Build #1 for sgrep-0.0

[all reports]

Package sgrep-0.0
Install InstallOk
Docs Ok
Tests NotTried
Time submitted unknown
Compiler ghc-7.6.3
OS linux
Arch x86_64
Dependencies regex-compat-0.95.1, bio-0.5.3, base-4.6.0.1
Flags none

Build log

[view raw]

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.Modifiers ( Test/QuickCheck/Modifiers.hs, dist/build/Test/QuickCheck/Modifiers.o )
[ 8 of 13] Compiling Test.QuickCheck.Function ( Test/QuickCheck/Function.hs, dist/build/Test/QuickCheck/Function.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.Monadic ( Test/QuickCheck/Monadic.hs, dist/build/Test/QuickCheck/Monadic.o )
[12 of 13] Compiling Test.QuickCheck  ( Test/QuickCheck.hs, dist/build/Test/QuickCheck.o )
[13 of 13] Compiling Test.QuickCheck.All ( Test/QuickCheck/All.hs, dist/build/Test/QuickCheck/All.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: rts-1.0, 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'
  92% ( 12 / 13) in 'Test.QuickCheck.Modifiers'
  14% (  1 /  7) in 'Test.QuickCheck.Function'
  59% ( 34 / 58) in 'Test.QuickCheck.Property'
  48% ( 13 / 27) in 'Test.QuickCheck.Test'
   7% (  1 / 15) in 'Test.QuickCheck.Monadic'
 100% (  9 /  9) in 'Test.QuickCheck.All'
  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/QuickCheck-2.6/ghc-7.6.3
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...
Warning: The documentation for the following packages are not installed. No
links will be generated to these packages: rts-1.0

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/binary-0.4.5/ghc-7.6.3
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...
Warning: The documentation for the following packages are not installed. No
links will be generated to these packages: rts-1.0
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/parallel-3.2.0.4/ghc-7.6.3
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: rts-1.0, 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/regex-base-0.93.2/ghc-7.6.3
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: rts-1.0, 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/tagsoup-0.13/ghc-7.6.3
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: rts-1.0, 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/regex-posix-0.95.2/ghc-7.6.3
Registering regex-posix-0.95.2...
Installed regex-posix-0.95.2
Configuring bio-0.5.3...
Building bio-0.5.3...
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.Phd ( Bio/Sequence/Phd.hs, dist/build/rselect-pe/rselect-pe-tmp/Bio/Sequence/Phd.o )
[ 7 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#]
[ 8 of 11] Compiling Bio.Sequence.SFF ( Bio/Sequence/SFF.hs, dist/build/rselect-pe/rselect-pe-tmp/Bio/Sequence/SFF.o )
[ 9 of 11] Compiling Bio.Sequence.HashWord ( Bio/Sequence/HashWord.lhs, dist/build/rselect-pe/rselect-pe-tmp/Bio/Sequence/HashWord.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 ...
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.Phd ( Bio/Sequence/Phd.hs, dist/build/orf/orf-tmp/Bio/Sequence/Phd.o )
[ 7 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#]
[ 8 of 11] Compiling Bio.Sequence.SFF ( Bio/Sequence/SFF.hs, dist/build/orf/orf-tmp/Bio/Sequence/SFF.o )
[ 9 of 11] Compiling Bio.Sequence.HashWord ( Bio/Sequence/HashWord.lhs, dist/build/orf/orf-tmp/Bio/Sequence/HashWord.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 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 '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 '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 '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 '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 '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 ...
Running Haddock for bio-0.5.3...
Running hscolour for bio-0.5.3...
Preprocessing executable 'rselect-pe' for bio-0.5.3...
Preprocessing executable 'orf' for bio-0.5.3...
Preprocessing library bio-0.5.3...
Preprocessing executable 'frename' for bio-0.5.3...
Preprocessing executable 'frecover' for bio-0.5.3...
Preprocessing executable 'flx' for bio-0.5.3...
Preprocessing executable 'flowclip' for bio-0.5.3...
Preprocessing executable 'fastout' for bio-0.5.3...
Preprocessing executable 'rselect-pe' for bio-0.5.3...
Preprocessing executable 'orf' 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: rts-1.0, 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 'frename' for bio-0.5.3...
Preprocessing executable 'frecover' for bio-0.5.3...
Preprocessing executable 'flx' for bio-0.5.3...
Preprocessing executable 'flowclip' for bio-0.5.3...
Preprocessing executable 'fastout' for bio-0.5.3...
Installing library in
/srv/hackage/var/build/tmp-install/lib/bio-0.5.3/ghc-7.6.3
Installing executable(s) in /srv/hackage/var/build/tmp-install/bin
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: rts-1.0, 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/regex-compat-0.95.1/ghc-7.6.3
Registering regex-compat-0.95.1...
Installed regex-compat-0.95.1
Downloading sgrep-0.0...
Configuring sgrep-0.0...
Building sgrep-0.0...
Preprocessing executable 'sgrep' for sgrep-0.0...
[1 of 1] Compiling Main             ( SGrep.hs, dist/build/sgrep/sgrep-tmp/Main.o )
Linking dist/build/sgrep/sgrep ...
Warning: No documentation was generated as this package does not contain a
library. Perhaps you want to use the --executables flag.
Installing executable(s) in /srv/hackage/var/build/tmp-install/bin
Installed sgrep-0.0