Build #1 for samtools-0.2

[all reports]

Package samtools-0.2
Install BuildFailed
Docs NotTried
Tests NotTried
Time submitted unknown
Compiler ghc-7.6.3
OS linux
Arch x86_64
Dependencies vector-0.10.9.1, seqloc-0.5.1.1, process-1.1.0.2, haskell98-2.0.0.2, filepath-1.3.0.1, bytestring-0.10.0.2, base-4.6.0.1
Flags -tests

Code Coverage

No Code Coverage was submitted for this report.

Build log

[view raw]

Resolving dependencies...
Configuring attoparsec-0.10.4.0...
Building attoparsec-0.10.4.0...
Preprocessing library attoparsec-0.10.4.0...
[ 1 of 18] Compiling Data.Attoparsec.Text.FastSet ( Data/Attoparsec/Text/FastSet.hs, dist/build/Data/Attoparsec/Text/FastSet.o )
[ 2 of 18] Compiling Data.Attoparsec.Zepto ( Data/Attoparsec/Zepto.hs, dist/build/Data/Attoparsec/Zepto.o )
[ 3 of 18] Compiling Data.Attoparsec.Number ( Data/Attoparsec/Number.hs, dist/build/Data/Attoparsec/Number.o )
[ 4 of 18] Compiling Data.Attoparsec.ByteString.FastSet ( Data/Attoparsec/ByteString/FastSet.hs, dist/build/Data/Attoparsec/ByteString/FastSet.o )
[ 5 of 18] Compiling Data.Attoparsec.Internal.Types ( Data/Attoparsec/Internal/Types.hs, dist/build/Data/Attoparsec/Internal/Types.o )
[ 6 of 18] Compiling Data.Attoparsec.Types ( Data/Attoparsec/Types.hs, dist/build/Data/Attoparsec/Types.o )
[ 7 of 18] Compiling Data.Attoparsec.Internal ( Data/Attoparsec/Internal.hs, dist/build/Data/Attoparsec/Internal.o )
[ 8 of 18] Compiling Data.Attoparsec.Combinator ( Data/Attoparsec/Combinator.hs, dist/build/Data/Attoparsec/Combinator.o )
[ 9 of 18] Compiling Data.Attoparsec.ByteString.Internal ( Data/Attoparsec/ByteString/Internal.hs, dist/build/Data/Attoparsec/ByteString/Internal.o )
[10 of 18] Compiling Data.Attoparsec.Text.Internal ( Data/Attoparsec/Text/Internal.hs, dist/build/Data/Attoparsec/Text/Internal.o )
[11 of 18] Compiling Data.Attoparsec.Text ( Data/Attoparsec/Text.hs, dist/build/Data/Attoparsec/Text.o )
[12 of 18] Compiling Data.Attoparsec.Text.Lazy ( Data/Attoparsec/Text/Lazy.hs, dist/build/Data/Attoparsec/Text/Lazy.o )
[13 of 18] Compiling Data.Attoparsec.ByteString ( Data/Attoparsec/ByteString.hs, dist/build/Data/Attoparsec/ByteString.o )
[14 of 18] Compiling Data.Attoparsec.ByteString.Char8 ( Data/Attoparsec/ByteString/Char8.hs, dist/build/Data/Attoparsec/ByteString/Char8.o )
[15 of 18] Compiling Data.Attoparsec.Char8 ( Data/Attoparsec/Char8.hs, dist/build/Data/Attoparsec/Char8.o )
[16 of 18] Compiling Data.Attoparsec.ByteString.Lazy ( Data/Attoparsec/ByteString/Lazy.hs, dist/build/Data/Attoparsec/ByteString/Lazy.o )
[17 of 18] Compiling Data.Attoparsec.Lazy ( Data/Attoparsec/Lazy.hs, dist/build/Data/Attoparsec/Lazy.o )
[18 of 18] Compiling Data.Attoparsec  ( Data/Attoparsec.hs, dist/build/Data/Attoparsec.o )
In-place registering attoparsec-0.10.4.0...
Running Haddock for attoparsec-0.10.4.0...
Running hscolour for attoparsec-0.10.4.0...
Preprocessing library attoparsec-0.10.4.0...
Preprocessing library attoparsec-0.10.4.0...
Haddock coverage:
  70% (  7 / 10) in 'Data.Attoparsec.Text.FastSet'
 100% (  7 /  7) in 'Data.Attoparsec.Zepto'
 100% (  2 /  2) in 'Data.Attoparsec.Number'
  69% (  9 / 13) in 'Data.Attoparsec.ByteString.FastSet'
  40% (  4 / 10) in 'Data.Attoparsec.Internal.Types'
 100% (  3 /  3) in 'Data.Attoparsec.Types'
 100% (  2 /  2) in 'Data.Attoparsec.Internal'
 100% ( 16 / 16) in 'Data.Attoparsec.Combinator'
  90% ( 37 / 41) in 'Data.Attoparsec.ByteString.Internal'
  95% ( 38 / 40) in 'Data.Attoparsec.Text.Internal'
  97% ( 71 / 73) in 'Data.Attoparsec.Text'
 100% (  9 /  9) in 'Data.Attoparsec.Text.Lazy'
  96% ( 48 / 50) in 'Data.Attoparsec.ByteString'
  97% ( 73 / 75) in 'Data.Attoparsec.ByteString.Char8'
 100% (  2 /  2) in 'Data.Attoparsec.Char8'
 100% (  9 /  9) in 'Data.Attoparsec.ByteString.Lazy'
 100% (  2 /  2) in 'Data.Attoparsec.Lazy'
 100% (  2 /  2) in 'Data.Attoparsec'
Documentation created: dist/doc/html/attoparsec/index.html
Installing library in
/srv/hackage/var/build/tmp-install/lib/x86_64-linux-ghc-7.6.3/attoparsec-0.10.4.0
Registering attoparsec-0.10.4.0...
Installed attoparsec-0.10.4.0
Configuring primitive-0.5.1.0...
Building primitive-0.5.1.0...
Preprocessing library primitive-0.5.1.0...
[ 1 of 10] Compiling Data.Primitive.Internal.Compat ( Data/Primitive/Internal/Compat.hs, dist/build/Data/Primitive/Internal/Compat.o )
[ 2 of 10] Compiling Data.Primitive.MachDeps ( Data/Primitive/MachDeps.hs, dist/build/Data/Primitive/MachDeps.o )
[ 3 of 10] Compiling Data.Primitive.Internal.Operations ( Data/Primitive/Internal/Operations.hs, dist/build/Data/Primitive/Internal/Operations.o )
[ 4 of 10] Compiling Control.Monad.Primitive ( Control/Monad/Primitive.hs, dist/build/Control/Monad/Primitive.o )
[ 5 of 10] Compiling Data.Primitive.Types ( Data/Primitive/Types.hs, dist/build/Data/Primitive/Types.o )
[ 6 of 10] Compiling Data.Primitive.Array ( Data/Primitive/Array.hs, dist/build/Data/Primitive/Array.o )
[ 7 of 10] Compiling Data.Primitive.ByteArray ( Data/Primitive/ByteArray.hs, dist/build/Data/Primitive/ByteArray.o )
[ 8 of 10] Compiling Data.Primitive.Addr ( Data/Primitive/Addr.hs, dist/build/Data/Primitive/Addr.o )
[ 9 of 10] Compiling Data.Primitive   ( Data/Primitive.hs, dist/build/Data/Primitive.o )
[10 of 10] Compiling Data.Primitive.MutVar ( Data/Primitive/MutVar.hs, dist/build/Data/Primitive/MutVar.o )
In-place registering primitive-0.5.1.0...
Running Haddock for primitive-0.5.1.0...
Running hscolour for primitive-0.5.1.0...
Preprocessing library primitive-0.5.1.0...
Preprocessing library primitive-0.5.1.0...
Haddock coverage:
  67% (  2 /  3) in 'Data.Primitive.Internal.Compat'
   3% (  1 / 35) in 'Data.Primitive.MachDeps'
   3% (  1 / 29) in 'Data.Primitive.Internal.Operations'
Warning: Control.Monad.Primitive: We do not support associated types in instances yet. These instances are affected:
Control.Monad.Primitive.PrimMonad GHC.Types.IO, Control.Monad.Primitive.PrimMonad (GHC.ST.ST s)
  71% ( 10 / 14) in 'Control.Monad.Primitive'
 100% (  3 /  3) in 'Data.Primitive.Types'
 100% ( 13 / 13) in 'Data.Primitive.Array'
  93% ( 27 / 29) in 'Data.Primitive.ByteArray'
 100% ( 16 / 16) in 'Data.Primitive.Addr'
 100% (  7 /  7) in 'Data.Primitive'
 100% (  7 /  7) in 'Data.Primitive.MutVar'
Documentation created: dist/doc/html/primitive/index.html
Installing library in
/srv/hackage/var/build/tmp-install/lib/x86_64-linux-ghc-7.6.3/primitive-0.5.1.0
Registering primitive-0.5.1.0...
Installed primitive-0.5.1.0
Configuring system-filepath-0.4.8...
Building system-filepath-0.4.8...
Preprocessing library system-filepath-0.4.8...
[1 of 4] Compiling Filesystem.Path.Internal ( lib/Filesystem/Path/Internal.hs, dist/build/Filesystem/Path/Internal.o )
[2 of 4] Compiling Filesystem.Path  ( lib/Filesystem/Path.hs, dist/build/Filesystem/Path.o )
[3 of 4] Compiling Filesystem.Path.Rules ( lib/Filesystem/Path/Rules.hs, dist/build/Filesystem/Path/Rules.o )
[4 of 4] Compiling Filesystem.Path.CurrentOS ( lib/Filesystem/Path/CurrentOS.hs, dist/build/Filesystem/Path/CurrentOS.o )
In-place registering system-filepath-0.4.8...
Running Haddock for system-filepath-0.4.8...
Running hscolour for system-filepath-0.4.8...
Preprocessing library system-filepath-0.4.8...
Preprocessing library system-filepath-0.4.8...
Haddock coverage:
   9% (  2 / 23) in 'Filesystem.Path.Internal'
  97% ( 33 / 34) in 'Filesystem.Path'
  94% ( 17 / 18) in 'Filesystem.Path.Rules'
  92% ( 12 / 13) in 'Filesystem.Path.CurrentOS'
Documentation created: dist/doc/html/system-filepath/index.html
Installing library in
/srv/hackage/var/build/tmp-install/lib/x86_64-linux-ghc-7.6.3/system-filepath-0.4.8
Registering system-filepath-0.4.8...
Installed system-filepath-0.4.8
Configuring vector-0.10.9.1...
Building vector-0.10.9.1...
Preprocessing library vector-0.10.9.1...
[ 1 of 19] Compiling Data.Vector.Storable.Internal ( Data/Vector/Storable/Internal.hs, dist/build/Data/Vector/Storable/Internal.o )
[ 2 of 19] Compiling Data.Vector.Fusion.Util ( Data/Vector/Fusion/Util.hs, dist/build/Data/Vector/Fusion/Util.o )
[ 3 of 19] Compiling Data.Vector.Fusion.Stream.Size ( Data/Vector/Fusion/Stream/Size.hs, dist/build/Data/Vector/Fusion/Stream/Size.o )

Data/Vector/Fusion/Stream/Size.hs:25:10: Warning:
    No explicit method or default declaration for `*'
    In the instance declaration for `Num Size'

Data/Vector/Fusion/Stream/Size.hs:25:10: Warning:
    No explicit method or default declaration for `abs'
    In the instance declaration for `Num Size'

Data/Vector/Fusion/Stream/Size.hs:25:10: Warning:
    No explicit method or default declaration for `signum'
    In the instance declaration for `Num Size'
[ 4 of 19] Compiling Data.Vector.Internal.Check ( Data/Vector/Internal/Check.hs, dist/build/Data/Vector/Internal/Check.o )
[ 5 of 19] Compiling Data.Vector.Fusion.Stream.Monadic ( Data/Vector/Fusion/Stream/Monadic.hs, dist/build/Data/Vector/Fusion/Stream/Monadic.o )
Loading package ghc-prim ... linking ... done.
Loading package integer-gmp ... linking ... done.
Loading package base ... linking ... done.
Loading package primitive-0.5.1.0 ... linking ... done.
Loading package array-0.4.0.1 ... linking ... done.
Loading package deepseq-1.3.0.1 ... linking ... done.
[ 6 of 19] Compiling Data.Vector.Fusion.Stream ( Data/Vector/Fusion/Stream.hs, dist/build/Data/Vector/Fusion/Stream.o )
[ 7 of 19] Compiling Data.Vector.Generic.Mutable ( Data/Vector/Generic/Mutable.hs, dist/build/Data/Vector/Generic/Mutable.o )
[ 8 of 19] Compiling Data.Vector.Generic.Base ( Data/Vector/Generic/Base.hs, dist/build/Data/Vector/Generic/Base.o )
[ 9 of 19] Compiling Data.Vector.Generic.New ( Data/Vector/Generic/New.hs, dist/build/Data/Vector/Generic/New.o )
[10 of 19] Compiling Data.Vector.Generic ( Data/Vector/Generic.hs, dist/build/Data/Vector/Generic.o )
[11 of 19] Compiling Data.Vector.Primitive.Mutable ( Data/Vector/Primitive/Mutable.hs, dist/build/Data/Vector/Primitive/Mutable.o )
[12 of 19] Compiling Data.Vector.Primitive ( Data/Vector/Primitive.hs, dist/build/Data/Vector/Primitive.o )
[13 of 19] Compiling Data.Vector.Storable.Mutable ( Data/Vector/Storable/Mutable.hs, dist/build/Data/Vector/Storable/Mutable.o )
[14 of 19] Compiling Data.Vector.Storable ( Data/Vector/Storable.hs, dist/build/Data/Vector/Storable.o )
[15 of 19] Compiling Data.Vector.Unboxed.Base ( Data/Vector/Unboxed/Base.hs, dist/build/Data/Vector/Unboxed/Base.o )
[16 of 19] Compiling Data.Vector.Unboxed ( Data/Vector/Unboxed.hs, dist/build/Data/Vector/Unboxed.o )
[17 of 19] Compiling Data.Vector.Unboxed.Mutable ( Data/Vector/Unboxed/Mutable.hs, dist/build/Data/Vector/Unboxed/Mutable.o )
[18 of 19] Compiling Data.Vector.Mutable ( Data/Vector/Mutable.hs, dist/build/Data/Vector/Mutable.o )
[19 of 19] Compiling Data.Vector      ( Data/Vector.hs, dist/build/Data/Vector.o )
In-place registering vector-0.10.9.1...
Running Haddock for vector-0.10.9.1...
Running hscolour for vector-0.10.9.1...
Preprocessing library vector-0.10.9.1...
Preprocessing library vector-0.10.9.1...

Data/Vector/Fusion/Stream/Size.hs:25:10: Warning:
    No explicit method or default declaration for `*'
    In the instance declaration for `Num Size'

Data/Vector/Fusion/Stream/Size.hs:25:10: Warning:
    No explicit method or default declaration for `abs'
    In the instance declaration for `Num Size'

Data/Vector/Fusion/Stream/Size.hs:25:10: Warning:
    No explicit method or default declaration for `signum'
    In the instance declaration for `Num Size'
Haddock coverage:
  25% (  1 /  4) in 'Data.Vector.Storable.Internal'
 100% (  5 /  5) in 'Data.Vector.Fusion.Util'
 100% (  6 /  6) in 'Data.Vector.Fusion.Stream.Size'
  11% (  1 /  9) in 'Data.Vector.Internal.Check'
  83% (104 /126) in 'Data.Vector.Fusion.Stream.Monadic'
  85% ( 88 /104) in 'Data.Vector.Fusion.Stream'
  64% ( 42 / 66) in 'Data.Vector.Generic.Mutable'
 100% (  3 /  3) in 'Data.Vector.Generic.Base'
   5% (  1 / 20) in 'Data.Vector.Generic.New'
  93% (215 /232) in 'Data.Vector.Generic'
  76% ( 38 / 50) in 'Data.Vector.Primitive.Mutable'
Warning: Data.Vector.Primitive: Instances of type and data families are not yet supported. Instances of the following families will be filtered out:
  Mutable
  97% (185 /191) in 'Data.Vector.Primitive'
  79% ( 46 / 58) in 'Data.Vector.Storable.Mutable'
Warning: Data.Vector.Storable: Instances of type and data families are not yet supported. Instances of the following families will be filtered out:
  Mutable
  97% (194 /200) in 'Data.Vector.Storable'
Warning: Data.Vector.Unboxed.Base: Instances of type and data families are not yet supported. Instances of the following families will be filtered out:
  Mutable, MVector, Vector
  17% (  1 /  6) in 'Data.Vector.Unboxed.Base'
  96% (201 /210) in 'Data.Vector.Unboxed'
  77% ( 47 / 61) in 'Data.Vector.Unboxed.Mutable'
  76% ( 37 / 49) in 'Data.Vector.Mutable'
Warning: Data.Vector: Instances of type and data families are not yet supported. Instances of the following families will be filtered out:
  Mutable
  94% (199 /212) in 'Data.Vector'
Documentation created: dist/doc/html/vector/index.html
Installing library in
/srv/hackage/var/build/tmp-install/lib/x86_64-linux-ghc-7.6.3/vector-0.10.9.1
Registering vector-0.10.9.1...
Installed vector-0.10.9.1
Configuring stringable-0.1.2...
Building stringable-0.1.2...
Preprocessing library stringable-0.1.2...
[1 of 1] Compiling Data.Stringable  ( Data/Stringable.hs, dist/build/Data/Stringable.o )
In-place registering stringable-0.1.2...
Running Haddock for stringable-0.1.2...
Running hscolour for stringable-0.1.2...
Preprocessing library stringable-0.1.2...
Preprocessing library stringable-0.1.2...
Haddock coverage:
   0% (  0 /  3) in 'Data.Stringable'
Documentation created: dist/doc/html/stringable/index.html
Installing library in
/srv/hackage/var/build/tmp-install/lib/x86_64-linux-ghc-7.6.3/stringable-0.1.2
Registering stringable-0.1.2...
Installed stringable-0.1.2
Configuring biocore-0.3.1...
Building biocore-0.3.1...
Preprocessing library biocore-0.3.1...
[1 of 3] Compiling Bio.Core.Strand  ( src/Bio/Core/Strand.hs, dist/build/Bio/Core/Strand.o )
[2 of 3] Compiling Bio.Core.Sequence ( src/Bio/Core/Sequence.hs, dist/build/Bio/Core/Sequence.o )
[3 of 3] Compiling Bio.Core         ( src/Bio/Core.hs, dist/build/Bio/Core.o )
In-place registering biocore-0.3.1...
Running Haddock for biocore-0.3.1...
Running hscolour for biocore-0.3.1...
Preprocessing library biocore-0.3.1...
Preprocessing library biocore-0.3.1...
Haddock coverage:
 100% (  2 /  2) in 'Bio.Core.Strand'
 100% ( 15 / 15) in 'Bio.Core.Sequence'
 100% (  3 /  3) in 'Bio.Core'
Documentation created: dist/doc/html/biocore/index.html
Installing library in
/srv/hackage/var/build/tmp-install/lib/x86_64-linux-ghc-7.6.3/biocore-0.3.1
Registering biocore-0.3.1...
Installed biocore-0.3.1
Configuring seqloc-0.5.1.1...
Building seqloc-0.5.1.1...
Preprocessing library seqloc-0.5.1.1...
[1 of 8] Compiling Bio.SeqLoc.SeqLike ( src/Bio/SeqLoc/SeqLike.hs, dist/build/Bio/SeqLoc/SeqLike.o )
[2 of 8] Compiling Bio.SeqLoc.LocRepr ( src/Bio/SeqLoc/LocRepr.hs, dist/build/Bio/SeqLoc/LocRepr.o )
[3 of 8] Compiling Bio.SeqLoc.Strand ( src/Bio/SeqLoc/Strand.hs, dist/build/Bio/SeqLoc/Strand.o )
[4 of 8] Compiling Bio.SeqLoc.Position ( src/Bio/SeqLoc/Position.hs, dist/build/Bio/SeqLoc/Position.o )

src/Bio/SeqLoc/Position.hs:24:1: Warning:
    The import of `Control.Arrow' is redundant
      except perhaps to import instances from `Control.Arrow'
    To import instances alone, use: import Control.Arrow()
[5 of 8] Compiling Bio.SeqLoc.Location ( src/Bio/SeqLoc/Location.hs, dist/build/Bio/SeqLoc/Location.o )
[6 of 8] Compiling Bio.SeqLoc.SpliceLocation ( src/Bio/SeqLoc/SpliceLocation.hs, dist/build/Bio/SeqLoc/SpliceLocation.o )
[7 of 8] Compiling Bio.SeqLoc.OnSeq ( src/Bio/SeqLoc/OnSeq.hs, dist/build/Bio/SeqLoc/OnSeq.o )

src/Bio/SeqLoc/OnSeq.hs:80:3: Warning:
    In the use of `seqlabel' (imported from Bio.Core.Sequence):
    Deprecated: "Warning: 'seqlabel' is deprecated, use 'seqid' or 'seqheader' instead."
[8 of 8] Compiling Bio.SeqLoc.Transcript ( src/Bio/SeqLoc/Transcript.hs, dist/build/Bio/SeqLoc/Transcript.o )
In-place registering seqloc-0.5.1.1...
Running Haddock for seqloc-0.5.1.1...
Running hscolour for seqloc-0.5.1.1...
Preprocessing library seqloc-0.5.1.1...
Preprocessing library seqloc-0.5.1.1...

dist/build/tmp-30894/src/Bio/SeqLoc/Position.hs:24:1: Warning:
    The import of `Control.Arrow' is redundant
      except perhaps to import instances from `Control.Arrow'
    To import instances alone, use: import Control.Arrow()

dist/build/tmp-30894/src/Bio/SeqLoc/OnSeq.hs:80:3: Warning:
    In the use of `seqlabel' (imported from Bio.Core.Sequence):
    Deprecated: "Warning: 'seqlabel' is deprecated, use 'seqid' or 'seqheader' instead."
Haddock coverage:
   0% (  0 /  2) in 'Bio.SeqLoc.SeqLike'
   0% (  0 /  6) in 'Bio.SeqLoc.LocRepr'
 100% (  5 /  5) in 'Bio.SeqLoc.Strand'
 100% (  8 /  8) in 'Bio.SeqLoc.Position'
  83% ( 10 / 12) in 'Bio.SeqLoc.Location'
  38% (  3 /  8) in 'Bio.SeqLoc.SpliceLocation'
  62% (  8 / 13) in 'Bio.SeqLoc.OnSeq'
  92% ( 12 / 13) in 'Bio.SeqLoc.Transcript'
Documentation created: dist/doc/html/seqloc/index.html
Installing library in
/srv/hackage/var/build/tmp-install/lib/x86_64-linux-ghc-7.6.3/seqloc-0.5.1.1
Registering seqloc-0.5.1.1...
Installed seqloc-0.5.1.1
Downloading samtools-0.2...
Configuring samtools-0.2...
Building samtools-0.2...
Preprocessing library samtools-0.2...

src/Bio/SamTools/Bam.hs:1:1:
    Ambiguous module name `Prelude':
      it was found in multiple packages: base haskell98-2.0.0.2
Failed to install samtools-0.2
cabal: Error: some packages failed to install:
samtools-0.2 failed during the building phase. The exception was:
ExitFailure 1

Test log

No test log was submitted for this report.