sci-biology/tree-puzzle: Mask stupid test, which fails due to precision reached depending on optimization used at compile time, #297646; fix move to EAPI=4, #429354

Package-Manager: portage-2.2.0_alpha120/cvs/Linux x86_64

4 files changed, 39 insertions, 11 deletions

diff --git a/sci-biology/tree-puzzle/ChangeLog b/sci-biology/tree-puzzle/ChangeLog
index 4c9ef5988c2c..34e72f3c6128 100644
--- a/sci-biology/tree-puzzle/ChangeLog
+++ b/sci-biology/tree-puzzle/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-biology/tree-puzzle
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/tree-puzzle/ChangeLog,v 1.18 2012/05/24 10:28:51 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/tree-puzzle/ChangeLog,v 1.19 2012/08/01 15:41:29 jlec Exp $
+
+  01 Aug 2012; Justin Lecher <jlec@gentoo.org> tree-puzzle-5.2.ebuild,
+  +files/tree-puzzle-impl-dec.patch:
+  Mask stupid test, which fails due to precision reached depending on
+  optimization used at compile time, #297646; fix move to EAPI=4, #429354
 
   24 May 2012; Justin Lecher <jlec@gentoo.org> tree-puzzle-5.2.ebuild:
   Corrected dep from sys-cluster/lam-mpi to virtual/mpi, #415765
diff --git a/sci-biology/tree-puzzle/Manifest b/sci-biology/tree-puzzle/Manifest
index c2e6c9d7b4cf..544fd4858178 100644
--- a/sci-biology/tree-puzzle/Manifest
+++ b/sci-biology/tree-puzzle/Manifest
@@ -1,15 +1,16 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA512
+Hash: SHA256
 
-DIST tree-puzzle-5.2.tar.gz 875142 RMD160 8a69f5ab2ad56a05c0faa6cd02e344c19271bf7a SHA1 fd52a9f04dc871b765d9f7464f68bdb8edc22e37 SHA256 3396d3b80b03b0600afb479dc33f0bd3e5631298337295a4fa454211ac44c3fb
-EBUILD tree-puzzle-5.2.ebuild 1377 RMD160 e4dfb4e1836c7d68cfe9b3444c4397a846f3f789 SHA1 58e2f5abcf6b568a79599d2ae8ae98a47e715085 SHA256 4a078a92816909a941c7478353f12b9ea5d8fbb7dd1327c387e419be0b2368c1
-MISC ChangeLog 3162 RMD160 1f1c9dfc08024fefc7091dbde8d71d52a16d34fa SHA1 4aefbb91e14aa00623f6c9366d6c54ac5532fac3 SHA256 4f956bb9b063c4d6f1a8e3b1ac1891f69c109a6890979001c72bda7846d6ca31
-MISC metadata.xml 1459 RMD160 1fd787e9bb6887264319e3484e30fd3612b855e0 SHA1 e3bcb0cffa751c79b5c61cb38e8006f368bd01d2 SHA256 ccefdd7d49206f9e090218494a5857e711977a75f24136f3916a34d4dab6219d
+AUX tree-puzzle-impl-dec.patch 380 SHA256 0d0941cb6030e089e224a2390a28193ec848c4b2aabf021888292e41df1a1f50 SHA512 092743fff8a305a41ef55afde3e058c1892d9c608bd05cb87de38a451c2b9cafc7749825347d5c245f1c6b1e84cf9d28b63bd4e7389440da5604766412290110 WHIRLPOOL d12a213adb3aefff795814859c02d9e8ed925b37bae31ad95d39344c6bc6514c05a3d03ef080ac9b8e7aff33f3a55d637c79c8df754c3ba6105e430b88b58282
+DIST tree-puzzle-5.2.tar.gz 875142 SHA256 3396d3b80b03b0600afb479dc33f0bd3e5631298337295a4fa454211ac44c3fb SHA512 5b9a729b120cba59f59ba426acd439cf396826ea01e75361b23387ccb9baf295d2512f21af96071a5f7b7507db4ff4d6b135cf6c5b6233a8b438532d31abe751 WHIRLPOOL 145afdfc266809638d7b049beb65cdfc8fb6c108ecba831ba36fae938d58edd141fdf1762d9ce86269f0098043e7314b0ddefaa5e7f9b11cc6fd56a480b54d61
+EBUILD tree-puzzle-5.2.ebuild 1475 SHA256 bfefe7801331667dbda4e266d7d96c6c1fd49133a18841fb1c40414ed6c97b18 SHA512 a482a3c2b138c3683e1cfcebd09a2e31b18c37181286cccdbc25e448d1f685c9f5e4469a9783ba43530c72f84af32b7d2c6f32b69d183a2593987a920635d2d8 WHIRLPOOL 0733edbf781314580b8de98623ad2f9440a949119d40d5a96ae95fd7d4e7beb79d44d0ac3afd228eeb7726bf446093f3f732a68d313e8e353bf80bc6bbaee1d0
+MISC ChangeLog 3415 SHA256 73662fc7bcbd74f8b2da79455934d8b6b40267e0b403c92d33866f6ceb156bfe SHA512 f9547f4a6f63a55aa98c0703d269a222a4cea38b4c7ac32dfc9965467b14f4e0be0fd0e502cb33b003cd6099c44dfed1c1ab5a49f2bf31a1777890d644d6a0a3 WHIRLPOOL 76a2553e06efafdf9864d87a2a774b05d48b3d13f2ad50bbcc20cc1f4cc54f841e5c3c1af97f43b6d9e4a76c60f1852ec71604cb73379f99ba1b70db3b20bf6d
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diff --git a/sci-biology/tree-puzzle/files/tree-puzzle-impl-dec.patch b/sci-biology/tree-puzzle/files/tree-puzzle-impl-dec.patch
new file mode 100644
index 000000000000..93b960f5c2b4
--- /dev/null
+++ b/sci-biology/tree-puzzle/files/tree-puzzle-impl-dec.patch
@@ -0,0 +1,14 @@
+ src/sprng/primes-lcg64.c |    1 +
+ 1 files changed, 1 insertions(+), 0 deletions(-)
+
+diff --git a/src/sprng/primes-lcg64.c b/src/sprng/primes-lcg64.c
+index 8e5a7c9..fb04373 100644
+--- a/src/sprng/primes-lcg64.c
++++ b/src/sprng/primes-lcg64.c
+@@ -1,5 +1,6 @@
+ #include <stdio.h>
+ #include <stdlib.h>
++#include <string.h>
+ #include "primes-lcg64.h"
+ #include "primelist-lcg64.h"
+ 
diff --git a/sci-biology/tree-puzzle/tree-puzzle-5.2.ebuild b/sci-biology/tree-puzzle/tree-puzzle-5.2.ebuild
index a567e9c34961..033fd7f49b7c 100644
--- a/sci-biology/tree-puzzle/tree-puzzle-5.2.ebuild
+++ b/sci-biology/tree-puzzle/tree-puzzle-5.2.ebuild
@@ -1,10 +1,10 @@
 # Copyright 1999-2012 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/tree-puzzle/tree-puzzle-5.2.ebuild,v 1.13 2012/05/24 10:28:51 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/tree-puzzle/tree-puzzle-5.2.ebuild,v 1.14 2012/08/01 15:41:29 jlec Exp $
 
 EAPI=4
 
-inherit toolchain-funcs
+inherit eutils toolchain-funcs
 
 DESCRIPTION="Maximum likelihood analysis for nucleotide, amino acid, and two-state data"
 HOMEPAGE="http://www.tree-puzzle.de"
@@ -18,6 +18,8 @@ IUSE="mpi"
 DEPEND="mpi? ( virtual/mpi )"
 RDEPEND="${DEPEND}"
 
+RESTRICT="test"
+
 pkg_setup () {
 	use mpi && [ $(tc-getCC) = icc ] && die "The parallelized version of tree-puzzle cannot be compiled using icc.
 	Either disable the \"mpi\" USE flag to compile only the non-parallelized
@@ -25,6 +27,12 @@ pkg_setup () {
 }
 
 src_prepare() {
+	epatch "${FILESDIR}"/${PN}-impl-dec.patch
+}
+
+src_configure() {
+	default
+
 	if ! use mpi; then
 			sed \
 				-e 's:bin_PROGRAMS = puzzle$(EXEEXT) ppuzzle:bin_PROGRAMS = puzzle :' \