[gentoo-commits] repo/gentoo:master commit in: dev-haskell/bio/, profiles/, dev-haskell/bio/files/

[Sergei Trofimovich]

commit:     2061aae04d054cdabfcea55a92c5cdb55a8e10b9
Author:     Sergei Trofimovich <slyfox <AT> gentoo <DOT> org>
AuthorDate: Sat Sep 26 20:53:51 2020 +0000
Commit:     Sergei Trofimovich <slyfox <AT> gentoo <DOT> org>
CommitDate: Sat Sep 26 20:55:08 2020 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=2061aae0

dev-haskell/bio: drop masked package

Signed-off-by: Sergei Trofimovich <slyfox <AT> gentoo.org>

 dev-haskell/bio/Manifest                       |  1 -
 dev-haskell/bio/bio-0.5.3-r2.ebuild            | 64 --------------------------
 dev-haskell/bio/files/bio-0.5.3-ghc-7.10.patch |  7 ---
 dev-haskell/bio/metadata.xml                   | 25 ----------
 profiles/package.mask                          |  5 --
 5 files changed, 102 deletions(-)

diff --git a/dev-haskell/bio/Manifest b/dev-haskell/bio/Manifest
deleted file mode 100644
index f9f2f698b89..00000000000
--- a/dev-haskell/bio/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST bio-0.5.3.tar.gz 103707 BLAKE2B 31c9e354ba33f20d6129a20d6272063498bfd4b4ea2cba9eddab8ede62ee894659eb5e6383ef022f5e003deab8bb3c92a98bcadae44db22e7b0346471cad5e4d SHA512 fbe09240a600abbcac952f52f05f28f9b305a1ae3def8b4144bd73bdb160acfbe5457086ef829057d5a73df1df5061668487b2ca5621df73628c8c4990b6b544

diff --git a/dev-haskell/bio/bio-0.5.3-r2.ebuild b/dev-haskell/bio/bio-0.5.3-r2.ebuild
deleted file mode 100644
index 9d49efd38d8..00000000000
--- a/dev-haskell/bio/bio-0.5.3-r2.ebuild
+++ /dev/null
@@ -1,64 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-# ebuild generated by hackport 0.3.2.9999
-
-CABAL_FEATURES="bin lib profile haddock hoogle hscolour"
-inherit eutils haskell-cabal
-
-DESCRIPTION="A bioinformatics library"
-HOMEPAGE="http://biohaskell.org/Libraries/Bio"
-SRC_URI="https://hackage.haskell.org/package/${P}/${P}.tar.gz"
-
-LICENSE="LGPL-2.1"
-SLOT="0/${PV}"
-KEYWORDS="~amd64 ~x86"
-IUSE="+examples test"
-RESTRICT="!test? ( test )"
-
-RDEPEND=">=dev-haskell/binary-0.4:=[profile?]
-		dev-haskell/mtl:=[profile?]
-		dev-haskell/old-time:=[profile?]
-		dev-haskell/parallel:=[profile?]
-		dev-haskell/parsec:=[profile?]
-		>=dev-haskell/quickcheck-2:2=[profile?]
-		dev-haskell/random:=[profile?]
-		>=dev-haskell/tagsoup-0.8:=[profile?]
-		>=dev-lang/ghc-6.10.4:="
-DEPEND="${RDEPEND}
-		>=dev-haskell/cabal-1.6"
-
-src_prepare() {
-	epatch "${FILESDIR}"/${P}-ghc-7.10.patch
-
-	cabal_chdeps \
-		'binary >=0.4 && <0.5' 'binary >=0.4'
-}
-
-src_configure() {
-	haskell-cabal_src_configure \
-		$(cabal_flag examples examples) \
-		$(cabal_flag test test)
-}
-
-src_test() {
-	dist/build/qc/qc || die
-}
-
-src_install() {
-	haskell-cabal_src_install
-
-	use test && rm "${ED}"/usr/bin/qc
-	# many examples collide with dev-haskell/flower
-	if use examples ; then
-		pushd "${ED}"/usr/bin
-		local example
-		for example in *
-		do
-			mv "${example}" "${PN}-example-${example}"
-		done
-		popd
-	fi
-}

diff --git a/dev-haskell/bio/files/bio-0.5.3-ghc-7.10.patch b/dev-haskell/bio/files/bio-0.5.3-ghc-7.10.patch
deleted file mode 100644
index d570d22917a..00000000000
--- a/dev-haskell/bio/files/bio-0.5.3-ghc-7.10.patch
+++ /dev/null
@@ -1,7 +0,0 @@
-diff --git a/Bio/Alignment/Bowtie.hs b/Bio/Alignment/Bowtie.hs
-index 883b057..3e58f0e 100644
---- a/Bio/Alignment/Bowtie.hs
-+++ b/Bio/Alignment/Bowtie.hs
-@@ -1 +1,2 @@
-+{-# LANGUAGE FlexibleContexts #-}
- {-| This module provides a data type to represent an alignment

diff --git a/dev-haskell/bio/metadata.xml b/dev-haskell/bio/metadata.xml
deleted file mode 100644
index 8927e5f9907..00000000000
--- a/dev-haskell/bio/metadata.xml
+++ /dev/null
@@ -1,25 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>haskell@g.o</email>
-		<name>Gentoo Haskell</name>
-	</maintainer>
-	<longdescription>
-		This is a collection of data structures and algorithms
-		useful for building bioinformatics-related tools
-		and utilities.
-		
-		Current list of features includes: a Sequence data type supporting
-		protein and nucleotide sequences and conversion between them.  As of version
-		0.4, different kinds of sequence have different types.  Support for quality
-		data, reading and writing Fasta formatted files, reading TwoBit and
-		phd formats, and Roche/454 SFF files.  Rudimentary (i.e. unoptimized) support
-		for doing alignments - including dynamic adjustment of scores based on sequence quality.
-		Also Blast output parsing.  Partly implemented single linkage clustering, and
-		multiple alignment.  Reading Gene Ontology (GO) annotations (GOA) and
-		definitions\/hierarchy.
-		
-		The Darcs repository is at: &lt;http://malde.org/~ketil/biohaskell/biolib&gt;.
-	</longdescription>
-</pkgmetadata>

diff --git a/profiles/package.mask b/profiles/package.mask
index 9e82fe40d47..ac73a4255de 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -675,11 +675,6 @@ dev-haskell/cryptocipher
 # Dead upstream. Removal in 30 days
 net-mail/maildirtree
 
-# Sergei Trofimovich <slyfox@g.o> (2020-08-27)
-# Abandoned upstream.
-# Does not compile against ghc-8.8. Removal in 30 days.
-dev-haskell/bio
-
 # Piotr Karbowski <slashbeast@g.o> (2020-08-28)
 # Temporary mask due to multiple reports of segfaults at startup, bug #739056
 =x11-base/xorg-server-1.20.9