sci-biology/allpaths: Fix for gcc-4.7

Package-Manager: portage-2.2.0_alpha123/cvs/Linux x86_64

4 files changed, 158 insertions, 26 deletions

diff --git a/sci-biology/allpaths/ChangeLog b/sci-biology/allpaths/ChangeLog
index 521be3cf8b2a..57be0ddeb00c 100644
--- a/sci-biology/allpaths/ChangeLog
+++ b/sci-biology/allpaths/ChangeLog
@@ -1,6 +1,10 @@
 # ChangeLog for sci-biology/allpaths
-# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/allpaths/ChangeLog,v 1.6 2010/01/26 20:43:21 weaver Exp $
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/allpaths/ChangeLog,v 1.7 2012/08/30 07:32:21 jlec Exp $
+
+  30 Aug 2012; Justin Lecher <jlec@gentoo.org> allpaths-3.1.ebuild,
+  +files/allpaths-3.1-gcc4.7.patch:
+  Fix for gcc-4.7
 
 *allpaths-3.1 (26 Jan 2010)
 
diff --git a/sci-biology/allpaths/Manifest b/sci-biology/allpaths/Manifest
index 92891efd0c7c..30aee6c4ec49 100644
--- a/sci-biology/allpaths/Manifest
+++ b/sci-biology/allpaths/Manifest
@@ -1,9 +1,21 @@
-AUX allpaths-2.0-gcc-x86-no-autocast.patch 1481 RMD160 06ce2c1fe608621527e3af1b0e01e5efa8b8329a SHA1 565c480b4d48400b42af72c61919b2b52fd7c829 SHA256 933377d2066d6dd3c8015ad005a12fd60cb1b8e90e7a966d9ff52b8fa30c2338
-DIST AllPathsV3_Manual_r1.0.docx 287870 RMD160 ca694ca153e81663629ebd9738befd866f150d06 SHA1 e42b925f2c6d21b28f88692d2bd5f44fbe046952 SHA256 497ce1649e627c542ac676cca2a6ab054347534b8521583795ae11d995b7680e
-DIST allpaths-2.0.manual.docx 287123 RMD160 41a3792e2bc135462c22ee15c992a606b928145a SHA1 307bb76b8acedff289511d10a3e8a3b65278a4a4 SHA256 f89d15f31d511d6bad587562fa2539c1d5a37a097e4c3f33bb5a00d47fba7e69
-DIST allpaths-2.0.tar.gz 11211652 RMD160 cedffb29289c9229615c2ab72dca149722c4236a SHA1 a9cf07b59838aae714645f90cbf6f1407da69330 SHA256 16dce075e7b4ebd8924a79c765a7a7b87c01a68502e256ec200680ba42d95f02
-DIST allpaths-3.1.tgz 1482541 RMD160 9552ce07353110d4b585b951ba3525257b30ce99 SHA1 77f7f19a9b1df5da1d72051ae98cb2454d0a8803 SHA256 bbdc43f82586fc0b67d3a2584e245c452c377f8b532c81e9fe4e2c309ac1a46b
-EBUILD allpaths-2.0.ebuild 1182 RMD160 e2b93df7d63be93d6ff0e2476193e0214186a735 SHA1 db18f3cfa7c0a0d4c2478ec63aa89e47bed7ef17 SHA256 38d3f146740ba679abbd759f8f4122839a05d0edfe908c83e6be969128912df6
-EBUILD allpaths-3.1.ebuild 1079 RMD160 207b16171cbce9d178dba67dfda4f6183e173775 SHA1 df99bf087f779689eab5f9ae94899a959155ab07 SHA256 b8cf4f7f609c6635ca43f207e800c8a1156fc8485f682281b6d6145317f9b93d
-MISC ChangeLog 941 RMD160 e8b77b25cba161abf8b10a401676143863daf03e SHA1 ee2a3d49df54066b50029baa0a4acf3f5b1cbd62 SHA256 88d0120a1848328153fd867f052a2a53906355335fa1c229f0a6f17edb287a8b
-MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA256
+
+AUX allpaths-2.0-gcc-x86-no-autocast.patch 1481 SHA256 933377d2066d6dd3c8015ad005a12fd60cb1b8e90e7a966d9ff52b8fa30c2338 SHA512 4fd9788fd1283cac2453a357e0af6c243afaba457cf840ceb873b5504367eacb1b41fd74889374a06d088d7de88307e84999632766409a1713d42737b7704c73 WHIRLPOOL 629c9e6921eab98c09ca7ae29a373954a0bbdfc476d8a7119b3f07fb9995a86fb349db0dbee05a20184c050b380f305990421ff8ca407992e44ef75ab63a0a87
+AUX allpaths-3.1-gcc4.7.patch 3977 SHA256 77178076fe881be713cd16bf192aefc7b8c00786d8d2867fb710016a2769ccf9 SHA512 9474e937d78875e2daeb95d872869cc633416e80825047017302b307de081aa6860cbd2c84ba1208eed667f5b9e250b98c1ba5cade8277845eff8ef131d64879 WHIRLPOOL 92c7a22d16b09d8af5d7a3225e75c8a503aac5d34eaf8e2023bde217030c7f01409aa76d973d58fb9cb0d3bcb4301f2dee42896349d9cd4fd3bee15e794fbfcf
+DIST AllPathsV3_Manual_r1.0.docx 287870 SHA256 497ce1649e627c542ac676cca2a6ab054347534b8521583795ae11d995b7680e SHA512 60646b79bcc94e47c04039b9778b637c0ae565dd7193caa90d2300197de996272397792bcc43fb9b58dd1a29941a04e3e498e395242c862f31e51105e6aceb34 WHIRLPOOL 3220858d2fc44acfe1d5667e5247b0af7dd5eaafba0fb936e8ecfe70d21df4b7eba4cf509c6db546945b9466bf6c57c2f0de8c25ca9866d0c1a02fc999b48702
+DIST allpaths-2.0.manual.docx 287123 SHA256 f89d15f31d511d6bad587562fa2539c1d5a37a097e4c3f33bb5a00d47fba7e69
+DIST allpaths-2.0.tar.gz 11211652 SHA256 16dce075e7b4ebd8924a79c765a7a7b87c01a68502e256ec200680ba42d95f02
+DIST allpaths-3.1.tgz 1482541 SHA256 bbdc43f82586fc0b67d3a2584e245c452c377f8b532c81e9fe4e2c309ac1a46b SHA512 c82fb89a9d2f9d6cf21082f54999546c8e5d9ce470e0ae4b6c57ad0f95c4e35ab8b5965b098f4444c38e40d1ee434ed22adf70dff4fe8320d9c154e2b904f4e2 WHIRLPOOL c3ceaaaec9ce40668796d72a864c9d903dd795825c2f2a6dcf9b4dff10e4b9b9d278b10c2b15982a8afd75f256f11e48a09fbd934e814b092666d14216678ab5
+EBUILD allpaths-2.0.ebuild 1182 SHA256 38d3f146740ba679abbd759f8f4122839a05d0edfe908c83e6be969128912df6 SHA512 9434603c0da9690bc7209dffb67d0da6553785b959a37d9fde510274691ca0878f748e81cf7c314f310fed4e0046022389fa062a08e3c1e9eb186d9c7ee5365c WHIRLPOOL e9084bee45ab437b8de69dbcf64b02c6f35b2bb18d11acf388a423354e8f4fe5cd449c26f968e2d95446f182efee961d3bee07b0a6970b4d4fff7fc8dd481b0d
+EBUILD allpaths-3.1.ebuild 1039 SHA256 33052151a60ebc2b48cd40c56b6cf338c0be3ec2173f1518be379a5a5787480a SHA512 a18604a2cc56de2f5ee952e0b8b374f5f12f22ba0977237c124af8180419a8b723d9180e88b72c22540c4336604400dd5f2c9cf4cbfeb5ecbdcf537688625fbe WHIRLPOOL 264ff1c58c4e35cfb28c19126cb20c5f771e2c011e9fb3659758226819a6f897d499de2e1d297be54f842d53dce68ad908858aaa35d9652b25e45e063b1bdbd5
+MISC ChangeLog 1062 SHA256 14624ab7f220b97ecf04260cd177f862261238ca86a392369ef41acd26004254 SHA512 4be46082196944e2c7797cb391671256a0a29863a42fe50723875ede112562aad6f872a4c96d79b516d1e2324cda66293fd7b090c37296d17d646cb38a602e67 WHIRLPOOL 9b8a59f7760fa52ae46798f543c72ba083fed1ccd1d7822c7c97f011358bf4cc3450090fc337eed53947fd9ca7a1e5d783041998d6c252b823e6e552372997cf
+MISC metadata.xml 259 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110 SHA512 c3aea4d69d75075af0108a03b7e109cfed6a1fe324f8ccbda3d4e5ca8a5070f1b24ddeb46b64787e10fd22252d867abcee1f31316d602f7e32fe3c990ae60d74 WHIRLPOOL e50da2f26fd4c908446d22da3edb595d60e61d72def374be46440358802a211fc34045b7ad970c4f94b57f7b17ff24cfe64dc94254fea20e047f1fbbbcae0c64
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.19 (GNU/Linux)
+Comment: GPGTools - http://gpgtools.org
+
+iEYEAREIAAYFAlA/FwoACgkQgAnW8HDreRYX8wCffKlTDOory5C+iKcZMV9Z3btZ
+JkYAni8OP7DjsJ3wm/71Np5W8Jng2R+W
+=z7uf
+-----END PGP SIGNATURE-----
diff --git a/sci-biology/allpaths/allpaths-3.1.ebuild b/sci-biology/allpaths/allpaths-3.1.ebuild
index 31ac65d432a1..7b271ade0f05 100644
--- a/sci-biology/allpaths/allpaths-3.1.ebuild
+++ b/sci-biology/allpaths/allpaths-3.1.ebuild
@@ -1,37 +1,39 @@
-# Copyright 1999-2010 Gentoo Foundation
+# Copyright 1999-2012 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/allpaths/allpaths-3.1.ebuild,v 1.1 2010/01/26 20:43:21 weaver Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/allpaths/allpaths-3.1.ebuild,v 1.2 2012/08/30 07:32:21 jlec Exp $
 
-EAPI="2"
+EAPI=4
 
 inherit base
 
 DESCRIPTION="De novo assembly of whole-genome shotgun microreads"
 HOMEPAGE="http://www.broadinstitute.org/science/programs/genome-biology/crd"
-SRC_URI="ftp://ftp.broad.mit.edu/pub/crd/ALLPATHS/Release-3-0/allpaths-${PV}.tgz
+SRC_URI="
+	ftp://ftp.broad.mit.edu/pub/crd/ALLPATHS/Release-3-0/allpaths-${PV}.tgz
 	ftp://ftp.broad.mit.edu/pub/crd/ALLPATHS/Release-3-0/AllPathsV3_Manual_r1.0.docx"
 
 LICENSE="Whitehead-MIT"
 SLOT="3"
 IUSE=""
-KEYWORDS="~amd64"
-
-DEPEND=">=sys-devel/gcc-4.3.2"
-RDEPEND=""
+KEYWORDS="~amd64 ~x86"
 
 S="${WORKDIR}/AllPaths"
 
+PATCHES=( "${FILESDIR}"/${P}-gcc4.7.patch )
+
 src_compile() {
 	base_src_compile
-	emake install_scripts || die
+	emake install_scripts
 }
 
 src_install() {
-	exeinto /usr/share/${P}/bin
+	exeinto /usr/libexec/${P}/
 	find bin -type f -executable | xargs doexe || die
-	echo "PATH=\"/usr/share/${P}/bin\"" > "${S}/99${P}"
-	doenvd "${S}/99${P}" || die
-	dosym /usr/share/${P}/bin/RunAllPaths3G /usr/bin/RunAllPaths3G || die
-	insinto /usr/share/doc/${PF}
-	doins "${DISTDIR}/AllPathsV3_Manual_r1.0.docx"
+
+	echo "PATH=\"/usr/libexec/${P}/\"" > "${S}/50${P}"
+	doenvd "${S}/50${P}" || die
+
+	dosym /usr/libexec/${P}/RunAllPaths3G /usr/bin/RunAllPaths3G
+
+	dodoc "${DISTDIR}/AllPathsV3_Manual_r1.0.docx"
 }
diff --git a/sci-biology/allpaths/files/allpaths-3.1-gcc4.7.patch b/sci-biology/allpaths/files/allpaths-3.1-gcc4.7.patch
new file mode 100644
index 000000000000..08383f4ff4bc
--- /dev/null
+++ b/sci-biology/allpaths/files/allpaths-3.1-gcc4.7.patch
@@ -0,0 +1,114 @@
+ MakeDepend.cc                | 1 +
+ Vec.h                        | 4 ++--
+ feudal/FeudalControlBlock.cc | 1 +
+ feudal/FeudalFileReader.h    | 1 +
+ feudal/MasterVec.h           | 6 +++---
+ feudal/SerfVec.h             | 4 ++--
+ 6 files changed, 10 insertions(+), 7 deletions(-)
+
+diff --git a/MakeDepend.cc b/MakeDepend.cc
+index 93032e8..619e6f7 100644
+--- a/MakeDepend.cc
++++ b/MakeDepend.cc
+@@ -25,6 +25,7 @@
+ #include <iterator>
+ #include <iostream>
+ #include <ctype.h>
++#include <unistd.h>
+ 
+ using namespace std;
+ 
+diff --git a/Vec.h b/Vec.h
+index f26f3f4..57eeff9 100644
+--- a/Vec.h
++++ b/Vec.h
+@@ -259,7 +259,7 @@ template <class T> class vec : public vector<T> {
+ 
+   template <class U>
+   void append( const vec<U>& y ) 
+-  {    insert( this->end( ), y.begin( ), y.end( ) );    }
++  {    this->insert( this->end( ), y.begin( ), y.end( ) );    }
+   
+   void append( const vec<T>& y, size_type i, size_type j ) {
+     if ( j == y.size( ) ) insert( this->end( ), y.begin( ) + i, y.end( ) );
+@@ -402,7 +402,7 @@ template <class T> class vec : public vector<T> {
+ 
+   /// EraseValue: erase all entries having the given value.
+   void EraseValue( const T& x ) {
+-    erase(remove(this->begin(), this->end(), x), this->end());
++    this->erase(remove(this->begin(), this->end(), x), this->end());
+   }
+ 
+   /// print values to ostream, separated by sep.
+diff --git a/feudal/FeudalControlBlock.cc b/feudal/FeudalControlBlock.cc
+index bc64ecd..a709320 100644
+--- a/feudal/FeudalControlBlock.cc
++++ b/feudal/FeudalControlBlock.cc
+@@ -24,6 +24,7 @@
+ #include <string.h>
+ #include <errno.h>
+ #include <iostream>
++#include <unistd.h>
+ 
+ using std::cout;
+ using std::endl;
+diff --git a/feudal/FeudalFileReader.h b/feudal/FeudalFileReader.h
+index b71bf6d..073a1a1 100644
+--- a/feudal/FeudalFileReader.h
++++ b/feudal/FeudalFileReader.h
+@@ -13,6 +13,7 @@
+ #include <string>
+ #include <cassert>
+ #include <sstream>
++#include <unistd.h>
+ #include "feudal/BinaryStream.h"
+ 
+ /**
+diff --git a/feudal/MasterVec.h b/feudal/MasterVec.h
+index e6477d9..45a8640 100644
+--- a/feudal/MasterVec.h
++++ b/feudal/MasterVec.h
+@@ -60,7 +60,7 @@ public:
+     /// This function is deprecated: Use reserve() instead.
+     /// The pool size argument is ignored, anyway.
+     MasterVec& Reserve( unsigned long raw_mem_size_ignored, size_type capacity )
+-    { reserve(capacity); return *this; }
++    { this->reserve(capacity); return *this; }
+ 
+     /// This function is deprecated:  Use clear().shrink_to_fit().
+     MasterVec& destroy() { BaseT::clear(); BaseT::shrink_to_fit(); return *this; }
+@@ -73,7 +73,7 @@ public:
+     MasterVec& push_back_reserve( T const& val,
+                                   size_type growthIncr = 0,
+                                   float growthFact = 1.3f )
+-    { push_back(val,growthFact,growthIncr); return *this; }
++    { this->push_back(val,growthFact,growthIncr); return *this; }
+ 
+     /// This function is deprecated:  Use append().
+     MasterVec& Append( MasterVec const& that )
+@@ -99,7 +99,7 @@ public:
+     { if ( !append ) BaseT::clear();
+       FeudalFileReader rdr(fileName.c_str(),T::fixedDataLen());
+       size_type siz = rdr.getNElements();
+-      reserve(BaseT::size()+siz);
++      this->reserve(BaseT::size()+siz);
+       for ( size_type iii = 0; iii < siz; ++iii )
+         appendFromReader(rdr,iii);
+       return *this; }
+diff --git a/feudal/SerfVec.h b/feudal/SerfVec.h
+index e91847c..d5f053d 100644
+--- a/feudal/SerfVec.h
++++ b/feudal/SerfVec.h
+@@ -79,10 +79,10 @@ public:
+     /// Deprecated:  Use assign().
+     SerfVec& SetToSubOf( SerfVec const& that, size_type pos, size_type len )
+     { if ( this != &that )
+-      { assign(that.begin(pos),that.begin(pos+len)); }
++      { this->assign(that.begin(pos),that.begin(pos+len)); }
+       else
+       { assert(that.size()>=pos+len);
+-        erase(BaseT::begin(),BaseT::begin(pos));
++        this->erase(BaseT::begin(),BaseT::begin(pos));
+         BaseT::resize(len); }
+       return *this; }
+