diff options
Diffstat (limited to 'sci-biology')
| -rw-r--r-- | sci-biology/mcl/Manifest | 1 | ||||
| -rw-r--r-- | sci-biology/mcl/files/mcl-14.137-qa-implicit-declarations.patch | 27 | ||||
| -rw-r--r-- | sci-biology/mcl/mcl-14.137.ebuild | 36 |
3 files changed, 64 insertions, 0 deletions
diff --git a/sci-biology/mcl/Manifest b/sci-biology/mcl/Manifest index 88b4aef28107..dcdaee7f54f5 100644 --- a/sci-biology/mcl/Manifest +++ b/sci-biology/mcl/Manifest @@ -1,2 +1,3 @@ DIST mcl-08-312.tar.gz 2749006 SHA256 0061da0661e99f783d97e6ae10149fe5ce11fa332b24cc8a4a491a072867bb6e SHA512 9f89f81af398710ebb9135c93653d892fc9daef360d70f3b890a3133d8a17dddffe568b110d3370602cead895562bc0dc5a71020834b3b3e9b6d2abf4bf64b0b WHIRLPOOL 6d00665c545edb55605fb0438cc79a412150e68b9c63ffc51c93f8f8c33b9bcd6e4e5e435b3be89a64407a0a8f6f1b8e77567f653e45c08f1675dbf2b9e0b59e DIST mcl-12-135.tar.gz 2970824 SHA256 3f5e0e7ad1074c7c4ef0139aa3318f92971fede7292dc3571eca2fd1da20a283 SHA512 97234e88f3430f223e1f303577b2b8853f40de6b204de415466719f691f529a795b17bf2fd48d4cc73d05900c87a10ba9afabbe54bce9367ee59215e7db0a8f5 WHIRLPOOL 1505643a460ba5bd6b834d070278a108fba57c9dc2a90a72a8e0726bd54a1b8fe3e4792a63397d58db62b036d22c325db2dd76f696a8692473987395c556a279 +DIST mcl-14-137.tar.gz 3035491 SHA256 b5786897a8a8ca119eb355a5630806a4da72ea84243dba85b19a86f14757b497 SHA512 7e399e571de60da5e1ba9e643b7f0cd98fe484cc8cef517222a57322b5c7a04afa675c7cf0ab88b5801efa9565e5e67a14c4914987964308391d88dd4be1bea2 WHIRLPOOL 6a4afda86cc91c3ddacb64740f020cec2235e22411430281cde9106fb8399663c7854eb1ba5f477624d825280a7762cf5a3f7c6ec824a784a7e200e92d42a168 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 new file mode 100644 index 000000000000..df4309874d48 --- /dev/null +++ b/sci-biology/mcl/files/mcl-14.137-qa-implicit-declarations.patch @@ -0,0 +1,27 @@ +Fix QA issues related to implicit declarations. + +* QA Notice: Package triggers severe warnings which indicate that it +* may exhibit random runtime failures. +* clmadjust.c:184:10: warning: implicit declaration of function ‘mcxFree’ [-Wimplicit-function-declaration] +* mcxi.c:42:16: warning: implicit declaration of function ‘isatty’ [-Wimplicit-function-declaration] + +--- mcl-14-137/src/shcl/clmadjust.c ++++ mcl-14-137/src/shcl/clmadjust.c +@@ -14,6 +14,7 @@ + #include "report.h" + #include "clmadjust.h" + ++#include "util/alloc.h" + #include "util/io.h" + #include "util/types.h" + #include "util/err.h" +--- mcl-14-137/src/shmcx/mcxi.c ++++ mcl-14-137/src/shmcx/mcxi.c +@@ -8,6 +8,7 @@ + */ + + #include <stdio.h> ++#include <unistd.h> + + #include "stack.h" + #include "glob.h" diff --git a/sci-biology/mcl/mcl-14.137.ebuild b/sci-biology/mcl/mcl-14.137.ebuild new file mode 100644 index 000000000000..6912351fd2ed --- /dev/null +++ b/sci-biology/mcl/mcl-14.137.ebuild @@ -0,0 +1,36 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=6 + +inherit autotools + +MY_P="${PN}-${PV/./-}" + +DESCRIPTION="A Markov Cluster Algorithm implementation" +HOMEPAGE="http://micans.org/mcl/" +SRC_URI="http://micans.org/mcl/src/${MY_P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="+blast" + +PATCHES=("${FILESDIR}/${P}-qa-implicit-declarations.patch") +S="${WORKDIR}/${MY_P}" + +src_prepare() { + find \ + -name Makefile.am \ + -exec sed \ + -e '/docdir/d' \ + -e '/exampledir/s:doc::g' \ + -i '{}' + || die + default + eautoreconf +} + +src_configure() { + econf $(use_enable blast) +} |