ccp4-apps

transmission ccp4 --> ccp4-apps and ccp4 as meta package

5 files changed, 62 insertions, 20 deletions

diff --git a/sci-chemistry/ccp4-apps/ChangeLog b/sci-chemistry/ccp4-apps/ChangeLog
index 5d239ff57..139b7e0a3 100644
--- a/sci-chemistry/ccp4-apps/ChangeLog
+++ b/sci-chemistry/ccp4-apps/ChangeLog
@@ -1,7 +1,12 @@
-# ChangeLog for sci-chemistry/ccp4
+# ChangeLog for sci-chemistry/ccp4-apps
 # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  03 Aug 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
+  files/6.1.2-dont-build-libs.patch, ccp4-apps-6.1.2.ebuild,
+  +files/6.1.2-gcc4.4.patch:
+  transmission ccp4 --> ccp4-apps and ccp4 as meta package
+
 *ccp4-6.1.1-r6 (07 Jul 2009)
 
   07 Jul 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
diff --git a/sci-chemistry/ccp4-apps/Manifest b/sci-chemistry/ccp4-apps/Manifest
index f1204695a..0f3623554 100644
--- a/sci-chemistry/ccp4-apps/Manifest
+++ b/sci-chemistry/ccp4-apps/Manifest
@@ -1,13 +1,14 @@
 AUX 6.1.2-clipper-mmdbold-ggc-4.3.patch 656 RMD160 6b302779b48217a14f5ac9110bc307db3a3b51eb SHA1 f5813d6769fa9dc11605425cdbda85691d3016bc SHA256 982eff0336a6dfaf4e280d51a59cf722fc063ca89d15ca0af46ce83727fb9a8a
 AUX 6.1.2-dont-build-double-and-make-bindir.patch 688 RMD160 f5f93cbec122ce81a1ddb1cf57a852d51fa5e5d6 SHA1 4c924554c5c1991ed691fe3474eeffbd108493a9 SHA256 037a3d9042c784c895083fe5348ed3bde74620c1b6b3b2cd4eea53bdbfe77d53
-AUX 6.1.2-dont-build-libs.patch 1255 RMD160 6454c2f61a13dbb8238b5ceed69c233fcf336ed4 SHA1 ff23480016731940279b8742707024f5a6e10bf3 SHA256 0d4a083d6c6bce38db0b84f9dccf0f339d746f9c0dd316eeb745f8427401be75
+AUX 6.1.2-dont-build-libs.patch 1266 RMD160 95d2960fbd2f3d8661187ea9ed7ffc5f2f30e61f SHA1 7b5fa26432f57a11c8bedff79209f687b6bd95cb SHA256 329d29c58e18403105ed06fdd6b012a481b7c2b43af53b86395204b2acea51ed
 AUX 6.1.2-dont-build-scala.patch 2195 RMD160 c09296e33acb2f10d69c8543163606d5867ba15f SHA1 a6bcbc519edeac0cfd47f677d8d6c79aa2a3b02a SHA256 73d4af040eef67e597b11877cc3719f5b15c5e357c3882449dc993a84857c4a3
 AUX 6.1.2-dont-make-dirs-in-configure.patch 2866 RMD160 ba49e45ab609a42a2d93b96f55af913bf9625610 SHA1 36c9329c3768c08687ef062c9ab649d32833b422 SHA256 1b5997f17526a4fd60ffa9eccf4b765aadf3a78c9394657000e0454f364240ca
 AUX 6.1.2-fix-setup-bash-incompatibility.patch 422 RMD160 e7e886ab030cf3324302c8fd0c866b48eeb34f8c SHA1 4e549abcd3ced1e6ecf9d3f2bddfed70425d61aa SHA256 109a0e806f9c0e1b8bf5e5f0c58be6f1dae06396b62ee4dae9f579ff7dcb5a01
+AUX 6.1.2-gcc4.4.patch 1006 RMD160 5d66b599da41649b836080f18dcea292917c88eb SHA1 0d7ed670e46f8433555fe63b0b7443fa27f42b0f SHA256 09d0cc3333e75d85ef057ba4f239e2c79ed76623cfa7ecc6e62a813d9bac2423
 AUX 6.1.2-nomolref.patch 559 RMD160 93a81aec6548fa909c67546958878fc27632b392 SHA1 e16dafd552839128f81bc2e8e8f9953258e1c398 SHA256 1ba59db41f93c02494beb7a5d816dea966341009344805df4dfb873ab4e98eca
 AUX 6.1.2-rename-rapper.patch 2856 RMD160 37504bed3cb4e1858d88331305deef6564616b02 SHA1 31f513c987e1408b868f8c9de4aaa9f2c35cb378 SHA256 d9fed1ec65089c4130358aeed771b32c1253e48a73e90f0ce7b92bd0abbb0c2b
 AUX 6.1.2-rename-truncate.patch 1515 RMD160 eff332faa67a1732e0f99cc6cdcb846932eadc87 SHA1 b504542cf710e1b54a684b0fa0e8d73d967c96ac SHA256 50a59a1856867daa3de1f8f53e92bcfe74dea3a6d3c4ba238a9ea83dbcdfbf07
 DIST ccp4-6.1.2-core-src.tar.gz 247203373 RMD160 d2ead65da0a2561a8a256cdaa15a6b1a02b6d49e SHA1 fe94461fcafa7074231e01221760e24bb886d605 SHA256 875137beb74cb385b89fe3e49feeda78330c175861a590ee5f7cdbec26bc0e8a
-EBUILD ccp4-apps-6.1.2.ebuild 9837 RMD160 72f50158de5e577927157bd4e908bba709840377 SHA1 f52cfbfdf6b020e318a75954f9dd7260b8e80056 SHA256 8f76f655d60b7a78db5a85889c1e03885e0a8a7326f3d0e613cd35782c1da75c
-MISC ChangeLog 5725 RMD160 a561282ea9bd67da0b6e17eaaf47d559c711b055 SHA1 23ba90946cda15225ebabf48309e41267d30f22e SHA256 0b9ab8e5fe091a7a79a394c355e7d253711b08f7f0ce4fbb65e4860d30229308
+EBUILD ccp4-apps-6.1.2.ebuild 10010 RMD160 83994ee0362055614365b9826447b3958bd3152f SHA1 de727c1e2bacec2f428b0e08feec4cd2281e6c85 SHA256 71abc6ff2b5e075117258e3bc51d3c2ff60b39839be2f24fb20d03e96adef81d
+MISC ChangeLog 5937 RMD160 6edb135e374358d2f4f5c5174d0d142ad0783c90 SHA1 132bd54847a869c0e5e369fec89067718b51858c SHA256 0dd7ab9bccd495d68ba6f8a0777179dfc64202348df20ded040117df0820b580
 MISC metadata.xml 166 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 SHA1 cb0b513473c0348f4f6f6cd9a132e4884155fddb SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852
diff --git a/sci-chemistry/ccp4-apps/ccp4-apps-6.1.2.ebuild b/sci-chemistry/ccp4-apps/ccp4-apps-6.1.2.ebuild
index 0487237aa..8e5ee5ca4 100644
--- a/sci-chemistry/ccp4-apps/ccp4-apps-6.1.2.ebuild
+++ b/sci-chemistry/ccp4-apps/ccp4-apps-6.1.2.ebuild
@@ -29,9 +29,9 @@ DESCRIPTION="Protein X-ray crystallography toolkit"
 HOMEPAGE="http://www.ccp4.ac.uk/"
 RESTRICT="mirror"
 SRC_URI="${SRC}/${PV}/${MY_P}-core-src.tar.gz"
-# plain files which were copied over
+# patch tarball from upstream
 	[[ -n ${UPDATE} ]] && SRC_URI="${SRC_URI} ${SRC}/${PV}/updates/${P}-src-patch-${UPDATE}.tar.gz"
-# real patches
+# patches created by us
 	[[ -n ${PATCHDATE} ]] && SRC_URI="${SRC_URI} http://dev.gentooexperimental.org/~jlec/science-dist/${PV}-${PATCHDATE}-updates.patch.bz2"
 
 for i in $(seq $PATCH_TOT); do
@@ -84,7 +84,8 @@ RDEPEND="X? ( ${X11DEPS} )
 	dev-python/pyxml
 	dev-libs/libxml2
 	dev-libs/boehm-gc
-	!app-office/sc"
+	!app-office/sc
+	!<sci-chemistry/ccp4-6.1.2"
 DEPEND="${RDEPEND}
 	=sys-devel/automake-1.6*
 	X? (
@@ -93,7 +94,7 @@ DEPEND="${RDEPEND}
 		x11-proto/xextproto
 	)"
 
-S="${WORKDIR}/${PN}-${PV}"
+S="${WORKDIR}/${PN/-apps}-${PV}"
 
 src_unpack() {
 	unpack ${A}
@@ -141,6 +142,9 @@ src_unpack() {
 	# We build scala ourself
 	ccp_patch "${FILESDIR}"/${PV}-dont-build-scala.patch
 
+	# gcc-4.3.3
+	ccp_patch "${FILESDIR}"/${PV}-gcc4.4.patch
+
 	einfo "Done." # done applying Gentoo patches
 	echo
 
@@ -303,10 +307,11 @@ src_install() {
 
 	# Setup scripts
 	insinto /etc/profile.d
-	newins "${S}"/include/ccp4.setup-bash ccp4.setup.sh || die
-	newins "${S}"/include/ccp4.setup-dist ccp4.setup.csh || die
-	rm -f "${S}"/include/ccp4.setup-bash
-	rm -f "${S}"/include/ccp4.setup-dist
+#	newins "${S}"/include/ccp4.setup-bash ccp4.setup.bash || die
+	newins "${S}"/include/ccp4.setup-csh ccp4.setup.csh || die
+#	newins "${S}"/include/ccp4.setup-zsh ccp4.setup.zsh || die
+	newins "${S}"/include/ccp4.setup-sh ccp4.setup.sh || die
+	rm -f "${S}"/include/ccp4.setup*
 
 	# Environment files, setup scripts, etc.
 	insinto /usr/share/ccp4/include
diff --git a/sci-chemistry/ccp4-apps/files/6.1.2-dont-build-libs.patch b/sci-chemistry/ccp4-apps/files/6.1.2-dont-build-libs.patch
index 5859093e7..2ef878bc1 100644
--- a/sci-chemistry/ccp4-apps/files/6.1.2-dont-build-libs.patch
+++ b/sci-chemistry/ccp4-apps/files/6.1.2-dont-build-libs.patch
@@ -1,20 +1,20 @@
---- ./Makefile.in.orig	2008-08-01 10:27:23.000000000 -0700
-+++ ./Makefile.in	2008-08-01 14:30:22.000000000 -0700
-@@ -3,7 +3,7 @@
- # $Header: /nfs/ccpdisk/xtal/CVSROOT/ccp4/Makefile.in,v 1.57 2008/04/09 10:41:58 fr45 Exp $
+--- Makefile.in	2009-06-19 15:13:29.000000000 +0200
++++ Makefile.in.new	2009-08-02 23:06:41.000000000 +0200
+@@ -2,7 +2,7 @@
+ # $Header: /nfs/ccpdisk/xtal/CVSROOT/ccp4/Makefile.in,v 1.60.2.1 2009/06/19 13:13:29 ccb Exp $
  
  SHELL = /bin/sh
--DIRS = $(fftwdir) $(clipperdir) $(diffimdir) $(lapackdir) $(ccifdir) lib/src $(ssmdir) src lib/data unsupported/src x-windows share $(prereleasedir)
-+DIRS = src lib/data unsupported/src x-windows share $(prereleasedir)
+-DIRS = $(fftwdir) $(clipperdir) $(diffimdir) $(lapackdir) $(ccifdir) lib/src $(ssmdir) src lib/data unsupported/src x-windows share ccp4i $(prereleasedir)
++DIRS = src lib/data unsupported/src x-windows share ccp4i $(prereleasedir)
  # this is for the benefit of makes that don't pass variable values in
  # recursive invocations, so that you can override these values on the
  # command line at the top level
-@@ -67,19 +67,19 @@
+@@ -69,19 +69,19 @@
  	$(MAKE) -i $(MFLAGS) $(MVARS) install; else true; fi ; \
  	$(MAKE) install
  
 -srcdir :  FORCE libdir
-+srcdir :  FORCE
++srcdir :  FORCE 
  	if test -d src; then cd src; $(MAKE) $(MFLAGS) $(MVARS); else true; fi
  
  supported : srcdir
diff --git a/sci-chemistry/ccp4-apps/files/6.1.2-gcc4.4.patch b/sci-chemistry/ccp4-apps/files/6.1.2-gcc4.4.patch
new file mode 100644
index 000000000..25b01fd93
--- /dev/null
+++ b/sci-chemistry/ccp4-apps/files/6.1.2-gcc4.4.patch
@@ -0,0 +1,31 @@
+--- src/clipper_progs/src/ctruncate_utils.cpp	2008-04-22 10:46:51.000000000 +0200
++++ src/clipper_progs/src/ctruncate_utils.cpp.new	2009-08-02 23:13:47.000000000 +0200
+@@ -13,6 +13,7 @@
+ #include <iostream>
+ #include <vector>
+ #include <math.h>
++#include <cstdio>
+ 
+ 
+ int bisect(double (*f)(double), double x1, double x2, double &xmid)
+--- src/clipper_progs/src/cphasematch.cpp	2008-07-14 15:03:11.000000000 +0200
++++ src/clipper_progs/src/cphasematch.cpp.new	2009-08-03 19:58:42.000000000 +0200
+@@ -4,6 +4,7 @@
+ #include <clipper/clipper.h>
+ #include <clipper/clipper-contrib.h>
+ #include <clipper/clipper-ccp4.h>
++#include <cstdio>
+ 
+ 
+ int main( int argc, char** argv )
+--- src/clipper_progs/src/csigmaa.cpp	2006-07-28 11:54:59.000000000 +0200
++++ src/clipper_progs/src/csigmaa.cpp.new	2009-08-03 20:08:34.000000000 +0200
+@@ -4,7 +4,7 @@
+ #include <clipper/clipper.h>
+ #include <clipper/clipper-contrib.h>
+ #include <clipper/clipper-ccp4.h>
+-
++#include <cstdio>
+ 
+ int main( int argc, char** argv )
+ {