_space.cc
+@@ -1,6 +1,7 @@
+ #include <iostream>
+ #include <cmath>
+ #include <cstdlib>
++#include <cstdio>
+ 
+ #include <psifiles.h>
+ #include <liboptions/liboptions.h>
+@@ -322,4 +323,4 @@ vector<string> MOInfo::get_matrix_names(std::string str)
+   return(names);
+ }
+ 
+-}
+\ No newline at end of file
++}
+diff --git a/src/lib/libmoinfo/moinfo_slaterdeterminant.cc b/src/lib/libmoinfo/moinfo_slaterdeterminant.cc
+index 8831cd5..a046679 100644
+--- a/src/lib/libmoinfo/moinfo_slaterdeterminant.cc
++++ b/src/lib/libmoinfo/moinfo_slaterdeterminant.cc
+@@ -1,4 +1,5 @@
+ #include <iostream>
++#include <cstdio>
+ #include "moinfo.h"
+ 
+ extern FILE *infile, *outfile;
+diff --git a/src/lib/libutil/stl_string.cc b/src/lib/libutil/stl_string.cc
+index 0ec247d..f719dcd 100644
+--- a/src/lib/libutil/stl_string.cc
++++ b/src/lib/libutil/stl_string.cc
+@@ -2,6 +2,7 @@
+ #include <cmath>
+ #include <iomanip>
+ #include <algorithm>
++#include <cstdio>
+ 
+ #include "libutil.h"
+ 
diff --git a/sci-chemistry/psi/files/psi-3.4.0-parallel-make.patch b/sci-chemistry/psi/files/psi-3.4.0-parallel-make.patch
new file mode 100644
index 000000000000..2805cb195e24
--- /dev/null
+++ b/sci-chemistry/psi/files/psi-3.4.0-parallel-make.patch
@@ -0,0 +1,19 @@
+diff --git a/src/lib/libipv1/Makefile.in b/src/lib/libipv1/Makefile.in
+index eafe8e2..141bf3b 100644
+--- a/src/lib/libipv1/Makefile.in
++++ b/src/lib/libipv1/Makefile.in
+@@ -33,10 +33,12 @@ LIBOBJ = $(ALLCSRC:%.c=%.o) $(ALLCXXSRC:%.cc=%.o)
+ 
+ include ../MakeRules
+ 
+-y.tab.c y.tab.h: parse.y
++y.tab.h: y.tab.c
++
++y.tab.c: parse.y
+ 	$(YACC) -v -d $<
+ 
+-scan.c: scan.l
++scan.c: scan.l y.tab.h
+ 	$(LEX) -t $^ > scan.c
+ 
+ install_inc:: $(ALLINCLUDE)
diff --git a/sci-chemistry/psi/psi-3.4.0.ebuild b/sci-chemistry/psi/psi-3.4.0.ebuild
new file mode 100644
index 000000000000..1d80d075dc69
--- /dev/null
+++ b/sci-chemistry/psi/psi-3.4.0.ebuild
@@ -0,0 +1,71 @@
+# 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 $
+
+EAPI="3"
+
+inherit autotools eutils
+
+DESCRIPTION="Suite of ab initio quantum chemistry programs to compute various molecular properties"
+HOMEPAGE="http://www.psicode.org/"
+SRC_URI="mirror://sourceforge/psicode/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+
+# File collision, see bug #249423
+RDEPEND="
+	!sci-visualization/extrema
+	virtual/blas
+	virtual/lapack
+	>=sci-libs/libint-1.1.4"
+DEPEND="${RDEPEND}
+	test? ( dev-lang/perl )"
+
+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=${LDFLAGS}:g" -i configure.ac || die
+	# Broken test
+	sed \
+		-e 's:scf-mvd-opt ::g' \
+		-e 's:scf-mvd-opt-puream ::g' \
+		-i tests/Makefile.in || die
+	eautoreconf
+}
+
+src_configure() {
+	# This variable gets set sometimes to /usr/lib/src and breaks stuff
+	unset CLIBS
+
+	econf \
+		--with-opt="${CFLAGS}" \
+		--datadir="${EPREFIX}"/usr/share/${PN} \
+		--with-blas="$(pkg-config blas --libs)"
+}
+
+src_compile() {
+	emake -j1 \
+		SCRATCH="${WORKDIR}/libint" \
+		|| die "make failed"
+}
+
+src_test() {
+	emake \
+		EXECDIR="${S}"/bin \
+		TESTFLAGS="" \
+		-j1 tests || die
+}
+
+src_install() {
+	emake -j1 \
+		DESTDIR="${D}" \
+		install || die "install failed"
+}