From 89ab6a3d9d32bcb93e27580298094a875a530685 Mon Sep 17 00:00:00 2001
From: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
Date: Thu, 13 Jan 2022 12:20:26 +0100
Subject: sci-biology/abyss: drop version 2.0.3

Closes: https://bugs.gentoo.org/741154
Closes: https://bugs.gentoo.org/715718
Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
---
 sci-biology/abyss/Manifest                        |  1 -
 sci-biology/abyss/abyss-2.0.3-r2.ebuild           | 64 -----------------------
 sci-biology/abyss/files/abyss-2.0.3-prog-AR.patch | 11 ----
 3 files changed, 76 deletions(-)
 delete mode 100644 sci-biology/abyss/abyss-2.0.3-r2.ebuild
 delete mode 100644 sci-biology/abyss/files/abyss-2.0.3-prog-AR.patch

(limited to 'sci-biology')

diff --git a/sci-biology/abyss/Manifest b/sci-biology/abyss/Manifest
index 32cead3a3a6e..9c9041e2c936 100644
--- a/sci-biology/abyss/Manifest
+++ b/sci-biology/abyss/Manifest
@@ -1,2 +1 @@
-DIST abyss-2.0.3.tar.gz 1049144 BLAKE2B 1a320cac735747225723f0d636af435ffcac9efb3273323150f258c0f4c27ed81bb104cb06a726aa664118cc9d2224b745d9deebfcac055face01dae3fc9de15 SHA512 15bc833e89839be89dfa35a23ae22ad0f9a19e8efd36211010c9f59e974de7c569576db36e26d6ab302543ff427604b5efb1b7badf62489a5e82a193ef155570
 DIST abyss-2.3.4.tar.gz 3511137 BLAKE2B 2b7449233055d22330f44951f9f6d5ff1a116fa3e19c09c17cd4fa517d2fc055c4f00ccb82c7e09b1b939ac6f7a1caf73cf73c33bd3c8aa9ff11879c227a2aaa SHA512 9d4e418399dd62883b53e831f51a0bd2ba228da73eda6c6459cd729c002eb0487f9613fca1c9bd0f4fbb076eed8a9b952505ee97143ab7dde537c23e4a246cd4
diff --git a/sci-biology/abyss/abyss-2.0.3-r2.ebuild b/sci-biology/abyss/abyss-2.0.3-r2.ebuild
deleted file mode 100644
index b9aed09d3eec..000000000000
--- a/sci-biology/abyss/abyss-2.0.3-r2.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 -> ${P}.tar.gz"
-
-LICENSE="abyss"
-SLOT="0"
-IUSE="+mpi openmp misc-haskell"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
-	dev-cpp/sparsehash
-	dev-libs/boost:=
-	misc-haskell? (
-		dev-libs/gmp:0=
-		dev-libs/libffi:0=
-	)
-	mpi? ( sys-cluster/openmpi )"
-DEPEND="${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 $(use_enable openmp)
-}
diff --git a/sci-biology/abyss/files/abyss-2.0.3-prog-AR.patch b/sci-biology/abyss/files/abyss-2.0.3-prog-AR.patch
deleted file mode 100644
index d41c58ad261a..000000000000
--- a/sci-biology/abyss/files/abyss-2.0.3-prog-AR.patch
+++ /dev/null
@@ -1,11 +0,0 @@
-https://bugs.gentoo.org/725300
---- a/configure.ac
-+++ b/configure.ac
-@@ -17,6 +17,7 @@ AC_CHECK_TOOL(GHC, ghc)
- AM_CONDITIONAL([HAVE_GHC], ["$GHC" --version])
- AC_CHECK_PROG(PANDOC, pandoc, yes)
- AM_CONDITIONAL([HAVE_PANDOC], [test x"$PANDOC" = x"yes"])
-+AM_PROG_AR
- 
- # Checks for header files.
- AC_CHECK_HEADERS([dlfcn.h fcntl.h float.h limits.h \
-- 
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