Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci

* 'master' of git+ssh://git.overlays.gentoo.org/proj/sci:
  sys-cluster/scalasca missing dep bug #290560
  64bit fix
  app-arch/lbzip2 version bump
  In main tree

15 files changed, 378 insertions, 112 deletions

diff --git a/app-arch/lbzip2/ChangeLog b/app-arch/lbzip2/ChangeLog
index b92d09626..f4569acd0 100644
--- a/app-arch/lbzip2/ChangeLog
+++ b/app-arch/lbzip2/ChangeLog
@@ -2,6 +2,12 @@
 # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*lbzip2-0.17 (29 Oct 2009)
+
+  29 Oct 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
+  +files/0.17-Makefile.patch, +lbzip2-0.17.ebuild:
+  bump
+
 *lbzip2-0.16 (26 Oct 2009)
 
   26 Oct 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
diff --git a/app-arch/lbzip2/Manifest b/app-arch/lbzip2/Manifest
index 758eeb1e5..f34a562d1 100644
--- a/app-arch/lbzip2/Manifest
+++ b/app-arch/lbzip2/Manifest
@@ -3,16 +3,19 @@ Hash: SHA1
 
 AUX 0.15-Makefile.patch 1423 RMD160 80f4c71195942d47268679533299199eb49eb4cd SHA1 148aedd17d55c3216d143e060cad7684e737d660 SHA256 185e84d290eae5f9fc3050c0fb4fe66cf77e140708c873d1b966ff991e352b1c
 AUX 0.16-Makefile.patch 1423 RMD160 80f4c71195942d47268679533299199eb49eb4cd SHA1 148aedd17d55c3216d143e060cad7684e737d660 SHA256 185e84d290eae5f9fc3050c0fb4fe66cf77e140708c873d1b966ff991e352b1c
+AUX 0.17-Makefile.patch 1423 RMD160 80f4c71195942d47268679533299199eb49eb4cd SHA1 148aedd17d55c3216d143e060cad7684e737d660 SHA256 185e84d290eae5f9fc3050c0fb4fe66cf77e140708c873d1b966ff991e352b1c
 DIST lbzip2-0.15.tar.gz 62774 RMD160 7a5c5e0acc4772141eccaa3b22778146f1a8f69f SHA1 f547ddbb39e4fcceb25c3ebdd586aa8a053a4ae0 SHA256 4b49477a4854984520995d75dab7bdc4abcb4e463a949df3db4cf635f8dadb5e
 DIST lbzip2-0.16.tar.gz 71038 RMD160 d21f69a2e523dc6ce71135c963f7d419412af0ec SHA1 d7175fa85861868a7416565051d911e96a4f93a8 SHA256 7db9018b11ef1982105d60e51ae077fa796e59edb899ac30ccec4f5430231f85
+DIST lbzip2-0.17.tar.gz 71304 RMD160 67c1c7dcef48f9e8d3fa7ffa8f61fb26c858297b SHA1 cf5c3a174a7ab9c4371ea927b5e7240b8d75b532 SHA256 8485d9892fb077f9735c5362b1bb94f8dda3fd1c64a938f04c524c640fc14ffc
 EBUILD lbzip2-0.15.ebuild 1192 RMD160 e640f038dedef908799d216628d4ee0558414c84 SHA1 748a4dc9d3a4686ec1dbecef11967049e55be877 SHA256 a7eee0b8283daecdef0d35c2bb4f0fca16526ff9ec8865dbdde79e97895a5290
 EBUILD lbzip2-0.16.ebuild 1164 RMD160 6722ff01e70429a0cede6a58c85b8bcb95f85b0f SHA1 671cd811a7d4b7e12cd7db3d6a32ca629f93ed52 SHA256 7a7618ff65f9b1387f68f818a6aa9ad6544cbe1af6c317eadc2de72c03ef8407
-MISC ChangeLog 1311 RMD160 f69e4c3750107a3e9d150049cfe3e9b565c6f86f SHA1 d540e350390f93f33a14d5087a5e8b3c5f1cf9a9 SHA256 f37e1a4d1fb26297aff31d6edac0b4085c29b014c81b4acb1a7c987b6e4a11dc
+EBUILD lbzip2-0.17.ebuild 1164 RMD160 6722ff01e70429a0cede6a58c85b8bcb95f85b0f SHA1 671cd811a7d4b7e12cd7db3d6a32ca629f93ed52 SHA256 7a7618ff65f9b1387f68f818a6aa9ad6544cbe1af6c317eadc2de72c03ef8407
+MISC ChangeLog 1455 RMD160 47b5027cbba2b61a61218f189c9d9c763a80143a SHA1 db68f4b78d1e68189be9fecd09ae6f2b5427d8e0 SHA256 c6929c2cf98ffff8eee605933d605110600ec90d3f3a2f0858cf5372d3cf51f1
 MISC metadata.xml 170 RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 SHA1 ac7f48a14fec325926f9ce1be8fbf1f311b4f2e4 SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42
 -----BEGIN PGP SIGNATURE-----
 Version: GnuPG v2.0.11 (GNU/Linux)
 
-iEYEARECAAYFAkrlUnUACgkQgAnW8HDreRZ60ACgl74CuztC7VimZn9kR/RDOJqW
-TjIAni1FKb3l1glQKrciS72VMnfYIwbb
-=nzbs
+iEYEARECAAYFAkrpWYcACgkQgAnW8HDreRaH0QCfY5f3aVWUYIb1x9xsj0/F3q79
+v2wAn1EZ2G93oOB11h5aGpz85n76tsPe
+=+tJ3
 -----END PGP SIGNATURE-----
diff --git a/app-arch/lbzip2/files/0.17-Makefile.patch b/app-arch/lbzip2/files/0.17-Makefile.patch
new file mode 100644
index 000000000..5bca44468
--- /dev/null
+++ b/app-arch/lbzip2/files/0.17-Makefile.patch
@@ -0,0 +1,45 @@
+--- Makefile	2009-04-04 00:33:49.000000000 +0200
++++ Makefile.new	2009-04-15 21:12:02.886390550 +0200
+@@ -1,34 +1,27 @@
+ # Makefile,v 1.9 2009-04-03 22:33:49 lacos Exp
+ .POSIX:
+ 
+-CC=gcc
+-CFLAGS=$$($(SHELL) lfs.sh CFLAGS) -D _XOPEN_SOURCE=500 -pipe -ansi -pedantic \
+-    -O2
+-
+-
+-
+-
+-LDFLAGS=-s $$($(SHELL) lfs.sh LDFLAGS)
+-LIBS=-l pthread -l bz2 $$($(SHELL) lfs.sh LIBS)
++CFLAGS += -D _XOPEN_SOURCE=500
++LIBS=-l pthread -l bz2
+ 
+ lbzip2: main.o lbzip2.o lbunzip2.o lbunzip2_single.o lacos_rbtree.o
+-	$(CC) -o lbzip2 $(LDFLAGS) main.o lbzip2.o lbunzip2.o \
++	$(CC) $(CPPFLAGS) $(LDFLAGS) -o lbzip2 main.o lbzip2.o lbunzip2.o \
+   lbunzip2_single.o lacos_rbtree.o $(LIBS)
+ 
+ main.o: main.c main.h lbunzip2_single.h lbunzip2.h lbzip2.h
+-	$(CC) $(CFLAGS) -c main.c
++	$(CC) $(CFLAGS) $(CPPFLAGS) -c main.c
+ 
+ lbzip2.o: lbzip2.c main.h lbzip2.h lacos_rbtree.h
+-	$(CC) $(CFLAGS) -c lbzip2.c
++	$(CC) $(CFLAGS) $(CPPFLAGS) -c lbzip2.c
+ 
+ lbunzip2.o: lbunzip2.c main.h lbunzip2.h lacos_rbtree.h
+-	$(CC) $(CFLAGS) -c lbunzip2.c
++	$(CC) $(CFLAGS) $(CPPFLAGS) -c lbunzip2.c
+ 
+ lbunzip2_single.o: lbunzip2_single.c main.h lbunzip2_single.h
+-	$(CC) $(CFLAGS) -c lbunzip2_single.c
++	$(CC) $(CFLAGS) $(CPPFLAGS) -c lbunzip2_single.c
+ 
+ lacos_rbtree.o: lacos_rbtree.c lacos_rbtree.h
+-	$(CC) $(CFLAGS) -c lacos_rbtree.c
++	$(CC) $(CFLAGS) $(CPPFLAGS) -c lacos_rbtree.c
+ 
+ clean:
+ 	rm -f lbzip2 main.o lbzip2.o lbunzip2.o lbunzip2_single.o \
diff --git a/app-arch/lbzip2/lbzip2-0.17.ebuild b/app-arch/lbzip2/lbzip2-0.17.ebuild
new file mode 100644
index 000000000..259d06c42
--- /dev/null
+++ b/app-arch/lbzip2/lbzip2-0.17.ebuild
@@ -0,0 +1,53 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI="2"
+
+inherit eutils flag-o-matic toolchain-funcs
+
+DESCRIPTION="Pthreads-based parallel bzip2/bunzip2 filter, passable to GNU tar"
+HOMEPAGE="http://lacos.hu/"
+SRC_URI="http://lacos.web.elte.hu/pub/${PN}/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+
+RDEPEND=""
+DEPEND="
+	test? (
+		app-shells/dash
+		sys-process/time
+	)"
+
+S=${WORKDIR}/${PN}
+
+src_prepare() {
+	epatch "${FILESDIR}"/${PV}-Makefile.patch
+}
+
+src_compile() {
+	append-lfs-flags
+	emake CC=$(tc-getCC) || die "emake failed"
+}
+
+src_test() {
+	if [ -t 0 ] || return; then
+		rm -rf "${T}/scratch" "${T}/results" "${T}/rnd"
+		hexdump -n 10485760 /dev/urandom > "${T}/rnd"
+		emake -j1 SHELL=/bin/dash PATH="${S}:${PATH}" TESTFILE="${T}/rnd" check \
+			|| die "make check failed"
+	else
+		ewarn "make check must be run attached to a terminal"
+	fi
+}
+
+src_install() {
+	dobin ${PN} || die "Installation of ${PN} failed"
+	dodoc ChangeLog README || die "no docs"
+	doman ${PN}.1 || die "no man"
+	insinto "/usr/share/${PN}"
+	doins corr-perf.sh malloc_trace.pl || die
+}
diff --git a/sci-biology/ucsc-genome-browser/ChangeLog b/sci-biology/ucsc-genome-browser/ChangeLog
deleted file mode 100644
index aca31855f..000000000
--- a/sci-biology/ucsc-genome-browser/ChangeLog
+++ /dev/null
@@ -1,7 +0,0 @@
-# ChangeLog for sci-biology/ucsc-genome-browser
-# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: $
-
-  23 Oct 2009; Andrey Kislyuk <weaver@gentoo.org> ChangeLog:
-  New package, bug 155780. Ebuild written by me and dawe <daweonline@gmail.com>
-
diff --git a/sci-biology/ucsc-genome-browser/Manifest b/sci-biology/ucsc-genome-browser/Manifest
deleted file mode 100644
index 01ebaa964..000000000
--- a/sci-biology/ucsc-genome-browser/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-DIST jksrc.v217.zip 118362449 RMD160 65ca4e0caefaf42cdf7885e55063216fd69fd8f2 SHA1 3df81e7dfd4fd56a6afac69590f9ecb53e9174c5 SHA256 53e95bfcc68644cc20e0d3707161044b0d231c94199e4b0702b91ae72db21c20
-EBUILD ucsc-genome-browser-217.ebuild 2467 RMD160 9f0579a467c5cc39c81d212684bd55b56f27e1ba SHA1 f09e479659bc6b9b5b6f918340f3fe6bb8395da2 SHA256 4abc71324506de21b851a801d7246832ab2b8c8c15716445f23f267b01cf9993
-MISC ChangeLog 274 RMD160 8999c8189cd55c5964ffcbe258482af9cefc952b SHA1 9abdde17b399b2cfb4a25471ad7b03e230e286a4 SHA256 193a442df34a33a92337da94b7ae64ee47b11a3c03f1a0bc04f776d6abe1c281
-MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
diff --git a/sci-biology/ucsc-genome-browser/metadata.xml b/sci-biology/ucsc-genome-browser/metadata.xml
deleted file mode 100644
index 3302123e5..000000000
--- a/sci-biology/ucsc-genome-browser/metadata.xml
+++ /dev/null
@@ -1,9 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer>
-		<email>weaver@gentoo.org</email>
-		<name>Andrey Kislyuk</name>
-	</maintainer>
-	<herd>sci-biology</herd>
-</pkgmetadata>
diff --git a/sci-biology/ucsc-genome-browser/ucsc-genome-browser-217.ebuild b/sci-biology/ucsc-genome-browser/ucsc-genome-browser-217.ebuild
deleted file mode 100644
index 5092aed70..000000000
--- a/sci-biology/ucsc-genome-browser/ucsc-genome-browser-217.ebuild
+++ /dev/null
@@ -1,82 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI="2"
-
-inherit toolchain-funcs flag-o-matic webapp
-
-DESCRIPTION="The UCSC genome browser suite, also known as Jim Kent's library and GoldenPath"
-HOMEPAGE="http://genome.ucsc.edu"
-SRC_URI="http://hgdownload.cse.ucsc.edu/admin/jksrc.v${PV}.zip"
-
-LICENSE="blat"
-# webapp ebuilds do not set SLOT
-KEYWORDS="~amd64 ~x86"
-IUSE="server"
-
-DEPEND="app-arch/unzip
-	virtual/mysql
-	server? ( virtual/httpd-cgi )" # TODO: test with other webservers
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/kent"
-
-src_prepare() {
-	use server && webapp_src_preinst
-	sed -i -e 's/-Werror//' \
-		-e "s/CC=gcc/CC=$(tc-getCC) ${CFLAGS}/" \
-		src/inc/common.mk || die
-	find -name makefile -or -name cgi_build_rules.mk \
-		| xargs sed -i -e 's/-${USER}//g' -e 's/-$(USER)//g' || die
-}
-
-src_compile() {
-	export MACHTYPE=${MACHTYPE/-*/} \
-		BINDIR="${WORKDIR}/destdir/opt/${PN}/bin" \
-		SCRIPTS="${WORKDIR}/destdir/opt/${PN}/cluster/scripts" \
-		ENCODE_PIPELINE_BIN="${WORKDIR}/destdir/opt/${PN}/cluster/data/encode/pipeline/bin" \
-		PATH="${BINDIR}:${PATH}" \
-		STRIP="echo 'skipping strip' "
-
-	export MYSQLLIBS="none" MYSQLINC="none" DOCUMENTROOT="none" CGI_BIN="none"
-
-	# use mysql &&
-	export MYSQLLIBS="${ROOT}usr/lib/mysql/libmysqlclient.a -lz -lssl" \
-		MYSQLINC="${ROOT}usr/include/mysql"
-
-	use server && export DOCUMENTROOT="${WORKDIR}/destdir/${MY_HTDOCSDIR}" \
-		CGI_BIN="${WORKDIR}/destdir/${MY_HTDOCSDIR}/cgi-bin"
-
-	mkdir -p "$BINDIR" "$SCRIPTS" "$ENCODE_PIPELINE_BIN" || die
-	use server && mkdir -p "$CGI_BIN" "$DOCUMENTROOT"
-
-	emake -C src clean || die
-	emake -C src/lib || die
-	emake -C src/jkOwnLib || die
-	emake -C src/utils/stringify || die
-	emake -j1 -C src/hg utils || die
-	emake -j1 -C src utils || die
-	emake -C src blatSuite userApps || die
-	if use server; then
-		emake -j1 -C src/hg || die
-		emake -j1 -C src || die
-	fi
-}
-
-src_install() {
-	cp -a "${WORKDIR}"/destdir/* "${D}" || die
-	# dolib.a src/lib/*.a src/hg/altSplice/lib/x86_64/libSpliceGraph.a
-	echo "PATH=/opt/${PN}/bin" > "${S}/99${PN}"
-	doenvd "${S}/99${PN}"
-	# TODO
-	use server && webapp_postinst_txt en src/product/README.QuickStart
-	use server && webapp_src_install
-
-	insinto "/opt/${PN}/include"
-	doins src/inc/*.h
-	insinto "/usr/share/${PN}"
-	doins -r src/product
-	keepdir "/usr/share/doc/${PF}"
-	find -name 'README*' -or -name '*.doc' | grep -v test | cpio -padv "${D}/usr/share/doc/${PF}" || die
-}
diff --git a/sci-libs/ccp4-libs/ChangeLog b/sci-libs/ccp4-libs/ChangeLog
index 7d26746b7..de1824b92 100644
--- a/sci-libs/ccp4-libs/ChangeLog
+++ b/sci-libs/ccp4-libs/ChangeLog
@@ -2,6 +2,12 @@
 # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*ccp4-libs-6.1.2-r1 (29 Oct 2009)
+
+  29 Oct 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
+  +ccp4-libs-6.1.2-r1.ebuild, +files/6.1.2-64bit.patch:
+  64bit fix in diffdump
+
   26 Aug 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
   ccp4-libs-6.1.2.ebuild:
   QA
diff --git a/sci-libs/ccp4-libs/Manifest b/sci-libs/ccp4-libs/Manifest
index d2cf71c17..70c30b53a 100644
--- a/sci-libs/ccp4-libs/Manifest
+++ b/sci-libs/ccp4-libs/Manifest
@@ -1,7 +1,11 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
 AUX 6.0.2-ppc-double-define-gerror.patch 424 RMD160 4f012233446fffa61e8d775a19a0dacea4ae2234 SHA1 209fa1bdf1e59b4055177e343b69e487d9183fb3 SHA256 09c2c1e0176bee94673b21609b2b00118b2bb4f5942f3feb35c64c61c99ebc61
 AUX 6.1.1-dont-make-dirs-in-configure.patch 2866 RMD160 ba49e45ab609a42a2d93b96f55af913bf9625610 SHA1 36c9329c3768c08687ef062c9ab649d32833b422 SHA256 1b5997f17526a4fd60ffa9eccf4b765aadf3a78c9394657000e0454f364240ca
 AUX 6.1.1-glibc2.10.patch 1018 RMD160 577ee4a6174df36bb8bac82738523f5c757df4b9 SHA1 48ad6d0d024c43d64277e4decba420d51e75a510 SHA256 d2a2ddf2a66738d94723b50797e279f64c8e057a3e584e33f9eb9c8d7ea0e532
 AUX 6.1.1-link-proberly.patch 9325 RMD160 0457062deb5d71f7419d134e89d3d99989fc12b7 SHA1 c7c0453b82b85ae22ea42b562dd2d4ac95b134e7 SHA256 81c4eda497ffa3a0f2d757b7c6b3f6cc35a06ced18ebede2faa31f18667ea8b7
+AUX 6.1.2-64bit.patch 1410 RMD160 7faa966989440dc0a6442b2f4a238a383f5cb667 SHA1 a9ca29271bd16e8532604765af8011d1907a98ea SHA256 33c9fda727a407c83007a8812bc18294804755507cc4aaa54c1e6a4d08e7eb96
 AUX 6.1.2-ccif-shared.patch 1668 RMD160 803687b13dbe93aaeed8264a73dfe7303b5fcdfb SHA1 3d833aefea874c08e61140613b0a5c75a90e0382 SHA256 57c201ee81e3fd95f174fecfd810ddf12509f0c2bfb1b2f317f893561eb60e3f
 AUX 6.1.2-dont-build-mmdb.patch 861 RMD160 f2cfce178bb421c36e1b1114435f8e0ee97102d8 SHA1 d39439dfd9c23781a232551ef9690df6f9ea7681 SHA256 fb4711188e41e6be0a86464425fd9b04ae5dba58fb00202c7234182d002dc795
 AUX 6.1.2-dont-make-dirs-in-configure.patch 2866 RMD160 ba49e45ab609a42a2d93b96f55af913bf9625610 SHA1 36c9329c3768c08687ef062c9ab649d32833b422 SHA256 1b5997f17526a4fd60ffa9eccf4b765aadf3a78c9394657000e0454f364240ca
@@ -16,6 +20,14 @@ EBUILD ccp4-libs-6.1.1-r4.ebuild 5776 RMD160 3a36e4a2fff69e2a17028c39f8849a4cfd7
 EBUILD ccp4-libs-6.1.1-r6.ebuild 5956 RMD160 88f4d6e5c9067225501f214002bc5924bc07c1a2 SHA1 8e61890578007833d8a923eeada3bdf064354056 SHA256 1e7bde2c6f9319d699cf95565aa74bd26372b9d1275fdeaaa8ee75fb4001b30a
 EBUILD ccp4-libs-6.1.1-r7.ebuild 6093 RMD160 99176fde51fd41e7b29610a15720859e97b22d01 SHA1 6a52cfb8e4cddd9454db90bb90bad600c3b753ec SHA256 2143d0c1a7905107b9699cce41d7f33a6fedc99cf9046de33d7b42ddafdfa937
 EBUILD ccp4-libs-6.1.1.ebuild 5211 RMD160 6f3705f7ab0c48bbda073eb7dc1a283b3dcaa39a SHA1 8b09909daae034fc393b49b5fda7e06a783bcd14 SHA256 e9b4a3183a8f753ced59968b261bb655c87d13ade8c9964c71f1f2948c42067e
+EBUILD ccp4-libs-6.1.2-r1.ebuild 5841 RMD160 83d0f6b8c6635e630a45b8adcd0f7564112f0c02 SHA1 9ba4da47a9227f1f91fb3cce0b7cd99202030975 SHA256 d526dfd1368290cd15e395338655f57e33bb3fce410a6642ceefe38bef707b7d
 EBUILD ccp4-libs-6.1.2.ebuild 5766 RMD160 aa4054b10c8122ac719c7300a3395d210e648a31 SHA1 29a5d1d07c87f78aea587ac5f2d4fc50a4e5afee SHA256 58c14a0f2def77683bd3db096fa28f30a8dd0fce4adaf7774c307c7e478d5eca
-MISC ChangeLog 2637 RMD160 4c2a747bb6980e07994a32b0c3e75a23b8a4ff20 SHA1 f8cc6b4e908516e6585203b8b5208d10ebed7684 SHA256 7cba8660239b24ab0425315fa7373652e2646100ce90951cc8a63de2a6be574f
+MISC ChangeLog 2810 RMD160 aea56b0049c3e25a108018a3c2417736519c8f30 SHA1 fff879d14890be376cfb626cb80e988ae163c9d4 SHA256 7454aaf9fcec6eb37a6a518790c69fe4b9c3aaf8324fe2a347d040a071c59424
 MISC metadata.xml 309 RMD160 b9d7f0a63f8fb51e9b4e2d6b4f4028541df5400c SHA1 26ee4b64e0e4d52b1afe00957d53b0cc2956da00 SHA256 04f156de856eae11c0cf8af213f74a9852213844cdd5133aa01dbe60371d57e7
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.11 (GNU/Linux)
+
+iEYEARECAAYFAkrphaAACgkQgAnW8HDreRZ7VgCeOF5CJ5CvDuGydkmbohWfX3M7
+slwAnjkAlNxLDdAv24Usrr1jIY00luQ0
+=QMBG
+-----END PGP SIGNATURE-----
diff --git a/sci-libs/ccp4-libs/ccp4-libs-6.1.2-r1.ebuild b/sci-libs/ccp4-libs/ccp4-libs-6.1.2-r1.ebuild
new file mode 100644
index 000000000..3d6ac6880
--- /dev/null
+++ b/sci-libs/ccp4-libs/ccp4-libs-6.1.2-r1.ebuild
@@ -0,0 +1,213 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+inherit fortran eutils gnuconfig toolchain-funcs
+
+FORTRAN="g77 gfortran ifc"
+
+SRC="ftp://ftp.ccp4.ac.uk/ccp4"
+
+#UPDATE="04_03_09"
+#PATCHDATE="090511"
+
+MY_P="${P/-libs}"
+
+PATCH_TOT="0"
+# Here's a little scriptlet to generate this list from the provided
+# index.patches file
+#
+# i=1; while read -a line; do [[ ${line//#} != ${line} ]] && continue;
+# echo "PATCH${i}=( ${line[1]}"; echo "${line[0]} )"; (( i++ )); done <
+# index.patches
+#PATCH1=( src/topp_
+#topp.f-r1.16.2.5-r1.16.2.6.diff )
+#PATCH2=( .
+#configure-r1.372.2.18-r1.372.2.19.diff )
+
+DESCRIPTION="Protein X-ray crystallography toolkit"
+HOMEPAGE="http://www.ccp4.ac.uk/"
+SRC_URI="${SRC}/${PV}/${MY_P}-core-src.tar.gz"
+# patch tarball from upstream
+	[[ -n ${UPDATE} ]] && SRC_URI="${SRC_URI} ${SRC}/${PV}/updates/${P}-src-patch-${UPDATE}.tar.gz"
+# 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 $PATCH_TOT); do
+	NAME="PATCH${i}[1]"
+	SRC_URI="${SRC_URI}
+		${SRC}/${PV}/patches/${!NAME}"
+done
+
+LICENSE="ccp4"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+RDEPEND="
+	app-shells/tcsh
+	!<sci-chemistry/ccp4-6.0.99
+	=sci-libs/fftw-2*
+	sci-libs/mmdb
+	sci-libs/monomer-db
+	virtual/lapack
+	virtual/blas"
+DEPEND="${RDEPEND}"
+
+RESTRICT="mirror"
+
+S="${WORKDIR}/${MY_P}"
+
+src_unpack() {
+	unpack ${A}
+	cd "${S}"
+
+	einfo "Applying upstream patches ..."
+	for patch in $(seq $PATCH_TOT); do
+		base="PATCH${patch}"
+		dir=$(eval echo \${${base}[0]})
+		p=$(eval echo \${${base}[1]})
+		pushd "${dir}" >& /dev/null
+		ccp_patch "${DISTDIR}/${p}"
+		popd >& /dev/null
+	done
+	einfo "Done."
+	echo
+
+	[[ -n ${PATCHDATE} ]] && epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch
+
+	einfo "Applying Gentoo patches ..."
+	# it tries to create libdir, bindir etc on live system in configure
+	ccp_patch "${FILESDIR}"/${PV}-dont-make-dirs-in-configure.patch
+
+	# gerror_ gets defined twice on ppc if you're using gfortran/g95
+	ccp_patch "${FILESDIR}"/6.0.2-ppc-double-define-gerror.patch
+
+	# make creation of libccif.so smooth
+	ccp_patch "${FILESDIR}"/${PV}-ccif-shared.patch
+
+	# lets try to build libmmdb seperatly
+	ccp_patch "${FILESDIR}"/${PV}-dont-build-mmdb.patch
+
+	# 64bit long -> int32_t patch
+	ccp_patch "${FILESDIR}"/${PV}-64bit.patch
+
+	einfo "Done." # done applying Gentoo patches
+	echo
+
+	gnuconfig_update
+}
+
+src_compile() {
+	# Build system is broken if we set LDFLAGS
+	userldflags="${LDFLAGS}"
+	export SHARED_LIB_FLAGS="${LDFLAGS}"
+	unset LDFLAGS
+
+	# GENTOO_OSNAME can be one of:
+	# irix irix64 sunos sunos64 aix hpux osf1 linux freebsd
+	# linux_compaq_compilers linux_intel_compilers generic Darwin
+	# ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers
+	if [[ "${FORTRANC}" = "ifc" ]]; then
+		if use ia64; then
+			GENTOO_OSNAME="ia64_linux_intel"
+		else
+			# Should be valid for x86, maybe amd64
+			GENTOO_OSNAME="linux_intel_compilers"
+		fi
+	else
+		# Should be valid for x86 and amd64, at least
+		GENTOO_OSNAME="linux"
+	fi
+
+	# Sets up env
+	ln -s \
+		ccp4.setup-bash \
+		"${S}"/include/ccp4.setup
+
+	# We agree to the license by emerging this, set in LICENSE
+	sed -i \
+		-e "s~^\(^agreed=\).*~\1yes~g" \
+		"${S}"/configure
+
+	# Fix up variables -- need to reset CCP4_MASTER at install-time
+	sed -i \
+		-e "s~^\(setenv CCP4_MASTER.*\)/.*~\1"${WORKDIR}"~g" \
+		-e "s~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1/usr/bin~g" \
+		"${S}"/include/ccp4.setup*
+
+	# Set up variables for build
+	source "${S}"/include/ccp4.setup
+
+	export CC=$(tc-getCC)
+	export CXX=$(tc-getCXX)
+	export COPTIM=${CFLAGS}
+	export CXXOPTIM=${CXXFLAGS}
+	# Default to -O2 if FFLAGS is unset
+	export FC=${FORTRANC}
+	export FOPTIM=${FFLAGS:- -O2}
+#	export CCP4_SCR="${T}"
+
+	# Fix linking
+#	$(tc-getCC) ${userldflags} -shared -Wl,-soname,libmmdb.so -o libmmdb.so \${MMDBOBJS} $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lm -lstdc++ && \
+	export SHARE_LIB="\
+		$(tc-getCC) ${userldflags} -shared -Wl,-soname,libccp4c.so -o libccp4c.so \${CORELIBOBJS} \${CGENERALOBJS} \${CUCOBJS} \${CMTZOBJS} \${CMAPOBJS} \${CSYMOBJS} -L.. -lccif $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lm && \
+		${FORTRANC} ${userldflags} -shared -Wl,-soname,libccp4f.so -o libccp4f.so \${FORTRANLOBJS} \${FINTERFACEOBJS} -L.. -lccif -L. -lccp4c -lmmdb $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lstdc++ -lgfortran -lm"
+
+	# Can't use econf, configure rejects unknown options like --prefix
+	./configure \
+		--onlylibs \
+		--with-shared-libs \
+		--with-fftw=/usr \
+		--with-warnings \
+		--disable-cctbx \
+		--disable-clipper \
+		--tmpdir="${TMPDIR}" \
+		${GENTOO_OSNAME} || die "econf failed"
+	emake -j1 onlylib || die "emake failed"
+}
+
+src_install() {
+	# Set up variables for build
+	source "${S}"/include/ccp4.setup
+
+	einstall || die "install failed"
+
+	# Libs
+	for file in "${S}"/lib/*; do
+		if [[ -d ${file} ]]; then
+			continue
+		elif [[ -x ${file} ]]; then
+			dolib.so ${file} || die
+		else
+			insinto /usr/$(get_libdir)
+			doins ${file} || die
+		fi
+	done
+
+	# Bins
+	dobin bin/{automask,diff2jpeg,diffdump,printpeaks} || die
+	newbin bin/superpose superpose-ccp4 || die
+
+	# Fix libdir in all *.la files
+	sed -i \
+		-e "s:^\(libdir=\).*:\1\'/usr/$(get_libdir)\':g" \
+		"${D}"/usr/$(get_libdir)/*.la
+
+	# Data
+	insinto /usr/share/ccp4/data/
+	doins -r "${S}"/lib/data/{*.PARM,*.prt,*.lib,*.dic,*.idl,*.cif,*.resource,*.york,*.hist,fraglib,reference_structures} || die
+	dodoc "${S}"/lib/data/*.doc
+	newdoc "${S}"/lib/data/README DATA-README
+
+	# Include files
+	insinto /usr/include
+	for i in ccp4; do
+		doins -r "${S}"/include/${i} || die
+	done
+}
+
+# Epatch wrapper for bulk patching
+ccp_patch() {
+	EPATCH_SINGLE_MSG="  ${1##*/} ..." epatch ${1}
+}
diff --git a/sci-libs/ccp4-libs/files/6.1.2-64bit.patch b/sci-libs/ccp4-libs/files/6.1.2-64bit.patch
new file mode 100644
index 000000000..10dd46b07
--- /dev/null
+++ b/sci-libs/ccp4-libs/files/6.1.2-64bit.patch
@@ -0,0 +1,26 @@
+diff --git a/ccp4-6.1.2/lib/DiffractionImage/Rigaku/RaxisImage.h b/ccp4-6.1.2/lib/DiffractionImage/Rigaku/RaxisImage.h
+index e02b72b..41de8ef 100755
+--- a/ccp4-6.1.2/lib/DiffractionImage/Rigaku/RaxisImage.h
++++ b/ccp4-6.1.2/lib/DiffractionImage/Rigaku/RaxisImage.h
+@@ -216,7 +216,7 @@ unsigned short Swap(unsigned short Value);
+    // This routine swaps the long <VAR>Value</VAR> so that the endianness 
+    // of <VAR>Value</VAR> is reversed and then returns the swapped value.
+    // This routine assumes that the size of a long is 4 bytes.
+-long Swap(long Value);
++int32_t Swap(int32_t Value);
+ 
+    // This routine swaps the float <VAR>Value</VAR> so that the endianness 
+    // of <VAR>Value</VAR> is reversed and then returns the swapped value.
+diff --git a/ccp4-6.1.2/lib/DiffractionImage/Rigaku/ReadRAXISImages.cpp b/ccp4-6.1.2/lib/DiffractionImage/Rigaku/ReadRAXISImages.cpp
+index 882d93d..0ff12a3 100755
+--- a/ccp4-6.1.2/lib/DiffractionImage/Rigaku/ReadRAXISImages.cpp
++++ b/ccp4-6.1.2/lib/DiffractionImage/Rigaku/ReadRAXISImages.cpp
+@@ -153,7 +153,7 @@ unsigned short Swap(const unsigned short Value)
+ 
+ /****************************************************************************
+  ****************************************************************************/
+-long Swap(const long Value)
++int32_t Swap(const int32_t Value)
+ {
+    long swap = Value;
+    char *p = reinterpret_cast<char *>(&swap);
diff --git a/sys-cluster/scalasca/ChangeLog b/sys-cluster/scalasca/ChangeLog
index 000d83f15..3efb0e2c7 100644
--- a/sys-cluster/scalasca/ChangeLog
+++ b/sys-cluster/scalasca/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  29 Oct 2009; Christoph Junghans <kleiner_otti@gmx.de> scalasca-1.2.ebuild:
+  missing dep bug #290560
+
   13 Aug 2009; Christoph Junghans <kleiner_otti@gmx.de> scalasca-1.2.ebuild:
   DOCDIR fix
 
diff --git a/sys-cluster/scalasca/Manifest b/sys-cluster/scalasca/Manifest
index 62a077eeb..b94ed5d6d 100644
--- a/sys-cluster/scalasca/Manifest
+++ b/sys-cluster/scalasca/Manifest
@@ -2,13 +2,13 @@
 Hash: SHA1
 
 DIST scalasca-1.2.tar.gz 4441027 RMD160 6cf1a96c22f6ef7c3b81754593f107ad269dc2b9 SHA1 d9198e5cdbc749caab92c76298f79c68f8a23475 SHA256 cce72dba92d957fcf45980e5a2f0b685e008b243d3420132caa7e4c9345ce1ec
-EBUILD scalasca-1.2.ebuild 1526 RMD160 28f78c78972bfd85b2e04473489d6765f105add4 SHA1 59ae09fadf335b9c1063f896dbf3c36dec8cb25e SHA256 037c6597f7339335dabbe2bcf461678080cfbc97586e08af5934a95cddfcdb46
-MISC ChangeLog 757 RMD160 858aff507422a78604e7a8e31fc79105b64d0611 SHA1 d078abdd50003f0429374b284cf1abbb43ae9382 SHA256 a1e3a7d99eebf51055b772777b1cf48dfdfd33518447f9699a0823ae1cc228ef
+EBUILD scalasca-1.2.ebuild 1545 RMD160 66b8de4ead8cc666de18b6f586cc17504ebc758a SHA1 a462726cb0b9f9de810d838ec7068b4958d5159e SHA256 e24cf8686bc11bdcc7b96388c1e6eefb4f761aaa4c21b9bace8f346bb253e233
+MISC ChangeLog 861 RMD160 76d459c753ab2e999f1ef22135488ed863c0d822 SHA1 3db753c786dd033586cdf0c88a43245c60afd83a SHA256 d48eb596e6965ad76759dadf773f7ffbfab35714df0ad710b274159088655dfc
 MISC metadata.xml 257 RMD160 df843d207f9d7b644df9d807c3a2747d3c0c1c86 SHA1 4b3b240062a031a98ab4f9309410dae3f7b0502a SHA256 e01b96ab62b3eef03eba7c6d35addeaf415cd00271fb8fa4197c866308ee18e9
 -----BEGIN PGP SIGNATURE-----
 Version: GnuPG v2.0.11 (GNU/Linux)
 
-iEYEARECAAYFAkqEYKcACgkQy0OE/ans1/nAIQCfWbFdSkCF8nhY+f77JXSBtWr4
-RGIAn2j/0khUx7An24l2EQrOucAwfJBI
-=YccB
+iEYEARECAAYFAkrpiiIACgkQy0OE/ans1/k6GACeLHDos+zFGO2woDJ/GebTiIBj
+SrYAni9JzCPgmMwlkz9uGP+16pBQwe9y
+=lTo+
 -----END PGP SIGNATURE-----
diff --git a/sys-cluster/scalasca/scalasca-1.2.ebuild b/sys-cluster/scalasca/scalasca-1.2.ebuild
index d16ade10e..ee3f51a09 100644
--- a/sys-cluster/scalasca/scalasca-1.2.ebuild
+++ b/sys-cluster/scalasca/scalasca-1.2.ebuild
@@ -19,6 +19,7 @@ IUSE="doc examples fortran mpi openmp wxwidgets"
 
 DEPEND="mpi? ( virtual/mpi )
 	x11-libs/qt-core:4
+	x11-libs/qt-gui:4
 	wxwidgets? ( x11-libs/wxGTK:2.6 )"
 
 RDEPEND="${DEPEND}"