clipper version bump

4 files changed, 91 insertions, 1 deletions

diff --git a/sci-libs/clipper/ChangeLog b/sci-libs/clipper/ChangeLog
index d089724eb..3407e337d 100644
--- a/sci-libs/clipper/ChangeLog
+++ b/sci-libs/clipper/ChangeLog
@@ -2,6 +2,12 @@
 # Copyright 1999-2009 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 $
 
+*clipper-20090522 (25 May 2009)
+
+  25 May 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
+  +files/20090522-missing-var.patch, +clipper-20090522.ebuild:
+  version bump and inclusion of some docs
+
 *clipper-20090520 (22 May 2009)
 
   22 May 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
diff --git a/sci-libs/clipper/Manifest b/sci-libs/clipper/Manifest
index 8143dbf86..4c9b36946 100644
--- a/sci-libs/clipper/Manifest
+++ b/sci-libs/clipper/Manifest
@@ -1,10 +1,13 @@
 AUX 20081201-as-needed.patch 3487 RMD160 698e9a72306643e49d6a7165bd3afbbba2ab5d9d SHA1 6ddead8d6c2e45b16bb45d756fce7fc67dd49ac9 SHA256 4fba3f3cd7a0c48c8ce6cc80bd77d4ef4870e6f642f3ea6ff470f0f49809ae56
 AUX 20081201-typo.patch 915 RMD160 4e1eeb005a7100596428154d0cb74b1958c164fb SHA1 a077543e0360efa17fe0d99dd37b1b52ca2926de SHA256 f72b79d8e7678f03ed684821a99ed8ed8f15f2ef7ca621c1fbdde9e8c370bd0d
 AUX 20090520-missing-var.patch 914 RMD160 ae0ffe28b79de0d2f1f6df02d4778f0bdf9e3f1a SHA1 247ed434ed9a17fb28509a1773ad41f4fe6ddc1b SHA256 741192b5bcd211f0a207ff82c3357297b7e624f80c3f9b0efa1c850ee4737727
+AUX 20090522-missing-var.patch 914 RMD160 ae0ffe28b79de0d2f1f6df02d4778f0bdf9e3f1a SHA1 247ed434ed9a17fb28509a1773ad41f4fe6ddc1b SHA256 741192b5bcd211f0a207ff82c3357297b7e624f80c3f9b0efa1c850ee4737727
 DIST clipper-2.1-090210-ac.tar.gz 967967 RMD160 e806be6f28cf2422225037ab01eff0a0f6a381e6 SHA1 0c2ae5ed2336a8fc39e29f094b37fdf87a8173ad SHA256 aafe5a838587b90bf463c3a5d291d4419c3b358927e3e845b44aafcf0856d97e
 DIST clipper-2.1-090520-ac.tar.gz 969990 RMD160 e309b2c815150de731e630d4169cfecd1582c6ca SHA1 fb1e01e7591b0a1faa3e41869cdfb15d486d458f SHA256 d5ba261584f8fd3a7108d060939fb3dd60bdc7b2f139e147684b5ef6b674707c
+DIST clipper-2.1-090522-ac.tar.gz 970014 RMD160 7d88c1f15f716328fd06c7c637d90d5412f3bbf9 SHA1 1a447aeed33a3e16d8552675af9aa89021d6274e SHA256 b784c08207bf31d40e91e2f652eb0e6fe16cc23a7f10f055a60d473488bb37d5
 EBUILD clipper-20090210-r2.ebuild 1447 RMD160 7c409e5555b82bbdb415b778ad519e9f16124e2a SHA1 97aad8411f6769f983ed218c8e92a89c0164dcca SHA256 2caf6169e0b9c36493d1b8140618de6af88886db27dfddb6bcb57ee5200f17dc
 EBUILD clipper-20090210.ebuild 1409 RMD160 40572993a0260d26692f2fbb7b0b70b54d83e915 SHA1 3785c82baf33765b3eb129d4a467b3842ca5a477 SHA256 3eb05ff167984f35aa6bff906a80a23ab8157f418282ad4a30a8c2fc2e4273a8
 EBUILD clipper-20090520.ebuild 1451 RMD160 b2c1ef21b57c2d5e0d6de2ba8092733c199030a3 SHA1 824b2359c86663efd0df6f42668c7a57b6ce226c SHA256 36b8e121c4fe0b7243ec1bd3ebc4cae8b839118146accc46cfe1ca504f943074
-MISC ChangeLog 1683 RMD160 3428d199556a4f9ce02ac807f9be2b588664cda2 SHA1 1e9a747b871a35c678540023d734771ad485ee46 SHA256 bb01952aada02880d7214100fa006ad86756f08cd003c7b7149d98796b972cd5
+EBUILD clipper-20090522.ebuild 1560 RMD160 9e8971d117dc26a5fc9263071fc73c6290720723 SHA1 3ec658af81c237cefaa454e254eccca6a97d9ace SHA256 89b285f222c1aa86f1cc5d8af097fff13dd6e8ca7f0d2cdadec52e8a709b5545
+MISC ChangeLog 1879 RMD160 0ae6434c118a5b2fc81066ffe24e13fba5012564 SHA1 f8ca05dda4e5636faee072defa3a920e336bed78 SHA256 e6d6ac7e438a79ad6676cb9ac9c47f9323a4f738326cc09842fb1a61be148164
 MISC metadata.xml 166 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 SHA1 cb0b513473c0348f4f6f6cd9a132e4884155fddb SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852
diff --git a/sci-libs/clipper/clipper-20090522.ebuild b/sci-libs/clipper/clipper-20090522.ebuild
new file mode 100644
index 000000000..d99fd3a0a
--- /dev/null
+++ b/sci-libs/clipper/clipper-20090522.ebuild
@@ -0,0 +1,63 @@
+# Copyright 1999-2009 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 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 ~ppc ~amd64"
+IUSE=""
+RDEPEND="sci-libs/ccp4-libs"
+DEPEND="${RDEPEND}"
+S=${WORKDIR}/clipper-2.1
+
+src_unpack() {
+	unpack ${A}
+	cd "${S}"
+
+	# ccp4 provides these, and more.
+	sed -i -e "s:examples::g" "${S}"/Makefile.am
+
+	epatch "${FILESDIR}"/20081201-as-needed.patch \
+		"${FILESDIR}"/${PV}-missing-var.patch
+
+	AT_M4DIR="config" eautoreconf
+}
+
+src_compile() {
+	# Recommended on ccp4bb/coot ML to fix crashes when calculating maps
+	# on 64-bit systems
+	append-flags -fno-strict-aliasing
+
+	# Slot programs with a '-2' suffix
+	econf \
+		--enable-contrib \
+		--enable-phs \
+		--enable-mmdb \
+		--with-mmdb=/usr \
+		--enable-minimol \
+		--enable-cif \
+		--enable-ccp4 \
+		--enable-cns \
+		|| die
+	# We don't have a cctbx ebuild yet
+	#		--enable-cctbx \
+
+	emake || die
+}
+
+src_test() {
+	cd examples
+	emake || die
+	./maketestdata || die "test failed"
+}
+
+src_install() {
+	emake DESTDIR="${D}" install || die
+	dodoc README ChangeLog NEWS
+}
diff --git a/sci-libs/clipper/files/20090522-missing-var.patch b/sci-libs/clipper/files/20090522-missing-var.patch
new file mode 100644
index 000000000..ace86b777
--- /dev/null
+++ b/sci-libs/clipper/files/20090522-missing-var.patch
@@ -0,0 +1,18 @@
+--- clipper-config.in	2009-02-10 18:42:47.000000000 +0100
++++ clipper-config.in.new	2009-05-20 14:30:52.000000000 +0200
+@@ -79,13 +79,13 @@
+ 
+ if test "$echo_cflags" = "yes" ; then
+  # and include mccp4 cflags? yes
+- cflags="-I${includedir} @CCP4_CXXFLAGS@ @MCCP4_CXXFLAGS@ @MMDB_CXXFLAGS@ @FFTW_CXXFLAGS@"
++ cflags="-I${includedir} @CCP4_CXXFLAGS@ @MMDB_CXXFLAGS@ @FFTW_CXXFLAGS@"
+  echo $cflags
+ fi
+ 
+ if test "$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