sci-biology/samtools: Drop old; use pkg-config to check for libncurses

(Portage version: 2.2.0_alpha159/cvs/Linux x86_64, signed Manifest commit with key 8009D6F070EB7916)

5 files changed, 23 insertions, 106 deletions

diff --git a/sci-biology/samtools/ChangeLog b/sci-biology/samtools/ChangeLog
index bafb11674633..3b5f84fde598 100644
--- a/sci-biology/samtools/ChangeLog
+++ b/sci-biology/samtools/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-biology/samtools
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/ChangeLog,v 1.8 2011/09/26 15:18:39 weaver Exp $
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/ChangeLog,v 1.9 2013/01/23 10:51:13 jlec Exp $
+
+*samtools-0.1.18-r1 (23 Jan 2013)
+
+  23 Jan 2013; Justin Lecher <jlec@gentoo.org> -samtools-0.1.12a-r1.ebuild,
+  -samtools-0.1.16.ebuild, -samtools-0.1.17.ebuild, +samtools-0.1.18-r1.ebuild,
+  metadata.xml:
+  Drop old; use pkg-config to check for libncurses
 
 *samtools-0.1.18 (26 Sep 2011)
 
diff --git a/sci-biology/samtools/metadata.xml b/sci-biology/samtools/metadata.xml
index 3302123e5718..fc7c76942a10 100644
--- a/sci-biology/samtools/metadata.xml
+++ b/sci-biology/samtools/metadata.xml
@@ -1,9 +1,9 @@
 <?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>
+  <maintainer>
+    <email>weaver@gentoo.org</email>
+    <name>Andrey Kislyuk</name>
+  </maintainer>
+  <herd>sci-biology</herd>
 </pkgmetadata>
diff --git a/sci-biology/samtools/samtools-0.1.12a-r1.ebuild b/sci-biology/samtools/samtools-0.1.12a-r1.ebuild
deleted file mode 100644
index 5c689a266cee..000000000000
--- a/sci-biology/samtools/samtools-0.1.12a-r1.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/samtools-0.1.12a-r1.ebuild,v 1.3 2011/07/18 01:50:51 jlec Exp $
-
-EAPI=2
-
-inherit toolchain-funcs multilib
-
-DESCRIPTION="Utilities for SAM (Sequence Alignment/Map), a format for large nucleotide sequence alignments"
-HOMEPAGE="http://samtools.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
-
-LICENSE="MIT"
-SLOT="0"
-IUSE="examples"
-KEYWORDS="~amd64 ~x86 ~x64-macos"
-
-src_prepare() {
-	sed \
-		-e '/^CFLAGS=/d' \
-		-e "s/\$(CC) \$(CFLAGS)/& \$(LDFLAGS)/g" \
-		-e "s/-shared/& \$(LDFLAGS)/" \
-		-i "${S}"/{Makefile,misc/Makefile} || die #358563
-	sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die
-}
-
-src_compile() {
-	emake CC="$(tc-getCC)" dylib || die
-	emake CC="$(tc-getCC)" || die
-}
-
-src_install() {
-	dobin samtools || die
-	dobin $(find misc -type f -executable) || die
-	dolib.so libbam.so.1 || die
-	dosym libbam.so.1 /usr/$(get_libdir)/libbam.so || die
-	insinto /usr/include/bam
-	doins bam.h bgzf.h faidx.h kaln.h khash.h kprobaln.h kseq.h ksort.h sam.h || die
-
-	doman ${PN}.1 || die
-	dodoc AUTHORS ChangeLog NEWS
-
-	if use examples; then
-		insinto /usr/share/${PN}
-		doins -r examples || die
-	fi
-}
diff --git a/sci-biology/samtools/samtools-0.1.16.ebuild b/sci-biology/samtools/samtools-0.1.16.ebuild
deleted file mode 100644
index a2181d1f6cfc..000000000000
--- a/sci-biology/samtools/samtools-0.1.16.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/samtools-0.1.16.ebuild,v 1.2 2011/07/18 01:50:51 jlec Exp $
-
-EAPI=2
-
-inherit multilib toolchain-funcs
-
-DESCRIPTION="Utilities for SAM (Sequence Alignment/Map), a format for large nucleotide sequence alignments"
-HOMEPAGE="http://samtools.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
-
-LICENSE="MIT"
-SLOT="0"
-IUSE="examples"
-KEYWORDS="~amd64 ~x86 ~x64-macos"
-
-src_prepare() {
-	sed \
-		-e '/^CFLAGS=/d' \
-		-e "s/\$(CC) \$(CFLAGS)/& \$(LDFLAGS)/g" \
-		-e "s/-shared/& \$(LDFLAGS)/" \
-		-i "${S}"/{Makefile,misc/Makefile} || die #358563
-	sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die
-}
-
-src_compile() {
-	emake CC="$(tc-getCC)" dylib || die
-	emake CC="$(tc-getCC)" || die
-}
-
-src_install() {
-	dobin samtools || die
-	dobin $(find misc -type f -executable) || die
-	dolib.so libbam.so.1 || die
-	dosym libbam.so.1 /usr/$(get_libdir)/libbam.so || die
-	insinto /usr/include/bam
-	doins bam.h bgzf.h faidx.h kaln.h khash.h kprobaln.h kseq.h ksort.h sam.h || die
-
-	doman ${PN}.1 || die
-	dodoc AUTHORS ChangeLog NEWS
-
-	if use examples; then
-		insinto /usr/share/${PN}
-		doins -r examples || die
-	fi
-}
diff --git a/sci-biology/samtools/samtools-0.1.17.ebuild b/sci-biology/samtools/samtools-0.1.18-r1.ebuild
index dbdcbb777a18..30ae8d10d078 100644
--- a/sci-biology/samtools/samtools-0.1.17.ebuild
+++ b/sci-biology/samtools/samtools-0.1.18-r1.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2011 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/samtools-0.1.17.ebuild,v 1.1 2011/07/18 01:50:51 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/samtools-0.1.18-r1.ebuild,v 1.1 2013/01/23 10:51:13 jlec Exp $
 
-EAPI=4
+EAPI=5
 
 inherit multilib toolchain-funcs
 
@@ -17,16 +17,20 @@ KEYWORDS="~amd64 ~x86 ~x64-macos"
 
 src_prepare() {
 	sed \
+		-e '/CC/s:=:?=:g' \
+		-e "/LIBCURSES/s:=.*$:= $(pkg-config --libs ncurses):g" \
 		-e '/^CFLAGS=/d' \
 		-e "s/\$(CC) \$(CFLAGS)/& \$(LDFLAGS)/g" \
 		-e "s/-shared/& \$(LDFLAGS)/" \
 		-i "${S}"/{Makefile,misc/Makefile} || die #358563
 	sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die
+
+	tc-export CC
 }
 
 src_compile() {
-	emake CC="$(tc-getCC)" dylib || die
-	emake CC="$(tc-getCC)" || die
+	emake dylib
+	emake
 }
 
 src_install() {