sci-biology/bowtie: Version Bump, Fix compilation with gcc-4.7, #421919

Package-Manager: portage-2.2.0_alpha110/cvs/Linux x86_64

4 files changed, 107 insertions, 8 deletions

diff --git a/sci-biology/bowtie/ChangeLog b/sci-biology/bowtie/ChangeLog
index 3dd84e690308..519ba8efed2f 100644
--- a/sci-biology/bowtie/ChangeLog
+++ b/sci-biology/bowtie/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/bowtie
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/bowtie/ChangeLog,v 1.13 2011/03/06 17:18:05 jlec Exp $
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/bowtie/ChangeLog,v 1.14 2012/06/19 11:34:11 jlec Exp $
+
+*bowtie-0.12.8 (19 Jun 2012)
+
+  19 Jun 2012; Justin Lecher <jlec@gentoo.org> +bowtie-0.12.8.ebuild,
+  +files/bowtie-0.12.8-gcc-47.patch:
+  Version Bump, Fix compilation with gcc-4.7, #421919
 
 *bowtie-0.12.7 (06 Mar 2011)
 
diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest
index 1363b8e38cb5..2392af4e90f0 100644
--- a/sci-biology/bowtie/Manifest
+++ b/sci-biology/bowtie/Manifest
@@ -1,18 +1,22 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
+Hash: SHA512
 
+AUX bowtie-0.12.8-gcc-47.patch 1077 RMD160 09785339898f9e3d96b7e02ff0be10d1600bf5bb SHA1 d019ab32fd4eec23cf083cd49c94dce68eb611dc SHA256 1516e8c3ca57cba14e28a864042a0637998fb2633f8fe3b4d7529e0f5c2a275f
 DIST bowtie-0.12.3-src.zip 10314474 RMD160 a5e9fc5de69c8c4e64e30bcfaf8303b3021e5b8f SHA1 7bf3ca4071638d36ff5139f8ccd976315e98c4b3 SHA256 aac6e02cc95058e19092f6f56e87ed2eac3df11ecce889050c6feea2b2344b84
 DIST bowtie-0.12.5-src.zip 10319902 RMD160 41e02aec08e77ce7944eb5440fdd78efb99d5a97 SHA1 90448c971d30797a63dcbc72246874a163174215 SHA256 244aa3ccbc15c88970196b0fb958c8455504902b5414987bf224c9dd92984cce
 DIST bowtie-0.12.7-src.zip 7697786 RMD160 7b2210d4526c4818936b729b0e68f4c13a101fc6 SHA1 0eb752db072a2da6fc6dac55d2ab825422e994ce SHA256 609a6a0ad0b1a5d97908ca17da7bbf5d6dc407c7b9c49713cdc9c40f056a586a
+DIST bowtie-0.12.8-src.zip 15569919 RMD160 a1fb27c8a5c14bb343ca03aa001d6400d882448d SHA1 56fd4dfd1d8ef995f041d11ce6078dd1e22a655f SHA256 f074a0f25e156976c4951fd69651d60caab925af9829054d107ec8b19af3082d
 EBUILD bowtie-0.12.3.ebuild 919 RMD160 b372dda86b94c59ba0dc9c71107c95efc31bde20 SHA1 ae85bfd3054996ec82274aaf9da78ae8e02b4eb1 SHA256 a48446e9cb918d99b3488e9b9ef3125ad2d8df2f2c8cd0fc0a1524a22663d301
 EBUILD bowtie-0.12.5.ebuild 931 RMD160 3bef3c346e7e5b1f5a8d11b2dd7f7d1ae5b57ea4 SHA1 dffb1225ae29c88e099355ceb525e4bb9c7d977e SHA256 cb12a3f471f9dd8e0b0eee6fff065929177895ce1d1f5995071380d944628d1f
 EBUILD bowtie-0.12.7.ebuild 1113 RMD160 ab7fd92e2198de8abeb753ecb802c4034100c6d2 SHA1 9b53b20d6e3f41c0a21f91939a7ec648365d5ff6 SHA256 ffc3c1ccaef5fb1b19f53946d19b4f1528076c7dc5b23d5d1ba1924612a820ec
-MISC ChangeLog 1959 RMD160 f33dedc34a7402580c50a5c6541abc0fcdf0bb05 SHA1 c3c3caa25113487cb8b9e58482b563f9af56765b SHA256 38288cf679c0fccde58767977cc176dfe8a7e03fecd25e4e58cf1057552ec327
+EBUILD bowtie-0.12.8.ebuild 1045 RMD160 06ee4337f6dab4a95076d098fa0d238f8d5d8569 SHA1 990bfe54398d48e30d832e8c1bd37c569ce1c272 SHA256 a3ff2f39d8f5f1e59dcbf121769d1c866d22d42181c9104f3d3a4d59e6d4492f
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 MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
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diff --git a/sci-biology/bowtie/bowtie-0.12.8.ebuild b/sci-biology/bowtie/bowtie-0.12.8.ebuild
new file mode 100644
index 000000000000..eb6670183490
--- /dev/null
+++ b/sci-biology/bowtie/bowtie-0.12.8.ebuild
@@ -0,0 +1,44 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/bowtie/bowtie-0.12.8.ebuild,v 1.1 2012/06/19 11:34:11 jlec Exp $
+
+EAPI=4
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="An ultrafast memory-efficient short read aligner"
+HOMEPAGE="http://bowtie-bio.sourceforge.net/"
+SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip"
+
+LICENSE="Artistic"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86 ~x64-macos"
+
+DEPEND="app-arch/unzip"
+RDEPEND=""
+
+# NB: Bundles code from Maq (http://maq.sf.net) and the SeqAn library (http://www.seqan.de)
+# TODO: properly report system CFLAGS in -DCOMPILE_OPTIONS
+
+src_prepare() {
+	epatch "${FILESDIR}"/${P}-gcc-47.patch
+}
+
+src_compile() {
+	unset CFLAGS
+	emake \
+		CC="$(tc-getCC)" \
+		CPP="$(tc-getCXX)" \
+		CXX="$(tc-getCXX)" \
+		EXTRA_FLAGS="${LDFLAGS}" \
+		RELEASE_FLAGS=""
+}
+
+src_install() {
+	dobin bowtie bowtie-*
+	exeinto /usr/share/${PN}/scripts
+	doexe scripts/*
+	newman MANUAL bowtie.1
+	dodoc AUTHORS NEWS TUTORIAL
+}
diff --git a/sci-biology/bowtie/files/bowtie-0.12.8-gcc-47.patch b/sci-biology/bowtie/files/bowtie-0.12.8-gcc-47.patch
new file mode 100644
index 000000000000..3c8a1e1d9ca4
--- /dev/null
+++ b/sci-biology/bowtie/files/bowtie-0.12.8-gcc-47.patch
@@ -0,0 +1,45 @@
+ alphabet.h |   24 ++++++++++++------------
+ 1 files changed, 12 insertions(+), 12 deletions(-)
+
+diff --git a/alphabet.h b/alphabet.h
+index b464ddf..08d0281 100644
+--- a/alphabet.h
++++ b/alphabet.h
+@@ -38,6 +38,18 @@ static inline TStr reverseComplement(const TStr& s, bool color) {
+ 	return s_rc;
+ }
+ 
++/// Reverse a string in-place
++template <typename TStr>
++static inline void reverseInPlace(TStr& s) {
++	typedef typename Value<TStr>::Type TVal;
++	size_t len = length(s);
++	for(size_t i = 0; i < (len>>1); i++) {
++		TVal tmp = s[i];
++		s[i] = s[len-i-1];
++		s[len-i-1] = tmp;
++	}
++}
++
+ /**
+  * Reverse-complement s in-place.  Ns go to Ns.
+  */
+@@ -69,18 +81,6 @@ static inline void reverseComplementInPlace(TStr& s, bool color) {
+ 	}
+ }
+ 
+-/// Reverse a string in-place
+-template <typename TStr>
+-static inline void reverseInPlace(TStr& s) {
+-	typedef typename Value<TStr>::Type TVal;
+-	size_t len = length(s);
+-	for(size_t i = 0; i < (len>>1); i++) {
+-		TVal tmp = s[i];
+-		s[i] = s[len-i-1];
+-		s[len-i-1] = tmp;
+-	}
+-}
+-
+ /**
+  * Return the reverse-complement of s.
+  */