*** setup configure

Configuring bio-0.3.3.1...
Dependency base>3: using base-3.0.1.0
Dependency QuickCheck<2: using QuickCheck-1.1.0.0
Dependency binary-any: using binary-0.4.2
Dependency tagsoup>=0.4: using tagsoup-0.6
Dependency bytestring-any: using bytestring-0.9.1.0
Dependency containers-any: using containers-0.1.0.1
Dependency array-any: using array-0.1.0.0
Dependency interlude-any: using interlude-0.1.1
Dependency parallel-any: using parallel-1.0.0.1
Dependency parsec-any: using parsec-3.0.0
Using compiler: ghc-6.8.2
Using install prefix: /usr/local/tmp/archive/install
Binaries installed in: /usr/local/tmp/archive/install/bin
Libraries installed in:
/usr/local/tmp/archive/install/lib/bio-0.3.3.1/ghc-6.8.2
Private binaries installed in: /usr/local/tmp/archive/install/libexec
Data files installed in: /usr/local/tmp/archive/install/share/bio-0.3.3.1
Documentation installed in:
/usr/local/tmp/archive/install/share/doc/bio-0.3.3.1
Using alex version 2.0.1 found on system at: /usr/local/bin/alex
Using ar found on system at: /usr/bin/ar
Using c2hs version 0.15.1 found on system at: /usr/local/bin/c2hs
Using cpphs version 0.7 found on system at: /usr/bin/cpphs
Using ffihugs found on system at: /usr/local/bin/ffihugs
Using ghc version 6.8.2 found on system at: /usr/local/bin/ghc
Using ghc-pkg version 6.8.2 found on system at: /usr/local/bin/ghc-pkg
No greencard found
Using haddock version 2.1.0 found on system at: /usr/local/bin/haddock
Using happy version 1.17 found on system at: /usr/local/bin/happy
No hmake found
Using hsc2hs version 0.66-ghc found on system at: /usr/local/bin/hsc2hs
Using hscolour version 1.9 found on system at: /usr/local/bin/HsColour
Using hugs found on system at: /usr/local/bin/hugs
No jhc found
Using ld found on system at: /usr/bin/ld
No nhc98 found
Using pkg-config version 0.22 found on system at: /usr/bin/pkg-config
Using ranlib found on system at: /usr/bin/ranlib
Using strip found on system at: /usr/bin/strip
Using tar found on system at: /bin/tar

*** setup build

Creating dist/build (and its parents)
Creating dist/build/autogen (and its parents)
Preprocessing library bio-0.3.3.1...
Building bio-0.3.3.1...
Building library...
Creating dist/build (and its parents)
/usr/local/bin/ghc -package-name bio-0.3.3.1 --make -hide-all-packages -i -idist/build/autogen -idist/build -i. -Idist/build -odir dist/build -hidir dist/build -stubdir dist/build -package base-3.0.1.0 -package QuickCheck-1.1.0.0 -package binary-0.4.2 -package tagsoup-0.6 -package bytestring-0.9.1.0 -package containers-0.1.0.1 -package array-0.1.0.0 -package interlude-0.1.1 -package parallel-1.0.0.1 -package parsec-3.0.0 -O -Wall -O2 -fexcess-precision -funbox-strict-fields -auto-all -XCPP -XParallelListComp Bio.Sequence Bio.Sequence.SeqData Bio.Sequence.Fasta Bio.Sequence.TwoBit Bio.Sequence.Phd Bio.Sequence.Entropy Bio.Sequence.HashWord Bio.Sequence.GOA Bio.Alignment.BlastData Bio.Alignment.BlastFlat Bio.Alignment.Blast Bio.Alignment.BlastXML Bio.Alignment.AlignData Bio.Alignment.Matrices Bio.Alignment.SAlign Bio.Alignment.AAlign Bio.Alignment.QAlign Bio.Alignment.Multiple Bio.Alignment.ACE Bio.Clustering Bio.Util Bio.Util.Parsex
[ 1 of 22] Compiling Bio.Util.Parsex  ( Bio/Util/Parsex.hs, dist/build/Bio/Util/Parsex.o )
[ 2 of 22] Compiling Bio.Util         ( Bio/Util.hs, dist/build/Bio/Util.o )

Bio/Util.hs:13:0:
    Warning: Definition but no type signature for `Bio.Util.lines'
             Inferred type: Bio.Util.lines :: B.ByteString -> [B.ByteString]

Bio/Util.hs:15:0:
    Warning: Definition but no type signature for `mylines'
             Inferred type: mylines :: B.ByteString -> [B.ByteString]

Bio/Util.hs:13:8:
    Warning: Pattern match(es) are non-exhaustive
             In a case alternative:
                 Patterns not matched: GHC.Base.I# #x with #x `notElem` [1#, 0#]
[ 3 of 22] Compiling Bio.Clustering   ( Bio/Clustering.hs, dist/build/Bio/Clustering.o )
[ 4 of 22] Compiling Bio.Alignment.BlastData ( Bio/Alignment/BlastData.hs, dist/build/Bio/Alignment/BlastData.o )
[ 5 of 22] Compiling Bio.Alignment.BlastFlat ( Bio/Alignment/BlastFlat.hs, dist/build/Bio/Alignment/BlastFlat.o )
[ 6 of 22] Compiling Bio.Alignment.Blast ( Bio/Alignment/Blast.hs, dist/build/Bio/Alignment/Blast.o )

Bio/Alignment/Blast.hs:39:0:
    Warning: Definition but no type signature for `str_query'
             Inferred type: str_query :: ByteString

Bio/Alignment/Blast.hs:40:0:
    Warning: Definition but no type signature for `str_gt'
             Inferred type: str_gt :: ByteString

Bio/Alignment/Blast.hs:41:0:
    Warning: Definition but no type signature for `str_score'
             Inferred type: str_score :: ByteString

Bio/Alignment/Blast.hs:42:0:
    Warning: Definition but no type signature for `str_refer'
             Inferred type: str_refer :: ByteString

Bio/Alignment/Blast.hs:43:0:
    Warning: Definition but no type signature for `str_datab'
             Inferred type: str_datab :: ByteString

Bio/Alignment/Blast.hs:44:0:
    Warning: Definition but no type signature for `str_search'
             Inferred type: str_search :: ByteString

Bio/Alignment/Blast.hs:74:0:
    Warning: Definition but no type signature for `parse_preamble'
             Inferred type: parse_preamble :: [ByteString] -> BlastResult

Bio/Alignment/Blast.hs:84:0:
    Warning: Definition but no type signature for `parse_query'
             Inferred type: parse_query :: [ByteString] -> BlastRecord

Bio/Alignment/Blast.hs:86:272:
    Warning: Defaulting the following constraint(s) to type `Integer'
             `Num t'
               arising from the literal `86' at Bio/Alignment/Blast.hs:86:272-273
    In the first argument of `show', namely `86'
    In the second argument of `(++)', namely `show 86'
    In the second argument of `(++)', namely `" line: " ++ show 86'

Bio/Alignment/Blast.hs:86:411:
    Warning: Defaulting the following constraint(s) to type `Integer'
             `Num t'
               arising from the literal `86' at Bio/Alignment/Blast.hs:86:411-412
    In the first argument of `show', namely `86'
    In the second argument of `(++)', namely `show 86'
    In the second argument of `(++)', namely `" line: " ++ show 86'

Bio/Alignment/Blast.hs:90:0:
    Warning: Definition but no type signature for `parse_hit'
             Inferred type: parse_hit :: [ByteString] -> BlastHit

Bio/Alignment/Blast.hs:95:0:
    Warning: Definition but no type signature for `parse_match'
             Inferred type: parse_match :: [ByteString] -> BlastMatch

Bio/Alignment/Blast.hs:99:252:
    Warning: Defaulting the following constraint(s) to type `Integer'
             `Num t'
               arising from the literal `99' at Bio/Alignment/Blast.hs:99:252-253
    In the first argument of `show', namely `99'
    In the second argument of `(++)', namely `show 99'
    In the second argument of `(++)', namely `" line: " ++ show 99'

Bio/Alignment/Blast.hs:99:391:
    Warning: Defaulting the following constraint(s) to type `Integer'
             `Num t'
               arising from the literal `99' at Bio/Alignment/Blast.hs:99:391-392
    In the first argument of `show', namely `99'
    In the second argument of `(++)', namely `show 99'
    In the second argument of `(++)', namely `" line: " ++ show 99'

Bio/Alignment/Blast.hs:100:253:
    Warning: Defaulting the following constraint(s) to type `Integer'
             `Num t'
               arising from the literal `100'
                            at Bio/Alignment/Blast.hs:100:253-255
    In the first argument of `show', namely `100'
    In the second argument of `(++)', namely `show 100'
    In the second argument of `(++)', namely `" line: " ++ show 100'

Bio/Alignment/Blast.hs:100:393:
    Warning: Defaulting the following constraint(s) to type `Integer'
             `Num t'
               arising from the literal `100'
                            at Bio/Alignment/Blast.hs:100:393-395
    In the first argument of `show', namely `100'
    In the second argument of `(++)', namely `show 100'
    In the second argument of `(++)', namely `" line: " ++ show 100'

Bio/Alignment/Blast.hs:102:260:
    Warning: Defaulting the following constraint(s) to type `Integer'
             `Num t'
               arising from the literal `102'
                            at Bio/Alignment/Blast.hs:102:260-262
    In the first argument of `show', namely `102'
    In the second argument of `(++)', namely `show 102'
    In the second argument of `(++)', namely `" line: " ++ show 102'

Bio/Alignment/Blast.hs:102:400:
    Warning: Defaulting the following constraint(s) to type `Integer'
             `Num t'
               arising from the literal `102'
                            at Bio/Alignment/Blast.hs:102:400-402
    In the first argument of `show', namely `102'
    In the second argument of `(++)', namely `show 102'
    In the second argument of `(++)', namely `" line: " ++ show 102'

Bio/Alignment/Blast.hs:102:643:
    Warning: Defaulting the following constraint(s) to type `Integer'
             `Num t'
               arising from the literal `102'
                            at Bio/Alignment/Blast.hs:102:643-645
    In the first argument of `show', namely `102'
    In the second argument of `(++)', namely `show 102'
    In the second argument of `(++)', namely `" line: " ++ show 102'

Bio/Alignment/Blast.hs:102:783:
    Warning: Defaulting the following constraint(s) to type `Integer'
             `Num t'
               arising from the literal `102'
                            at Bio/Alignment/Blast.hs:102:783-785
    In the first argument of `show', namely `102'
    In the second argument of `(++)', namely `show 102'
    In the second argument of `(++)', namely `" line: " ++ show 102'

Bio/Alignment/Blast.hs:74:0:
    Warning: Pattern match(es) are non-exhaustive
             In the definition of `parse_preamble': Patterns not matched: []

Bio/Alignment/Blast.hs:95:0:
    Warning: Pattern match(es) are non-exhaustive
             In the definition of `parse_match':
                 Patterns not matched:
                     []
                     [_]
                     [_, _]
[ 7 of 22] Compiling Bio.Alignment.BlastXML ( Bio/Alignment/BlastXML.hs, dist/build/Bio/Alignment/BlastXML.o )

Bio/Alignment/BlastXML.hs:26:0:
    Warning: Definition but no type signature for `getFrom'
             Inferred type: getFrom :: [Tag] -> String -> String

Bio/Alignment/BlastXML.hs:34:0:
    Warning: Definition but no type signature for `showSome'
             Inferred type: showSome :: forall a. (Show a) => [a] -> [Char]

Bio/Alignment/BlastXML.hs:81:53:
    Warning: This binding for `_o' shadows an existing binding
             In a case alternative

Bio/Alignment/BlastXML.hs:81:67:
    Warning: This binding for `_c' shadows an existing binding
             In a case alternative

Bio/Alignment/BlastXML.hs:85:29:
    Warning: Defaulting the following constraint(s) to type `Integer'
             `Num a'
               arising from a use of `strand''
                            at Bio/Alignment/BlastXML.hs:85:29-35
             `Read a'
               arising from a use of `read' at Bio/Alignment/BlastXML.hs:85:48-53
    In the first argument of `($)', namely `strand''
    In the first argument of `Frame', namely
        `(strand' $ signum $ read f)'
    In the expression: Frame (strand' $ signum $ read f) (abs $ read f)

Bio/Alignment/BlastXML.hs:86:35:
    Warning: Defaulting the following constraint(s) to type `Integer'
             `Num a'
               arising from a use of `strand''
                            at Bio/Alignment/BlastXML.hs:86:35-41
             `Read a'
               arising from a use of `read' at Bio/Alignment/BlastXML.hs:86:45-50
    In the first argument of `($)', namely `strand''
    In the first argument of `Strands', namely `(strand' $ read h)'
    In the expression: Strands (strand' $ read h) (strand' $ read q)

Bio/Alignment/BlastXML.hs:86:54:
    Warning: Defaulting the following constraint(s) to type `Integer'
             `Num a'
               arising from a use of `strand''
                            at Bio/Alignment/BlastXML.hs:86:54-60
             `Read a'
               arising from a use of `read' at Bio/Alignment/BlastXML.hs:86:64-69
    In the first argument of `($)', namely `strand''
    In the second argument of `Strands', namely `(strand' $ read q)'
    In the expression: Strands (strand' $ read h) (strand' $ read q)

Bio/Alignment/BlastXML.hs:79:49:
    Warning: Pattern match(es) are non-exhaustive
             In a case alternative:
                 Patterns not matched:
                     [] : _
                     [_] : _
                     (_ : ((TagClose _) : _)) : _
                     (_ : ((TagOpen _ _) : _)) : _
                     ...
[ 8 of 22] Compiling Bio.Sequence.GOA ( Bio/Sequence/GOA.hs, dist/build/Bio/Sequence/GOA.o )

Bio/Sequence/GOA.hs:34:14: Warning: Defined but not used: `n'

Bio/Sequence/GOA.hs:52:10:
    Warning: Pattern match(es) are non-exhaustive
             In the definition of `pick':
                 Patterns not matched:
                     []
                     [_]

Bio/Sequence/GOA.hs:53:10:
    Warning: Pattern match(es) are non-exhaustive
             In the definition of `pick'':
                 Patterns not matched:
                     _ []
                     _ [_]
                     _ [_, _]
[ 9 of 22] Compiling Bio.Sequence.Entropy ( Bio/Sequence/Entropy.hs, dist/build/Bio/Sequence/Entropy.o )
[10 of 22] Compiling Bio.Sequence.SeqData ( Bio/Sequence/SeqData.hs, dist/build/Bio/Sequence/SeqData.o )

Bio/Sequence/SeqData.hs:77:0:
    Warning: Pattern match(es) are non-exhaustive
             In the definition of `?': Patterns not matched: Seq _ _ Nothing

Bio/Sequence/SeqData.hs:97:0:
    Warning: Pattern match(es) are non-exhaustive
             In the definition of `seqqual':
                 Patterns not matched: Seq _ _ Nothing
[11 of 22] Compiling Bio.Sequence.Fasta ( Bio/Sequence/Fasta.hs, dist/build/Bio/Sequence/Fasta.o )

Bio/Sequence/Fasta.hs:147:11:
    Warning: This binding for `l' shadows an existing binding
             In a lambda abstraction

Bio/Sequence/Fasta.hs:182:0:
    Warning: Definition but no type signature for `mkSeq'
             Inferred type: mkSeq :: [ByteString] -> Sequence

Bio/Sequence/Fasta.hs:94:6:
    Warning: Pattern match(es) are non-exhaustive
             In the definition of `mkseq':
                 Patterns not matched: (Seq _ _ _) (Seq _ _ Nothing)

Bio/Sequence/Fasta.hs:188:10:
    Warning: Pattern match(es) are non-exhaustive
             In the definition of `f': Patterns not matched: []
[12 of 22] Compiling Bio.Sequence.TwoBit ( Bio/Sequence/TwoBit.hs, dist/build/Bio/Sequence/TwoBit.o )

Bio/Sequence/TwoBit.hs:54:0:
    Warning: No explicit method nor default method for `coarbitrary'
    In the instance declaration for `Arbitrary Word8'

Bio/Sequence/TwoBit.hs:58:0:
    Warning: Defined but not used: `prop_bswap'

Bio/Sequence/TwoBit.hs:61:38:
    Warning: Defined but not used: `version'

Bio/Sequence/TwoBit.hs:61:54:
    Warning: Defined but not used: `reserved'

Bio/Sequence/TwoBit.hs:73:16: Warning: Defined but not used: `m'

Bio/Sequence/TwoBit.hs:73:18: Warning: Defined but not used: `v'

Bio/Sequence/TwoBit.hs:73:22: Warning: Defined but not used: `r'

Bio/Sequence/TwoBit.hs:82:0:
    Warning: Definition but no type signature for `swapEntry'
             Inferred type: swapEntry :: Entry -> Entry

Bio/Sequence/TwoBit.hs:87:6:
    Warning: This binding for `name' shadows an existing binding
             In a pattern binding in
                a 'do' expression

Bio/Sequence/TwoBit.hs:88:6:
    Warning: This binding for `offset' shadows an existing binding
             In a pattern binding in
                a 'do' expression

Bio/Sequence/TwoBit.hs:90:18:
    Warning: This binding for `offset' shadows an existing binding
             In the definition of `put'

Bio/Sequence/TwoBit.hs:99:0:
    Warning: No explicit method nor default method for `put'
    In the instance declaration for `Binary Entries'

Bio/Sequence/TwoBit.hs:121:27:
    Warning: Defined but not used: `reserved2'

Bio/Sequence/TwoBit.hs:128:0:
    Warning: No explicit method nor default method for `put'
    In the instance declaration for `Binary SRBE'

Bio/Sequence/TwoBit.hs:173:22:
    Warning: This binding for `ns' shadows an existing binding
             In the definition of `go'

Bio/Sequence/TwoBit.hs:178:17:
    Warning: This binding for `ns' shadows an existing binding
             In the definition of `go'

Bio/Sequence/TwoBit.hs:198:0:
    Warning: Definition but no type signature for `splits'
             Inferred type: splits :: [Int64] -> B.ByteString -> [B.ByteString]

Bio/Sequence/TwoBit.hs:202:0:
    Warning: Definition but no type signature for `unSRBE'
             Inferred type: unSRBE :: SRBE -> SR

Bio/Sequence/TwoBit.hs:203:0:
    Warning: Definition but no type signature for `unSRLE'
             Inferred type: unSRLE :: SRLE -> SR

Bio/Sequence/TwoBit.hs:206:0: Warning: Defined but not used: `toSR'

Bio/Sequence/TwoBit.hs:206:5: Warning: Defined but not used: `bs'

Bio/Sequence/TwoBit.hs:218:0:
    Warning: Defined but not used: `write2Bit'

Bio/Sequence/TwoBit.hs:222:0:
    Warning: Defined but not used: `hWrite2Bit'
Warning: orphan instances:
  instance Test.QuickCheck.Arbitrary [GHC.Word.Word8] = Bio.Sequence.TwoBit.$f8

[13 of 22] Compiling Bio.Sequence.Phd ( Bio/Sequence/Phd.hs, dist/build/Bio/Sequence/Phd.o )
[14 of 22] Compiling Bio.Sequence.HashWord ( Bio/Sequence/HashWord.lhs, dist/build/Bio/Sequence/HashWord.o )

Bio/Sequence/HashWord.lhs:141:14:
    Warning: Defined but not used: `c1'

Bio/Sequence/HashWord.lhs:141:17:
    Warning: Defined but not used: `c2'

Bio/Sequence/HashWord.lhs:141:21:
    Warning: Defined but not used: `i'

Bio/Sequence/HashWord.lhs:195:0:
    Warning: Definition but no type signature for `k2n''
             Inferred type: k2n' :: forall a a1.
                                    (Integral a, Integral a1) =>
                                    a -> a1 -> [Char]
[15 of 22] Compiling Bio.Alignment.AlignData ( Bio/Alignment/AlignData.hs, dist/build/Bio/Alignment/AlignData.o )

Bio/Alignment/AlignData.hs:57:0:
    Warning: Definition but no type signature for `showalign'
             Inferred type: showalign :: EditList -> [Char]

Bio/Alignment/AlignData.hs:119:0:
    Warning: Definition but no type signature for `on'
             Inferred type: on :: forall t t1 t2.
                                  (t1 -> t1 -> t2) -> (t -> t1) -> t -> t -> t2

Bio/Alignment/AlignData.hs:110:8:
    Warning: Pattern match(es) are non-exhaustive
             In the definition of `mkcol': Patterns not matched: ([], _)
[16 of 22] Compiling Bio.Alignment.Matrices ( Bio/Alignment/Matrices.hs, dist/build/Bio/Alignment/Matrices.o )
[17 of 22] Compiling Bio.Alignment.SAlign ( Bio/Alignment/SAlign.hs, dist/build/Bio/Alignment/SAlign.o )
[18 of 22] Compiling Bio.Alignment.AAlign ( Bio/Alignment/AAlign.hs, dist/build/Bio/Alignment/AAlign.o )

Bio/Alignment/AAlign.hs:40:13:
    Warning: This binding for `minf' shadows an existing binding
             In the definition of `score_select'

Bio/Alignment/AAlign.hs:50:0:
    Warning: Definition but no type signature for `max''
             Inferred type: max' :: forall t t1.
                                    (Ord t) =>
                                    (t, t1) -> (t, t1) -> (t, t1)

Bio/Alignment/AAlign.hs:51:0:
    Warning: Definition but no type signature for `fp'
             Inferred type: fp :: forall t t1.
                                  (Num t) =>
                                  (t, [t1]) -> (t, t1) -> (t, [t1])

Bio/Alignment/AAlign.hs:64:0:
    Warning: Definition but no type signature for `revsnd'
             Inferred type: revsnd :: forall t a. (t, [a]) -> (t, [a])

Bio/Alignment/AAlign.hs:68:13:
    Warning: This binding for `minf' shadows an existing binding
             In the definition of `align_select'
[19 of 22] Compiling Bio.Alignment.QAlign ( Bio/Alignment/QAlign.hs, dist/build/Bio/Alignment/QAlign.o )

Bio/Alignment/QAlign.hs:33:72:
    Warning: Imported from `Bio.Alignment.AlignData' but not used:
               `showalign'

Bio/Alignment/QAlign.hs:91:71:
    Warning: This binding for `x' shadows an existing binding
             In a pattern binding in
                a list comprehension

Bio/Alignment/QAlign.hs:91:85:
    Warning: This binding for `y' shadows an existing binding
             In a pattern binding in
                a list comprehension

Bio/Alignment/QAlign.hs:92:72:
    Warning: This binding for `x' shadows an existing binding
             In a pattern binding in
                a list comprehension

Bio/Alignment/QAlign.hs:92:86:
    Warning: This binding for `y' shadows an existing binding
             In a pattern binding in
                a list comprehension

Bio/Alignment/QAlign.hs:118:13:
    Warning: This binding for `minf' shadows an existing binding
             In the definition of `score_select'

Bio/Alignment/QAlign.hs:154:0:
    Warning: Definition but no type signature for `revsnd'
             Inferred type: revsnd :: forall t a. (t, [a]) -> (t, [a])

Bio/Alignment/QAlign.hs:158:13:
    Warning: This binding for `minf' shadows an existing binding
             In the definition of `align_select'

Bio/Alignment/QAlign.hs:166:0:
    Warning: Definition but no type signature for `snd''
             Inferred type: snd' :: forall t t1 t2 t3. (t, t1, t2, t3) -> t1

Bio/Alignment/QAlign.hs:58:8:
    Warning: Pattern match(es) are non-exhaustive
             In the definition of `mkcol': Patterns not matched: (_, [], _)
[20 of 22] Compiling Bio.Alignment.ACE ( Bio/Alignment/ACE.hs, dist/build/Bio/Alignment/ACE.o )
[21 of 22] Compiling Bio.Sequence     ( Bio/Sequence.hs, dist/build/Bio/Sequence.o )

Bio/Sequence.hs:56:0:
    Warning: Module `Bio.Sequence.Entropy' is imported, but nothing from it is used,
               except perhaps instances visible in `Bio.Sequence.Entropy'
             To suppress this warning, use: import Bio.Sequence.Entropy()
[22 of 22] Compiling Bio.Alignment.Multiple ( Bio/Alignment/Multiple.hs, dist/build/Bio/Alignment/Multiple.o )

Bio/Alignment/Multiple.hs:12:0:
    Warning: Module `Bio.Clustering' is imported, but nothing from it is used,
               except perhaps instances visible in `Bio.Clustering'
             To suppress this warning, use: import Bio.Clustering()

Bio/Alignment/Multiple.hs:24:18:
    Warning: Defined but not used: `x2'

Bio/Alignment/Multiple.hs:24:31:
    Warning: Defined but not used: `y1'

Bio/Alignment/Multiple.hs:26:29:
    Warning: Defined but not used: `y1'

Bio/Alignment/Multiple.hs:30:14:
    Warning: Defined but not used: `x1'

Bio/Alignment/Multiple.hs:31:14:
    Warning: Defined but not used: `x1'

Bio/Alignment/Multiple.hs:31:26:
    Warning: Defined but not used: `y1'
Linking...
/usr/bin/ar q dist/build/libHSbio-0.3.3.1.a dist/build/Bio/Sequence.o dist/build/Bio/Sequence/SeqData.o dist/build/Bio/Sequence/Fasta.o dist/build/Bio/Sequence/TwoBit.o dist/build/Bio/Sequence/Phd.o dist/build/Bio/Sequence/Entropy.o dist/build/Bio/Sequence/HashWord.o dist/build/Bio/Sequence/GOA.o dist/build/Bio/Alignment/BlastData.o dist/build/Bio/Alignment/BlastFlat.o dist/build/Bio/Alignment/Blast.o dist/build/Bio/Alignment/BlastXML.o dist/build/Bio/Alignment/AlignData.o dist/build/Bio/Alignment/Matrices.o dist/build/Bio/Alignment/SAlign.o dist/build/Bio/Alignment/AAlign.o dist/build/Bio/Alignment/QAlign.o dist/build/Bio/Alignment/Multiple.o dist/build/Bio/Alignment/ACE.o dist/build/Bio/Clustering.o dist/build/Bio/Util.o dist/build/Bio/Util/Parsex.o
/usr/bin/ar: creating dist/build/libHSbio-0.3.3.1.a
/usr/bin/ld -x -r -o dist/build/HSbio-0.3.3.1.o.tmp dist/build/Bio/Sequence.o dist/build/Bio/Sequence/SeqData.o dist/build/Bio/Sequence/Fasta.o dist/build/Bio/Sequence/TwoBit.o dist/build/Bio/Sequence/Phd.o dist/build/Bio/Sequence/Entropy.o dist/build/Bio/Sequence/HashWord.o dist/build/Bio/Sequence/GOA.o dist/build/Bio/Alignment/BlastData.o dist/build/Bio/Alignment/BlastFlat.o dist/build/Bio/Alignment/Blast.o dist/build/Bio/Alignment/BlastXML.o dist/build/Bio/Alignment/AlignData.o dist/build/Bio/Alignment/Matrices.o dist/build/Bio/Alignment/SAlign.o dist/build/Bio/Alignment/AAlign.o dist/build/Bio/Alignment/QAlign.o dist/build/Bio/Alignment/Multiple.o dist/build/Bio/Alignment/ACE.o dist/build/Bio/Clustering.o dist/build/Bio/Util.o dist/build/Bio/Util/Parsex.o

*** setup haddock

Creating dist/doc/html/bio (and its parents)
Preprocessing library bio-0.3.3.1...
Running hscolour for bio-0.3.3.1...
Creating dist/doc/html/bio/src (and its parents)
/usr/local/bin/HsColour -print-css -odist/doc/html/bio/src/hscolour.css
/usr/local/bin/HsColour -css -anchor -odist/doc/html/bio/src/Bio-Sequence.html Bio/Sequence.hs
/usr/local/bin/HsColour -css -anchor -odist/doc/html/bio/src/Bio-Sequence-SeqData.html Bio/Sequence/SeqData.hs
/usr/local/bin/HsColour -css -anchor -odist/doc/html/bio/src/Bio-Sequence-Fasta.html Bio/Sequence/Fasta.hs
/usr/local/bin/HsColour -css -anchor -odist/doc/html/bio/src/Bio-Sequence-TwoBit.html Bio/Sequence/TwoBit.hs
/usr/local/bin/HsColour -css -anchor -odist/doc/html/bio/src/Bio-Sequence-Phd.html Bio/Sequence/Phd.hs
/usr/local/bin/HsColour -css -anchor -odist/doc/html/bio/src/Bio-Sequence-Entropy.html Bio/Sequence/Entropy.hs
/usr/local/bin/HsColour -css -anchor -odist/doc/html/bio/src/Bio-Sequence-HashWord.html Bio/Sequence/HashWord.lhs
/usr/local/bin/HsColour -css -anchor -odist/doc/html/bio/src/Bio-Sequence-GOA.html Bio/Sequence/GOA.hs
/usr/local/bin/HsColour -css -anchor -odist/doc/html/bio/src/Bio-Alignment-BlastData.html Bio/Alignment/BlastData.hs
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/usr/local/bin/HsColour -css -anchor -odist/doc/html/bio/src/Bio-Alignment-Blast.html Bio/Alignment/Blast.hs
/usr/local/bin/HsColour -css -anchor -odist/doc/html/bio/src/Bio-Alignment-BlastXML.html Bio/Alignment/BlastXML.hs
/usr/local/bin/HsColour -css -anchor -odist/doc/html/bio/src/Bio-Alignment-AlignData.html Bio/Alignment/AlignData.hs
/usr/local/bin/HsColour -css -anchor -odist/doc/html/bio/src/Bio-Alignment-Matrices.html Bio/Alignment/Matrices.hs
/usr/local/bin/HsColour -css -anchor -odist/doc/html/bio/src/Bio-Alignment-SAlign.html Bio/Alignment/SAlign.hs
/usr/local/bin/HsColour -css -anchor -odist/doc/html/bio/src/Bio-Alignment-AAlign.html Bio/Alignment/AAlign.hs
/usr/local/bin/HsColour -css -anchor -odist/doc/html/bio/src/Bio-Alignment-QAlign.html Bio/Alignment/QAlign.hs
/usr/local/bin/HsColour -css -anchor -odist/doc/html/bio/src/Bio-Alignment-Multiple.html Bio/Alignment/Multiple.hs
/usr/local/bin/HsColour -css -anchor -odist/doc/html/bio/src/Bio-Alignment-ACE.html Bio/Alignment/ACE.hs
/usr/local/bin/HsColour -css -anchor -odist/doc/html/bio/src/Bio-Clustering.html Bio/Clustering.hs
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Creating dist/build/tmp (and its parents)
Creating dist/doc/html/bio (and its parents)
Preprocessing library bio-0.3.3.1...
Running Haddock for bio-0.3.3.1...
/usr/local/bin/haddock --use-contents=http://hackage.haskell.org/cgi-bin/hackage-scripts/package/bio-0.3.3.1 --ghc-version
/usr/local/bin/ghc --print-libdir
Creating dist/build (and its parents)
Creating dist/build/autogen (and its parents)
Preprocessing library bio-0.3.3.1...
/usr/local/bin/haddock --use-contents=http://hackage.haskell.org/cgi-bin/hackage-scripts/package/bio-0.3.3.1 --html --odir=dist/doc/html/bio --title=bio-0.3.3.1: A bioinformatics library --dump-interface=dist/doc/html/bio/bio.haddock --prologue=dist/bio-0.3.3.1-haddock-prolog5752.txt --optghc=-package-name --optghc=bio-0.3.3.1 --source-module=src/%{MODULE/./-}.html --source-entity=src/%{MODULE/./-}.html#%{NAME} --read-interface=http://hackage.haskell.org/packages/archive/base/3.0.1.0/doc/html,/usr/local/share/doc/ghc/libraries/base/base.haddock --read-interface=http://hackage.haskell.org/packages/archive/QuickCheck/1.1.0.0/doc/html,/usr/local/tmp/archive/install/share/doc/QuickCheck-1.1.0.0/html/QuickCheck.haddock --read-interface=http://hackage.haskell.org/packages/archive/binary/0.4.2/doc/html,/usr/local/tmp/archive/install/share/doc/binary-0.4.2/html/binary.haddock --read-interface=http://hackage.haskell.org/packages/archive/tagsoup/0.6/doc/html,/usr/local/tmp/archive/install/share/doc/tagsoup-0.6/html/tagsoup.haddock --read-interface=http://hackage.haskell.org/packages/archive/bytestring/0.9.1.0/doc/html,/usr/local/tmp/archive/install/share/doc/bytestring-0.9.1.0/html/bytestring.haddock --read-interface=http://hackage.haskell.org/packages/archive/containers/0.1.0.1/doc/html,/usr/local/share/doc/ghc/libraries/containers/containers.haddock --read-interface=http://hackage.haskell.org/packages/archive/array/0.1.0.0/doc/html,/usr/local/share/doc/ghc/libraries/array/array.haddock --read-interface=http://hackage.haskell.org/packages/archive/interlude/0.1.1/doc/html,/usr/local/tmp/archive/install/share/doc/interlude-0.1.1/html/interlude.haddock --read-interface=http://hackage.haskell.org/packages/archive/parallel/1.0.0.1/doc/html,/usr/local/tmp/archive/install/share/doc/parallel-1.0.0.1/html/parallel.haddock --read-interface=http://hackage.haskell.org/packages/archive/parsec/3.0.0/doc/html,/usr/local/tmp/archive/install/share/doc/parsec-3.0.0/html/parsec.haddock --use-contents=http://hackage.haskell.org/cgi-bin/hackage-scripts/package/bio-0.3.3.1 -B/usr/local/lib/ghc-6.8.2 --optghc=-hide-all-packages --optghc=-package --optghc=base-3.0.1.0 --optghc=-package --optghc=QuickCheck-1.1.0.0 --optghc=-package --optghc=binary-0.4.2 --optghc=-package --optghc=tagsoup-0.6 --optghc=-package --optghc=bytestring-0.9.1.0 --optghc=-package --optghc=containers-0.1.0.1 --optghc=-package --optghc=array-0.1.0.0 --optghc=-package --optghc=interlude-0.1.1 --optghc=-package --optghc=parallel-1.0.0.1 --optghc=-package --optghc=parsec-3.0.0 --optghc=-i --optghc=-Wall --optghc=-O2 --optghc=-fexcess-precision --optghc=-funbox-strict-fields --optghc=-auto-all --optghc=-idist/build/autogen --optghc=-i. --optghc=-idist/build --optghc=-odir --optghc=dist/build --optghc=-hidir --optghc=dist/build --optghc=-XCPP --optghc=-XParallelListComp Bio.Sequence Bio.Sequence.SeqData Bio.Sequence.Fasta Bio.Sequence.TwoBit Bio.Sequence.Phd Bio.Sequence.Entropy Bio.Sequence.HashWord Bio.Sequence.GOA Bio.Alignment.BlastData Bio.Alignment.BlastFlat Bio.Alignment.Blast Bio.Alignment.BlastXML Bio.Alignment.AlignData Bio.Alignment.Matrices Bio.Alignment.SAlign Bio.Alignment.AAlign Bio.Alignment.QAlign Bio.Alignment.Multiple Bio.Alignment.ACE Bio.Clustering Bio.Util Bio.Util.Parsex

Bio/Util.hs:13:0:
    Warning: Definition but no type signature for `Bio.Util.lines'
             Inferred type: Bio.Util.lines :: B.ByteString -> [B.ByteString]

Bio/Util.hs:15:0:
    Warning: Definition but no type signature for `mylines'
             Inferred type: mylines :: B.ByteString -> [B.ByteString]

Bio/Alignment/Blast.hs:39:0:
    Warning: Definition but no type signature for `str_query'
             Inferred type: str_query :: ByteString

Bio/Alignment/Blast.hs:40:0:
    Warning: Definition but no type signature for `str_gt'
             Inferred type: str_gt :: ByteString

Bio/Alignment/Blast.hs:41:0:
    Warning: Definition but no type signature for `str_score'
             Inferred type: str_score :: ByteString

Bio/Alignment/Blast.hs:42:0:
    Warning: Definition but no type signature for `str_refer'
             Inferred type: str_refer :: ByteString

Bio/Alignment/Blast.hs:43:0:
    Warning: Definition but no type signature for `str_datab'
             Inferred type: str_datab :: ByteString

Bio/Alignment/Blast.hs:44:0:
    Warning: Definition but no type signature for `str_search'
             Inferred type: str_search :: ByteString

Bio/Alignment/Blast.hs:74:0:
    Warning: Definition but no type signature for `parse_preamble'
             Inferred type: parse_preamble :: [ByteString] -> BlastResult

Bio/Alignment/Blast.hs:84:0:
    Warning: Definition but no type signature for `parse_query'
             Inferred type: parse_query :: [ByteString] -> BlastRecord

Bio/Alignment/Blast.hs:86:272:
    Warning: Defaulting the following constraint(s) to type `Integer'
             `Num t'
               arising from the literal `86' at Bio/Alignment/Blast.hs:86:272-273
    In the first argument of `show', namely `86'
    In the second argument of `(++)', namely `show 86'
    In the second argument of `(++)', namely `" line: " ++ show 86'

Bio/Alignment/Blast.hs:86:411:
    Warning: Defaulting the following constraint(s) to type `Integer'
             `Num t'
               arising from the literal `86' at Bio/Alignment/Blast.hs:86:411-412
    In the first argument of `show', namely `86'
    In the second argument of `(++)', namely `show 86'
    In the second argument of `(++)', namely `" line: " ++ show 86'

Bio/Alignment/Blast.hs:90:0:
    Warning: Definition but no type signature for `parse_hit'
             Inferred type: parse_hit :: [ByteString] -> BlastHit

Bio/Alignment/Blast.hs:95:0:
    Warning: Definition but no type signature for `parse_match'
             Inferred type: parse_match :: [ByteString] -> BlastMatch

Bio/Alignment/Blast.hs:99:252:
    Warning: Defaulting the following constraint(s) to type `Integer'
             `Num t'
               arising from the literal `99' at Bio/Alignment/Blast.hs:99:252-253
    In the first argument of `show', namely `99'
    In the second argument of `(++)', namely `show 99'
    In the second argument of `(++)', namely `" line: " ++ show 99'

Bio/Alignment/Blast.hs:99:391:
    Warning: Defaulting the following constraint(s) to type `Integer'
             `Num t'
               arising from the literal `99' at Bio/Alignment/Blast.hs:99:391-392
    In the first argument of `show', namely `99'
    In the second argument of `(++)', namely `show 99'
    In the second argument of `(++)', namely `" line: " ++ show 99'

Bio/Alignment/Blast.hs:100:253:
    Warning: Defaulting the following constraint(s) to type `Integer'
             `Num t'
               arising from the literal `100'
                            at Bio/Alignment/Blast.hs:100:253-255
    In the first argument of `show', namely `100'
    In the second argument of `(++)', namely `show 100'
    In the second argument of `(++)', namely `" line: " ++ show 100'

Bio/Alignment/Blast.hs:100:393:
    Warning: Defaulting the following constraint(s) to type `Integer'
             `Num t'
               arising from the literal `100'
                            at Bio/Alignment/Blast.hs:100:393-395
    In the first argument of `show', namely `100'
    In the second argument of `(++)', namely `show 100'
    In the second argument of `(++)', namely `" line: " ++ show 100'

Bio/Alignment/Blast.hs:102:260:
    Warning: Defaulting the following constraint(s) to type `Integer'
             `Num t'
               arising from the literal `102'
                            at Bio/Alignment/Blast.hs:102:260-262
    In the first argument of `show', namely `102'
    In the second argument of `(++)', namely `show 102'
    In the second argument of `(++)', namely `" line: " ++ show 102'

Bio/Alignment/Blast.hs:102:400:
    Warning: Defaulting the following constraint(s) to type `Integer'
             `Num t'
               arising from the literal `102'
                            at Bio/Alignment/Blast.hs:102:400-402
    In the first argument of `show', namely `102'
    In the second argument of `(++)', namely `show 102'
    In the second argument of `(++)', namely `" line: " ++ show 102'

Bio/Alignment/Blast.hs:102:643:
    Warning: Defaulting the following constraint(s) to type `Integer'
             `Num t'
               arising from the literal `102'
                            at Bio/Alignment/Blast.hs:102:643-645
    In the first argument of `show', namely `102'
    In the second argument of `(++)', namely `show 102'
    In the second argument of `(++)', namely `" line: " ++ show 102'

Bio/Alignment/Blast.hs:102:783:
    Warning: Defaulting the following constraint(s) to type `Integer'
             `Num t'
               arising from the literal `102'
                            at Bio/Alignment/Blast.hs:102:783-785
    In the first argument of `show', namely `102'
    In the second argument of `(++)', namely `show 102'
    In the second argument of `(++)', namely `" line: " ++ show 102'

Bio/Alignment/BlastXML.hs:26:0:
    Warning: Definition but no type signature for `getFrom'
             Inferred type: getFrom :: [Tag] -> String -> String

Bio/Alignment/BlastXML.hs:34:0:
    Warning: Definition but no type signature for `showSome'
             Inferred type: showSome :: forall a. (Show a) => [a] -> [Char]

Bio/Alignment/BlastXML.hs:81:53:
    Warning: This binding for `_o' shadows an existing binding
             In a case alternative

Bio/Alignment/BlastXML.hs:81:67:
    Warning: This binding for `_c' shadows an existing binding
             In a case alternative

Bio/Alignment/BlastXML.hs:85:29:
    Warning: Defaulting the following constraint(s) to type `Integer'
             `Num a'
               arising from a use of `strand''
                            at Bio/Alignment/BlastXML.hs:85:29-35
             `Read a'
               arising from a use of `read' at Bio/Alignment/BlastXML.hs:85:48-53
    In the first argument of `($)', namely `strand''
    In the first argument of `Frame', namely
        `(strand' $ signum $ read f)'
    In the expression: Frame (strand' $ signum $ read f) (abs $ read f)

Bio/Alignment/BlastXML.hs:86:35:
    Warning: Defaulting the following constraint(s) to type `Integer'
             `Num a'
               arising from a use of `strand''
                            at Bio/Alignment/BlastXML.hs:86:35-41
             `Read a'
               arising from a use of `read' at Bio/Alignment/BlastXML.hs:86:45-50
    In the first argument of `($)', namely `strand''
    In the first argument of `Strands', namely `(strand' $ read h)'
    In the expression: Strands (strand' $ read h) (strand' $ read q)

Bio/Alignment/BlastXML.hs:86:54:
    Warning: Defaulting the following constraint(s) to type `Integer'
             `Num a'
               arising from a use of `strand''
                            at Bio/Alignment/BlastXML.hs:86:54-60
             `Read a'
               arising from a use of `read' at Bio/Alignment/BlastXML.hs:86:64-69
    In the first argument of `($)', namely `strand''
    In the second argument of `Strands', namely `(strand' $ read q)'
    In the expression: Strands (strand' $ read h) (strand' $ read q)

Bio/Sequence/GOA.hs:34:14: Warning: Defined but not used: `n'

Bio/Sequence/Fasta.hs:147:11:
    Warning: This binding for `l' shadows an existing binding
             In a lambda abstraction

Bio/Sequence/Fasta.hs:182:0:
    Warning: Definition but no type signature for `mkSeq'
             Inferred type: mkSeq :: [ByteString] -> Sequence

Bio/Sequence/TwoBit.hs:54:0:
    Warning: No explicit method nor default method for `coarbitrary'
    In the instance declaration for `Arbitrary Word8'

Bio/Sequence/TwoBit.hs:58:0:
    Warning: Defined but not used: `prop_bswap'

Bio/Sequence/TwoBit.hs:61:38:
    Warning: Defined but not used: `version'

Bio/Sequence/TwoBit.hs:61:54:
    Warning: Defined but not used: `reserved'

Bio/Sequence/TwoBit.hs:73:16: Warning: Defined but not used: `m'

Bio/Sequence/TwoBit.hs:73:18: Warning: Defined but not used: `v'

Bio/Sequence/TwoBit.hs:73:22: Warning: Defined but not used: `r'

Bio/Sequence/TwoBit.hs:82:0:
    Warning: Definition but no type signature for `swapEntry'
             Inferred type: swapEntry :: Entry -> Entry

Bio/Sequence/TwoBit.hs:87:6:
    Warning: This binding for `name' shadows an existing binding
             In a pattern binding in
                a 'do' expression

Bio/Sequence/TwoBit.hs:88:6:
    Warning: This binding for `offset' shadows an existing binding
             In a pattern binding in
                a 'do' expression

Bio/Sequence/TwoBit.hs:90:18:
    Warning: This binding for `offset' shadows an existing binding
             In the definition of `put'

Bio/Sequence/TwoBit.hs:99:0:
    Warning: No explicit method nor default method for `put'
    In the instance declaration for `Binary Entries'

Bio/Sequence/TwoBit.hs:121:27:
    Warning: Defined but not used: `reserved2'

Bio/Sequence/TwoBit.hs:128:0:
    Warning: No explicit method nor default method for `put'
    In the instance declaration for `Binary SRBE'

Bio/Sequence/TwoBit.hs:173:22:
    Warning: This binding for `ns' shadows an existing binding
             In the definition of `go'

Bio/Sequence/TwoBit.hs:178:17:
    Warning: This binding for `ns' shadows an existing binding
             In the definition of `go'

Bio/Sequence/TwoBit.hs:198:0:
    Warning: Definition but no type signature for `splits'
             Inferred type: splits :: [Int64] -> B.ByteString -> [B.ByteString]

Bio/Sequence/TwoBit.hs:202:0:
    Warning: Definition but no type signature for `unSRBE'
             Inferred type: unSRBE :: SRBE -> SR

Bio/Sequence/TwoBit.hs:203:0:
    Warning: Definition but no type signature for `unSRLE'
             Inferred type: unSRLE :: SRLE -> SR

Bio/Sequence/TwoBit.hs:206:0: Warning: Defined but not used: `toSR'

Bio/Sequence/TwoBit.hs:206:5: Warning: Defined but not used: `bs'

Bio/Sequence/TwoBit.hs:218:0:
    Warning: Defined but not used: `write2Bit'

Bio/Sequence/TwoBit.hs:222:0:
    Warning: Defined but not used: `hWrite2Bit'

Bio/Sequence/HashWord.lhs:141:14:
    Warning: Defined but not used: `c1'

Bio/Sequence/HashWord.lhs:141:17:
    Warning: Defined but not used: `c2'

Bio/Sequence/HashWord.lhs:141:21:
    Warning: Defined but not used: `i'

Bio/Sequence/HashWord.lhs:195:0:
    Warning: Definition but no type signature for `k2n''
             Inferred type: k2n' :: forall a a1.
                                    (Integral a, Integral a1) =>
                                    a -> a1 -> [Char]

Bio/Alignment/AlignData.hs:57:0:
    Warning: Definition but no type signature for `showalign'
             Inferred type: showalign :: EditList -> [Char]

Bio/Alignment/AlignData.hs:119:0:
    Warning: Definition but no type signature for `on'
             Inferred type: on :: forall t t1 t2.
                                  (t1 -> t1 -> t2) -> (t -> t1) -> t -> t -> t2

Bio/Alignment/AAlign.hs:40:13:
    Warning: This binding for `minf' shadows an existing binding
             In the definition of `score_select'

Bio/Alignment/AAlign.hs:50:0:
    Warning: Definition but no type signature for `max''
             Inferred type: max' :: forall t t1.
                                    (Ord t) =>
                                    (t, t1) -> (t, t1) -> (t, t1)

Bio/Alignment/AAlign.hs:51:0:
    Warning: Definition but no type signature for `fp'
             Inferred type: fp :: forall t t1.
                                  (Num t) =>
                                  (t, [t1]) -> (t, t1) -> (t, [t1])

Bio/Alignment/AAlign.hs:64:0:
    Warning: Definition but no type signature for `revsnd'
             Inferred type: revsnd :: forall t a. (t, [a]) -> (t, [a])

Bio/Alignment/AAlign.hs:68:13:
    Warning: This binding for `minf' shadows an existing binding
             In the definition of `align_select'

Bio/Alignment/QAlign.hs:33:72:
    Warning: Imported from `Bio.Alignment.AlignData' but not used:
               `showalign'

Bio/Alignment/QAlign.hs:91:71:
    Warning: This binding for `x' shadows an existing binding
             In a pattern binding in
                a list comprehension

Bio/Alignment/QAlign.hs:91:85:
    Warning: This binding for `y' shadows an existing binding
             In a pattern binding in
                a list comprehension

Bio/Alignment/QAlign.hs:92:72:
    Warning: This binding for `x' shadows an existing binding
             In a pattern binding in
                a list comprehension

Bio/Alignment/QAlign.hs:92:86:
    Warning: This binding for `y' shadows an existing binding
             In a pattern binding in
                a list comprehension

Bio/Alignment/QAlign.hs:118:13:
    Warning: This binding for `minf' shadows an existing binding
             In the definition of `score_select'

Bio/Alignment/QAlign.hs:154:0:
    Warning: Definition but no type signature for `revsnd'
             Inferred type: revsnd :: forall t a. (t, [a]) -> (t, [a])

Bio/Alignment/QAlign.hs:158:13:
    Warning: This binding for `minf' shadows an existing binding
             In the definition of `align_select'

Bio/Alignment/QAlign.hs:166:0:
    Warning: Definition but no type signature for `snd''
             Inferred type: snd' :: forall t t1 t2 t3. (t, t1, t2, t3) -> t1

Bio/Alignment/ACE.hs:169:0: parse error in doc string
haddock: Failed to check module: Bio.Alignment.ACE