gregoryschwartz / blosum Goto Github PK
View Code? Open in Web Editor NEWBLOSUM matrix generator with the addition of any generic characters for special amino acids
License: GNU General Public License v3.0
BLOSUM matrix generator with the addition of any generic characters for special amino acids
License: GNU General Public License v3.0
Preprocessing executable 'blosum' for blosum-0.1.1.2...
[1 of 1] Compiling Main ( app/Main.hs, dist/build/blosum/blosum-tmp/Main.o )
app/Main.hs:47:10: error:
• Variable not in scope: (<>) :: Mod f0 a0 -> Mod f1 a1 -> t1
• Perhaps you meant one of these:
data constructor ‘Seq.:>’ (imported from Data.Sequence),
‘<$>’ (imported from Options.Applicative),
‘<*>’ (imported from Options.Applicative)
app/Main.hs:48:10: error:
• Variable not in scope: (<>) :: t1 -> Mod f2 a2 -> t0
• Perhaps you meant one of these:
data constructor ‘Seq.:>’ (imported from Data.Sequence),
‘<$>’ (imported from Options.Applicative),
‘<*>’ (imported from Options.Applicative)
app/Main.hs:49:10: error:
• Variable not in scope:
(<>) :: t0 -> Mod f3 a3 -> Mod OptionFields String
• Perhaps you meant one of these:
data constructor ‘Seq.:>’ (imported from Data.Sequence),
‘<$>’ (imported from Options.Applicative),
This is blocking the new blosum version from being included in stackage LTS 7. If you are fine with that you can close this issue.
Preprocessing library blosum-0.1.1.3...
[1 of 5] Compiling Types ( src/Types.hs, dist/build/Types.o )
[2 of 5] Compiling Print ( src/Print.hs, dist/build/Print.o )
[3 of 5] Compiling Utility ( src/Utility.hs, dist/build/Utility.o )
[4 of 5] Compiling Cluster ( src/Cluster.hs, dist/build/Cluster.o )
[5 of 5] Compiling Matrix ( src/Matrix.hs, dist/build/Matrix.o )
Preprocessing executable 'blosum' for blosum-0.1.1.3...
[1 of 1] Compiling Main ( app/Main.hs, dist/build/blosum/blosum-tmp/Main.o )
app/Main.hs:48:10: error:
Ambiguous occurrence ‘<>’
It could refer to either ‘Options.Applicative.<>’,
imported from ‘Options.Applicative’ at app/Main.hs:24:1-26
(and originally defined in ‘Data.Monoid’)
or ‘Data.Semigroup.<>’,
imported from ‘Data.Semigroup’ at app/Main.hs:14:24-27
See http://matrix.hackage.haskell.org/package/blosum
src/Types.hs:47:10:
Not in scope: type constructor or class ‘Monoid’
Perhaps you meant ‘Monad’ (imported from Prelude)
Configuring blosum-0.1.1.1...
Dependency base ==4.8.2.0: using base-4.8.2.0
Dependency blosum -any: using blosum-0.1.1.1
Dependency containers ==0.5.6.2: using containers-0.5.6.2
Dependency fasta ==0.10.2.0: using fasta-0.10.2.0
Dependency lens ==4.14: using lens-4.14
Dependency optparse-applicative ==0.12.1.0: using
optparse-applicative-0.12.1.0
Dependency pipes ==4.1.9: using pipes-4.1.9
Dependency pipes-text ==0.0.2.1: using pipes-text-0.0.2.1
Dependency split ==0.2.3.1: using split-0.2.3.1
Dependency text ==1.2.2.1: using text-1.2.2.1
Dependency text-show ==3.2.2: using text-show-3.2.2
src/Types.hs:33:60:
Ambiguous occurrence ‘AA’
It could refer to either ‘Types.AA’, defined at src/Types.hs:18:1
or ‘Data.Fasta.Text.AA’,
Fails to find a build-plan. I'm not sure where the problem is, as fasta matrix.h.h.o
seems to read backjump limit too on GHC-8.0.
EDIT this might explain: http://matrix.hackage.haskell.org/package/pipes-text
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