From bfc501a0582e9c60cd27624cc23d3cfa56cf0004 Mon Sep 17 00:00:00 2001 From: Michael Orlitzky Date: Mon, 21 Sep 2015 11:18:33 -0400 Subject: sci-biology/flower: remove package masked in bug #553636. --- sci-biology/flower/Manifest | 1 - .../flower/files/flower-0.7.2-ghc-7.8.patch | 27 ----------------- sci-biology/flower/flower-0.7.2.ebuild | 35 ---------------------- sci-biology/flower/metadata.xml | 24 --------------- 4 files changed, 87 deletions(-) delete mode 100644 sci-biology/flower/Manifest delete mode 100644 sci-biology/flower/files/flower-0.7.2-ghc-7.8.patch delete mode 100644 sci-biology/flower/flower-0.7.2.ebuild delete mode 100644 sci-biology/flower/metadata.xml diff --git a/sci-biology/flower/Manifest b/sci-biology/flower/Manifest deleted file mode 100644 index 727ec9661be4..000000000000 --- a/sci-biology/flower/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST flower-0.7.2.tar.gz 10455 SHA256 0b8d60e8af5114e496e401af344c3f7338ecb42c1b8b8a96220efa19d21a3465 SHA512 1c96173b8e3a881b2c65f3dcabd27e71a9341a73e56c056534e7d8eb53bc3222d8d32c6397a3a80413ee361bce42a40f20d7280d5e9748a1c1b828d42fefba74 WHIRLPOOL 8fec1ce45acb41e3da63eee27911fa7a738c7b9e259cecdc01df1f1c06974099b50505a0e51c041e8ae96f60cff9a283aa2b887d12cf7a800b1a129d2cc0ad0c diff --git a/sci-biology/flower/files/flower-0.7.2-ghc-7.8.patch b/sci-biology/flower/files/flower-0.7.2-ghc-7.8.patch deleted file mode 100644 index 90dfb2326918..000000000000 --- a/sci-biology/flower/files/flower-0.7.2-ghc-7.8.patch +++ /dev/null @@ -1,27 +0,0 @@ -diff --git a/src/Flower.hs b/src/Flower.hs -index fca5814..9424222 100644 ---- a/src/Flower.hs -+++ b/src/Flower.hs -@@ -25,6 +25,7 @@ import qualified Data.ByteString.Lazy as L1 - - import Data.Array.Unboxed - import Data.Array.ST -+import qualified Data.Array.Unsafe as U - import Control.Monad.ST - import Control.Monad.State - -@@ -238,10 +239,10 @@ histogram fl scores = runST $ do - ins1 (x,_) = error ("Illegal character "++show x++" in flow!") - bump ar i = readArray ar i >>= \x -> writeArray ar i (x+1) - mapM_ ins1 (zip (cycle fl) (map (\x->if x>9999 || x<0 then 9999 else x) $ concat scores)) -- a' <- unsafeFreeze a -- c' <- unsafeFreeze c -- g' <- unsafeFreeze g -- t' <- unsafeFreeze t -+ a' <- U.unsafeFreeze a -+ c' <- U.unsafeFreeze c -+ g' <- U.unsafeFreeze g -+ t' <- U.unsafeFreeze t - return (a',c',g',t') - - showHist :: (Hist,Hist,Hist,Hist) -> String diff --git a/sci-biology/flower/flower-0.7.2.ebuild b/sci-biology/flower/flower-0.7.2.ebuild deleted file mode 100644 index 25e24c3aa26f..000000000000 --- a/sci-biology/flower/flower-0.7.2.ebuild +++ /dev/null @@ -1,35 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -# ebuild generated by hackport 0.2.17.9999 - -EAPI=5 - -CABAL_FEATURES="bin" -inherit eutils haskell-cabal - -DESCRIPTION="Analyze 454 flowgrams (.SFF files)" -HOMEPAGE="http://biohaskell.org/Applications/Flower" -SRC_URI="mirror://hackage/packages/archive/${PN}/${PV}/${P}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -RDEPEND="" -DEPEND="${RDEPEND} - >=dev-haskell/binary-0.4 =dev-haskell/bio-0.4.9 - >=dev-haskell/cabal-1.6 - >=dev-haskell/cmdargs-0.5 - dev-haskell/mtl - dev-haskell/random - >=dev-lang/ghc-6.10.1" - -src_prepare() { - epatch "${FILESDIR}"/${P}-ghc-7.8.patch - cabal_chdeps \ - 'binary == 0.4.*' 'binary >= 0.4 && <0.8' -} diff --git a/sci-biology/flower/metadata.xml b/sci-biology/flower/metadata.xml deleted file mode 100644 index dcaae2095b0e..000000000000 --- a/sci-biology/flower/metadata.xml +++ /dev/null @@ -1,24 +0,0 @@ - - - - haskell - - haskell@gentoo.org - - - flower - FLOWgram ExtractoR tools - - The flower executable reads files in SFF-format and produces various output, - including sequences with quality, or flowgram data in tabular format. By default, - it outputs a textual representation of the data in the SFF-file, much like - 'sffinfo' from Roche does. - - The fselect executable extracts reads from SFF-files, generating a new - SFF-file with a subset of the reads based on various criteria. - - Sometimes SFF files will appear to be corrupted, with all-zero blocks in the - file. The frecover program ignores these and tries to resync with the file after an - invalid region. This was likely a one-time bug in the 454 software, so this program - is probably not so useful any more. - - -- cgit v1.2.3-18-g5258