From 1fe19b7d55eb2b0b650b105c45740c408c6c966e Mon Sep 17 00:00:00 2001 From: Sergei Trofimovich Date: Mon, 19 Jan 2015 22:44:11 +0000 Subject: Port to ghc-7.8 (bug #537052 by Toralf Förster). MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Package-Manager: portage-2.2.15/cvs/Linux x86_64 Manifest-Sign-Key: 0x611FF3AA --- sci-biology/flower/ChangeLog | 8 +++-- sci-biology/flower/Manifest | 17 ++++++++--- .../flower/files/flower-0.7.2-ghc-7.8.patch | 27 +++++++++++++++++ sci-biology/flower/flower-0.7-r1.ebuild | 34 ---------------------- sci-biology/flower/flower-0.7.2.ebuild | 9 ++++-- 5 files changed, 52 insertions(+), 43 deletions(-) create mode 100644 sci-biology/flower/files/flower-0.7.2-ghc-7.8.patch delete mode 100644 sci-biology/flower/flower-0.7-r1.ebuild (limited to 'sci-biology') diff --git a/sci-biology/flower/ChangeLog b/sci-biology/flower/ChangeLog index d6b508d77dec..c53233cd223a 100644 --- a/sci-biology/flower/ChangeLog +++ b/sci-biology/flower/ChangeLog @@ -1,6 +1,10 @@ # ChangeLog for sci-biology/flower -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/flower/ChangeLog,v 1.2 2013/09/22 14:16:14 cynede Exp $ +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/flower/ChangeLog,v 1.3 2015/01/19 22:44:09 slyfox Exp $ + + 19 Jan 2015; Sergei Trofimovich + +files/flower-0.7.2-ghc-7.8.patch, -flower-0.7-r1.ebuild, flower-0.7.2.ebuild: + Port to ghc-7.8 (bug #537052 by Toralf Förster). *flower-0.7.2 (22 Sep 2013) diff --git a/sci-biology/flower/Manifest b/sci-biology/flower/Manifest index 70fee1e2b22e..f50332116009 100644 --- a/sci-biology/flower/Manifest +++ b/sci-biology/flower/Manifest @@ -1,6 +1,15 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA256 + +AUX flower-0.7.2-ghc-7.8.patch 879 SHA256 c08eaf6d156bb7617f46b8f6d2ce991aa13161aec7ed353ce0af784418248105 SHA512 c2ed46cf16dbf9bd9957a9166d63978e6453a5b8a0172ed6cb3cc676b8b34909373dcfdc83152b9ee7a28700473ca3b22b8a2b1fd094e2fb80f58ce494d7e67a WHIRLPOOL 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71ae5703a5ba6df9a24ac5f7c11fc078ccd064fb00ef9326913e287616ad32dbff15d4af35692caba741f99f631b571d62cc02682a948e1e510a4171bad016f5 WHIRLPOOL 23ac76ea1d42d9ff062d0b4768dd42852ac3e575104ddb415dc00ec6cbfd02b9420b9f7e1d446f5f4e4e4ba17d81ac9dcee40e391ea0a16a901b1e0f5b69d590 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2 + +iEYEAREIAAYFAlS9iLsACgkQcaHudmEf86otzgCfawvOKa9NljPiXM9jRe9TL5/l +KSAAmgLxIF3kzvf9gXyaTnSq0NI4Mpf3 +=vQvM +-----END PGP SIGNATURE----- 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 new file mode 100644 index 000000000000..90dfb2326918 --- /dev/null +++ b/sci-biology/flower/files/flower-0.7.2-ghc-7.8.patch @@ -0,0 +1,27 @@ +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-r1.ebuild b/sci-biology/flower/flower-0.7-r1.ebuild deleted file mode 100644 index 4f5b566d9acb..000000000000 --- a/sci-biology/flower/flower-0.7-r1.ebuild +++ /dev/null @@ -1,34 +0,0 @@ -# Copyright 1999-2013 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/flower/flower-0.7-r1.ebuild,v 1.1 2013/09/12 20:23:27 slyfox Exp $ - -# ebuild generated by hackport 0.2.17.9999 - -EAPI=5 - -CABAL_FEATURES="bin" -inherit 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() { - cabal_chdeps \ - 'binary == 0.4.*' 'binary >= 0.4 && <0.8' -} diff --git a/sci-biology/flower/flower-0.7.2.ebuild b/sci-biology/flower/flower-0.7.2.ebuild index e2986ed050b1..6064b581eee1 100644 --- a/sci-biology/flower/flower-0.7.2.ebuild +++ b/sci-biology/flower/flower-0.7.2.ebuild @@ -1,11 +1,13 @@ -# Copyright 1999-2013 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/flower/flower-0.7.2.ebuild,v 1.1 2013/09/22 14:16:14 cynede Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/flower/flower-0.7.2.ebuild,v 1.2 2015/01/19 22:44:09 slyfox Exp $ + +# ebuild generated by hackport 0.2.17.9999 EAPI=5 CABAL_FEATURES="bin" -inherit haskell-cabal +inherit eutils haskell-cabal DESCRIPTION="Analyze 454 flowgrams (.SFF files)" HOMEPAGE="http://biohaskell.org/Applications/Flower" @@ -27,6 +29,7 @@ DEPEND="${RDEPEND} >=dev-lang/ghc-6.10.1" src_prepare() { + epatch "${FILESDIR}"/${P}-ghc-7.8.patch cabal_chdeps \ 'binary == 0.4.*' 'binary >= 0.4 && <0.8' } -- cgit v1.2.3-65-gdbad