Version Bump, fix for bug 246293 & bug 250087

Removed old versions
Package-Manager: portage-2.2_rc62/cvs/Linux x86_64

6 files changed, 100 insertions, 149 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/Manifest b/sci-libs/clipper/Manifest
index 551b6dff60f3..b7501b72336c 100644
--- a/sci-libs/clipper/Manifest
+++ b/sci-libs/clipper/Manifest
@@ -1,8 +1,17 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
 AUX 20070528-as-needed.patch 884 RMD160 9bf79566b547f700b136c645c59b6aaf7126880f SHA1 6bbe32356d0cc6a1737dbfa8d0e68792f2b61ae7 SHA256 e6654df312419335c0e1886a23b685462f5ce08f5745e36f78f29a509fd6acbd
 AUX 20070907-as-needed.patch 1879 RMD160 fb87f61edb1e0abc09eb60d8702f3c0536dbefa5 SHA1 699ea4c3e8ada36b8f597f660e23c5bd07002796 SHA256 799740dcacb98ba2f00a9f57c909e213d5d3b620fdfd8149dbe652a27a8d6d62
-DIST clipper20ac.latest-20070528.tar.gz 1121873 RMD160 fe0db88ebdff7beebe947a29ec3f07732d19ebfc SHA1 ac4095e1968831b74cc45141144883b1fb27d948 SHA256 9da6189965b8742b35af8bece8575938c5257eb5bf81eae296726c31e0569691
-DIST clipper20ac.latest-20070907.tar.gz 1123329 RMD160 c150042c858d17d0f3e59717aedf532e9488d68d SHA1 feb1eee652fc8b41b9550846509361e56c232875 SHA256 c33454ec0d1f1dc394a286708d8928e7c2e49c6c0366305a22947f0544b275fd
-EBUILD clipper-20070528.ebuild 1925 RMD160 1bb564219d907c340cf30f803d7838e59b17d0d8 SHA1 5ac2cf74f3315ca40e88c34adf7b34d19df1d5a8 SHA256 46be23809a5196623f76510a706385f16d323c771ca2e5928d889d65196b2a0e
-EBUILD clipper-20070907.ebuild 2050 RMD160 82596ac56885e33f1d63e6a8dd003f9def71850f SHA1 2f4f0e3541f4fb22df25e2a7c853236b8c213d09 SHA256 e5d25c883c4651b55b99169b4d2910820e27a03431b5baa21b7cbdbe2ad679ce
-MISC ChangeLog 893 RMD160 5724a442cc483300461f839c5030e93627da87db SHA1 c6df530f02a1eefa5708bf0324c6746305752663 SHA256 9165ffb7b83c3df8d6a5611b8969f20dd6dfd1388a2f45ddb4dfdf436ed3a7d8
+AUX 20091215-missing-var.patch 663 RMD160 ef35c47c98f599f2633f90c12bccd8691d994954 SHA1 e3d2df3b82ba359e95930c09e86a6449e885fb1f SHA256 abb3e83e3bcdfa1ba4ce8d382a8f490e70c2c761d574484a38741bba438a00d4
+DIST clipper-2.1-091215-ac.tar.gz 991480 RMD160 de1c64634ddfa33dd8877138734905518b527964 SHA1 50dc24186bc3cbe798c0e7a68e43cfb62fec4127 SHA256 395f0338ca405805fa577d19105430cc740630ab8eea37d753864722a157ed85
+EBUILD clipper-20091215.ebuild 1447 RMD160 6bade86df00618aae7810df0fd4c2d711fa0cf13 SHA1 f916c52425c709ffce2cf8c7370bec2eeb6b9bf3 SHA256 fef20b30a819139e912842dc731e0548d9342828967a501f88e5d54e369e597e
+MISC ChangeLog 1160 RMD160 372dabc5226f2163995eb92ddbb0fb5699d4519f SHA1 e787fe948f55932057d62a6d35c80d3245cb8950 SHA256 2892d6588bf7a459b6598bf133acff2e554446f666cb84b001553c3d7117cc60
 MISC metadata.xml 166 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 SHA1 cb0b513473c0348f4f6f6cd9a132e4884155fddb SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.14 (GNU/Linux)
+
+iEYEARECAAYFAktrO5QACgkQgAnW8HDreRYwzwCfWUpHGSqvY6tss+gi4NymgV1j
+KVwAoKebA4/NjnDix3dtT9648myrYMK2
+=QTMx
+-----END PGP SIGNATURE-----
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