Port to ghc-7.8 (bug #537052 by Toralf Förster).

Package-Manager: portage-2.2.15/cvs/Linux x86_64
Manifest-Sign-Key: 0x611FF3AA

5 files changed, 52 insertions, 43 deletions

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 <slyfox@gentoo.org>
+  +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 4a9e0d6490b06aac5b7e665640af8c5ef16ab37b5088cada0ee8d0067141c33d50622d7b5dc9999a020c561994bfb39ae017d41d05b2b18a37110f7e3ee8bc4b
 DIST flower-0.7.2.tar.gz 10455 SHA256 0b8d60e8af5114e496e401af344c3f7338ecb42c1b8b8a96220efa19d21a3465 SHA512 1c96173b8e3a881b2c65f3dcabd27e71a9341a73e56c056534e7d8eb53bc3222d8d32c6397a3a80413ee361bce42a40f20d7280d5e9748a1c1b828d42fefba74 WHIRLPOOL 8fec1ce45acb41e3da63eee27911fa7a738c7b9e259cecdc01df1f1c06974099b50505a0e51c041e8ae96f60cff9a283aa2b887d12cf7a800b1a129d2cc0ad0c
-DIST flower-0.7.tar.gz 10781 SHA256 df24ba9831603d09af29599d8ab229cf636fe9ec9edcb723eb96ca0f297b7129 SHA512 3f7fe93943e3fcc005dc9c91669e820b9ddbc32501c388381ba6a2c9e35dea2e4c42d0db8919e7a98ae5e40866643af4b90c387bee7868d51f0aa0c01bd85d6c WHIRLPOOL d2db86dcd559e0a3d8c1823db4af3bad80275af56181e6f620c5addc90c185973cad5948e4138a035dd794f6a9ab9745edb3736ad1256fd1378bc571fc58d585
-EBUILD flower-0.7-r1.ebuild 851 SHA256 6af98c8a3784c0cc554d01b288068bc6f7e32c45051e1b96435087de6bf3f1ed SHA512 2cc7caef8fe4fecad4e92f3c1d64626053e26583cb03b00e9b8a9e1e5e3223e35cc8c220568801fa3b4baafa72787fba7bf9f7876ac45a1e3ae76f9b67dcaed6 WHIRLPOOL 4700be7912b1e12703c11297be9dcda24f7888f1c89aab5fbb8b7a452e3f7939f161cff42278008609cc43b2598926614079ece4336cb7e2fcea7110cb16e28a
-EBUILD flower-0.7.2.ebuild 806 SHA256 94b12cc7d7fbb038093f5f7356522352f9d501c943adab58942f8f0e706db46a SHA512 ce4231d8d30fba9a772429dfb99a9866cde961d60b93098fb41108d77c3fa19a554f3228f1bcdd30160f492489044a90b5fa408967858b3b8abe00ef3ba4d42b WHIRLPOOL 22379fa98b3e953087d1ad9fd2a79b0f38a2dd6c619aa9ccfcf31039078bdef537cd0509c4305011fd39a386cbf807708620f544599ce617c3ad048238445c47
-MISC ChangeLog 527 SHA256 5471cfe009623067c92afd41a174073bf55f5a784229e07c31740e0d65a51368 SHA512 74fc056b967b4091109ca643650de40cb84e25e8634ecf408bd1205fdaafb96df9a327522d6f67de3f98d80fdac72dcaf956681f3e25c1b7014dd6dbd1c0e4d6 WHIRLPOOL 254765327e648ffaa6cd1b7dda1dfe9ec73f7971ca3d927cb1b393f6b3a25c756149b4a355d15266a3e367133b5394226e66b1ee163de0548e9742ee0130a7ff
+EBUILD flower-0.7.2.ebuild 898 SHA256 45ad77df8e5ab0b8b313d833d0b72ef6486b8de990b6fb49a794a779ba542d4e SHA512 cd3a8c8f92a0ff172f8ce5958d1d1e8ca1dfdd1a0a1b8e110119f8c66c859735bbfa298f6b09b60722bd1fd0f0c1b0cf4441e748ebe2274982d177230baf1f89 WHIRLPOOL 2b752805d2230766139e73ff43fcb065100fb4333852ded22bbb887175e393740629ea1b083cbb1875013be9323aac9f25f992aeeade45070106e3e434792428
+MISC ChangeLog 715 SHA256 bfc66fe97d213c26c7559c14f6fcd289e19f00b26e4e82a3ed1e2ae3a0296688 SHA512 dc37c2136cffecaaa7b126561cc34cd41dd13c80d6dbcd460181ca8dd71f13ff13795de20fbdf03bd1ccc11837c9cf32631682245f8e4aa5e46f7393f589fa7d WHIRLPOOL ee918415fb4bcecf71aec40f490ee8ec1889e414cb747fbf2c18915f326589efc699f6806930d07acc904a79bd99414c55dc04579e39ab1d0f654c90b4bfce3e
 MISC metadata.xml 1016 SHA256 f953d05cd071c0f4bc8d8ce67f42f7e5d7afa6d2c992c3cd4444ea7f4609e029 SHA512 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/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() {
-	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'
 }