[gentoo-commits] repo/gentoo:master commit in: dev-haskell/biocore/, dev-haskell/biocore/files/

[Sergei Trofimovich]

commit:     2dc441dd028362e5463f8bdddabc73c73a46c388
Author:     Sergei Trofimovich <slyfox <AT> gentoo <DOT> org>
AuthorDate: Fri Aug 14 22:59:58 2020 +0000
Commit:     Sergei Trofimovich <slyfox <AT> gentoo <DOT> org>
CommitDate: Fri Aug 14 23:00:04 2020 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=2dc441dd

dev-haskell/biocore: tweak for ghc-8.8

Reported-by: Agostino Sarubbo
Closes: https://bugs.gentoo.org/735860
Package-Manager: Portage-3.0.2, Repoman-2.3.23
Signed-off-by: Sergei Trofimovich <slyfox <AT> gentoo.org>

 dev-haskell/biocore/biocore-0.3.1.ebuild           |  8 +++++--
 .../biocore/files/biocore-0.3.1-ghc84.patch        | 28 ++++++++++++++++++++++
 2 files changed, 34 insertions(+), 2 deletions(-)

diff --git a/dev-haskell/biocore/biocore-0.3.1.ebuild b/dev-haskell/biocore/biocore-0.3.1.ebuild
index a03f1244d73..54d16dfe8cd 100644
--- a/dev-haskell/biocore/biocore-0.3.1.ebuild
+++ b/dev-haskell/biocore/biocore-0.3.1.ebuild
@@ -1,7 +1,7 @@
 # Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=6
 
 # ebuild generated by hackport 0.3.3.9999
 
@@ -9,7 +9,7 @@ CABAL_FEATURES="lib profile haddock hoogle hscolour"
 inherit haskell-cabal
 
 DESCRIPTION="A bioinformatics library"
-HOMEPAGE="https://hackage.haskell.org/package/biocore"
+HOMEPAGE="http://hackage.haskell.org/package/biocore"
 SRC_URI="https://hackage.haskell.org/package/${P}/${P}.tar.gz"
 
 LICENSE="LGPL-2.1"
@@ -23,3 +23,7 @@ RDEPEND="dev-haskell/stringable:=[profile?]
 DEPEND="${RDEPEND}
 	>=dev-haskell/cabal-1.6.0.3
 "
+
+PATCHES=(
+	"${FILESDIR}"/${P}-ghc84.patch
+)

diff --git a/dev-haskell/biocore/files/biocore-0.3.1-ghc84.patch b/dev-haskell/biocore/files/biocore-0.3.1-ghc84.patch
new file mode 100644
index 00000000000..b0a404eb8b4
--- /dev/null
+++ b/dev-haskell/biocore/files/biocore-0.3.1-ghc84.patch
@@ -0,0 +1,28 @@
+--- a/src/Bio/Core/Sequence.hs
++++ b/src/Bio/Core/Sequence.hs
+@@ -37,2 +37,3 @@ import Data.Stringable hiding (length)
+ import Data.Monoid
++import qualified Data.Semigroup as S
+ 
+@@ -42,2 +43,5 @@ newtype SeqData  = SeqData { unSD :: LC.ByteString }
+ 
++instance S.Semigroup SeqData where
++  (<>) (SeqData s1) (SeqData s2) = SeqData (mappend s1 s2)
++
+ instance Monoid SeqData where
+@@ -51,2 +55,9 @@ newtype SeqLabel = SeqLabel { unSL :: LC.ByteString }
+ 
++instance S.Semigroup SeqLabel where
++  (<>) (SeqLabel s1) (SeqLabel s2) = let
++    (i1:r1) = LC.words s1
++    (i2:r2) = LC.words s2
++    sid = mconcat [i1,(LC.pack ":"),i2]
++    in SeqLabel (LC.unwords ([sid]++r1++[LC.pack ":"]++r2))
++
+ instance Monoid SeqLabel where
+@@ -68,2 +79,5 @@ newtype QualData = QualData { unQD :: L.ByteString }
+ 
++instance S.Semigroup QualData where
++  (<>) (QualData s1) (QualData s2) = QualData (mappend s1 s2)
++
+ instance Monoid QualData where