From 4499edbc478106c4f7a04062c8ee2f273474c8cb Mon Sep 17 00:00:00 2001
From: Sergei Trofimovich <slyfox@gentoo.org>
Date: Sun, 21 Jun 2020 17:46:53 +0100
Subject: sci-biology/abyss: switch from virtual/libffi

Package-Manager: Portage-2.3.101, Repoman-2.3.22
Signed-off-by: Sergei Trofimovich <slyfox@gentoo.org>
---
 sci-biology/abyss/abyss-2.0.3-r1.ebuild | 64 ---------------------------------
 sci-biology/abyss/abyss-2.0.3-r2.ebuild | 64 +++++++++++++++++++++++++++++++++
 2 files changed, 64 insertions(+), 64 deletions(-)
 delete mode 100644 sci-biology/abyss/abyss-2.0.3-r1.ebuild
 create mode 100644 sci-biology/abyss/abyss-2.0.3-r2.ebuild

(limited to 'sci-biology')

diff --git a/sci-biology/abyss/abyss-2.0.3-r1.ebuild b/sci-biology/abyss/abyss-2.0.3-r1.ebuild
deleted file mode 100644
index 800a45964cd0..000000000000
--- a/sci-biology/abyss/abyss-2.0.3-r1.ebuild
+++ /dev/null
@@ -1,64 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-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 -> ${P}.tar.gz"
-
-LICENSE="abyss"
-SLOT="0"
-IUSE="+mpi openmp misc-haskell"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
-	dev-cpp/sparsehash
-	dev-libs/boost:=
-	misc-haskell? (
-		dev-libs/gmp:0=
-		virtual/libffi:0=
-	)
-	mpi? ( sys-cluster/openmpi )"
-DEPEND="${RDEPEND}
-	misc-haskell? (
-		dev-lang/ghc
-	)"
-
-PATCHES=("${FILESDIR}"/${PN}-2.0.3-prog-AR.patch)
-
-# GHC uses it's own native code generator. Portage's
-# QA check generates false positive because it assumes
-# presence of GCC-specific sections.
-#
-# Workaround false positiove by disabling the check completely.
-# bug #677600
-QA_FLAGS_IGNORED='/usr/bin/abyss-samtobreak'
-
-# todo: --enable-maxk=N configure option
-# todo: fix automagic mpi toggling
-
-pkg_pretend() {
-	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-}
-
-pkg_setup() {
-	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-}
-
-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 $(use_enable openmp)
-}
diff --git a/sci-biology/abyss/abyss-2.0.3-r2.ebuild b/sci-biology/abyss/abyss-2.0.3-r2.ebuild
new file mode 100644
index 000000000000..b9aed09d3eec
--- /dev/null
+++ b/sci-biology/abyss/abyss-2.0.3-r2.ebuild
@@ -0,0 +1,64 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit autotools toolchain-funcs
+
+DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler"
+HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/"
+SRC_URI="https://github.com/bcgsc/abyss/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="abyss"
+SLOT="0"
+IUSE="+mpi openmp misc-haskell"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+	dev-cpp/sparsehash
+	dev-libs/boost:=
+	misc-haskell? (
+		dev-libs/gmp:0=
+		dev-libs/libffi:0=
+	)
+	mpi? ( sys-cluster/openmpi )"
+DEPEND="${RDEPEND}
+	misc-haskell? (
+		dev-lang/ghc
+	)"
+
+PATCHES=("${FILESDIR}"/${PN}-2.0.3-prog-AR.patch)
+
+# GHC uses it's own native code generator. Portage's
+# QA check generates false positive because it assumes
+# presence of GCC-specific sections.
+#
+# Workaround false positiove by disabling the check completely.
+# bug #677600
+QA_FLAGS_IGNORED='/usr/bin/abyss-samtobreak'
+
+# todo: --enable-maxk=N configure option
+# todo: fix automagic mpi toggling
+
+pkg_pretend() {
+	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
+}
+
+pkg_setup() {
+	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
+}
+
+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)
+}
-- 
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