gentoo-mirror/gentoo
1
0
Fork 0
mirror of https://github.com/gentoo-mirror/gentoo.git synced 2026-08-06 12:58:16 -07:00
Code Issues Projects Releases Wiki Activity

sci-biology/abyss: bump up to 2.0.2, bug #596018

Browse Source 
Fixes gcc-6 and boost-1.62 build failures.

Reported-by: Toralf Förster
Bug: https://bugs.gentoo.org/596018

Package-Manager: portage-2.3.2
This commit is contained in:
Sergei Trofimovich
2016-11-06 13:12:25 +00:00
parent edb7931695
commit 4c8a5799cd
3 changed files with 49 additions and 1 deletions
Download Patch File Download Diff File Expand all files Collapse all files

1
sci-biology/abyss/Manifest
View File

@@ -1,3 +1,4 @@
DIST abyss-1.3.3.tar.gz 621480 SHA256 60396e2c8813952ceb1c66a3ad7c87eda984aa1e4952a14265217d9f639706a0 SHA512 4ec7fdd24bdb1e3d66e2bda50929122ff347107010701703e81ca1609fb1b4913c713991b3fe84a48ccfbc069e126f4f4120aafbab81e54e567a95a2f1099fb2 WHIRLPOOL 35f6fdfe60b70316e67bcbbb0a9c67e952302333e9ec71d893f2de7a94482dca1a604dc8cfef1ecee49e464244bb5df7469a8ad7bdc37bd54ff455b0f75b7914
DIST abyss-1.3.6.tar.gz 678880 SHA256 4432a8b5046bdcb548b6f1b22069a6cade4dea26fc6f83ad5467548e4f3e7c95 SHA512 2c6d72e0227c4af2d5740a989168ad35a84b9236dc53b65a29a010c4e5f77e5c4bfaa38bfaa2f14fd530ae6df204294ff167bd40e79f61e8bad6a7489bf34ace WHIRLPOOL 0677b1fd4090ba155fb876c0047a1ccd2ec2e220950e1e9940e1f3df05ef0abd3ba2e3dbabd500d6fab39a8f7d94e02e0a07410934733682a70fa605d2a8bc07
DIST abyss-1.9.0.tar.gz 985480 SHA256 82e4050766a9c7fb87fd736f94724a02388efb1df847b40870a0fbf842917239 SHA512 d9da19f004bb97f9301f3be83ceb5361eb70f42139a1ef17129de99e03bda5de7680d718d76aed26d26f24c1d26c37e050801ff343acad007b76d2214955b83f WHIRLPOOL bd322afa9bf99a53aec177c79ca9618f39043cda606eb4e3d5dcfb46c26298d218fc154e2c46efadac59febb69dd625fe597101a1efbccc62ab8228b555596cc
DIST abyss-2.0.2.tar.gz 1036135 SHA256 6482b81eb5439703c0dbf6cd7ac25cd0df7541d9e04ef7865343b241e21db460 SHA512 b19325b9d51e80378fc9818942c4005c94f470f0ad8ff6c1b8b593ad0216d35f9a99c0aa7c627082372690a6a7094ced8ca8efeb0bff6014ca46a67d7eb16a30 WHIRLPOOL 23447cb00b0bb9b5b8a724ba44f8d7193d9640ccd19956b42bbbd83b67557b66b7c68141d6f292c4ab11ab523286471d5ee1c938f22749a61162de056a0d903e

2
sci-biology/abyss/abyss-1.9.0-r1.ebuild
View File

@@ -8,7 +8,7 @@ inherit autotools toolchain-funcs
DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler"
HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/"
SRC_URI="https://github.com/bcgsc/abyss/archive/1.9.0.tar.gz -> ${P}.tar.gz"
SRC_URI="https://github.com/bcgsc/abyss/archive/${PV}.tar.gz -> ${P}.tar.gz"
LICENSE="abyss"
SLOT="0"

47
sci-biology/abyss/abyss-2.0.2.ebuild Normal file
View File

@@ -0,0 +1,47 @@
# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
EAPI=6
inherit autotools toolchain-funcs
DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler"
HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/"
SRC_URI="https://github.com/bcgsc/abyss/archive/${PV}.tar.gz -> ${P}.tar.gz"
LICENSE="abyss"
SLOT="0"
IUSE="+mpi openmp misc-haskell"
KEYWORDS="~amd64 ~x86"
RDEPEND="
dev-cpp/sparsehash
dev-libs/boost:=
misc-haskell? ( dev-libs/gmp:0=
virtual/libffi:0=
)
mpi? ( virtual/mpi )
"
DEPEND="${RDEPEND}
misc-haskell? ( dev-lang/ghc
dev-haskell/mmap )
"
# todo: --enable-maxk=N configure option
# todo: fix automagic mpi toggling
src_prepare() {
default
sed -i -e "s/-Werror//" configure.ac || die #365195
sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die
eautoreconf
}
src_configure() {
# disable building haskell tool Misc/samtobreak
# unless request by user: bug #534412
use misc-haskell || export ac_cv_prog_ac_ct_GHC=
econf $(use_enable openmp)
}