1 |
commit: 61b8654f706e0c48f79a631ee797be9ba5135b2c |
2 |
Author: Ted Tanberry <ted.tanberry <AT> gmail <DOT> com> |
3 |
AuthorDate: Thu Dec 24 20:12:54 2015 +0000 |
4 |
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org> |
5 |
CommitDate: Fri Dec 25 11:44:51 2015 +0000 |
6 |
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=61b8654f |
7 |
|
8 |
sci-biology/mcl: Version bump, fix bug 569040 and QA issues. |
9 |
|
10 |
Package-Manager: portage-2.2.26 |
11 |
|
12 |
sci-biology/mcl/Manifest | 1 + |
13 |
.../mcl-14.137-qa-implicit-declarations.patch | 27 ++++++++++++++++ |
14 |
sci-biology/mcl/mcl-14.137.ebuild | 36 ++++++++++++++++++++++ |
15 |
3 files changed, 64 insertions(+) |
16 |
|
17 |
diff --git a/sci-biology/mcl/Manifest b/sci-biology/mcl/Manifest |
18 |
index 88b4aef..dcdaee7 100644 |
19 |
--- a/sci-biology/mcl/Manifest |
20 |
+++ b/sci-biology/mcl/Manifest |
21 |
@@ -1,2 +1,3 @@ |
22 |
DIST mcl-08-312.tar.gz 2749006 SHA256 0061da0661e99f783d97e6ae10149fe5ce11fa332b24cc8a4a491a072867bb6e SHA512 9f89f81af398710ebb9135c93653d892fc9daef360d70f3b890a3133d8a17dddffe568b110d3370602cead895562bc0dc5a71020834b3b3e9b6d2abf4bf64b0b WHIRLPOOL 6d00665c545edb55605fb0438cc79a412150e68b9c63ffc51c93f8f8c33b9bcd6e4e5e435b3be89a64407a0a8f6f1b8e77567f653e45c08f1675dbf2b9e0b59e |
23 |
DIST mcl-12-135.tar.gz 2970824 SHA256 3f5e0e7ad1074c7c4ef0139aa3318f92971fede7292dc3571eca2fd1da20a283 SHA512 97234e88f3430f223e1f303577b2b8853f40de6b204de415466719f691f529a795b17bf2fd48d4cc73d05900c87a10ba9afabbe54bce9367ee59215e7db0a8f5 WHIRLPOOL 1505643a460ba5bd6b834d070278a108fba57c9dc2a90a72a8e0726bd54a1b8fe3e4792a63397d58db62b036d22c325db2dd76f696a8692473987395c556a279 |
24 |
+DIST mcl-14-137.tar.gz 3035491 SHA256 b5786897a8a8ca119eb355a5630806a4da72ea84243dba85b19a86f14757b497 SHA512 7e399e571de60da5e1ba9e643b7f0cd98fe484cc8cef517222a57322b5c7a04afa675c7cf0ab88b5801efa9565e5e67a14c4914987964308391d88dd4be1bea2 WHIRLPOOL 6a4afda86cc91c3ddacb64740f020cec2235e22411430281cde9106fb8399663c7854eb1ba5f477624d825280a7762cf5a3f7c6ec824a784a7e200e92d42a168 |
25 |
|
26 |
diff --git a/sci-biology/mcl/files/mcl-14.137-qa-implicit-declarations.patch b/sci-biology/mcl/files/mcl-14.137-qa-implicit-declarations.patch |
27 |
new file mode 100644 |
28 |
index 0000000..df43098 |
29 |
--- /dev/null |
30 |
+++ b/sci-biology/mcl/files/mcl-14.137-qa-implicit-declarations.patch |
31 |
@@ -0,0 +1,27 @@ |
32 |
+Fix QA issues related to implicit declarations. |
33 |
+ |
34 |
+* QA Notice: Package triggers severe warnings which indicate that it |
35 |
+* may exhibit random runtime failures. |
36 |
+* clmadjust.c:184:10: warning: implicit declaration of function ‘mcxFree’ [-Wimplicit-function-declaration] |
37 |
+* mcxi.c:42:16: warning: implicit declaration of function ‘isatty’ [-Wimplicit-function-declaration] |
38 |
+ |
39 |
+--- mcl-14-137/src/shcl/clmadjust.c |
40 |
++++ mcl-14-137/src/shcl/clmadjust.c |
41 |
+@@ -14,6 +14,7 @@ |
42 |
+ #include "report.h" |
43 |
+ #include "clmadjust.h" |
44 |
+ |
45 |
++#include "util/alloc.h" |
46 |
+ #include "util/io.h" |
47 |
+ #include "util/types.h" |
48 |
+ #include "util/err.h" |
49 |
+--- mcl-14-137/src/shmcx/mcxi.c |
50 |
++++ mcl-14-137/src/shmcx/mcxi.c |
51 |
+@@ -8,6 +8,7 @@ |
52 |
+ */ |
53 |
+ |
54 |
+ #include <stdio.h> |
55 |
++#include <unistd.h> |
56 |
+ |
57 |
+ #include "stack.h" |
58 |
+ #include "glob.h" |
59 |
|
60 |
diff --git a/sci-biology/mcl/mcl-14.137.ebuild b/sci-biology/mcl/mcl-14.137.ebuild |
61 |
new file mode 100644 |
62 |
index 0000000..6912351 |
63 |
--- /dev/null |
64 |
+++ b/sci-biology/mcl/mcl-14.137.ebuild |
65 |
@@ -0,0 +1,36 @@ |
66 |
+# Copyright 1999-2015 Gentoo Foundation |
67 |
+# Distributed under the terms of the GNU General Public License v2 |
68 |
+# $Id$ |
69 |
+ |
70 |
+EAPI=6 |
71 |
+ |
72 |
+inherit autotools |
73 |
+ |
74 |
+MY_P="${PN}-${PV/./-}" |
75 |
+ |
76 |
+DESCRIPTION="A Markov Cluster Algorithm implementation" |
77 |
+HOMEPAGE="http://micans.org/mcl/" |
78 |
+SRC_URI="http://micans.org/mcl/src/${MY_P}.tar.gz" |
79 |
+ |
80 |
+LICENSE="GPL-2" |
81 |
+SLOT="0" |
82 |
+KEYWORDS="~amd64 ~x86" |
83 |
+IUSE="+blast" |
84 |
+ |
85 |
+PATCHES=("${FILESDIR}/${P}-qa-implicit-declarations.patch") |
86 |
+S="${WORKDIR}/${MY_P}" |
87 |
+ |
88 |
+src_prepare() { |
89 |
+ find \ |
90 |
+ -name Makefile.am \ |
91 |
+ -exec sed \ |
92 |
+ -e '/docdir/d' \ |
93 |
+ -e '/exampledir/s:doc::g' \ |
94 |
+ -i '{}' + || die |
95 |
+ default |
96 |
+ eautoreconf |
97 |
+} |
98 |
+ |
99 |
+src_configure() { |
100 |
+ econf $(use_enable blast) |
101 |
+} |