Bump as a dependency of Coot 0.4 prereleases.

Package-Manager: portage-2.1.4_rc9

5 files changed, 157 insertions, 5 deletions

diff --git a/sci-libs/clipper/ChangeLog b/sci-libs/clipper/ChangeLog
index 71abe4d931db..7d693eda4475 100644
--- a/sci-libs/clipper/ChangeLog
+++ b/sci-libs/clipper/ChangeLog
@@ -1,6 +1,12 @@
 # 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 1.2 2007/05/30 22:00:27 dberkholz Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/clipper/ChangeLog,v 1.3 2007/12/19 18:43:12 dberkholz Exp $
+
+*clipper-20070907 (19 Dec 2007)
+
+  19 Dec 2007; Donnie Berkholz <dberkholz@gentoo.org>;
+  +files/20070907-as-needed.patch, +clipper-20070907.ebuild:
+  Bump as a dependency of Coot 0.4 prereleases.
 
   30 May 2007; Donnie Berkholz <dberkholz@gentoo.org>;
   clipper-20070528.ebuild:
diff --git a/sci-libs/clipper/Manifest b/sci-libs/clipper/Manifest
index a873ccec1a05..1bacf0543bbf 100644
--- a/sci-libs/clipper/Manifest
+++ b/sci-libs/clipper/Manifest
@@ -1,16 +1,28 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
 AUX 20070528-as-needed.patch 884 RMD160 9bf79566b547f700b136c645c59b6aaf7126880f SHA1 6bbe32356d0cc6a1737dbfa8d0e68792f2b61ae7 SHA256 e6654df312419335c0e1886a23b685462f5ce08f5745e36f78f29a509fd6acbd
 MD5 02986c51c33f3b22465bb5a6e01e812a files/20070528-as-needed.patch 884
 RMD160 9bf79566b547f700b136c645c59b6aaf7126880f files/20070528-as-needed.patch 884
 SHA256 e6654df312419335c0e1886a23b685462f5ce08f5745e36f78f29a509fd6acbd files/20070528-as-needed.patch 884
+AUX 20070907-as-needed.patch 1879 RMD160 fb87f61edb1e0abc09eb60d8702f3c0536dbefa5 SHA1 699ea4c3e8ada36b8f597f660e23c5bd07002796 SHA256 799740dcacb98ba2f00a9f57c909e213d5d3b620fdfd8149dbe652a27a8d6d62
+MD5 645b3899eafcf653eb49fa3e644982df files/20070907-as-needed.patch 1879
+RMD160 fb87f61edb1e0abc09eb60d8702f3c0536dbefa5 files/20070907-as-needed.patch 1879
+SHA256 799740dcacb98ba2f00a9f57c909e213d5d3b620fdfd8149dbe652a27a8d6d62 files/20070907-as-needed.patch 1879
 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
 MD5 5c49bc13d5dbe45951d4a17512f87923 clipper-20070528.ebuild 1925
 RMD160 1bb564219d907c340cf30f803d7838e59b17d0d8 clipper-20070528.ebuild 1925
 SHA256 46be23809a5196623f76510a706385f16d323c771ca2e5928d889d65196b2a0e clipper-20070528.ebuild 1925
-MISC ChangeLog 695 RMD160 611fc5643f69c73d7c89290f397415e4b8a9c8b5 SHA1 f5e757817aca0ef060c2babcb885bc80ff957fc4 SHA256 28b67ae4e751ee836cad45ee34c25082d212cab0e98ce2cb948980df676aa8d7
-MD5 372b958d2d2d3f87b6f70d9ac021d053 ChangeLog 695
-RMD160 611fc5643f69c73d7c89290f397415e4b8a9c8b5 ChangeLog 695
-SHA256 28b67ae4e751ee836cad45ee34c25082d212cab0e98ce2cb948980df676aa8d7 ChangeLog 695
+EBUILD clipper-20070907.ebuild 2050 RMD160 82596ac56885e33f1d63e6a8dd003f9def71850f SHA1 2f4f0e3541f4fb22df25e2a7c853236b8c213d09 SHA256 e5d25c883c4651b55b99169b4d2910820e27a03431b5baa21b7cbdbe2ad679ce
+MD5 35a8a97d963f231cd076be1428cae259 clipper-20070907.ebuild 2050
+RMD160 82596ac56885e33f1d63e6a8dd003f9def71850f clipper-20070907.ebuild 2050
+SHA256 e5d25c883c4651b55b99169b4d2910820e27a03431b5baa21b7cbdbe2ad679ce clipper-20070907.ebuild 2050
+MISC ChangeLog 893 RMD160 5724a442cc483300461f839c5030e93627da87db SHA1 c6df530f02a1eefa5708bf0324c6746305752663 SHA256 9165ffb7b83c3df8d6a5611b8969f20dd6dfd1388a2f45ddb4dfdf436ed3a7d8
+MD5 7970c59be16d2060b45df43e3cc2ab31 ChangeLog 893
+RMD160 5724a442cc483300461f839c5030e93627da87db ChangeLog 893
+SHA256 9165ffb7b83c3df8d6a5611b8969f20dd6dfd1388a2f45ddb4dfdf436ed3a7d8 ChangeLog 893
 MISC metadata.xml 166 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 SHA1 cb0b513473c0348f4f6f6cd9a132e4884155fddb SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852
 MD5 43628e9f5743b5c3b018a82669a76bc7 metadata.xml 166
 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 metadata.xml 166
@@ -18,3 +30,13 @@ SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852 metadata
 MD5 2f7dee8b7b0f8a283ac3d13d89668dfb files/digest-clipper-20070528 286
 RMD160 d3b0b0d6403742cbc2f8dc4c01ef01e82225e61b files/digest-clipper-20070528 286
 SHA256 96147e14b267907488da11c4d86ed35814dded7ff172743ea34d5df3864029ea files/digest-clipper-20070528 286
+MD5 ca456f4a519f13c046aaca32ffae82c6 files/digest-clipper-20070907 286
+RMD160 f1a8740789463868bd633349c32c47675f12efeb files/digest-clipper-20070907 286
+SHA256 a8d546246e0d097dd210f3b34db90f495a2fe94e414ec705ffdee0b03e4a6243 files/digest-clipper-20070907 286
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.7 (GNU/Linux)
+
+iD8DBQFHaWZJXVaO67S1rtsRAvHCAKD3I4BfmOXium9O64i6MHDiza2z7gCgvXyK
+10TJeArO0ca4CuJTVfdfiAY=
+=Oy0P
+-----END PGP SIGNATURE-----
diff --git a/sci-libs/clipper/clipper-20070907.ebuild b/sci-libs/clipper/clipper-20070907.ebuild
new file mode 100644
index 000000000000..103dff060a39
--- /dev/null
+++ b/sci-libs/clipper/clipper-20070907.ebuild
@@ -0,0 +1,74 @@
+# 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/files/20070907-as-needed.patch b/sci-libs/clipper/files/20070907-as-needed.patch
new file mode 100644
index 000000000000..b8c7103bdf12
--- /dev/null
+++ b/sci-libs/clipper/files/20070907-as-needed.patch
@@ -0,0 +1,47 @@
+diff -urN clipper.orig/clipper/ccp4/Makefile.am clipper/clipper/ccp4/Makefile.am
+--- clipper.orig/clipper/ccp4/Makefile.am	2007-11-13 15:16:40.000000000 -0800
++++ clipper/clipper/ccp4/Makefile.am	2007-11-13 17:30:00.000000000 -0800
+@@ -12,6 +12,6 @@
+ 
+ library_includedir = $(pkgincludedir)/ccp4
+ 
+-libclipper_ccp4_la_LDFLAGS = -version-info @CLIPPER_LT_VERSION@
++libclipper_ccp4_la_LDFLAGS = -version-info @CLIPPER_LT_VERSION@ $(CCP4_LIBS)
+ 
+ ####
+diff -urN clipper.orig/clipper/core/Makefile.am clipper/clipper/core/Makefile.am
+--- clipper.orig/clipper/core/Makefile.am	2007-11-13 15:16:40.000000000 -0800
++++ clipper/clipper/core/Makefile.am	2007-11-13 17:30:00.000000000 -0800
+@@ -29,6 +29,6 @@
+ 
+ lib_LTLIBRARIES = libclipper-core.la
+ 
+-libclipper_core_la_LDFLAGS = -version-info @CLIPPER_LT_VERSION@
++libclipper_core_la_LDFLAGS = -version-info @CLIPPER_LT_VERSION@ $(FFTW_LIBS)
+ 
+ ####
+diff -urN clipper.orig/clipper/minimol/Makefile.am clipper/clipper/minimol/Makefile.am
+--- clipper.orig/clipper/minimol/Makefile.am	2007-11-13 15:16:40.000000000 -0800
++++ clipper/clipper/minimol/Makefile.am	2007-11-13 19:22:44.000000000 -0800
+@@ -24,6 +24,7 @@
+ 
+ library_includedir = $(pkgincludedir)/minimol
+ 
+-libclipper_minimol_la_LDFLAGS = -version-info @CLIPPER_LT_VERSION@
++libclipper_minimol_la_LDFLAGS = -version-info @CLIPPER_LT_VERSION@ \
++	$(top_builddir)/clipper/mmdb/libclipper-mmdb.la
+ 
+ ####
+diff -urN clipper.orig/clipper/mmdb/Makefile.am clipper/clipper/mmdb/Makefile.am
+--- clipper.orig/clipper/mmdb/Makefile.am	2007-11-13 15:16:40.000000000 -0800
++++ clipper/clipper/mmdb/Makefile.am	2007-11-13 19:22:15.000000000 -0800
+@@ -9,7 +9,8 @@
+ 
+ library_includedir = $(pkgincludedir)/mmdb
+ 
+-libclipper_mmdb_la_LDFLAGS = -version-info @CLIPPER_LT_VERSION@
++libclipper_mmdb_la_LDFLAGS = -version-info @CLIPPER_LT_VERSION@ \
++	$(MMDB_LIBS)
+ 
+ EXTRA_DIST = clipper_mmdb_dox
+ 
diff --git a/sci-libs/clipper/files/digest-clipper-20070907 b/sci-libs/clipper/files/digest-clipper-20070907
new file mode 100644
index 000000000000..87b7c03b74ba
--- /dev/null
+++ b/sci-libs/clipper/files/digest-clipper-20070907
@@ -0,0 +1,3 @@
+MD5 cf5746cd7e040180c1e4cb429c7b2ac1 clipper20ac.latest-20070907.tar.gz 1123329
+RMD160 c150042c858d17d0f3e59717aedf532e9488d68d clipper20ac.latest-20070907.tar.gz 1123329
+SHA256 c33454ec0d1f1dc394a286708d8928e7c2e49c6c0366305a22947f0544b275fd clipper20ac.latest-20070907.tar.gz 1123329