sci-chemistry/apbs: Fix patching problem which lead to an empty pkg-config file, #425294

(Portage version: 2.2.0_alpha120/cvs/Linux x86_64)

3 files changed, 195 insertions, 1 deletions

diff --git a/sci-chemistry/apbs/ChangeLog b/sci-chemistry/apbs/ChangeLog
index 92425668ee09..cd2e6fb83fe6 100644
--- a/sci-chemistry/apbs/ChangeLog
+++ b/sci-chemistry/apbs/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-chemistry/apbs
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/apbs/ChangeLog,v 1.57 2012/06/16 15:37:21 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/apbs/ChangeLog,v 1.58 2012/07/19 10:20:51 jlec Exp $
+
+*apbs-1.3-r3 (19 Jul 2012)
+
+  19 Jul 2012; Justin Lecher <jlec@gentoo.org> +apbs-1.3-r3.ebuild,
+  +files/apbs-1.3/0016-apbs-1.3-apbs.pc-in-AC_CONFIG_FILES.patch:
+  Fix patching problem which lead to an empty pkg-config file, #425294
 
   25 Apr 2012; Justin Lecher <jlec@gentoo.org> apbs-1.3-r2.ebuild:
   Don't run libtoolize twice
diff --git a/sci-chemistry/apbs/apbs-1.3-r3.ebuild b/sci-chemistry/apbs/apbs-1.3-r3.ebuild
new file mode 100644
index 000000000000..653031fe466e
--- /dev/null
+++ b/sci-chemistry/apbs/apbs-1.3-r3.ebuild
@@ -0,0 +1,160 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/apbs/apbs-1.3-r3.ebuild,v 1.1 2012/07/19 10:20:51 jlec Exp $
+
+EAPI=4
+
+PYTHON_DEPEND="python? 2"
+
+inherit autotools-utils eutils fortran-2 python toolchain-funcs versionator
+
+MY_PV=$(get_version_component_range 1-3)
+MY_P="${PN}-${MY_PV}"
+
+DESCRIPTION="For evaluation of electrostatic properties of nanoscale biomolecular systems"
+HOMEPAGE="http://apbs.sourceforge.net/"
+SRC_URI="mirror://sourceforge/${PN}/${P}-source.tar.gz"
+
+SLOT="0"
+LICENSE="BSD"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
+IUSE="arpack doc examples fetk mpi openmp python static-libs tools"
+REQUIRED_USE="mpi? ( !python )"
+
+DEPEND="
+	dev-libs/maloc[mpi=]
+	virtual/blas
+	sys-libs/readline
+	virtual/fortran
+	arpack? ( sci-libs/arpack )
+	fetk? (
+		sci-libs/fetk
+		sci-libs/amd
+		sci-libs/umfpack
+		sci-libs/superlu )
+	mpi? ( virtual/mpi )"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/"${MY_P}-source"
+
+AUTOTOOLS_IN_SOURCE_BUILD=1
+MAKEOPTS+=" -j1"
+
+pkg_setup() {
+	fortran-2_pkg_setup
+	use python && python_set_active_version 2 && python_pkg_setup
+	if [[ -z ${MAXMEM} ]]; then
+		einfo "You can specify the max amount of RAM used"
+		einfo "by setting MAXMEM=\"your size in MB\""
+	else
+		einfo "Settings max memory usage to ${MAXMEM} MB"
+	fi
+}
+
+# git clone ssh://woodpecker/home/jlec/apbs.git
+PATCHES=( "${FILESDIR}"/${P}/00{01..16}* )
+
+src_prepare() {
+	rm -rf contrib/{blas,maloc,opal,zlib} || die
+	find -name "._*" -delete || die
+
+	EPATCH_OPTS="-p1" \
+		autotools-utils_src_prepare
+
+	sed \
+		-e "s:GENTOO_PKG_NAME:${PN}:g" \
+		-i Makefile.am || die "Cannot correct package name"
+	sed \
+		-e 's:libmaloc.a:libmaloc.so:g' \
+		-e 's:-lblas::g' \
+		-i configure.ac || die
+	sed -e 's:opal::g' -i contrib/Makefile.am || die
+	sed \
+		-e 's:noinst_PROGRAMS:bin_PROGRAMS:g' \
+		-i tools/*/Makefile.am || die
+	AT_NOELIBTOOLIZE=yes eautoreconf
+}
+
+src_configure() {
+	local myeconfargs=( --docdir="${EPREFIX}/usr/share/doc/${PF}" )
+	use arpack && myeconfargs+=( --with-arpack="${EPREFIX}/usr/$(get_libdir)" )
+
+	# check which mpi version is installed and tell configure
+	if use mpi; then
+		export CC="${EPREFIX}/usr/bin/mpicc"
+		export F77="${EPREFIX}/usr/bin/mpif77"
+
+		if has_version sys-cluster/mpich; then
+	 		myeconfargs+=( --with-mpich="${EPREFIX}/usr" )
+		elif has_version sys-cluster/mpich2; then
+			myeconfargs+=( --with-mpich2="${EPREFIX}/usr" )
+		elif has_version sys-cluster/openmpi; then
+			myeconfargs+=( --with-openmpi="${EPREFIX}/usr" )
+		fi
+	fi || die "Failed to select proper mpi implementation"
+
+	if use fetk; then
+		myeconfargs+=( --with-fetk-include="${EPREFIX}/usr/include" --with-fetk-library="${EPREFIX}/usr/$(get_libdir)" )
+	else
+		myeconfargs+=( --disable-fetk )
+	fi
+
+	[[ -n ${MAXMEM} ]] && myeconfargs+=( --with-maxmem=${MAXMEM} )
+
+	if use python; then
+		myeconfargs+=( --enable-tools  )
+	else
+		myeconfargs+=( $(use_enable tools) )
+	fi
+
+	myeconfargs+=(
+		--disable-maloc-rebuild
+		--enable-shared
+		$(use_enable openmp)
+		$(use_enable python)
+		)
+	autotools-utils_src_configure
+}
+
+src_test() {
+	export LC_NUMERIC=C
+	cd examples && make test \
+		|| die "Tests failed"
+	grep -q 'FAILED' "${S}"/examples/TESTRESULTS.log && die "Tests failed"
+}
+
+src_install() {
+	autotools-utils_src_install
+
+	use doc && dohtml -r doc/*
+	use examples && insinto /usr/share/${PN} && doins -r examples
+	use tools && emake DESTDIR="${D}" install-tools
+
+	if use python && ! use mpi; then
+		insinto $(python_get_sitedir)/${PN}
+		doins tools/manip/*.py
+		doins tools/python/{*.py,*.pqr}
+		doins tools/python/*/{*.py,*.so}
+		python_clean_installation_image
+	fi
+
+	if use python || use tools; then
+		mv "${ED}"/usr/bin/analysis{,_apbs} || die
+		mv "${ED}"/usr/bin/smooth{,_apbs} || die
+	fi
+}
+
+pkg_postinst() {
+	use python && python_mod_optimize ${PN}
+	if use python || use tools; then
+		echo
+		elog "Following apps have been renamed"
+		elog "${EPREFIX}/usr/bin/analysis -> ${EPREFIX}/usr/bin/analysis_apbs"
+		elog "${EPREFIX}/usr/bin/smooth -> ${EPREFIX}/usr/bin/smooth_apbs"
+		echo
+	fi
+}
+
+pkg_postrm() {
+	use python && python_mod_cleanup ${PN}
+}
diff --git a/sci-chemistry/apbs/files/apbs-1.3/0016-apbs-1.3-apbs.pc-in-AC_CONFIG_FILES.patch b/sci-chemistry/apbs/files/apbs-1.3/0016-apbs-1.3-apbs.pc-in-AC_CONFIG_FILES.patch
new file mode 100644
index 000000000000..8a5e59d0a838
--- /dev/null
+++ b/sci-chemistry/apbs/files/apbs-1.3/0016-apbs-1.3-apbs.pc-in-AC_CONFIG_FILES.patch
@@ -0,0 +1,28 @@
+From ba195e1ea7e023ab442c4699c9c329bacc646c6a Mon Sep 17 00:00:00 2001
+Message-Id: <ba195e1ea7e023ab442c4699c9c329bacc646c6a.1342692605.git.jlec@gentoo.org>
+In-Reply-To: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1342692605.git.jlec@gentoo.org>
+References: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1342692605.git.jlec@gentoo.org>
+From: Justin Lecher <jlec@gentoo.org>
+Date: Thu, 19 Jul 2012 12:07:59 +0200
+Subject: [PATCH 16/16] apbs 1.3 apbs.pc in AC_CONFIG_FILES
+
+---
+ configure.ac |    2 +-
+ 1 files changed, 1 insertions(+), 1 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index d39a0a5..6855929 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -1269,7 +1269,7 @@ AC_CONFIG_FILES([
+     
+     bin/Makefile
+ 
+-    apbs.pc:apbs.pc.in
++    apbs.pc
+ 
+ ])
+ AC_OUTPUT
+-- 
+1.7.8.6
+