Version Bump, fix for bug 246293 & bug 250087

Removed old versions
(Portage version: 2.2_rc62/cvs/Linux x86_64)

5 files changed, 86 insertions, 144 deletions

diff --git a/sci-libs/clipper/ChangeLog b/sci-libs/clipper/ChangeLog
index 7d693eda4475..1d3a17d6445d 100644
--- a/sci-libs/clipper/ChangeLog
+++ b/sci-libs/clipper/ChangeLog
@@ -1,6 +1,14 @@
 # ChangeLog for sci-libs/clipper
-# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/clipper/ChangeLog,v 1.3 2007/12/19 18:43:12 dberkholz Exp $
+# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/clipper/ChangeLog,v 1.4 2010/02/04 21:26:38 jlec Exp $
+
+*clipper-20091215 (04 Feb 2010)
+
+  04 Feb 2010; Justin Lecher (jlec) <jlec@gentoo.org>
+  +files/20091215-missing-var.patch, -clipper-20070528.ebuild,
+  -clipper-20070907.ebuild, +clipper-20091215.ebuild:
+  Version Bump, fix for bug 246293 & 250087
+  Removed old versions
 
 *clipper-20070907 (19 Dec 2007)
 
diff --git a/sci-libs/clipper/clipper-20070528.ebuild b/sci-libs/clipper/clipper-20070528.ebuild
deleted file mode 100644
index 428349f6e2ff..000000000000
--- a/sci-libs/clipper/clipper-20070528.ebuild
+++ /dev/null
@@ -1,68 +0,0 @@
-# Copyright 1999-2007 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/clipper/clipper-20070528.ebuild,v 1.2 2007/05/30 22:00:27 dberkholz Exp $
-
-inherit autotools
-
-DESCRIPTION="Aset of object-oriented libraries for the organisation of crystallographic data and the performance of crystallographic computation"
-HOMEPAGE="http://www.ysbl.york.ac.uk/~cowtan/clipper/clipper.html"
-#SRC_URI="http://www.ysbl.york.ac.uk/~cowtan/clipper/clipper20ac.latest.tar.gz"
-SRC_URI="http://dev.gentoo.org/~dberkholz/distfiles/clipper20ac.latest-${PV}.tar.gz"
-LICENSE="LGPL-2.1"
-SLOT="0"
-KEYWORDS="~x86 ~ppc"
-IUSE=""
-RDEPEND="sci-chemistry/ccp4"
-DEPEND="${RDEPEND}"
-S="${WORKDIR}"
-
-src_unpack() {
-	unpack ${A}
-
-	epatch "${FILESDIR}"/${PV}-as-needed.patch
-
-	# Slot libraries with a '-2' suffix so we don't overlap with ccp4
-	ebegin "versioning libraries with -2 suffix"
-		find . -name Makefile.am \
-			| xargs sed -i \
-				-e "s~\(lib[[:alnum:]_]*\)_la~\1_2_la~g" \
-				-e "s~\(lib[[:alnum:]-]*\).la~\1-2.la~g" \
-				-e "s~\(-lclipper[[:alnum:]-]*\)~\1-2~g" \
-				|| die "sed to version libs with -2 failed"
-	eend $?
-
-	AT_M4DIR="config" eautoreconf
-}
-
-src_compile() {
-	# Slot programs with a '-2' suffix
-	econf \
-		--enable-contrib \
-		--enable-phs \
-		--enable-mmdb \
-		--enable-mmdbold \
-		--enable-minimol \
-		--enable-cif \
-		--enable-ccp4 \
-		--enable-cns \
-		--with-mmdb=/usr \
-		--program-suffix=-2 \
-		|| die "econf failed"
-	emake || die "emake failed"
-}
-src_install() {
-	# Slot includes with a '-2' suffix
-	emake \
-		DESTDIR="${D}" \
-		pkgincludedir=/usr/include/clipper-2 \
-		install \
-		|| die "emake install failed"
-
-	# Use '-2' suffix in headers
-	ebegin "changing headers to use -2 suffix"
-	grep 'include.*clipper' -rl "${D}" \
-		| xargs sed -i \
-			-e "s~\(include.*clipper\)/~\1-2/~g" \
-			|| die "sed to find -2 slotted headers failed"
-	eend $?
-}
diff --git a/sci-libs/clipper/clipper-20070907.ebuild b/sci-libs/clipper/clipper-20070907.ebuild
deleted file mode 100644
index 103dff060a39..000000000000
--- a/sci-libs/clipper/clipper-20070907.ebuild
+++ /dev/null
@@ -1,74 +0,0 @@
-# Copyright 1999-2007 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/clipper/clipper-20070907.ebuild,v 1.1 2007/12/19 18:43:12 dberkholz Exp $
-
-inherit autotools
-
-DESCRIPTION="Object-oriented libraries for the organisation of crystallographic data and the performance of crystallographic computation"
-HOMEPAGE="http://www.ysbl.york.ac.uk/~cowtan/clipper/clipper.html"
-#SRC_URI="http://www.ysbl.york.ac.uk/~cowtan/clipper/clipper20ac.latest.tar.gz"
-SRC_URI="http://dev.gentoo.org/~dberkholz/distfiles/clipper20ac.latest-${PV}.tar.gz"
-LICENSE="LGPL-2.1"
-SLOT="0"
-KEYWORDS="~x86 ~ppc"
-IUSE=""
-RDEPEND="sci-chemistry/ccp4"
-DEPEND="${RDEPEND}"
-S=${WORKDIR}
-
-src_unpack() {
-	unpack ${A}
-
-	epatch "${FILESDIR}"/${PV}-as-needed.patch
-
-	# Slot libraries with a '-2' suffix so we don't overlap with ccp4
-	ebegin "versioning libraries with -2 suffix"
-		find . -name Makefile.am \
-			| xargs sed -i \
-				-e "s~\(lib[[:alnum:]_]*\)_la~\1_2_la~g" \
-				-e "s~\(lib[[:alnum:]-]*\).la~\1-2.la~g" \
-				-e "s~\(-lclipper[[:alnum:]-]*\)~\1-2~g" \
-				|| die "sed to version libs with -2 failed"
-	eend $?
-
-	AT_M4DIR="config" eautoreconf
-}
-
-src_compile() {
-	# Slot programs with a '-2' suffix
-	econf \
-		--enable-contrib \
-		--enable-phs \
-		--enable-mmdb \
-		--with-mmdb=/usr \
-		--enable-mmdbold \
-		--enable-minimol \
-		--enable-cif \
-		--enable-ccp4 \
-		--enable-cns \
-		--program-suffix=-2 \
-		|| die
-	# We don't have a cctbx ebuild yet
-	#		--enable-cctbx \
-	# This is a GPL replacement for CCP4 libraries
-	# http://www.bioxray.dk/~mok/node/100
-	#		--enable-gpp4 \
-
-	emake || die
-}
-src_install() {
-	# Slot includes with a '-2' suffix
-	emake \
-		DESTDIR="${D}" \
-		pkgincludedir=/usr/include/clipper-2 \
-		install \
-		|| die "emake install failed"
-
-	# Use '-2' suffix in headers
-	ebegin "changing headers to use -2 suffix"
-	grep 'include.*clipper' -rl "${D}" \
-		| xargs sed -i \
-			-e "s~\(include.*clipper\)/~\1-2/~g" \
-			|| die "sed to find -2 slotted headers failed"
-	eend $?
-}
diff --git a/sci-libs/clipper/clipper-20091215.ebuild b/sci-libs/clipper/clipper-20091215.ebuild
new file mode 100644
index 000000000000..b41eea306c9d
--- /dev/null
+++ b/sci-libs/clipper/clipper-20091215.ebuild
@@ -0,0 +1,63 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/clipper/clipper-20091215.ebuild,v 1.1 2010/02/04 21:26:38 jlec Exp $
+
+EAPI="3"
+
+WANT_AUTOMAKE="1.11"
+
+inherit autotools eutils flag-o-matic
+
+DESCRIPTION="Object-oriented libraries for the organisation of crystallographic data and the performance of crystallographic computation"
+HOMEPAGE="http://www.ysbl.york.ac.uk/~cowtan/clipper/clipper.html"
+# Transform 4-digit year to 2 digits
+SRC_URI="http://www.ysbl.york.ac.uk/~cowtan/clipper/clipper-2.1-${PV:2:${#PV}}-ac.tar.gz"
+
+LICENSE="LGPL-2.1"
+SLOT="0"
+KEYWORDS="~x86 ~amd64"
+IUSE="debug"
+
+RDEPEND="
+	sci-libs/ccp4-libs
+	sci-libs/fftw"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}"/${PN}-2.1
+
+src_prepare() {
+	epatch "${FILESDIR}"/${PV}-missing-var.patch
+
+	# ccp4 provides these, and more.
+	sed -i -e "s:examples::g" "${S}"/Makefile.am
+
+	AT_M4DIR="config" eautoreconf
+}
+
+src_configure() {
+	# Recommended on ccp4bb/coot ML to fix crashes when calculating maps
+	# on 64-bit systems
+	append-flags -fno-strict-aliasing
+
+	econf \
+		--enable-ccp4 \
+		--enable-cif \
+		--enable-cns \
+		--enable-contrib \
+		--enable-minimol \
+		--enable-mmdb \
+		--enable-phs \
+		--with-mmdb=${EPREFIX}/usr \
+		$(use_enable debug)
+}
+
+src_test() {
+	emake \
+		-C examples \
+		check || die
+}
+
+src_install() {
+	emake DESTDIR="${D}" install || die
+	dodoc README ChangeLog NEWS || die
+}
diff --git a/sci-libs/clipper/files/20091215-missing-var.patch b/sci-libs/clipper/files/20091215-missing-var.patch
new file mode 100644
index 000000000000..9ba4b007e9d0
--- /dev/null
+++ b/sci-libs/clipper/files/20091215-missing-var.patch
@@ -0,0 +1,13 @@
+diff --git a/clipper-config.in b/clipper-config.in
+index df0b77b..3ae536e 100644
+--- a/clipper-config.in
++++ b/clipper-config.in
+@@ -84,7 +84,7 @@ fi
+ 
+ if test "$echo_libs" = "yes" ; then
+  # note BOOST_LIBS should be part of CCTBX_LIBS
+- libs="-lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-cif -lclipper-contrib -lclipper-ccp4 -lclipper-phs -lclipper-core @CCP4_LIBS@ @MMDB_LIBS@ @FFTW_LIBS@ @CCTBX_LIBS@"
++ libs="-lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-cif -lclipper-contrib -lclipper-ccp4 -lclipper-phs -lclipper-core @CCP4_LIBS@ @MMDB_LIBS@ @FFTW_LIBS@"
+  if test "${libdir}" != "/usr/lib" ; then
+   echo -L${libdir} $libs
+  else