Version bump and fixed compilation with autoconf 2.64 (fixes bug #294453 and #295537).

Package-Manager: portage-2.1.7.10/cvs/Linux x86_64

4 files changed, 132 insertions, 2 deletions

diff --git a/sci-chemistry/apbs/ChangeLog b/sci-chemistry/apbs/ChangeLog
index 5f38dafade0a..de779bafa61a 100644
--- a/sci-chemistry/apbs/ChangeLog
+++ b/sci-chemistry/apbs/ChangeLog
@@ -1,6 +1,13 @@
 # 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 1.22 2009/11/03 05:30:06 markusle Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/apbs/ChangeLog,v 1.23 2009/12/04 04:09:15 markusle Exp $
+
+*apbs-1.2.1b (04 Dec 2009)
+
+  04 Dec 2009; Markus Dittrich <markusle@gentoo.org> +apbs-1.2.1b.ebuild,
+  +files/apbs-1.2.1b-autoconf-2.64.patch:
+  Version bump and fixed compilation with autoconf 2.64 (fixes bug
+  #294453 and #295537).
 
 *apbs-1.2.0 (03 Nov 2009)
 
diff --git a/sci-chemistry/apbs/Manifest b/sci-chemistry/apbs/Manifest
index 51dc2894f89a..e61e615adc75 100644
--- a/sci-chemistry/apbs/Manifest
+++ b/sci-chemistry/apbs/Manifest
@@ -5,9 +5,12 @@ AUX apbs-1.0.0-openmpi.patch 1458 RMD160 27e786dcb212348e14400442d11543038a1015b
 AUX apbs-1.2.0-contrib.patch 382 RMD160 4c0c75e57fb6a0c298606d87785a5b9daa8db457 SHA1 653295c9ff7ac075613dd82ce332b41b0e2ea37e SHA256 0b2a1c518c66de6010954f101c1622cfd570bbfcc4774d98607174e57e67f1b3
 AUX apbs-1.2.0-install-fix.patch 1417 RMD160 4dbf96c23c2c2b150d48dc2983c293aac8be5492 SHA1 591339b9f994ee3853f6f6c38ab2cb4a280d3216 SHA256 cb805d3b12b7457c9c9a28277159516b5ea3724b6c5647b567c9683865a160b8
 AUX apbs-1.2.0-link.patch 1716 RMD160 904e7123d32f628171aa728a761c9d7fd95e967d SHA1 63265d0c7c636749292d90efe6a989e7e48251b6 SHA256 37faa758d6439f22853aa9d4524e3e8770437d3986e00649a193b0a97f369bba
+AUX apbs-1.2.1b-autoconf-2.64.patch 952 RMD160 80ed2f351c52764b1c3221b4f5f0e152652c8637 SHA1 dbe725035299182efe82d6ab4a8dcb721601592c SHA256 d9855b84b5b3ca404c463ad9ada7d75d7076d11a929b53bd61f42ed427be9984
 DIST apbs-1.0.0-source.tar.gz 11541303 RMD160 1eeb79f93a591835281bf8395308cddc065dac93 SHA1 fbcfe664defb09165e0eae3ff913a9d5a17cb27e SHA256 bd3803183ffb2bede9fca242d5432acb60b3cb8668eeccdbbced69aaf7a57604
 DIST apbs-1.2-source.tar.gz 10593537 RMD160 62cb82da9ca5276c3d7127a4d1f9737747dac315 SHA1 43e766a8c6166288c25229e0615a72dca5e8a3b5 SHA256 b8b74d80f8b4e553cd2e51727efc79436152cd4f5e02be076e7cdf994aa5424e
+DIST apbs-1.2.1b-source.tar.gz 40647966 RMD160 4ba1f72a7f9adcf7b283dc18743488143025b398 SHA1 dc3e6933a987ff9fdf88db510db79b3dacb100d6 SHA256 7d088def1ed7689127eb64014ea44069b9d7bfc995941fe5800ff753d48c87be
 EBUILD apbs-1.0.0-r1.ebuild 1995 RMD160 0efbe531fe27749a65a23d17958c411bcd15ad74 SHA1 9ff5761e0d8d01cdb49518cdf5d3372977c0f9ad SHA256 34b2bd026da29cec1224c91d9b4c86bdac3bec95747e167b2127aa329de2f4b2
 EBUILD apbs-1.2.0.ebuild 2514 RMD160 860994d50bc8a5d1657a5f3f6fa0dfef3c1e76e4 SHA1 d917e489ecc0e245e02796097a6aef07617e73ff SHA256 4f4229963c163b60012c091e84cf456a1215680358e3852174f2a972554546bf
-MISC ChangeLog 3858 RMD160 f8f2eb4d126b6e0db3c2a4019693dbde350047d0 SHA1 77c1d2641af825555957fb1f5fd725f4e607f79c SHA256 2c5fa87ba17878062b9a279621b00d3166b251611532fd6651f87434259a0841
+EBUILD apbs-1.2.1b.ebuild 2587 RMD160 0f1159c48ea537f1aa8393c2bca3fbe04de36a90 SHA1 bc852c472d96fc12d90babed8aede32139a8acd5 SHA256 19df7bc7c36fa57273cac61b8d5670c297f7675082b44231f4535f4c539e06fa
+MISC ChangeLog 4094 RMD160 fee4a6502780fbeb6a982f7233a842051ea7e2ed SHA1 21f3fe13cb25abb266c83cd883e0733407ab2978 SHA256 2729c3f259121b36b28c772cd0d01a4c86572784d511a38cb9a0fc09673f4a75
 MISC metadata.xml 358 RMD160 b98e2ce84589bbc6b62f9fb91007bae907f019bc SHA1 c15f33b50d731bda2c2f58a1fe601e0b23f7288c SHA256 9f33e69a8a217ad31fcad567e0d0889693c680631d9245c7bd9774caac95a74e
diff --git a/sci-chemistry/apbs/apbs-1.2.1b.ebuild b/sci-chemistry/apbs/apbs-1.2.1b.ebuild
new file mode 100644
index 000000000000..09247ced7d14
--- /dev/null
+++ b/sci-chemistry/apbs/apbs-1.2.1b.ebuild
@@ -0,0 +1,97 @@
+# 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-1.2.1b.ebuild,v 1.1 2009/12/04 04:09:15 markusle Exp $
+
+EAPI="2"
+
+inherit eutils fortran autotools python versionator flag-o-matic
+
+MY_PV=$(get_version_component_range 1-3)
+MY_P="${PN}-${MY_PV}"
+S="${WORKDIR}"/"${MY_P}-source"
+
+DESCRIPTION=" Software for evaluating the electrostatic properties of nanoscale biomolecular systems"
+LICENSE="BSD"
+HOMEPAGE="http://apbs.sourceforge.net/"
+SRC_URI="mirror://sourceforge/${PN}/${P}-source.tar.gz"
+
+SLOT="0"
+IUSE="arpack blas doc mpi python openmp"
+KEYWORDS="~x86 ~amd64 ~ppc"
+
+DEPEND="dev-libs/maloc[mpi=]
+	blas? ( virtual/blas )
+	python? ( dev-lang/python )
+	sys-libs/readline
+	arpack? ( sci-libs/arpack )
+	mpi? ( virtual/mpi )"
+RDEPEND="${DEPEND}"
+
+FORTRAN="g77 gfortran ifc"
+
+src_prepare() {
+	python_version
+
+	epatch "${FILESDIR}"/${PN}-1.2.0-install-fix.patch
+	epatch "${FILESDIR}"/${PN}-1.2.0-contrib.patch
+	epatch "${FILESDIR}"/${PN}-1.2.0-link.patch
+	epatch "${FILESDIR}"/${P}-autoconf-2.64.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-1.2.1b-autoconf-2.64.patch b/sci-chemistry/apbs/files/apbs-1.2.1b-autoconf-2.64.patch
new file mode 100644
index 000000000000..ab7015126f9b
--- /dev/null
+++ b/sci-chemistry/apbs/files/apbs-1.2.1b-autoconf-2.64.patch
@@ -0,0 +1,23 @@
+diff -Naur apbs-1.2.1-source/acinclude.m4 apbs-1.2.1-source.new/acinclude.m4
+--- apbs-1.2.1-source/acinclude.m4	2009-12-01 09:20:23.000000000 -0500
++++ apbs-1.2.1-source.new/acinclude.m4	2009-12-03 22:56:47.000000000 -0500
+@@ -54,14 +54,11 @@
+ AC_LANG_C
+ ac_save_LIBS="$LIBS"
+ LIBS="mangle-func.o $LIBS"
+-AC_TRY_LINK(,foobar();,
+-     ac_f77_mangle_type=lowercase,
+-     AC_TRY_LINK(,foobar_();,
+-          ac_f77_mangle_type=lowercase-underscore,
+-          AC_TRY_LINK(,FOOBAR();,
+-               ac_f77_mangle_type=uppercase,
+-               AC_TRY_LINK(,FOOBAR_();,
+-                    ac_f77_mangle_type=uppercase-underscore))))
++AC_TRY_LINK(,foobar();,ac_f77_mangle_type=lowercase)
++AC_TRY_LINK(,foobar_();,ac_f77_mangle_type=lowercase-underscore)
++AC_TRY_LINK(,FOOBAR();,ac_f77_mangle_type=uppercase)
++AC_TRY_LINK(,FOOBAR_();,ac_f77_mangle_type=uppercase-underscore)
++
+ LIBS="$ac_save_LIBS"
+ AC_LANG_RESTORE
+ AC_MSG_RESULT($ac_f77_mangle_type)