[gentoo-commits] repo/gentoo:master commit in: sci-biology/flower/, sci-biology/flower/files/

[Michael Orlitzky]

commit:     bfc501a0582e9c60cd27624cc23d3cfa56cf0004
Author:     Michael Orlitzky <mjo <AT> gentoo <DOT> org>
AuthorDate: Mon Sep 21 15:18:33 2015 +0000
Commit:     Michael Orlitzky <mjo <AT> gentoo <DOT> org>
CommitDate: Mon Sep 21 15:23:14 2015 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=bfc501a0

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(-)

diff --git a/sci-biology/flower/Manifest b/sci-biology/flower/Manifest
deleted file mode 100644
index 727ec96..0000000
--- 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 90dfb23..0000000
--- 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 25e24c3..0000000
--- 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/binary-0.8
-		>=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 dcaae20..0000000
--- a/sci-biology/flower/metadata.xml
+++ /dev/null
@@ -1,24 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<herd>haskell</herd>
-	<maintainer>
-		<email>haskell@g.o</email>
-	</maintainer>
-	<longdescription>
-		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
-		&#39;sffinfo&#39; 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.
-	</longdescription>
-</pkgmetadata>