Version bump (fixes bug #262905) and removed old ebuilds.

(Portage version: 2.1.7.3/cvs/Linux x86_64)

10 files changed, 183 insertions, 189 deletions

diff --git a/sci-chemistry/apbs/ChangeLog b/sci-chemistry/apbs/ChangeLog
index 48d3f53bd63e..5f38dafade0a 100644
--- a/sci-chemistry/apbs/ChangeLog
+++ b/sci-chemistry/apbs/ChangeLog
@@ -1,6 +1,17 @@
 # ChangeLog for sci-chemistry/apbs
 # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/apbs/ChangeLog,v 1.21 2009/05/06 21:05:52 maekke Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/apbs/ChangeLog,v 1.22 2009/11/03 05:30:06 markusle Exp $
+
+*apbs-1.2.0 (03 Nov 2009)
+
+  03 Nov 2009; Markus Dittrich <markusle@gentoo.org> -apbs-0.5.0.ebuild,
+  -apbs-0.5.1.ebuild, +apbs-1.2.0.ebuild, +files/apbs-1.2.0-contrib.patch,
+  +files/apbs-1.2.0-install-fix.patch, +files/apbs-1.2.0-link.patch,
+  -files/apbs-examples-gentoo.patch, -files/apbs-gcc4-gentoo.patch,
+  metadata.xml:
+  Version bump (fixes bug #262905) and removed old ebuilds. Currently 
+  missing is opal support (needs keywording by ppc) as well as fetk 
+  support. Thanks much to Justin Lecher for his ebuild.
 
   06 May 2009; Markus Meier <maekke@gentoo.org> apbs-1.0.0-r1.ebuild:
   amd64/x86 stable, bug #250903
diff --git a/sci-chemistry/apbs/apbs-0.5.0.ebuild b/sci-chemistry/apbs/apbs-0.5.0.ebuild
deleted file mode 100644
index 19043a78c5bf..000000000000
--- a/sci-chemistry/apbs/apbs-0.5.0.ebuild
+++ /dev/null
@@ -1,68 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/apbs/apbs-0.5.0.ebuild,v 1.4 2009/02/05 05:44:50 darkside Exp $
-
-inherit eutils fortran
-
-MY_P="${P}-source-2"
-S="${WORKDIR}"/"${MY_P}"
-
-DESCRIPTION=" Software for evaluating the electrostatic properties of nanoscale biomolecular systems"
-LICENSE="GPL-2"
-HOMEPAGE="http://apbs.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.gz"
-
-SLOT="0"
-IUSE="blas mpi"
-KEYWORDS="~ppc ~x86 ~amd64"
-
-DEPEND="blas? ( virtual/blas )
-		sys-libs/readline
-		mpi? ( virtual/mpi )"
-
-FORTRAN="g77 gfortran"
-
-pkg_setup() {
-	# It is important that you use the same compiler to compile
-	# APBS that you used when compiling MPI.
-	fortran_pkg_setup
-}
-
-src_compile() {
-
-	# use blas
-	use blas && local myconf="--with-blas=-lblas"
-
-	use mpi && myconf="${myconf} --with-mpiinc=/usr/include"
-
-	econf ${myconf} || die "configure failed"
-
-	# build
-	make DESTDIR="${D}" || die "make failed"
-}
-
-src_install() {
-
-	# install apbs binary
-	dobin bin/apbs || die "failed to install apbs binary"
-
-	# remove useless files and install docs
-	find ./examples -name 'test.sh' -exec rm -f {} \; || \
-		die "Failed to remove test.sh files"
-	find ./examples -name 'Makefile*' -exec rm -f {} \; || \
-		die "Failed to remove Makefiles"
-	find ./tools -name 'Makefile*' -exec rm -f {} \; || \
-		die "Failed to remove Makefiles"
-
-	dohtml -r doc/index.html doc/programmer doc/tutorial \
-		doc/user-guide doc/license || \
-			die "Failed to install html docs"
-
-	insinto /usr/share/doc/${PF}/examples
-	doins -r examples/* || \
-		die "Failed to install examples"
-
-	insinto /usr/share/${PF}/tools
-	doins -r tools/* || die "failed to install tools"
-
-}
diff --git a/sci-chemistry/apbs/apbs-0.5.1.ebuild b/sci-chemistry/apbs/apbs-0.5.1.ebuild
deleted file mode 100644
index 868d07fce050..000000000000
--- a/sci-chemistry/apbs/apbs-0.5.1.ebuild
+++ /dev/null
@@ -1,70 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/apbs/apbs-0.5.1.ebuild,v 1.4 2009/02/05 05:44:50 darkside Exp $
-
-inherit eutils fortran
-
-MY_P="${P}-source"
-S="${WORKDIR}"/"${MY_P}"
-
-DESCRIPTION=" Software for evaluating the electrostatic properties of nanoscale biomolecular systems"
-LICENSE="GPL-2"
-HOMEPAGE="http://apbs.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tgz"
-
-SLOT="0"
-IUSE="blas mpi"
-KEYWORDS="~ppc ~x86 ~amd64"
-
-DEPEND="blas? ( virtual/blas )
-		sys-libs/readline
-		mpi? ( virtual/mpi )"
-
-FORTRAN="g77 gfortran"
-
-pkg_setup() {
-	# It is important that you use the same compiler to compile
-	# APBS that you used when compiling MPI.
-	fortran_pkg_setup
-}
-
-src_compile() {
-	# fix apbsblas
-	sed -e "s:-L\${prefix}/lib -lapbsblas:${S}//contrib/blas/.libs/libapbsblas.a:" \
-		-i configure \
-		|| die "failed to fix configure"
-
-	# use blas
-	use blas && local myconf="--with-blas=-lblas"
-
-	use mpi && myconf="${myconf} --with-mpiinc=/usr/include"
-
-	econf ${myconf} || die "configure failed"
-
-	# build
-	make DESTDIR="${D}" || die "make failed"
-}
-
-src_install() {
-	# install apbs binary
-	dobin bin/apbs || die "failed to install apbs binary"
-
-	# remove useless files and install docs
-	find ./examples -name 'test.sh' -exec rm -f {} \; || \
-		die "Failed to remove test.sh files"
-	find ./examples -name 'Makefile*' -exec rm -f {} \; || \
-		die "Failed to remove Makefiles"
-	find ./tools -name 'Makefile*' -exec rm -f {} \; || \
-		die "Failed to remove Makefiles"
-
-	dohtml -r doc/index.html doc/programmer doc/tutorial \
-		doc/user-guide doc/license || \
-			die "Failed to install html docs"
-
-	insinto /usr/share/doc/${PF}/examples
-	doins -r examples/* || \
-		die "Failed to install examples"
-
-	insinto /usr/share/${PN}/tools
-	doins -r tools/* || die "failed to install tools"
-}
diff --git a/sci-chemistry/apbs/apbs-1.2.0.ebuild b/sci-chemistry/apbs/apbs-1.2.0.ebuild
new file mode 100644
index 000000000000..55c69b2aac41
--- /dev/null
+++ b/sci-chemistry/apbs/apbs-1.2.0.ebuild
@@ -0,0 +1,96 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/apbs/apbs-1.2.0.ebuild,v 1.1 2009/11/03 05:30:06 markusle Exp $
+
+EAPI="2"
+
+inherit eutils fortran autotools python versionator flag-o-matic
+
+MY_PV=$(get_version_component_range 1-2)
+MY_P="${PN}-${MY_PV}-source"
+S="${WORKDIR}"/"${MY_P}"
+
+DESCRIPTION=" Software for evaluating the electrostatic properties of nanoscale biomolecular systems"
+LICENSE="BSD"
+HOMEPAGE="http://apbs.sourceforge.net/"
+SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.gz"
+
+SLOT="0"
+IUSE="arpack blas doc mpi python openmp"
+KEYWORDS="~x86 ~amd64 ~ppc"
+
+DEPEND="dev-libs/maloc[mpi=]
+	blas? ( virtual/blas )
+	python? ( dev-lang/python )
+	sys-libs/readline
+	arpack? ( sci-libs/arpack )
+	mpi? ( virtual/mpi )"
+RDEPEND="${DEPEND}"
+
+FORTRAN="g77 gfortran ifc"
+
+src_prepare() {
+	python_version
+
+	epatch "${FILESDIR}"/${P}-install-fix.patch
+	epatch "${FILESDIR}"/${P}-contrib.patch
+	epatch "${FILESDIR}"/${P}-link.patch
+	sed "s:GENTOO_PKG_NAME:${PN}:g" \
+	-i Makefile.am || die "Cannot correct package name"
+	eautoreconf
+}
+
+src_configure() {
+	local myconf="--docdir=/usr/share/doc/${PF}"
+	use blas && myconf="${myconf} --with-blas=-lblas"
+	use arpack && myconf="${myconf} --with-arpack=/usr/$(get_libdir)"
+
+	# check which mpi version is installed and tell configure
+	if use mpi; then
+		export CC="/usr/bin/mpicc"
+		export F77="/usr/bin/mpif77"
+
+		if has_version sys-cluster/mpich; then
+	 		myconf="${myconf} --with-mpich=/usr"
+		elif has_version sys-cluster/mpich2; then
+			myconf="${myconf} --with-mpich2=/usr"
+		elif has_version sys-cluster/lam-mpi; then
+			myconf="${myconf} --with-lam=/usr"
+		elif has_version sys-cluster/openmpi; then
+			myconf="${myconf} --with-openmpi=/usr"
+		fi
+	fi || die "Failed to select proper mpi implementation"
+
+	# apbs' configure's openmp detection is broken; we'll
+	# work around this until it is fixed
+	if use openmp; then
+		append-flags -fopenmp
+	else
+		myconf="${myconf} --disable-openmp"
+	fi
+
+	econf $(use_enable python) \
+		--disable-maloc-rebuild \
+		${myconf} || die "configure failed"
+}
+
+src_compile() {
+	emake -j1 || die "make failed"
+}
+
+src_test() {
+	cd examples && make test \
+		|| die "Tests failed"
+}
+
+src_install() {
+	emake -j1 DESTDIR="${D}" install \
+		|| die "make install failed"
+
+	dodoc AUTHORS INSTALL README NEWS ChangeLog \
+		|| die "Failed to install docs"
+
+	if use doc; then
+		dohtml -r doc/* || die "Failed to install html docs"
+	fi
+}
diff --git a/sci-chemistry/apbs/files/apbs-1.2.0-contrib.patch b/sci-chemistry/apbs/files/apbs-1.2.0-contrib.patch
new file mode 100644
index 000000000000..6bfc9ffaa790
--- /dev/null
+++ b/sci-chemistry/apbs/files/apbs-1.2.0-contrib.patch
@@ -0,0 +1,10 @@
+--- contrib/Makefile.am	2009-03-05 21:30:09.000000000 +0100
++++ contrib/Makefile.am.new	2009-04-24 19:08:39.000000000 +0200
+@@ -9,6 +9,6 @@
+ AUTOMAKE_OPTIONS = no-dependencies
+ SUFFIXES = .H .h .C .c .f .o
+ 
+-always_built_SUBDIRS = @apbs_do_blas@ @apbs_do_maloc@ pmgZ aqua opal
++always_built_SUBDIRS = @apbs_do_blas@ @apbs_do_maloc@ pmgZ aqua
+ 
+ SUBDIRS = $(always_built_SUBDIRS) .
diff --git a/sci-chemistry/apbs/files/apbs-1.2.0-install-fix.patch b/sci-chemistry/apbs/files/apbs-1.2.0-install-fix.patch
new file mode 100644
index 000000000000..1d6f130a522a
--- /dev/null
+++ b/sci-chemistry/apbs/files/apbs-1.2.0-install-fix.patch
@@ -0,0 +1,39 @@
+diff -Naur apbs-1.2-source/Makefile.am apbs-1.2-source.new/Makefile.am
+--- apbs-1.2-source/Makefile.am	2009-10-14 13:20:55.000000000 -0400
++++ apbs-1.2-source.new/Makefile.am	2009-11-02 23:31:41.000000000 -0500
+@@ -28,10 +28,19 @@
+ 	-rm -f ./bin/apbs
+ 
+ install-data-local:
+-	mkdir -p ${prefix}/share
+-	-cp -rf examples ${prefix}/share 
+-	-cp -rf doc ${prefix}/share 
+-	-cp -rf tools ${prefix}/share
++	mkdir -p $(DESTDIR)${prefix}/share/GENTOO_PKG_NAME/examples 
++	mkdir -p $(DESTDIR)${prefix}/share/GENTOO_PKG_NAME/tools
++	-rm -f doc/LICENSE.txt
++	-rm -f tools/manip/*.pyc
++	-rm -f tools/**/*.o
++	-rm -f tools/**/Makefile*
++	-rm -f tools/**/**/*.o
++	-rm -f tools/**/**/Makefile*
++	-rm -f tools/Makefile*
++	-rm -f examples/Makefile*
++	-rm -f examples/**/Makefile*
++	-cp -rf examples $(DESTDIR)${prefix}/share/GENTOO_PKG_NAME/
++	-cp -rf tools $(DESTDIR)${prefix}/share/GENTOO_PKG_NAME/
+ 
+ test:
+ 	cd examples; make test
+diff -Naur apbs-1.2-source/bin/Makefile.am apbs-1.2-source.new/bin/Makefile.am
+--- apbs-1.2-source/bin/Makefile.am	2009-10-14 13:20:48.000000000 -0400
++++ apbs-1.2-source.new/bin/Makefile.am	2009-11-02 23:31:15.000000000 -0500
+@@ -40,6 +40,4 @@
+ include_HEADERS = routines.h
+ 	
+ install-data-local:
+-	-cp -p ${top_apbsdir}/bin/ApbsClient.py ${prefix}/bin
+-	-chmod 755 ${prefix}/bin/ApbsClient.py
+-	-rm -f ${prefix}/bin/wsdl2py 
+\ No newline at end of file
++	-rm -f $(DESTDIR)${prefix}/bin/wsdl2py 
diff --git a/sci-chemistry/apbs/files/apbs-1.2.0-link.patch b/sci-chemistry/apbs/files/apbs-1.2.0-link.patch
new file mode 100644
index 000000000000..ae64793423b7
--- /dev/null
+++ b/sci-chemistry/apbs/files/apbs-1.2.0-link.patch
@@ -0,0 +1,23 @@
+diff -Naur apbs-1.2-source/tools/python/Makefile.am apbs-1.2-source.new/tools/python/Makefile.am
+--- apbs-1.2-source/tools/python/Makefile.am	2009-10-14 13:20:57.000000000 -0400
++++ apbs-1.2-source.new/tools/python/Makefile.am	2009-10-29 16:08:18.000000000 -0400
+@@ -15,5 +15,5 @@
+ 
+ noinst_PROGRAMS       = _apbslib.so
+ _apbslib_so_SOURCES   = apbslib.c
+-_apbslib_so_LINK      = $(PY_CC) $(PY_LINKFLAGS) -o $@ $(PY_SHARED)
+-_apbslib_so_LDADD     = ${top_builddir}/bin/.libs/libapbsmainroutines.a ${top_builddir}/src/aaa_lib/.libs/libapbs.a ${top_builddir}/contrib/lib/libmaloc.a ${top_builddir}/contrib/blas/.libs/libapbsblas.a $(PY_LDFLAGS)
++_apbslib_so_LINK      = $(PY_CC) $(PY_LINKFLAGS) $(LDFLAGS) -o $@ $(PY_SHARED)
++_apbslib_so_LDADD     = ${top_builddir}/bin/.libs/libapbsmainroutines.a ${top_builddir}/src/aaa_lib/.libs/libapbs.a $(PY_LDFLAGS)
+diff -Naur apbs-1.2-source/tools/python/vgrid/Makefile.am apbs-1.2-source.new/tools/python/vgrid/Makefile.am
+--- apbs-1.2-source/tools/python/vgrid/Makefile.am	2009-10-14 13:20:57.000000000 -0400
++++ apbs-1.2-source.new/tools/python/vgrid/Makefile.am	2009-10-29 16:08:29.000000000 -0400
+@@ -15,6 +15,6 @@
+ if PY_PRESENT
+    noinst_PROGRAMS     = _vgrid.so
+    _vgrid_so_SOURCES   = vgridlib.c
+-   _vgrid_so_LINK      = $(PY_CC) $(PY_LINKFLAGS) -o $@ $(PY_SHARED)
+-   _vgrid_so_LDADD     = ${top_builddir}/bin/.libs/libapbsmainroutines.a ${top_builddir}/src/aaa_lib/.libs/libapbs.a $(PY_LDFLAGS) ${top_builddir}/contrib/lib/libmaloc.a @lib_list@
++   _vgrid_so_LINK      = $(PY_CC) $(PY_LINKFLAGS) $(LDFLAGS) -o $@ $(PY_SHARED)
++   _vgrid_so_LDADD     = ${top_builddir}/bin/.libs/libapbsmainroutines.a ${top_builddir}/src/aaa_lib/.libs/libapbs.a @lib_list@
+ endif
diff --git a/sci-chemistry/apbs/files/apbs-examples-gentoo.patch b/sci-chemistry/apbs/files/apbs-examples-gentoo.patch
deleted file mode 100644
index 5c82bc2882ab..000000000000
--- a/sci-chemistry/apbs/files/apbs-examples-gentoo.patch
+++ /dev/null
@@ -1,30 +0,0 @@
-diff -Naur apbs-0.4.0/examples/born/runme apbs-0.4.0-new/examples/born/runme
---- apbs-0.4.0/examples/born/runme	2002-08-13 14:35:41.000000000 +0000
-+++ apbs-0.4.0-new/examples/born/runme	2006-03-09 03:15:09.000000000 +0000
-@@ -8,5 +8,5 @@
-   echo "Generating ion with $i radius..."
-   echo "ATOM      1  I   ION     1       0.000   0.000  0.000  1.00  $i" \
-     > ion.pqr
--  ${bindir}/apbs apbs.in > OUTPUT-${i} 2>&1 
-+  /usr/bin/apbs apbs.in > OUTPUT-${i} 2>&1 
- done
-diff -Naur apbs-0.4.0/examples/ion-pmf/runme apbs-0.4.0-new/examples/ion-pmf/runme
---- apbs-0.4.0/examples/ion-pmf/runme	2002-08-13 14:35:41.000000000 +0000
-+++ apbs-0.4.0-new/examples/ion-pmf/runme	2006-03-09 03:16:11.000000000 +0000
-@@ -14,5 +14,5 @@
-   echo "ATOM      1  I   ION     1      $i    0.000   0.000  1.00 2.00"\
-      > mol2.pqr
-   cat mol1.pqr mol2.pqr > complex.pqr
--  ${bindir}/apbs apbs.in > OUTPUT_${i} 2>&1
-+  /usr/bin/apbs apbs.in > OUTPUT_${i} 2>&1
- done
-diff -Naur apbs-0.4.0/examples/point-pmf/runme.sh apbs-0.4.0-new/examples/point-pmf/runme.sh
---- apbs-0.4.0/examples/point-pmf/runme.sh	2004-02-12 17:14:02.000000000 +0000
-+++ apbs-0.4.0-new/examples/point-pmf/runme.sh	2006-03-09 03:17:11.000000000 +0000
-@@ -20,5 +20,5 @@
-   echo "ATOM      1  I   ION     1      $i    0.000   0.000  1.00 0.00"\
-      > mol2.pqr
-   cat mol1.pqr mol2.pqr > complex.pqr
--  ${bindir}/apbs apbs.in > OUTPUT_${i} 2>&1
-+  /usr/bin/apbs apbs.in > OUTPUT_${i} 2>&1
- done
diff --git a/sci-chemistry/apbs/files/apbs-gcc4-gentoo.patch b/sci-chemistry/apbs/files/apbs-gcc4-gentoo.patch
deleted file mode 100644
index 434a7fc0a05c..000000000000
--- a/sci-chemistry/apbs/files/apbs-gcc4-gentoo.patch
+++ /dev/null
@@ -1,20 +0,0 @@
---- apbs-0.4.0/configure	2005-12-14 14:11:17.000000000 -0500
-+++ apbs-0.4.0-new/configure	2006-05-23 17:01:07.000000000 -0400
-@@ -3513,7 +3513,7 @@
- ac_link='$F77 -o conftest$ac_exeext $FFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
- ac_compiler_gnu=$ac_cv_f77_compiler_gnu
- if test -n "$ac_tool_prefix"; then
--  for ac_prog in g77 f77 xlf frt pgf77 fl32 af77 fort77 f90 xlf90 pgf90 epcf90 f95 fort xlf95 lf95 g95
-+  for ac_prog in g77 gfortran f77 xlf frt pgf77 fl32 af77 fort77 f90 xlf90 pgf90 epcf90 f95 fort xlf95 lf95 g95
-   do
-     # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args.
- set dummy $ac_tool_prefix$ac_prog; ac_word=$2
-@@ -3555,7 +3555,7 @@
- fi
- if test -z "$F77"; then
-   ac_ct_F77=$F77
--  for ac_prog in g77 f77 xlf frt pgf77 fl32 af77 fort77 f90 xlf90 pgf90 epcf90 f95 fort xlf95 lf95 g95
-+  for ac_prog in g77 gfortran f77 xlf frt pgf77 fl32 af77 fort77 f90 xlf90 pgf90 epcf90 f95 fort xlf95 lf95 g95
- do
-   # Extract the first word of "$ac_prog", so it can be a program name with args.
- set dummy $ac_prog; ac_word=$2
diff --git a/sci-chemistry/apbs/metadata.xml b/sci-chemistry/apbs/metadata.xml
index dafc7c94643e..cc7f93f699b0 100644
--- a/sci-chemistry/apbs/metadata.xml
+++ b/sci-chemistry/apbs/metadata.xml
@@ -6,4 +6,7 @@
         <name>Markus Dittrich</name>
     </maintainer>
 	<herd>sci-chemistry</herd>
+	<use>
+		<flag name='arpack'>Include support for arpack libs</flag>
+	</use>
 </pkgmetadata>