Resolving dependencies... Configuring QuickCheck-2.6... Building QuickCheck-2.6... Preprocessing library QuickCheck-2.6... [ 1 of 13] Compiling Test.QuickCheck.Exception ( Test/QuickCheck/Exception.hs, dist/build/Test/QuickCheck/Exception.o ) [ 2 of 13] Compiling Test.QuickCheck.Text ( Test/QuickCheck/Text.hs, dist/build/Test/QuickCheck/Text.o ) [ 3 of 13] Compiling Test.QuickCheck.State ( Test/QuickCheck/State.hs, dist/build/Test/QuickCheck/State.o ) [ 4 of 13] Compiling Test.QuickCheck.Gen ( Test/QuickCheck/Gen.hs, dist/build/Test/QuickCheck/Gen.o ) [ 5 of 13] Compiling Test.QuickCheck.Arbitrary ( Test/QuickCheck/Arbitrary.hs, dist/build/Test/QuickCheck/Arbitrary.o ) [ 6 of 13] Compiling Test.QuickCheck.Poly ( Test/QuickCheck/Poly.hs, dist/build/Test/QuickCheck/Poly.o ) [ 7 of 13] Compiling Test.QuickCheck.Function ( Test/QuickCheck/Function.hs, dist/build/Test/QuickCheck/Function.o ) [ 8 of 13] Compiling Test.QuickCheck.Modifiers ( Test/QuickCheck/Modifiers.hs, dist/build/Test/QuickCheck/Modifiers.o ) [ 9 of 13] Compiling Test.QuickCheck.Property ( Test/QuickCheck/Property.hs, dist/build/Test/QuickCheck/Property.o ) [10 of 13] Compiling Test.QuickCheck.Test ( Test/QuickCheck/Test.hs, dist/build/Test/QuickCheck/Test.o ) [11 of 13] Compiling Test.QuickCheck.All ( Test/QuickCheck/All.hs, dist/build/Test/QuickCheck/All.o ) [12 of 13] Compiling Test.QuickCheck.Monadic ( Test/QuickCheck/Monadic.hs, dist/build/Test/QuickCheck/Monadic.o ) [13 of 13] Compiling Test.QuickCheck ( Test/QuickCheck.hs, dist/build/Test/QuickCheck.o ) In-place registering QuickCheck-2.6... Running Haddock for QuickCheck-2.6... Running hscolour for QuickCheck-2.6... Preprocessing library QuickCheck-2.6... Preprocessing library QuickCheck-2.6... Warning: The documentation for the following packages are not installed. No links will be generated to these packages: random-1.0.1.1 Haddock coverage: 12% ( 1 / 8) in 'Test.QuickCheck.Exception' 0% ( 0 / 18) in 'Test.QuickCheck.Text' 50% ( 1 / 2) in 'Test.QuickCheck.State' 95% ( 20 / 21) in 'Test.QuickCheck.Gen' 92% ( 23 / 25) in 'Test.QuickCheck.Arbitrary' 14% ( 1 / 7) in 'Test.QuickCheck.Poly' 14% ( 1 / 7) in 'Test.QuickCheck.Function' 92% ( 12 / 13) in 'Test.QuickCheck.Modifiers' 59% ( 34 / 58) in 'Test.QuickCheck.Property' 48% ( 13 / 27) in 'Test.QuickCheck.Test' 100% ( 9 / 9) in 'Test.QuickCheck.All' 7% ( 1 / 15) in 'Test.QuickCheck.Monadic' 93% ( 95 /102) in 'Test.QuickCheck' Warning: Test.QuickCheck.Text: could not find link destinations for: Test.QuickCheck.Text.Output Warning: Test.QuickCheck.State: could not find link destinations for: System.Random.StdGen Warning: Test.QuickCheck.Gen: could not find link destinations for: System.Random.StdGen System.Random.Random Warning: Test.QuickCheck.Arbitrary: could not find link destinations for: System.Random.Random Warning: Test.QuickCheck.Property: could not find link destinations for: Test.QuickCheck.Exception.AnException Warning: Test.QuickCheck.Test: could not find link destinations for: System.Random.StdGen Warning: Test.QuickCheck: could not find link destinations for: System.Random.StdGen System.Random.Random Documentation created: dist/doc/html/QuickCheck/index.html Installing library in /srv/hackage/var/build/tmp-install/lib/x86_64-linux-ghc-7.6.3/QuickCheck-2.6 Registering QuickCheck-2.6... Installed QuickCheck-2.6 Configuring binary-0.4.5... Building binary-0.4.5... Preprocessing library binary-0.4.5... src/Data/Binary/Get.hs:2:16: Warning: -fglasgow-exts is deprecated: Use individual extensions instead src/Data/Binary/Builder.hs:2:16: Warning: -fglasgow-exts is deprecated: Use individual extensions instead [1 of 4] Compiling Data.Binary.Builder ( src/Data/Binary/Builder.hs, dist/build/Data/Binary/Builder.o ) src/Data/Binary/Builder.hs:60:1: Warning: The import of `Data.Word' is redundant except perhaps to import instances from `Data.Word' To import instances alone, use: import Data.Word() src/Data/Binary/Builder.hs:70:1: Warning: The qualified import of `Data.ByteString.Lazy.Internal' is redundant except perhaps to import instances from `Data.ByteString.Lazy.Internal' To import instances alone, use: import Data.ByteString.Lazy.Internal() src/Data/Binary/Builder.hs:168:37: Warning: In the use of `unsafePerformIO' (imported from Foreign): Deprecated: "Use System.IO.Unsafe.unsafePerformIO instead; This function will be removed in the next release" [2 of 4] Compiling Data.Binary.Get ( src/Data/Binary/Get.hs, dist/build/Data/Binary/Get.o ) src/Data/Binary/Get.hs:99:1: Warning: The import of `GHC.Int' is redundant except perhaps to import instances from `GHC.Int' To import instances alone, use: import GHC.Int() src/Data/Binary/Get.hs:368:15: Warning: In the use of `unsafeInterleaveST' (imported from Control.Monad.ST): Deprecated: "Please import from Control.Monad.ST.Unsafe instead; This will be removed in the next release" src/Data/Binary/Get.hs:379:48: Warning: In the use of `unsafeInterleaveST' (imported from Control.Monad.ST): Deprecated: "Please import from Control.Monad.ST.Unsafe instead; This will be removed in the next release" [3 of 4] Compiling Data.Binary.Put ( src/Data/Binary/Put.hs, dist/build/Data/Binary/Put.o ) src/Data/Binary/Put.hs:64:16: Warning: Ignoring unusable UNPACK pragma on the second argument of `PairS' In the definition of data constructor `PairS' In the data declaration for `PairS' [4 of 4] Compiling Data.Binary ( src/Data/Binary.hs, dist/build/Data/Binary.o ) src/Data/Binary.hs:66:1: Warning: The import of `System.IO' is redundant except perhaps to import instances from `System.IO' To import instances alone, use: import System.IO() In-place registering binary-0.4.5... Running Haddock for binary-0.4.5... Running hscolour for binary-0.4.5... Preprocessing library binary-0.4.5... Preprocessing library binary-0.4.5... src/Data/Binary/Get.hs:2:16: Warning: -fglasgow-exts is deprecated: Use individual extensions instead src/Data/Binary/Builder.hs:2:16: Warning: -fglasgow-exts is deprecated: Use individual extensions instead src/Data/Binary/Get.hs:2:16: Warning: -fglasgow-exts is deprecated: Use individual extensions instead src/Data/Binary/Builder.hs:2:16: Warning: -fglasgow-exts is deprecated: Use individual extensions instead src/Data/Binary/Builder.hs:60:1: Warning: The import of `Data.Word' is redundant except perhaps to import instances from `Data.Word' To import instances alone, use: import Data.Word() src/Data/Binary/Builder.hs:70:1: Warning: The qualified import of `Data.ByteString.Lazy.Internal' is redundant except perhaps to import instances from `Data.ByteString.Lazy.Internal' To import instances alone, use: import Data.ByteString.Lazy.Internal() src/Data/Binary/Builder.hs:168:37: Warning: In the use of `unsafePerformIO' (imported from Foreign): Deprecated: "Use System.IO.Unsafe.unsafePerformIO instead; This function will be removed in the next release" src/Data/Binary/Get.hs:99:1: Warning: The import of `GHC.Int' is redundant except perhaps to import instances from `GHC.Int' To import instances alone, use: import GHC.Int() src/Data/Binary/Get.hs:368:15: Warning: In the use of `unsafeInterleaveST' (imported from Control.Monad.ST): Deprecated: "Please import from Control.Monad.ST.Unsafe instead; This will be removed in the next release" src/Data/Binary/Get.hs:379:48: Warning: In the use of `unsafeInterleaveST' (imported from Control.Monad.ST): Deprecated: "Please import from Control.Monad.ST.Unsafe instead; This will be removed in the next release" src/Data/Binary/Put.hs:64:16: Warning: Ignoring unusable UNPACK pragma on the second argument of `PairS' In the definition of data constructor `PairS' In the data declaration for `PairS' src/Data/Binary.hs:66:1: Warning: The import of `System.IO' is redundant except perhaps to import instances from `System.IO' To import instances alone, use: import System.IO() Haddock coverage: 100% ( 26 / 26) in 'Data.Binary.Builder' 100% ( 37 / 37) in 'Data.Binary.Get' 100% ( 24 / 24) in 'Data.Binary.Put' 100% ( 17 / 17) in 'Data.Binary' Warning: Data.Binary.Get: could not find link destinations for: Data.Binary.Get.get Warning: Data.Binary.Put: could not find link destinations for: Data.Binary.Put.PairS Documentation created: dist/doc/html/binary/index.html Installing library in /srv/hackage/var/build/tmp-install/lib/x86_64-linux-ghc-7.6.3/binary-0.4.5 Registering binary-0.4.5... Installed binary-0.4.5 Configuring parallel-3.2.0.4... Building parallel-3.2.0.4... Preprocessing library parallel-3.2.0.4... [1 of 3] Compiling Control.Parallel ( Control/Parallel.hs, dist/build/Control/Parallel.o ) [2 of 3] Compiling Control.Seq ( Control/Seq.hs, dist/build/Control/Seq.o ) [3 of 3] Compiling Control.Parallel.Strategies ( Control/Parallel/Strategies.hs, dist/build/Control/Parallel/Strategies.o ) In-place registering parallel-3.2.0.4... Running Haddock for parallel-3.2.0.4... Running hscolour for parallel-3.2.0.4... Preprocessing library parallel-3.2.0.4... Preprocessing library parallel-3.2.0.4... Haddock coverage: 100% ( 3 / 3) in 'Control.Parallel' 72% ( 21 / 29) in 'Control.Seq' 81% ( 68 / 84) in 'Control.Parallel.Strategies' Documentation created: dist/doc/html/parallel/index.html Installing library in /srv/hackage/var/build/tmp-install/lib/x86_64-linux-ghc-7.6.3/parallel-3.2.0.4 Registering parallel-3.2.0.4... Installed parallel-3.2.0.4 Configuring regex-base-0.93.2... Building regex-base-0.93.2... Preprocessing library regex-base-0.93.2... [1 of 4] Compiling Text.Regex.Base.RegexLike ( Text/Regex/Base/RegexLike.hs, dist/build/Text/Regex/Base/RegexLike.o ) [2 of 4] Compiling Text.Regex.Base.Context ( Text/Regex/Base/Context.hs, dist/build/Text/Regex/Base/Context.o ) [3 of 4] Compiling Text.Regex.Base ( Text/Regex/Base.hs, dist/build/Text/Regex/Base.o ) [4 of 4] Compiling Text.Regex.Base.Impl ( Text/Regex/Base/Impl.hs, dist/build/Text/Regex/Base/Impl.o ) In-place registering regex-base-0.93.2... Running Haddock for regex-base-0.93.2... Running hscolour for regex-base-0.93.2... Preprocessing library regex-base-0.93.2... Preprocessing library regex-base-0.93.2... Warning: The documentation for the following packages are not installed. No links will be generated to these packages: mtl-2.1.2, transformers-0.3.0.0 Haddock coverage: 94% ( 17 / 18) in 'Text.Regex.Base.RegexLike' 100% ( 1 / 1) in 'Text.Regex.Base.Context' 75% ( 3 / 4) in 'Text.Regex.Base' 33% ( 1 / 3) in 'Text.Regex.Base.Impl' Documentation created: dist/doc/html/regex-base/index.html Installing library in /srv/hackage/var/build/tmp-install/lib/x86_64-linux-ghc-7.6.3/regex-base-0.93.2 Registering regex-base-0.93.2... Installed regex-base-0.93.2 Configuring tagsoup-0.13... Building tagsoup-0.13... Preprocessing library tagsoup-0.13... [ 1 of 13] Compiling Text.HTML.TagSoup.Entity ( Text/HTML/TagSoup/Entity.hs, dist/build/Text/HTML/TagSoup/Entity.o ) [ 2 of 13] Compiling Text.StringLike ( Text/StringLike.hs, dist/build/Text/StringLike.o ) [ 3 of 13] Compiling Text.HTML.TagSoup.Type ( Text/HTML/TagSoup/Type.hs, dist/build/Text/HTML/TagSoup/Type.o ) [ 4 of 13] Compiling Text.HTML.TagSoup.Match ( Text/HTML/TagSoup/Match.hs, dist/build/Text/HTML/TagSoup/Match.o ) [ 5 of 13] Compiling Text.HTML.TagSoup.Tree ( Text/HTML/TagSoup/Tree.hs, dist/build/Text/HTML/TagSoup/Tree.o ) [ 6 of 13] Compiling Text.HTML.TagSoup.Options ( Text/HTML/TagSoup/Options.hs, dist/build/Text/HTML/TagSoup/Options.o ) [ 7 of 13] Compiling Text.HTML.TagSoup.Implementation ( Text/HTML/TagSoup/Implementation.hs, dist/build/Text/HTML/TagSoup/Implementation.o ) [ 8 of 13] Compiling Text.HTML.TagSoup.Specification ( Text/HTML/TagSoup/Specification.hs, dist/build/Text/HTML/TagSoup/Specification.o ) [ 9 of 13] Compiling Text.HTML.TagSoup.Manual ( Text/HTML/TagSoup/Manual.hs, dist/build/Text/HTML/TagSoup/Manual.o ) [10 of 13] Compiling Text.HTML.TagSoup.Generated ( Text/HTML/TagSoup/Generated.hs, dist/build/Text/HTML/TagSoup/Generated.o ) [11 of 13] Compiling Text.HTML.TagSoup.Render ( Text/HTML/TagSoup/Render.hs, dist/build/Text/HTML/TagSoup/Render.o ) [12 of 13] Compiling Text.HTML.TagSoup.Parser ( Text/HTML/TagSoup/Parser.hs, dist/build/Text/HTML/TagSoup/Parser.o ) [13 of 13] Compiling Text.HTML.TagSoup ( Text/HTML/TagSoup.hs, dist/build/Text/HTML/TagSoup.o ) In-place registering tagsoup-0.13... Running Haddock for tagsoup-0.13... Running hscolour for tagsoup-0.13... Preprocessing library tagsoup-0.13... Preprocessing library tagsoup-0.13... Warning: The documentation for the following packages are not installed. No links will be generated to these packages: text-0.11.2.3 Haddock coverage: 100% ( 7 / 7) in 'Text.HTML.TagSoup.Entity' 100% ( 3 / 3) in 'Text.StringLike' 81% ( 22 / 27) in 'Text.HTML.TagSoup.Type' 50% ( 9 / 18) in 'Text.HTML.TagSoup.Match' 67% ( 4 / 6) in 'Text.HTML.TagSoup.Tree' 83% ( 5 / 6) in 'Text.HTML.TagSoup.Options' 0% ( 0 / 32) in 'Text.HTML.TagSoup.Implementation' 0% ( 0 / 2) in 'Text.HTML.TagSoup.Specification' 0% ( 0 / 2) in 'Text.HTML.TagSoup.Manual' 0% ( 0 / 2) in 'Text.HTML.TagSoup.Generated' 100% ( 6 / 6) in 'Text.HTML.TagSoup.Render' 86% ( 6 / 7) in 'Text.HTML.TagSoup.Parser' 100% ( 39 / 39) in 'Text.HTML.TagSoup' Warning: Text.StringLike: could not find link destinations for: Data.Text.Internal.Text Data.Text.Lazy.Internal.Text Documentation created: dist/doc/html/tagsoup/index.html Installing library in /srv/hackage/var/build/tmp-install/lib/x86_64-linux-ghc-7.6.3/tagsoup-0.13 Registering tagsoup-0.13... Installed tagsoup-0.13 Configuring regex-posix-0.95.2... Building regex-posix-0.95.2... Preprocessing library regex-posix-0.95.2... [1 of 6] Compiling Text.Regex.Posix.Wrap ( dist/build/Text/Regex/Posix/Wrap.hs, dist/build/Text/Regex/Posix/Wrap.o ) [2 of 6] Compiling Text.Regex.Posix.String ( Text/Regex/Posix/String.hs, dist/build/Text/Regex/Posix/String.o ) [3 of 6] Compiling Text.Regex.Posix.Sequence ( Text/Regex/Posix/Sequence.hs, dist/build/Text/Regex/Posix/Sequence.o ) [4 of 6] Compiling Text.Regex.Posix.ByteString ( Text/Regex/Posix/ByteString.hs, dist/build/Text/Regex/Posix/ByteString.o ) [5 of 6] Compiling Text.Regex.Posix.ByteString.Lazy ( Text/Regex/Posix/ByteString/Lazy.hs, dist/build/Text/Regex/Posix/ByteString/Lazy.o ) [6 of 6] Compiling Text.Regex.Posix ( Text/Regex/Posix.hs, dist/build/Text/Regex/Posix.o ) In-place registering regex-posix-0.95.2... Running Haddock for regex-posix-0.95.2... Running hscolour for regex-posix-0.95.2... Preprocessing library regex-posix-0.95.2... Preprocessing library regex-posix-0.95.2... Warning: The documentation for the following packages are not installed. No links will be generated to these packages: mtl-2.1.2, transformers-0.3.0.0 Haddock coverage: 40% ( 17 / 42) in 'Text.Regex.Posix.Wrap' 68% ( 17 / 25) in 'Text.Regex.Posix.String' 67% ( 16 / 24) in 'Text.Regex.Posix.Sequence' 68% ( 17 / 25) in 'Text.Regex.Posix.ByteString' 68% ( 17 / 25) in 'Text.Regex.Posix.ByteString.Lazy' 80% ( 4 / 5) in 'Text.Regex.Posix' Warning: Text.Regex.Posix.Wrap: could not find link destinations for: Text.Regex.Posix.Wrap.retNoMatch Warning: Text.Regex.Posix.String: could not find link destinations for: Text.Regex.Posix.Wrap.retNoMatch Warning: Text.Regex.Posix.Sequence: could not find link destinations for: Text.Regex.Posix.Wrap.retNoMatch Warning: Text.Regex.Posix.ByteString: could not find link destinations for: Text.Regex.Posix.Wrap.retNoMatch Warning: Text.Regex.Posix.ByteString.Lazy: could not find link destinations for: Text.Regex.Posix.Wrap.retNoMatch Documentation created: dist/doc/html/regex-posix/index.html Installing library in /srv/hackage/var/build/tmp-install/lib/x86_64-linux-ghc-7.6.3/regex-posix-0.95.2 Registering regex-posix-0.95.2... Installed regex-posix-0.95.2 Configuring bio-0.5.3... Building bio-0.5.3... Preprocessing library bio-0.5.3... [ 1 of 46] Compiling Bio.GFF3.Escape ( Bio/GFF3/Escape.hs, dist/build/Bio/GFF3/Escape.o ) [ 2 of 46] Compiling Bio.Util.Parsex ( Bio/Util/Parsex.hs, dist/build/Bio/Util/Parsex.o ) [ 3 of 46] Compiling Bio.Clustering ( Bio/Clustering.hs, dist/build/Bio/Clustering.o ) [ 4 of 46] Compiling Bio.Alignment.PSL ( Bio/Alignment/PSL.hs, dist/build/Bio/Alignment/PSL.o ) [ 5 of 46] Compiling Bio.Util ( Bio/Util.hs, dist/build/Bio/Util.o ) [ 6 of 46] Compiling Bio.Alignment.BlastData ( Bio/Alignment/BlastData.hs, dist/build/Bio/Alignment/BlastData.o ) [ 7 of 46] Compiling Bio.Alignment.BlastXML ( Bio/Alignment/BlastXML.hs, dist/build/Bio/Alignment/BlastXML.o ) [ 8 of 46] Compiling Bio.Alignment.BlastFlat ( Bio/Alignment/BlastFlat.hs, dist/build/Bio/Alignment/BlastFlat.o ) [ 9 of 46] Compiling Bio.Alignment.Blast ( Bio/Alignment/Blast.hs, dist/build/Bio/Alignment/Blast.o ) [10 of 46] Compiling Bio.Sequence.SFF_name ( Bio/Sequence/SFF_name.hs, dist/build/Bio/Sequence/SFF_name.o ) [11 of 46] Compiling Bio.Sequence.GeneOntology ( Bio/Sequence/GeneOntology.hs, dist/build/Bio/Sequence/GeneOntology.o ) [12 of 46] Compiling Bio.Sequence.KEGG ( Bio/Sequence/KEGG.hs, dist/build/Bio/Sequence/KEGG.o ) [13 of 46] Compiling Bio.Sequence.GOA ( Bio/Sequence/GOA.hs, dist/build/Bio/Sequence/GOA.o ) [14 of 46] Compiling Bio.Sequence.Entropy ( Bio/Sequence/Entropy.hs, dist/build/Bio/Sequence/Entropy.o ) [15 of 46] Compiling Bio.Sequence.SeqData ( Bio/Sequence/SeqData.hs, dist/build/Bio/Sequence/SeqData.o ) [16 of 46] Compiling Bio.Sequence.Fasta ( Bio/Sequence/Fasta.hs, dist/build/Bio/Sequence/Fasta.o ) Bio/Sequence/Fasta.hs:31:1: Warning: The import of `chr' from module `Data.Char' is redundant [17 of 46] Compiling Bio.Sequence.FastQ ( Bio/Sequence/FastQ.hs, dist/build/Bio/Sequence/FastQ.o ) [18 of 46] Compiling Bio.Sequence.Phd ( Bio/Sequence/Phd.hs, dist/build/Bio/Sequence/Phd.o ) [19 of 46] Compiling Bio.Sequence.TwoBit ( Bio/Sequence/TwoBit.hs, dist/build/Bio/Sequence/TwoBit.o ) Bio/Sequence/TwoBit.hs:256:26: Warning: This binding for `ns' shadows the existing binding bound at Bio/Sequence/TwoBit.hs:234:8 Bio/Sequence/TwoBit.hs:261:21: Warning: This binding for `ns' shadows the existing binding bound at Bio/Sequence/TwoBit.hs:234:8 Bio/Sequence/TwoBit.hs:360:29: Warning: Pattern match(es) are non-exhaustive In a case alternative: Patterns not matched: ghc-prim:GHC.Types.C# #x with #x `notElem` ['T', 'C', 'A', 'G'] Bio/Sequence/TwoBit.hs:396:51: Warning: Pattern match(es) are non-exhaustive In a case alternative: Patterns not matched: ghc-prim:GHC.Types.I# #x with #x `notElem` [1#, 2#, 3#, 4#] [20 of 46] Compiling Bio.Sequence.SFF ( Bio/Sequence/SFF.hs, dist/build/Bio/Sequence/SFF.o ) [21 of 46] Compiling Bio.Sequence.SFF_filters ( Bio/Sequence/SFF_filters.hs, dist/build/Bio/Sequence/SFF_filters.o ) [22 of 46] Compiling Bio.Sequence.HashWord ( Bio/Sequence/HashWord.lhs, dist/build/Bio/Sequence/HashWord.o ) [23 of 46] Compiling Bio.Sequence.AminoProperties ( Bio/Sequence/AminoProperties.hs, dist/build/Bio/Sequence/AminoProperties.o ) [24 of 46] Compiling Bio.Alignment.AlignData ( Bio/Alignment/AlignData.hs, dist/build/Bio/Alignment/AlignData.o ) Bio/Alignment/AlignData.hs:59:1: Warning: Top-level binding with no type signature: showalign :: [Edit] -> [Char] Bio/Alignment/AlignData.hs:112:9: Warning: Pattern match(es) are non-exhaustive In an equation for `mkcol': Patterns not matched: ([], _) Bio/Alignment/AlignData.hs:121:1: Warning: Top-level binding with no type signature: on :: forall t t1 t2. (t1 -> t1 -> t) -> (t2 -> t1) -> t2 -> t2 -> t [25 of 46] Compiling Bio.Alignment.Matrices ( Bio/Alignment/Matrices.hs, dist/build/Bio/Alignment/Matrices.o ) [26 of 46] Compiling Bio.Alignment.SAlign ( Bio/Alignment/SAlign.hs, dist/build/Bio/Alignment/SAlign.o ) [27 of 46] Compiling Bio.Alignment.AAlign ( Bio/Alignment/AAlign.hs, dist/build/Bio/Alignment/AAlign.o ) Bio/Alignment/AAlign.hs:40:14: Warning: This binding for `minf' shadows the existing binding defined at Bio/Alignment/AAlign.hs:23:1 Bio/Alignment/AAlign.hs:50:1: Warning: Top-level binding with no type signature: max' :: forall t t1. Ord t => (t, t1) -> (t, t1) -> (t, t1) Bio/Alignment/AAlign.hs:51:1: Warning: Top-level binding with no type signature: fp :: forall t a. Num t => (t, [a]) -> (t, a) -> (t, [a]) Bio/Alignment/AAlign.hs:64:1: Warning: Top-level binding with no type signature: revsnd :: forall t a. (t, [a]) -> (t, [a]) Bio/Alignment/AAlign.hs:68:14: Warning: This binding for `minf' shadows the existing binding defined at Bio/Alignment/AAlign.hs:23:1 [28 of 46] Compiling Bio.Alignment.QAlign ( Bio/Alignment/QAlign.hs, dist/build/Bio/Alignment/QAlign.o ) Bio/Alignment/QAlign.hs:70:9: Warning: Pattern match(es) are non-exhaustive In an equation for `mkcol': Patterns not matched: (_, [], _) Bio/Alignment/QAlign.hs:103:72: Warning: This binding for `x' shadows the existing binding bound at Bio/Alignment/QAlign.hs:94:15 Bio/Alignment/QAlign.hs:103:86: Warning: This binding for `y' shadows the existing binding bound at Bio/Alignment/QAlign.hs:94:17 Bio/Alignment/QAlign.hs:104:73: Warning: This binding for `x' shadows the existing binding bound at Bio/Alignment/QAlign.hs:94:15 Bio/Alignment/QAlign.hs:104:87: Warning: This binding for `y' shadows the existing binding bound at Bio/Alignment/QAlign.hs:94:17 Bio/Alignment/QAlign.hs:140:11: Warning: Pattern match(es) are non-exhaustive In an equation for `overlap_score_select': Patterns not matched: [] [_, _] _ : (_ : (_ : (_ : _))) Bio/Alignment/QAlign.hs:145:14: Warning: This binding for `minf' shadows the existing binding defined at Bio/Alignment/QAlign.hs:89:1 Bio/Alignment/QAlign.hs:183:11: Warning: Pattern match(es) are non-exhaustive In an equation for `overlap_align_select': Patterns not matched: [] [_, _] _ : (_ : (_ : (_ : _))) Bio/Alignment/QAlign.hs:188:1: Warning: Defined but not used: overlap_align' Bio/Alignment/QAlign.hs:192:11: Warning: Pattern match(es) are non-exhaustive In an equation for `overlap_align_select': Patterns not matched: [] [(((_, _), (_, _)), _, _, _), _] (((_, _), (_, _)), _, _, _) : (_ : (_ : (_ : _))) Bio/Alignment/QAlign.hs:193:36: Warning: This binding for `s1' shadows the existing binding bound at Bio/Alignment/QAlign.hs:188:21 Bio/Alignment/QAlign.hs:193:36: Warning: Defined but not used: `s1' Bio/Alignment/QAlign.hs:193:39: Warning: Defined but not used: `es1' Bio/Alignment/QAlign.hs:193:45: Warning: This binding for `s2' shadows the existing binding bound at Bio/Alignment/QAlign.hs:188:24 Bio/Alignment/QAlign.hs:193:45: Warning: Defined but not used: `s2' Bio/Alignment/QAlign.hs:196:1: Warning: Top-level binding with no type signature: revsnd :: forall t a. (t, [a]) -> (t, [a]) Bio/Alignment/QAlign.hs:200:14: Warning: This binding for `minf' shadows the existing binding defined at Bio/Alignment/QAlign.hs:89:1 Bio/Alignment/QAlign.hs:208:1: Warning: Top-level binding with no type signature: snd' :: forall t t1 t2 t3. (t, t1, t2, t3) -> t1 Bio/Alignment/QAlign.hs:222:7: Warning: This binding for `or' shadows the existing binding imported from `Prelude' at Bio/Alignment/QAlign.hs:19:8-27 (and originally defined in `GHC.List') [29 of 46] Compiling Bio.Alignment.ACE ( Bio/Alignment/ACE.hs, dist/build/Bio/Alignment/ACE.o ) [30 of 46] Compiling Bio.Location.OnSeq ( Bio/Location/OnSeq.hs, dist/build/Bio/Location/OnSeq.o ) Bio/Location/OnSeq.hs:21:1: Warning: The import of `Data.List' is redundant except perhaps to import instances from `Data.List' To import instances alone, use: import Data.List() [31 of 46] Compiling Bio.Location.Strand ( Bio/Location/Strand.hs, dist/build/Bio/Location/Strand.o ) [32 of 46] Compiling Bio.Location.Position ( Bio/Location/Position.hs, dist/build/Bio/Location/Position.o ) Bio/Location/Position.hs:24:1: Warning: The import of `Data.List' is redundant except perhaps to import instances from `Data.List' To import instances alone, use: import Data.List() [33 of 46] Compiling Bio.Location.ContigLocation ( Bio/Location/ContigLocation.hs, dist/build/Bio/Location/ContigLocation.o ) [34 of 46] Compiling Bio.Location.Location ( Bio/Location/Location.hs, dist/build/Bio/Location/Location.o ) [35 of 46] Compiling Bio.Location.SeqLocation ( Bio/Location/SeqLocation.hs, dist/build/Bio/Location/SeqLocation.o ) [36 of 46] Compiling Bio.Alignment.Bowtie ( Bio/Alignment/Bowtie.hs, dist/build/Bio/Alignment/Bowtie.o ) Bio/Alignment/Bowtie.hs:35:1: Warning: The import of `Data.Char' is redundant except perhaps to import instances from `Data.Char' To import instances alone, use: import Data.Char() [37 of 46] Compiling Bio.Alignment.Soap ( Bio/Alignment/Soap.hs, dist/build/Bio/Alignment/Soap.o ) [38 of 46] Compiling Bio.Alignment.BED ( Bio/Alignment/BED.hs, dist/build/Bio/Alignment/BED.o ) [39 of 46] Compiling Bio.Location.LocMap ( Bio/Location/LocMap.hs, dist/build/Bio/Location/LocMap.o ) Bio/Location/LocMap.hs:29:1: Warning: The import of `Data.Maybe' is redundant except perhaps to import instances from `Data.Maybe' To import instances alone, use: import Data.Maybe() Bio/Location/LocMap.hs:50:10: Warning: Defined but not used: `zonesize' [40 of 46] Compiling Bio.Location.SeqLocMap ( Bio/Location/SeqLocMap.hs, dist/build/Bio/Location/SeqLocMap.o ) [41 of 46] Compiling Bio.GFF3.Feature ( Bio/GFF3/Feature.hs, dist/build/Bio/GFF3/Feature.o ) [42 of 46] Compiling Bio.GFF3.FeatureHier ( Bio/GFF3/FeatureHier.hs, dist/build/Bio/GFF3/FeatureHier.o ) [43 of 46] Compiling Bio.GFF3.FeatureHierSequences ( Bio/GFF3/FeatureHierSequences.hs, dist/build/Bio/GFF3/FeatureHierSequences.o ) [44 of 46] Compiling Bio.GFF3.SGD ( Bio/GFF3/SGD.hs, dist/build/Bio/GFF3/SGD.o ) [45 of 46] Compiling Bio.Sequence ( Bio/Sequence.hs, dist/build/Bio/Sequence.o ) [46 of 46] Compiling Bio.Alignment.Multiple ( Bio/Alignment/Multiple.hs, dist/build/Bio/Alignment/Multiple.o ) In-place registering bio-0.5.3... Preprocessing executable 'flx' for bio-0.5.3... [1 of 4] Compiling Bio.Sequence.SFF_name ( Bio/Sequence/SFF_name.hs, dist/build/flx/flx-tmp/Bio/Sequence/SFF_name.o ) [2 of 4] Compiling Bio.Sequence.SeqData ( Bio/Sequence/SeqData.hs, dist/build/flx/flx-tmp/Bio/Sequence/SeqData.o ) [3 of 4] Compiling Bio.Sequence.SFF ( Bio/Sequence/SFF.hs, dist/build/flx/flx-tmp/Bio/Sequence/SFF.o ) [4 of 4] Compiling Main ( examples/Flx.hs, dist/build/flx/flx-tmp/Main.o ) Linking dist/build/flx/flx ... Preprocessing executable 'fastout' for bio-0.5.3... [ 1 of 11] Compiling Bio.Sequence.SFF_name ( Bio/Sequence/SFF_name.hs, dist/build/fastout/fastout-tmp/Bio/Sequence/SFF_name.o ) [ 2 of 11] Compiling Bio.Sequence.Entropy ( Bio/Sequence/Entropy.hs, dist/build/fastout/fastout-tmp/Bio/Sequence/Entropy.o ) [ 3 of 11] Compiling Bio.Sequence.SeqData ( Bio/Sequence/SeqData.hs, dist/build/fastout/fastout-tmp/Bio/Sequence/SeqData.o ) [ 4 of 11] Compiling Bio.Sequence.Fasta ( Bio/Sequence/Fasta.hs, dist/build/fastout/fastout-tmp/Bio/Sequence/Fasta.o ) [ 5 of 11] Compiling Bio.Sequence.FastQ ( Bio/Sequence/FastQ.hs, dist/build/fastout/fastout-tmp/Bio/Sequence/FastQ.o ) [ 6 of 11] Compiling Bio.Sequence.TwoBit ( Bio/Sequence/TwoBit.hs, dist/build/fastout/fastout-tmp/Bio/Sequence/TwoBit.o ) [ 7 of 11] Compiling Bio.Sequence.Phd ( Bio/Sequence/Phd.hs, dist/build/fastout/fastout-tmp/Bio/Sequence/Phd.o ) [ 8 of 11] Compiling Bio.Sequence.HashWord ( Bio/Sequence/HashWord.lhs, dist/build/fastout/fastout-tmp/Bio/Sequence/HashWord.o ) [ 9 of 11] Compiling Bio.Sequence.SFF ( Bio/Sequence/SFF.hs, dist/build/fastout/fastout-tmp/Bio/Sequence/SFF.o ) [10 of 11] Compiling Bio.Sequence ( Bio/Sequence.hs, dist/build/fastout/fastout-tmp/Bio/Sequence.o ) [11 of 11] Compiling Main ( examples/FastOut.hs, dist/build/fastout/fastout-tmp/Main.o ) Linking dist/build/fastout/fastout ... Preprocessing executable 'frecover' for bio-0.5.3... [1 of 4] Compiling Bio.Sequence.SFF_name ( Bio/Sequence/SFF_name.hs, dist/build/frecover/frecover-tmp/Bio/Sequence/SFF_name.o ) [2 of 4] Compiling Bio.Sequence.SeqData ( Bio/Sequence/SeqData.hs, dist/build/frecover/frecover-tmp/Bio/Sequence/SeqData.o ) [3 of 4] Compiling Bio.Sequence.SFF ( Bio/Sequence/SFF.hs, dist/build/frecover/frecover-tmp/Bio/Sequence/SFF.o ) [4 of 4] Compiling Main ( examples/FRecover.hs, dist/build/frecover/frecover-tmp/Main.o ) Linking dist/build/frecover/frecover ... Preprocessing executable 'frename' for bio-0.5.3... [1 of 4] Compiling Bio.Sequence.SFF_name ( Bio/Sequence/SFF_name.hs, dist/build/frename/frename-tmp/Bio/Sequence/SFF_name.o ) [2 of 4] Compiling Bio.Sequence.SeqData ( Bio/Sequence/SeqData.hs, dist/build/frename/frename-tmp/Bio/Sequence/SeqData.o ) [3 of 4] Compiling Bio.Sequence.SFF ( Bio/Sequence/SFF.hs, dist/build/frename/frename-tmp/Bio/Sequence/SFF.o ) [4 of 4] Compiling Main ( examples/FRename.hs, dist/build/frename/frename-tmp/Main.o ) Linking dist/build/frename/frename ... Preprocessing executable 'flowclip' for bio-0.5.3... [1 of 4] Compiling Bio.Sequence.SFF_name ( Bio/Sequence/SFF_name.hs, dist/build/flowclip/flowclip-tmp/Bio/Sequence/SFF_name.o ) [2 of 4] Compiling Bio.Sequence.SeqData ( Bio/Sequence/SeqData.hs, dist/build/flowclip/flowclip-tmp/Bio/Sequence/SeqData.o ) [3 of 4] Compiling Bio.Sequence.SFF ( Bio/Sequence/SFF.hs, dist/build/flowclip/flowclip-tmp/Bio/Sequence/SFF.o ) [4 of 4] Compiling Main ( examples/FlowClip.hs, dist/build/flowclip/flowclip-tmp/Main.o ) Linking dist/build/flowclip/flowclip ... Preprocessing executable 'orf' for bio-0.5.3... [ 1 of 11] Compiling Bio.Sequence.SFF_name ( Bio/Sequence/SFF_name.hs, dist/build/orf/orf-tmp/Bio/Sequence/SFF_name.o ) [ 2 of 11] Compiling Bio.Sequence.Entropy ( Bio/Sequence/Entropy.hs, dist/build/orf/orf-tmp/Bio/Sequence/Entropy.o ) [ 3 of 11] Compiling Bio.Sequence.SeqData ( Bio/Sequence/SeqData.hs, dist/build/orf/orf-tmp/Bio/Sequence/SeqData.o ) [ 4 of 11] Compiling Bio.Sequence.Fasta ( Bio/Sequence/Fasta.hs, dist/build/orf/orf-tmp/Bio/Sequence/Fasta.o ) Bio/Sequence/Fasta.hs:31:1: Warning: The import of `chr' from module `Data.Char' is redundant [ 5 of 11] Compiling Bio.Sequence.FastQ ( Bio/Sequence/FastQ.hs, dist/build/orf/orf-tmp/Bio/Sequence/FastQ.o ) [ 6 of 11] Compiling Bio.Sequence.TwoBit ( Bio/Sequence/TwoBit.hs, dist/build/orf/orf-tmp/Bio/Sequence/TwoBit.o ) Bio/Sequence/TwoBit.hs:256:26: Warning: This binding for `ns' shadows the existing binding bound at Bio/Sequence/TwoBit.hs:234:8 Bio/Sequence/TwoBit.hs:261:21: Warning: This binding for `ns' shadows the existing binding bound at Bio/Sequence/TwoBit.hs:234:8 Bio/Sequence/TwoBit.hs:360:29: Warning: Pattern match(es) are non-exhaustive In a case alternative: Patterns not matched: ghc-prim:GHC.Types.C# #x with #x `notElem` ['T', 'C', 'A', 'G'] Bio/Sequence/TwoBit.hs:396:51: Warning: Pattern match(es) are non-exhaustive In a case alternative: Patterns not matched: ghc-prim:GHC.Types.I# #x with #x `notElem` [1#, 2#, 3#, 4#] [ 7 of 11] Compiling Bio.Sequence.Phd ( Bio/Sequence/Phd.hs, dist/build/orf/orf-tmp/Bio/Sequence/Phd.o ) [ 8 of 11] Compiling Bio.Sequence.HashWord ( Bio/Sequence/HashWord.lhs, dist/build/orf/orf-tmp/Bio/Sequence/HashWord.o ) [ 9 of 11] Compiling Bio.Sequence.SFF ( Bio/Sequence/SFF.hs, dist/build/orf/orf-tmp/Bio/Sequence/SFF.o ) [10 of 11] Compiling Bio.Sequence ( Bio/Sequence.hs, dist/build/orf/orf-tmp/Bio/Sequence.o ) [11 of 11] Compiling Main ( examples/Orf.hs, dist/build/orf/orf-tmp/Main.o ) examples/Orf.hs:11:1: Warning: Top-level binding with no type signature: doit :: Sequence Nuc -> String examples/Orf.hs:21:1: Warning: Top-level binding with no type signature: comp_orflength :: forall t t1 t2 t3 a. Ord a => (t, a, t1) -> (t2, a, t3) -> Ordering examples/Orf.hs:39:1: Warning: Top-level binding with no type signature: takeUntil :: forall t. (t -> Bool) -> [t] -> [t] Linking dist/build/orf/orf ... Preprocessing executable 'rselect-pe' for bio-0.5.3... [ 1 of 11] Compiling Bio.Sequence.SFF_name ( Bio/Sequence/SFF_name.hs, dist/build/rselect-pe/rselect-pe-tmp/Bio/Sequence/SFF_name.o ) [ 2 of 11] Compiling Bio.Sequence.Entropy ( Bio/Sequence/Entropy.hs, dist/build/rselect-pe/rselect-pe-tmp/Bio/Sequence/Entropy.o ) [ 3 of 11] Compiling Bio.Sequence.SeqData ( Bio/Sequence/SeqData.hs, dist/build/rselect-pe/rselect-pe-tmp/Bio/Sequence/SeqData.o ) [ 4 of 11] Compiling Bio.Sequence.Fasta ( Bio/Sequence/Fasta.hs, dist/build/rselect-pe/rselect-pe-tmp/Bio/Sequence/Fasta.o ) Bio/Sequence/Fasta.hs:31:1: Warning: The import of `chr' from module `Data.Char' is redundant [ 5 of 11] Compiling Bio.Sequence.FastQ ( Bio/Sequence/FastQ.hs, dist/build/rselect-pe/rselect-pe-tmp/Bio/Sequence/FastQ.o ) [ 6 of 11] Compiling Bio.Sequence.TwoBit ( Bio/Sequence/TwoBit.hs, dist/build/rselect-pe/rselect-pe-tmp/Bio/Sequence/TwoBit.o ) Bio/Sequence/TwoBit.hs:256:26: Warning: This binding for `ns' shadows the existing binding bound at Bio/Sequence/TwoBit.hs:234:8 Bio/Sequence/TwoBit.hs:261:21: Warning: This binding for `ns' shadows the existing binding bound at Bio/Sequence/TwoBit.hs:234:8 Bio/Sequence/TwoBit.hs:360:29: Warning: Pattern match(es) are non-exhaustive In a case alternative: Patterns not matched: ghc-prim:GHC.Types.C# #x with #x `notElem` ['T', 'C', 'A', 'G'] Bio/Sequence/TwoBit.hs:396:51: Warning: Pattern match(es) are non-exhaustive In a case alternative: Patterns not matched: ghc-prim:GHC.Types.I# #x with #x `notElem` [1#, 2#, 3#, 4#] [ 7 of 11] Compiling Bio.Sequence.Phd ( Bio/Sequence/Phd.hs, dist/build/rselect-pe/rselect-pe-tmp/Bio/Sequence/Phd.o ) [ 8 of 11] Compiling Bio.Sequence.HashWord ( Bio/Sequence/HashWord.lhs, dist/build/rselect-pe/rselect-pe-tmp/Bio/Sequence/HashWord.o ) [ 9 of 11] Compiling Bio.Sequence.SFF ( Bio/Sequence/SFF.hs, dist/build/rselect-pe/rselect-pe-tmp/Bio/Sequence/SFF.o ) [10 of 11] Compiling Bio.Sequence ( Bio/Sequence.hs, dist/build/rselect-pe/rselect-pe-tmp/Bio/Sequence.o ) [11 of 11] Compiling Main ( examples/RSelectPE.hs, dist/build/rselect-pe/rselect-pe-tmp/Main.o ) examples/RSelectPE.hs:9:1: Warning: Top-level binding with no type signature: main :: IO () examples/RSelectPE.hs:24:1: Warning: Pattern match(es) are non-exhaustive In an equation for `writer': Patterns not matched: _ _ (_, _) examples/RSelectPE.hs:35:1: Warning: Top-level binding with no type signature: sufchk :: [Char] -> [Char] -> Bool examples/RSelectPE.hs:37:1: Warning: Top-level binding with no type signature: hdchk :: forall a a1. Sequence a -> Sequence a1 -> Bool Linking dist/build/rselect-pe/rselect-pe ... Running Haddock for bio-0.5.3... Running hscolour for bio-0.5.3... Preprocessing library bio-0.5.3... Preprocessing executable 'flx' for bio-0.5.3... Preprocessing executable 'fastout' for bio-0.5.3... Preprocessing executable 'frecover' for bio-0.5.3... Preprocessing executable 'frename' for bio-0.5.3... Preprocessing executable 'flowclip' for bio-0.5.3... Preprocessing executable 'orf' for bio-0.5.3... Preprocessing executable 'rselect-pe' for bio-0.5.3... Preprocessing library bio-0.5.3... Warning: The documentation for the following packages are not installed. No links will be generated to these packages: mtl-2.1.2, parsec-3.1.3, random-1.0.1.1, text-0.11.2.3, transformers-0.3.0.0 Bio/Sequence/Fasta.hs:31:1: Warning: The import of `chr' from module `Data.Char' is redundant Bio/Sequence/TwoBit.hs:256:26: Warning: This binding for `ns' shadows the existing binding bound at Bio/Sequence/TwoBit.hs:234:8 Bio/Sequence/TwoBit.hs:261:21: Warning: This binding for `ns' shadows the existing binding bound at Bio/Sequence/TwoBit.hs:234:8 Bio/Alignment/AlignData.hs:59:1: Warning: Top-level binding with no type signature: showalign :: [Edit] -> [Char] Bio/Alignment/AlignData.hs:121:1: Warning: Top-level binding with no type signature: on :: forall t t1 t2. (t1 -> t1 -> t) -> (t2 -> t1) -> t2 -> t2 -> t Bio/Alignment/AAlign.hs:40:14: Warning: This binding for `minf' shadows the existing binding defined at Bio/Alignment/AAlign.hs:23:1 Bio/Alignment/AAlign.hs:50:1: Warning: Top-level binding with no type signature: max' :: forall t t1. Ord t => (t, t1) -> (t, t1) -> (t, t1) Bio/Alignment/AAlign.hs:51:1: Warning: Top-level binding with no type signature: fp :: forall t a. Num t => (t, [a]) -> (t, a) -> (t, [a]) Bio/Alignment/AAlign.hs:64:1: Warning: Top-level binding with no type signature: revsnd :: forall t a. (t, [a]) -> (t, [a]) Bio/Alignment/AAlign.hs:68:14: Warning: This binding for `minf' shadows the existing binding defined at Bio/Alignment/AAlign.hs:23:1 Bio/Alignment/QAlign.hs:103:72: Warning: This binding for `x' shadows the existing binding bound at Bio/Alignment/QAlign.hs:94:15 Bio/Alignment/QAlign.hs:103:86: Warning: This binding for `y' shadows the existing binding bound at Bio/Alignment/QAlign.hs:94:17 Bio/Alignment/QAlign.hs:104:73: Warning: This binding for `x' shadows the existing binding bound at Bio/Alignment/QAlign.hs:94:15 Bio/Alignment/QAlign.hs:104:87: Warning: This binding for `y' shadows the existing binding bound at Bio/Alignment/QAlign.hs:94:17 Bio/Alignment/QAlign.hs:145:14: Warning: This binding for `minf' shadows the existing binding defined at Bio/Alignment/QAlign.hs:89:1 Bio/Alignment/QAlign.hs:188:1: Warning: Defined but not used: overlap_align' Bio/Alignment/QAlign.hs:193:36: Warning: This binding for `s1' shadows the existing binding bound at Bio/Alignment/QAlign.hs:188:21 Bio/Alignment/QAlign.hs:193:36: Warning: Defined but not used: `s1' Bio/Alignment/QAlign.hs:193:39: Warning: Defined but not used: `es1' Bio/Alignment/QAlign.hs:193:45: Warning: This binding for `s2' shadows the existing binding bound at Bio/Alignment/QAlign.hs:188:24 Bio/Alignment/QAlign.hs:193:45: Warning: Defined but not used: `s2' Bio/Alignment/QAlign.hs:196:1: Warning: Top-level binding with no type signature: revsnd :: forall t a. (t, [a]) -> (t, [a]) Bio/Alignment/QAlign.hs:200:14: Warning: This binding for `minf' shadows the existing binding defined at Bio/Alignment/QAlign.hs:89:1 Bio/Alignment/QAlign.hs:208:1: Warning: Top-level binding with no type signature: snd' :: forall t t1 t2 t3. (t, t1, t2, t3) -> t1 Bio/Alignment/QAlign.hs:222:7: Warning: This binding for `or' shadows the existing binding imported from `Prelude' at Bio/Alignment/QAlign.hs:19:8-27 (and originally defined in `GHC.List') Bio/Location/OnSeq.hs:21:1: Warning: The import of `Data.List' is redundant except perhaps to import instances from `Data.List' To import instances alone, use: import Data.List() Bio/Location/Position.hs:24:1: Warning: The import of `Data.List' is redundant except perhaps to import instances from `Data.List' To import instances alone, use: import Data.List() Bio/Alignment/Bowtie.hs:35:1: Warning: The import of `Data.Char' is redundant except perhaps to import instances from `Data.Char' To import instances alone, use: import Data.Char() Bio/Location/LocMap.hs:29:1: Warning: The import of `Data.Maybe' is redundant except perhaps to import instances from `Data.Maybe' To import instances alone, use: import Data.Maybe() Bio/Location/LocMap.hs:50:10: Warning: Defined but not used: `zonesize' Haddock coverage: 0% ( 0 / 5) in 'Bio.GFF3.Escape' 50% ( 1 / 2) in 'Bio.Util.Parsex' 100% ( 3 / 3) in 'Bio.Clustering' 14% ( 1 / 7) in 'Bio.Alignment.PSL' 100% ( 6 / 6) in 'Bio.Util' 100% ( 8 / 8) in 'Bio.Alignment.BlastData' 100% ( 2 / 2) in 'Bio.Alignment.BlastXML' 53% ( 10 / 19) in 'Bio.Alignment.BlastFlat' 50% ( 1 / 2) in 'Bio.Alignment.Blast' 7% ( 1 / 14) in 'Bio.Sequence.SFF_name' 89% ( 16 / 18) in 'Bio.Sequence.GeneOntology' 83% ( 5 / 6) in 'Bio.Sequence.KEGG' Warning: bio-0.5.3:Bio.Sequence.GOA: Could not find documentation for exported module: GO 50% ( 1 / 2) in 'Bio.Sequence.GOA' 0% ( 0 / 3) in 'Bio.Sequence.Entropy' 90% ( 43 / 48) in 'Bio.Sequence.SeqData' 85% ( 17 / 20) in 'Bio.Sequence.Fasta' 32% ( 6 / 19) in 'Bio.Sequence.FastQ' 100% ( 3 / 3) in 'Bio.Sequence.Phd' 100% ( 7 / 7) in 'Bio.Sequence.TwoBit' 91% ( 29 / 32) in 'Bio.Sequence.SFF' 66% ( 19 / 29) in 'Bio.Sequence.SFF_filters' 29% ( 5 / 17) in 'Bio.Sequence.HashWord' 18% ( 3 / 17) in 'Bio.Sequence.AminoProperties' 71% ( 15 / 21) in 'Bio.Alignment.AlignData' 100% ( 14 / 14) in 'Bio.Alignment.Matrices' 86% ( 6 / 7) in 'Bio.Alignment.SAlign' 100% ( 7 / 7) in 'Bio.Alignment.AAlign' 88% ( 15 / 17) in 'Bio.Alignment.QAlign' 50% ( 3 / 6) in 'Bio.Alignment.ACE' 100% ( 13 / 13) in 'Bio.Location.OnSeq' 100% ( 4 / 4) in 'Bio.Location.Strand' 100% ( 10 / 10) in 'Bio.Location.Position' 100% ( 21 / 21) in 'Bio.Location.ContigLocation' 100% ( 19 / 19) in 'Bio.Location.Location' 100% ( 17 / 17) in 'Bio.Location.SeqLocation' 94% ( 17 / 18) in 'Bio.Alignment.Bowtie' 8% ( 1 / 12) in 'Bio.Alignment.Soap' 60% ( 3 / 5) in 'Bio.Alignment.BED' 92% ( 12 / 13) in 'Bio.Location.LocMap' 100% ( 10 / 10) in 'Bio.Location.SeqLocMap' 0% ( 0 / 14) in 'Bio.GFF3.Feature' 0% ( 0 / 13) in 'Bio.GFF3.FeatureHier' 0% ( 0 / 15) in 'Bio.GFF3.FeatureHierSequences' 0% ( 0 / 13) in 'Bio.GFF3.SGD' 76% ( 63 / 83) in 'Bio.Sequence' 100% ( 3 / 3) in 'Bio.Alignment.Multiple' Warning: Bio.GFF3.Escape: could not find link destinations for: Control.Monad.Trans.Error.Error Control.Monad.Error.Class.MonadError Warning: Bio.Util.Parsex: could not find link destinations for: Text.Parsec.String.GenParser Text.Parsec.Pos.SourceName Warning: Bio.Alignment.QAlign: could not find link destinations for: Bio.Alignment.QAlign.QualMx Warning: Bio.Alignment.ACE: could not find link destinations for: Bio.Alignment.ACE.AceParser Bio.Alignment.ACE.ACE Warning: Bio.Location.OnSeq: could not find link destinations for: Control.Monad.Trans.Error.Error Control.Monad.Error.Class.MonadError Warning: Bio.Location.Position: could not find link destinations for: Control.Monad.Trans.Error.Error Control.Monad.Error.Class.MonadError Warning: Bio.Location.ContigLocation: could not find link destinations for: Control.Monad.Trans.Error.Error Control.Monad.Error.Class.MonadError Warning: Bio.Location.Location: could not find link destinations for: Control.Monad.Trans.Error.Error Control.Monad.Error.Class.MonadError Warning: Bio.Location.SeqLocation: could not find link destinations for: Control.Monad.Trans.Error.Error Control.Monad.Error.Class.MonadError Warning: Bio.Alignment.Soap: could not find link destinations for: Control.Monad.Trans.Error.Error Control.Monad.Error.Class.MonadError Warning: Bio.GFF3.Feature: could not find link destinations for: Control.Monad.Trans.Error.Error Control.Monad.Error.Class.MonadError Warning: Bio.GFF3.FeatureHier: could not find link destinations for: Control.Monad.Trans.Error.Error Control.Monad.Error.Class.MonadError Control.Monad.Reader.Class.MonadReader Warning: Bio.GFF3.FeatureHierSequences: could not find link destinations for: Control.Monad.Trans.Error.Error Control.Monad.Error.Class.MonadError Control.Monad.Trans.Error.ErrorT Control.Monad.Trans.Reader.Reader Control.Monad.Trans.Reader.ReaderT Control.Monad.Reader.Class.MonadReader Warning: Bio.GFF3.SGD: could not find link destinations for: Control.Monad.Trans.Error.Error Control.Monad.Error.Class.MonadError Documentation created: dist/doc/html/bio/index.html Preprocessing executable 'flx' for bio-0.5.3... Preprocessing executable 'fastout' for bio-0.5.3... Preprocessing executable 'frecover' for bio-0.5.3... Preprocessing executable 'frename' for bio-0.5.3... Preprocessing executable 'flowclip' for bio-0.5.3... Preprocessing executable 'orf' for bio-0.5.3... Preprocessing executable 'rselect-pe' for bio-0.5.3... Installing library in /srv/hackage/var/build/tmp-install/lib/x86_64-linux-ghc-7.6.3/bio-0.5.3 Installing executable(s) in /srv/hackage/var/build/tmp-install/bin Warning: The directory /srv/hackage/var/build/tmp-install/bin is not in the system search path. Registering bio-0.5.3... Installed bio-0.5.3 Configuring regex-compat-0.95.1... Building regex-compat-0.95.1... Preprocessing library regex-compat-0.95.1... [1 of 1] Compiling Text.Regex ( Text/Regex.hs, dist/build/Text/Regex.o ) In-place registering regex-compat-0.95.1... Running Haddock for regex-compat-0.95.1... Running hscolour for regex-compat-0.95.1... Preprocessing library regex-compat-0.95.1... Preprocessing library regex-compat-0.95.1... Warning: The documentation for the following packages are not installed. No links will be generated to these packages: mtl-2.1.2, transformers-0.3.0.0 Haddock coverage: 100% ( 9 / 9) in 'Text.Regex' Documentation created: dist/doc/html/regex-compat/index.html Installing library in /srv/hackage/var/build/tmp-install/lib/x86_64-linux-ghc-7.6.3/regex-compat-0.95.1 Registering regex-compat-0.95.1... Installed regex-compat-0.95.1 Downloading dephd-0.1... Configuring dephd-0.1... Building dephd-0.1... Preprocessing executable 'dephd' for dephd-0.1... [1 of 1] Compiling Main ( src/Dephd.hs, dist/build/dephd/dephd-tmp/Main.o ) src/Dephd.hs:31:42: Expecting one more argument to `Sequence' In the type `[(FilePath, Sequence) -> IO ()]' In the definition of data constructor `O' In the data declaration for `MyOpts' Failed to install dephd-0.1 cabal: Error: some packages failed to install: dephd-0.1 failed during the building phase. The exception was: ExitFailure 1