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>hask...@gentoo.org</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: <http://malde.org/~ketil/biohaskell/biolib>. - </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 <sly...@gentoo.org> (2020-08-27) -# Abandoned upstream. -# Does not compile against ghc-8.8. Removal in 30 days. -dev-haskell/bio - # Piotr Karbowski <slashbe...@gentoo.org> (2020-08-28) # Temporary mask due to multiple reports of segfaults at startup, bug #739056 =x11-base/xorg-server-1.20.9
