*** setup configure

Configuring bio-0.3.3...
Dependency QuickCheck <2: using QuickCheck-1.2.0.0
Dependency array -any: using array-0.2.0.0
Dependency base >3: using base-4.1.0.0
Dependency binary -any: using binary-0.5.0.1
Dependency bytestring -any: using bytestring-0.9.1.4
Dependency containers -any: using containers-0.2.0.1
Dependency interlude -any: using interlude-0.1.1
Dependency parallel -any: using parallel-1.1.0.1
Dependency parsec -any: using parsec-3.0.0
Dependency tagsoup >=0.5: using tagsoup-0.6
Using Cabal-1.7.0 compiled by ghc-6.10
Using compiler: ghc-6.10.2
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/ghc-6.10.2
Private binaries installed in: /usr/local/tmp/archive/install/libexec
Data files installed in: /usr/local/tmp/archive/install/share/bio-0.3.3
Documentation installed in: /usr/local/tmp/archive/install/share/doc/bio-0.3.3
Using alex version 2.2 found on system at: /usr/bin/alex
Using ar found on system at: /usr/bin/ar
Using c2hs version 0.16.0 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 gcc version 4.3.3 found on system at: /usr/bin/gcc
Using ghc version 6.10.2 found on system at: /usr/local/bin/ghc
Using ghc-pkg version 6.10.2 found on system at: /usr/local/bin/ghc-pkg
Using greencard found on system at:
/usr/local/tmp/archive/install/bin/greencard
Using haddock version 2.4.2 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 0.67 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 lhc found
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
/usr/bin/gcc /tmp/29591.c -o /tmp/29591 -D__GLASGOW_HASKELL__=610 -I. -I/usr/local/tmp/archive/install/lib/network-2.2.1.4/ghc-6.10.2/include -I/usr/local/tmp/archive/install/lib/interlude-0.1.1/ghc-6.10.2/include -I/usr/local/lib/ghc-6.10.2/bytestring-0.9.1.4/include -I/usr/local/lib/ghc-6.10.2/old-time-1.0.0.2/include -I/usr/local/lib/ghc-6.10.2/base-4.1.0.0/include -I/usr/local/lib/ghc-6.10.2/include -IPAPI_INCLUDE_DIR

*** setup build

Creating dist/build (and its parents)
Creating dist/build/autogen (and its parents)
Preprocessing library bio-0.3.3...
Building bio-0.3.3...
Building library...
Creating dist/build (and its parents)
/usr/local/bin/ghc -package-name bio-0.3.3 --make -hide-all-packages -i -idist/build -i. -idist/build/autogen -Idist/build/autogen -Idist/build -optP-include -optPdist/build/autogen/cabal_macros.h -odir dist/build -hidir dist/build -stubdir dist/build -package QuickCheck-1.2.0.0 -package array-0.2.0.0 -package base-4.1.0.0 -package binary-0.5.0.1 -package bytestring-0.9.1.4 -package containers-0.2.0.1 -package interlude-0.1.1 -package parallel-1.1.0.1 -package parsec-3.0.0 -package tagsoup-0.6 -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 )
[ 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:79:49:
    Warning: Pattern match(es) are non-exhaustive
             In a case alternative:
                 Patterns not matched:
                     [] : _
                     [_] : _
                     (_ : ((TagOpen _ _) : _)) : _
                     (_ : ((TagClose _) : _)) : _
                     ...

Bio/Alignment/BlastXML.hs:81:53:
    Warning: This binding for `_o' shadows the existing binding
               bound at Bio/Alignment/BlastXML.hs:79:27
             In a case alternative

Bio/Alignment/BlastXML.hs:81:67:
    Warning: This binding for `_c' shadows the existing binding
               bound at Bio/Alignment/BlastXML.hs:79:41
             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)
[20 of 22] Compiling Bio.Alignment.ACE ( Bio/Alignment/ACE.hs, dist/build/Bio/Alignment/ACE.o )

Bio/Alignment/ACE.hs:79:0:
    Warning: Definition but no type signature for `uw'
             Inferred type: uw :: [ByteString] -> [Char]

Bio/Alignment/ACE.hs:90:10:
    Warning: This binding for `pred' shadows the existing binding
               imported from Interlude at Bio/Alignment/ACE.hs:(35,0)-(37,24)
             In the binding group for: sho, pos, pred

Bio/Alignment/ACE.hs:117:0:
    Warning: Definition but no type signature for `blank'
             Inferred type: blank :: Text.Parsec.Prim.ParsecT
                                       [(SourcePos, ACE)]
                                       ()
                                       mtl-1.1.0.2:Control.Monad.Identity.Identity
                                       ()

Bio/Alignment/ACE.hs:128:13:
    Warning: This binding for `str' shadows the existing binding
               bound at Bio/Alignment/ACE.hs:127:14
             In the definition of `go'

Bio/Alignment/ACE.hs:130:13:
    Warning: This binding for `str' shadows the existing binding
               bound at Bio/Alignment/ACE.hs:127:14
             In the definition of `go'

Bio/Alignment/ACE.hs:165:21:
    Warning: This binding for `as' shadows the existing binding
               defined at Bio/Alignment/ACE.hs:112:0
             In a pattern binding in
                a 'do' expression

Bio/Alignment/ACE.hs:186:16:
    Warning: Pattern match(es) are non-exhaustive
             In a case alternative:
                 Patterns not matched:
                     []
                     (ghc-prim:GHC.Types.C# #x) : _ with #x `notElem` ['U', 'C']
                     (ghc-prim:GHC.Types.C# 'U') : (_ : _)
                     (ghc-prim:GHC.Types.C# 'C') : (_ : _)

Bio/Alignment/ACE.hs:187:23:
    Warning: Pattern match(es) are non-exhaustive
             In a case alternative: Patterns not matched: Nothing

Bio/Alignment/ACE.hs:192:23:
    Warning: Pattern match(es) are non-exhaustive
             In a case alternative: Patterns not matched: Nothing

Bio/Alignment/ACE.hs:237:38:
    Warning: This binding for `bs' shadows the existing binding
               defined at Bio/Alignment/ACE.hs:190:0
             In a case alternative

Bio/Alignment/ACE.hs:237:49:
    Warning: This binding for `compl' shadows the existing binding
               imported from Bio.Sequence.SeqData at Bio/Alignment/ACE.hs:39:0-26
             In a case alternative
Linking...
/usr/bin/ar q dist/build/libHSbio-0.3.3.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.a
/usr/bin/ld -x -r -o dist/build/HSbio-0.3.3.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

Running Haddock for bio-0.3.3...
/usr/local/bin/haddock --use-contents=http://hackage.haskell.org/package/bio-0.3.3 --ghc-version
Creating dist/build (and its parents)
Creating dist/build/autogen (and its parents)
Preprocessing library bio-0.3.3...
Running hscolour for bio-0.3.3...
Creating dist/doc/html/bio (and its parents)
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
/usr/local/bin/HsColour -css -anchor -odist/doc/html/bio/src/Bio-Alignment-BlastFlat.html Bio/Alignment/BlastFlat.hs
/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
/usr/local/bin/HsColour -css -anchor -odist/doc/html/bio/src/Bio-Util.html Bio/Util.hs
/usr/local/bin/HsColour -css -anchor -odist/doc/html/bio/src/Bio-Util-Parsex.html Bio/Util/Parsex.hs
Warning: The documentation for the following packages are not installed. No
links will be generated to these packages: rts-1.0
/usr/local/bin/ghc --print-libdir
/usr/local/bin/ghc -E -cpp -x hs -optP-include -optPdist/build/autogen/cabal_macros.h -o dist/build/tmp29684/Bio/Sequence.hs Bio/Sequence.hs -Dlinux_BUILD_OS -Dlinux_HOST_OS -Di386_BUILD_ARCH -Di386_HOST_ARCH -D__GLASGOW_HASKELL__=610
/usr/local/bin/ghc -E -cpp -x hs -optP-include -optPdist/build/autogen/cabal_macros.h -o dist/build/tmp29684/Bio/Sequence/SeqData.hs Bio/Sequence/SeqData.hs -Dlinux_BUILD_OS -Dlinux_HOST_OS -Di386_BUILD_ARCH -Di386_HOST_ARCH -D__GLASGOW_HASKELL__=610
/usr/local/bin/ghc -E -cpp -x hs -optP-include -optPdist/build/autogen/cabal_macros.h -o dist/build/tmp29684/Bio/Sequence/Fasta.hs Bio/Sequence/Fasta.hs -Dlinux_BUILD_OS -Dlinux_HOST_OS -Di386_BUILD_ARCH -Di386_HOST_ARCH -D__GLASGOW_HASKELL__=610
/usr/local/bin/ghc -E -cpp -x hs -optP-include -optPdist/build/autogen/cabal_macros.h -o dist/build/tmp29684/Bio/Sequence/TwoBit.hs Bio/Sequence/TwoBit.hs -Dlinux_BUILD_OS -Dlinux_HOST_OS -Di386_BUILD_ARCH -Di386_HOST_ARCH -D__GLASGOW_HASKELL__=610
/usr/local/bin/ghc -E -cpp -x hs -optP-include -optPdist/build/autogen/cabal_macros.h -o dist/build/tmp29684/Bio/Sequence/Phd.hs Bio/Sequence/Phd.hs -Dlinux_BUILD_OS -Dlinux_HOST_OS -Di386_BUILD_ARCH -Di386_HOST_ARCH -D__GLASGOW_HASKELL__=610
/usr/local/bin/ghc -E -cpp -x hs -optP-include -optPdist/build/autogen/cabal_macros.h -o dist/build/tmp29684/Bio/Sequence/Entropy.hs Bio/Sequence/Entropy.hs -Dlinux_BUILD_OS -Dlinux_HOST_OS -Di386_BUILD_ARCH -Di386_HOST_ARCH -D__GLASGOW_HASKELL__=610
/usr/local/bin/ghc -E -cpp -x hs -optP-include -optPdist/build/autogen/cabal_macros.h -o dist/build/tmp29684/Bio/Sequence/HashWord.lhs Bio/Sequence/HashWord.lhs -Dlinux_BUILD_OS -Dlinux_HOST_OS -Di386_BUILD_ARCH -Di386_HOST_ARCH -D__GLASGOW_HASKELL__=610
/usr/local/bin/ghc -E -cpp -x hs -optP-include -optPdist/build/autogen/cabal_macros.h -o dist/build/tmp29684/Bio/Sequence/GOA.hs Bio/Sequence/GOA.hs -Dlinux_BUILD_OS -Dlinux_HOST_OS -Di386_BUILD_ARCH -Di386_HOST_ARCH -D__GLASGOW_HASKELL__=610
/usr/local/bin/ghc -E -cpp -x hs -optP-include -optPdist/build/autogen/cabal_macros.h -o dist/build/tmp29684/Bio/Alignment/BlastData.hs Bio/Alignment/BlastData.hs -Dlinux_BUILD_OS -Dlinux_HOST_OS -Di386_BUILD_ARCH -Di386_HOST_ARCH -D__GLASGOW_HASKELL__=610
/usr/local/bin/ghc -E -cpp -x hs -optP-include -optPdist/build/autogen/cabal_macros.h -o dist/build/tmp29684/Bio/Alignment/BlastFlat.hs Bio/Alignment/BlastFlat.hs -Dlinux_BUILD_OS -Dlinux_HOST_OS -Di386_BUILD_ARCH -Di386_HOST_ARCH -D__GLASGOW_HASKELL__=610
/usr/local/bin/ghc -E -cpp -x hs -optP-include -optPdist/build/autogen/cabal_macros.h -o dist/build/tmp29684/Bio/Alignment/Blast.hs Bio/Alignment/Blast.hs -Dlinux_BUILD_OS -Dlinux_HOST_OS -Di386_BUILD_ARCH -Di386_HOST_ARCH -D__GLASGOW_HASKELL__=610
/usr/local/bin/ghc -E -cpp -x hs -optP-include -optPdist/build/autogen/cabal_macros.h -o dist/build/tmp29684/Bio/Alignment/BlastXML.hs Bio/Alignment/BlastXML.hs -Dlinux_BUILD_OS -Dlinux_HOST_OS -Di386_BUILD_ARCH -Di386_HOST_ARCH -D__GLASGOW_HASKELL__=610
/usr/local/bin/ghc -E -cpp -x hs -optP-include -optPdist/build/autogen/cabal_macros.h -o dist/build/tmp29684/Bio/Alignment/AlignData.hs Bio/Alignment/AlignData.hs -Dlinux_BUILD_OS -Dlinux_HOST_OS -Di386_BUILD_ARCH -Di386_HOST_ARCH -D__GLASGOW_HASKELL__=610
/usr/local/bin/ghc -E -cpp -x hs -optP-include -optPdist/build/autogen/cabal_macros.h -o dist/build/tmp29684/Bio/Alignment/Matrices.hs Bio/Alignment/Matrices.hs -Dlinux_BUILD_OS -Dlinux_HOST_OS -Di386_BUILD_ARCH -Di386_HOST_ARCH -D__GLASGOW_HASKELL__=610
/usr/local/bin/ghc -E -cpp -x hs -optP-include -optPdist/build/autogen/cabal_macros.h -o dist/build/tmp29684/Bio/Alignment/SAlign.hs Bio/Alignment/SAlign.hs -Dlinux_BUILD_OS -Dlinux_HOST_OS -Di386_BUILD_ARCH -Di386_HOST_ARCH -D__GLASGOW_HASKELL__=610
/usr/local/bin/ghc -E -cpp -x hs -optP-include -optPdist/build/autogen/cabal_macros.h -o dist/build/tmp29684/Bio/Alignment/AAlign.hs Bio/Alignment/AAlign.hs -Dlinux_BUILD_OS -Dlinux_HOST_OS -Di386_BUILD_ARCH -Di386_HOST_ARCH -D__GLASGOW_HASKELL__=610
/usr/local/bin/ghc -E -cpp -x hs -optP-include -optPdist/build/autogen/cabal_macros.h -o dist/build/tmp29684/Bio/Alignment/QAlign.hs Bio/Alignment/QAlign.hs -Dlinux_BUILD_OS -Dlinux_HOST_OS -Di386_BUILD_ARCH -Di386_HOST_ARCH -D__GLASGOW_HASKELL__=610
/usr/local/bin/ghc -E -cpp -x hs -optP-include -optPdist/build/autogen/cabal_macros.h -o dist/build/tmp29684/Bio/Alignment/Multiple.hs Bio/Alignment/Multiple.hs -Dlinux_BUILD_OS -Dlinux_HOST_OS -Di386_BUILD_ARCH -Di386_HOST_ARCH -D__GLASGOW_HASKELL__=610
/usr/local/bin/ghc -E -cpp -x hs -optP-include -optPdist/build/autogen/cabal_macros.h -o dist/build/tmp29684/Bio/Alignment/ACE.hs Bio/Alignment/ACE.hs -Dlinux_BUILD_OS -Dlinux_HOST_OS -Di386_BUILD_ARCH -Di386_HOST_ARCH -D__GLASGOW_HASKELL__=610

Bio/Alignment/ACE.hs:34:0:
     error: interlude.h: No such file or directory

*** Trying again with preferred-versions

*** setup configure

Configuring bio-0.3.3...
Dependency QuickCheck <2 && <2: using QuickCheck-1.2.0.0
Dependency array -any: using array-0.2.0.0
Dependency base >3 && <4: using base-3.0.3.1
Dependency binary -any: using binary-0.5.0.1
Dependency bytestring -any: using bytestring-0.9.1.4
Dependency containers -any: using containers-0.2.0.1
Dependency interlude -any: using interlude-0.1.1
Dependency parallel -any: using parallel-1.1.0.1
Dependency parsec -any && <3: using parsec-2.1.0.1
Dependency tagsoup >=0.5: using tagsoup-0.6
Warning: This package indirectly depends on multiple versions of the same
package. This is highly likely to cause a compile failure.
package bio-0.3.3 requires parsec-2.1.0.1
package network-2.2.1.4 requires parsec-3.0.0
Using Cabal-1.7.0 compiled by ghc-6.10
Using compiler: ghc-6.10.2
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/ghc-6.10.2
Private binaries installed in: /usr/local/tmp/archive/install/libexec
Data files installed in: /usr/local/tmp/archive/install/share/bio-0.3.3
Documentation installed in: /usr/local/tmp/archive/install/share/doc/bio-0.3.3
Using alex version 2.2 found on system at: /usr/bin/alex
Using ar found on system at: /usr/bin/ar
Using c2hs version 0.16.0 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 gcc version 4.3.3 found on system at: /usr/bin/gcc
Using ghc version 6.10.2 found on system at: /usr/local/bin/ghc
Using ghc-pkg version 6.10.2 found on system at: /usr/local/bin/ghc-pkg
Using greencard found on system at:
/usr/local/tmp/archive/install/bin/greencard
Using haddock version 2.4.2 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 0.67 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 lhc found
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
/usr/bin/gcc /tmp/29843.c -o /tmp/29843 -D__GLASGOW_HASKELL__=610 -I. -I/usr/local/tmp/archive/install/lib/network-2.2.1.4/ghc-6.10.2/include -I/usr/local/tmp/archive/install/lib/interlude-0.1.1/ghc-6.10.2/include -I/usr/local/lib/ghc-6.10.2/bytestring-0.9.1.4/include -I/usr/local/lib/ghc-6.10.2/old-time-1.0.0.2/include -I/usr/local/lib/ghc-6.10.2/base-4.1.0.0/include -I/usr/local/lib/ghc-6.10.2/include -IPAPI_INCLUDE_DIR

*** setup build

Creating dist/build (and its parents)
Creating dist/build/autogen (and its parents)
Preprocessing library bio-0.3.3...
Building bio-0.3.3...
Building library...
Creating dist/build (and its parents)
/usr/local/bin/ghc -package-name bio-0.3.3 --make -hide-all-packages -i -idist/build -i. -idist/build/autogen -Idist/build/autogen -Idist/build -optP-include -optPdist/build/autogen/cabal_macros.h -odir dist/build -hidir dist/build -stubdir dist/build -package QuickCheck-1.2.0.0 -package array-0.2.0.0 -package base-3.0.3.1 -package binary-0.5.0.1 -package bytestring-0.9.1.4 -package containers-0.2.0.1 -package interlude-0.1.1 -package parallel-1.1.0.1 -package parsec-2.1.0.1 -package tagsoup-0.6 -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 )
[ 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:79:49:
    Warning: Pattern match(es) are non-exhaustive
             In a case alternative:
                 Patterns not matched:
                     [] : _
                     [_] : _
                     (_ : ((TagOpen _ _) : _)) : _
                     (_ : ((TagClose _) : _)) : _
                     ...

Bio/Alignment/BlastXML.hs:81:53:
    Warning: This binding for `_o' shadows the existing binding
               bound at Bio/Alignment/BlastXML.hs:79:27
             In a case alternative

Bio/Alignment/BlastXML.hs:81:67:
    Warning: This binding for `_c' shadows the existing binding
               bound at Bio/Alignment/BlastXML.hs:79:41
             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)
[20 of 22] Compiling Bio.Alignment.ACE ( Bio/Alignment/ACE.hs, dist/build/Bio/Alignment/ACE.o )

Bio/Alignment/ACE.hs:79:0:
    Warning: Definition but no type signature for `uw'
             Inferred type: uw :: [ByteString] -> [Char]

Bio/Alignment/ACE.hs:90:10:
    Warning: This binding for `pred' shadows the existing binding
               imported from Interlude at Bio/Alignment/ACE.hs:(35,0)-(37,24)
             In the binding group for: sho, pos, pred

Bio/Alignment/ACE.hs:117:0:
    Warning: Definition but no type signature for `blank'
             Inferred type: blank :: GenParser (SourcePos, ACE) () ()

Bio/Alignment/ACE.hs:128:13:
    Warning: This binding for `str' shadows the existing binding
               bound at Bio/Alignment/ACE.hs:127:14
             In the definition of `go'

Bio/Alignment/ACE.hs:130:13:
    Warning: This binding for `str' shadows the existing binding
               bound at Bio/Alignment/ACE.hs:127:14
             In the definition of `go'

Bio/Alignment/ACE.hs:165:21:
    Warning: This binding for `as' shadows the existing binding
               defined at Bio/Alignment/ACE.hs:112:0
             In a pattern binding in
                a 'do' expression

Bio/Alignment/ACE.hs:186:16:
    Warning: Pattern match(es) are non-exhaustive
             In a case alternative:
                 Patterns not matched:
                     []
                     (ghc-prim:GHC.Types.C# #x) : _ with #x `notElem` ['U', 'C']
                     (ghc-prim:GHC.Types.C# 'U') : (_ : _)
                     (ghc-prim:GHC.Types.C# 'C') : (_ : _)

Bio/Alignment/ACE.hs:187:23:
    Warning: Pattern match(es) are non-exhaustive
             In a case alternative: Patterns not matched: Nothing

Bio/Alignment/ACE.hs:192:23:
    Warning: Pattern match(es) are non-exhaustive
             In a case alternative: Patterns not matched: Nothing

Bio/Alignment/ACE.hs:237:38:
    Warning: This binding for `bs' shadows the existing binding
               defined at Bio/Alignment/ACE.hs:190:0
             In a case alternative

Bio/Alignment/ACE.hs:237:49:
    Warning: This binding for `compl' shadows the existing binding
               imported from Bio.Sequence.SeqData at Bio/Alignment/ACE.hs:39:0-26
             In a case alternative
Linking...
/usr/bin/ar q dist/build/libHSbio-0.3.3.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.a
/usr/bin/ld -x -r -o dist/build/HSbio-0.3.3.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

Running Haddock for bio-0.3.3...
/usr/local/bin/haddock --use-contents=http://hackage.haskell.org/package/bio-0.3.3 --ghc-version
Creating dist/build (and its parents)
Creating dist/build/autogen (and its parents)
Preprocessing library bio-0.3.3...
Running hscolour for bio-0.3.3...
Creating dist/doc/html/bio (and its parents)
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
/usr/local/bin/HsColour -css -anchor -odist/doc/html/bio/src/Bio-Alignment-BlastFlat.html Bio/Alignment/BlastFlat.hs
/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
/usr/local/bin/HsColour -css -anchor -odist/doc/html/bio/src/Bio-Util.html Bio/Util.hs
/usr/local/bin/HsColour -css -anchor -odist/doc/html/bio/src/Bio-Util-Parsex.html Bio/Util/Parsex.hs
Warning: The documentation for the following packages are not installed. No
links will be generated to these packages: rts-1.0
/usr/local/bin/ghc --print-libdir
/usr/local/bin/ghc -E -cpp -x hs -optP-include -optPdist/build/autogen/cabal_macros.h -o dist/build/tmp29938/Bio/Sequence.hs Bio/Sequence.hs -Dlinux_BUILD_OS -Dlinux_HOST_OS -Di386_BUILD_ARCH -Di386_HOST_ARCH -D__GLASGOW_HASKELL__=610
/usr/local/bin/ghc -E -cpp -x hs -optP-include -optPdist/build/autogen/cabal_macros.h -o dist/build/tmp29938/Bio/Sequence/SeqData.hs Bio/Sequence/SeqData.hs -Dlinux_BUILD_OS -Dlinux_HOST_OS -Di386_BUILD_ARCH -Di386_HOST_ARCH -D__GLASGOW_HASKELL__=610
/usr/local/bin/ghc -E -cpp -x hs -optP-include -optPdist/build/autogen/cabal_macros.h -o dist/build/tmp29938/Bio/Sequence/Fasta.hs Bio/Sequence/Fasta.hs -Dlinux_BUILD_OS -Dlinux_HOST_OS -Di386_BUILD_ARCH -Di386_HOST_ARCH -D__GLASGOW_HASKELL__=610
/usr/local/bin/ghc -E -cpp -x hs -optP-include -optPdist/build/autogen/cabal_macros.h -o dist/build/tmp29938/Bio/Sequence/TwoBit.hs Bio/Sequence/TwoBit.hs -Dlinux_BUILD_OS -Dlinux_HOST_OS -Di386_BUILD_ARCH -Di386_HOST_ARCH -D__GLASGOW_HASKELL__=610
/usr/local/bin/ghc -E -cpp -x hs -optP-include -optPdist/build/autogen/cabal_macros.h -o dist/build/tmp29938/Bio/Sequence/Phd.hs Bio/Sequence/Phd.hs -Dlinux_BUILD_OS -Dlinux_HOST_OS -Di386_BUILD_ARCH -Di386_HOST_ARCH -D__GLASGOW_HASKELL__=610
/usr/local/bin/ghc -E -cpp -x hs -optP-include -optPdist/build/autogen/cabal_macros.h -o dist/build/tmp29938/Bio/Sequence/Entropy.hs Bio/Sequence/Entropy.hs -Dlinux_BUILD_OS -Dlinux_HOST_OS -Di386_BUILD_ARCH -Di386_HOST_ARCH -D__GLASGOW_HASKELL__=610
/usr/local/bin/ghc -E -cpp -x hs -optP-include -optPdist/build/autogen/cabal_macros.h -o dist/build/tmp29938/Bio/Sequence/HashWord.lhs Bio/Sequence/HashWord.lhs -Dlinux_BUILD_OS -Dlinux_HOST_OS -Di386_BUILD_ARCH -Di386_HOST_ARCH -D__GLASGOW_HASKELL__=610
/usr/local/bin/ghc -E -cpp -x hs -optP-include -optPdist/build/autogen/cabal_macros.h -o dist/build/tmp29938/Bio/Sequence/GOA.hs Bio/Sequence/GOA.hs -Dlinux_BUILD_OS -Dlinux_HOST_OS -Di386_BUILD_ARCH -Di386_HOST_ARCH -D__GLASGOW_HASKELL__=610
/usr/local/bin/ghc -E -cpp -x hs -optP-include -optPdist/build/autogen/cabal_macros.h -o dist/build/tmp29938/Bio/Alignment/BlastData.hs Bio/Alignment/BlastData.hs -Dlinux_BUILD_OS -Dlinux_HOST_OS -Di386_BUILD_ARCH -Di386_HOST_ARCH -D__GLASGOW_HASKELL__=610
/usr/local/bin/ghc -E -cpp -x hs -optP-include -optPdist/build/autogen/cabal_macros.h -o dist/build/tmp29938/Bio/Alignment/BlastFlat.hs Bio/Alignment/BlastFlat.hs -Dlinux_BUILD_OS -Dlinux_HOST_OS -Di386_BUILD_ARCH -Di386_HOST_ARCH -D__GLASGOW_HASKELL__=610
/usr/local/bin/ghc -E -cpp -x hs -optP-include -optPdist/build/autogen/cabal_macros.h -o dist/build/tmp29938/Bio/Alignment/Blast.hs Bio/Alignment/Blast.hs -Dlinux_BUILD_OS -Dlinux_HOST_OS -Di386_BUILD_ARCH -Di386_HOST_ARCH -D__GLASGOW_HASKELL__=610
/usr/local/bin/ghc -E -cpp -x hs -optP-include -optPdist/build/autogen/cabal_macros.h -o dist/build/tmp29938/Bio/Alignment/BlastXML.hs Bio/Alignment/BlastXML.hs -Dlinux_BUILD_OS -Dlinux_HOST_OS -Di386_BUILD_ARCH -Di386_HOST_ARCH -D__GLASGOW_HASKELL__=610
/usr/local/bin/ghc -E -cpp -x hs -optP-include -optPdist/build/autogen/cabal_macros.h -o dist/build/tmp29938/Bio/Alignment/AlignData.hs Bio/Alignment/AlignData.hs -Dlinux_BUILD_OS -Dlinux_HOST_OS -Di386_BUILD_ARCH -Di386_HOST_ARCH -D__GLASGOW_HASKELL__=610
/usr/local/bin/ghc -E -cpp -x hs -optP-include -optPdist/build/autogen/cabal_macros.h -o dist/build/tmp29938/Bio/Alignment/Matrices.hs Bio/Alignment/Matrices.hs -Dlinux_BUILD_OS -Dlinux_HOST_OS -Di386_BUILD_ARCH -Di386_HOST_ARCH -D__GLASGOW_HASKELL__=610
/usr/local/bin/ghc -E -cpp -x hs -optP-include -optPdist/build/autogen/cabal_macros.h -o dist/build/tmp29938/Bio/Alignment/SAlign.hs Bio/Alignment/SAlign.hs -Dlinux_BUILD_OS -Dlinux_HOST_OS -Di386_BUILD_ARCH -Di386_HOST_ARCH -D__GLASGOW_HASKELL__=610
/usr/local/bin/ghc -E -cpp -x hs -optP-include -optPdist/build/autogen/cabal_macros.h -o dist/build/tmp29938/Bio/Alignment/AAlign.hs Bio/Alignment/AAlign.hs -Dlinux_BUILD_OS -Dlinux_HOST_OS -Di386_BUILD_ARCH -Di386_HOST_ARCH -D__GLASGOW_HASKELL__=610
/usr/local/bin/ghc -E -cpp -x hs -optP-include -optPdist/build/autogen/cabal_macros.h -o dist/build/tmp29938/Bio/Alignment/QAlign.hs Bio/Alignment/QAlign.hs -Dlinux_BUILD_OS -Dlinux_HOST_OS -Di386_BUILD_ARCH -Di386_HOST_ARCH -D__GLASGOW_HASKELL__=610
/usr/local/bin/ghc -E -cpp -x hs -optP-include -optPdist/build/autogen/cabal_macros.h -o dist/build/tmp29938/Bio/Alignment/Multiple.hs Bio/Alignment/Multiple.hs -Dlinux_BUILD_OS -Dlinux_HOST_OS -Di386_BUILD_ARCH -Di386_HOST_ARCH -D__GLASGOW_HASKELL__=610
/usr/local/bin/ghc -E -cpp -x hs -optP-include -optPdist/build/autogen/cabal_macros.h -o dist/build/tmp29938/Bio/Alignment/ACE.hs Bio/Alignment/ACE.hs -Dlinux_BUILD_OS -Dlinux_HOST_OS -Di386_BUILD_ARCH -Di386_HOST_ARCH -D__GLASGOW_HASKELL__=610

Bio/Alignment/ACE.hs:34:0:
     error: interlude.h: No such file or directory