*** setup configure Configuring clustertools-0.1... Dependency base >3: using base-4.1.0.0 Dependency bio >=0.3.3: using bio-0.3.5 Dependency bytestring -any: using bytestring-0.9.1.4 Dependency containers -any: using containers-0.2.0.1 Dependency regex-compat -any: using regex-compat-0.92 Dependency simpleargs >=0.1: using simpleargs-0.1 Using Cabal-1.6.0.1 compiled by ghc-6.8 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/clustertools-0.1/ghc-6.10.2 Private binaries installed in: /usr/local/tmp/archive/install/libexec Data files installed in: /usr/local/tmp/archive/install/share/clustertools-0.1 Documentation installed in: /usr/local/tmp/archive/install/share/doc/clustertools-0.1 Using alex version 2.2 found on system at: /usr/bin/alex Using ar found on system at: /usr/bin/ar Using c2hs version 0.15.1 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 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 No greencard found 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 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 executables for clustertools-0.1... Building clustertools-0.1... Building executable: filter... Creating dist/build/filter (and its parents) Creating dist/build/filter/filter-tmp (and its parents) /usr/local/bin/ghc -o dist/build/filter/filter --make -hide-all-packages -i -idist/build/filter/filter-tmp -isrc -idist/build/autogen -Idist/build/autogen -Idist/build/filter/filter-tmp -optP-include -optPdist/build/autogen/cabal_macros.h -odir dist/build/filter/filter-tmp -hidir dist/build/filter/filter-tmp -stubdir dist/build/filter/filter-tmp -package base-4.1.0.0 -package bio-0.3.5 -package bytestring-0.9.1.4 -package containers-0.2.0.1 -package regex-compat-0.92 -package simpleargs-0.1 -O -Wall -O2 -funbox-strict-fields src/Filter.hs [1 of 1] Compiling Main ( src/Filter.hs, dist/build/filter/filter-tmp/Main.o ) Linking dist/build/filter/filter ... Building executable: clusc... Creating dist/build/clusc (and its parents) Creating dist/build/clusc/clusc-tmp (and its parents) /usr/local/bin/ghc -o dist/build/clusc/clusc --make -hide-all-packages -i -idist/build/clusc/clusc-tmp -isrc -idist/build/autogen -Idist/build/autogen -Idist/build/clusc/clusc-tmp -optP-include -optPdist/build/autogen/cabal_macros.h -odir dist/build/clusc/clusc-tmp -hidir dist/build/clusc/clusc-tmp -stubdir dist/build/clusc/clusc-tmp -package base-4.1.0.0 -package bio-0.3.5 -package bytestring-0.9.1.4 -package containers-0.2.0.1 -package regex-compat-0.92 -package simpleargs-0.1 -O src/Cluscomp.lhs [1 of 1] Compiling Main ( src/Cluscomp.lhs, dist/build/clusc/clusc-tmp/Main.o ) Linking dist/build/clusc/clusc ... Building executable: add_single... Creating dist/build/add_single (and its parents) Creating dist/build/add_single/add_single-tmp (and its parents) /usr/local/bin/ghc -o dist/build/add_single/add_single --make -hide-all-packages -i -idist/build/add_single/add_single-tmp -isrc -idist/build/autogen -Idist/build/autogen -Idist/build/add_single/add_single-tmp -optP-include -optPdist/build/autogen/cabal_macros.h -odir dist/build/add_single/add_single-tmp -hidir dist/build/add_single/add_single-tmp -stubdir dist/build/add_single/add_single-tmp -package base-4.1.0.0 -package bio-0.3.5 -package bytestring-0.9.1.4 -package containers-0.2.0.1 -package regex-compat-0.92 -package simpleargs-0.1 -O src/AddSingletons.hs [1 of 1] Compiling Main ( src/AddSingletons.hs, dist/build/add_single/add_single-tmp/Main.o ) Linking dist/build/add_single/add_single ... Building executable: ace2contigs... Creating dist/build/ace2contigs (and its parents) Creating dist/build/ace2contigs/ace2contigs-tmp (and its parents) /usr/local/bin/ghc -o dist/build/ace2contigs/ace2contigs --make -hide-all-packages -i -idist/build/ace2contigs/ace2contigs-tmp -isrc -idist/build/autogen -Idist/build/autogen -Idist/build/ace2contigs/ace2contigs-tmp -optP-include -optPdist/build/autogen/cabal_macros.h -odir dist/build/ace2contigs/ace2contigs-tmp -hidir dist/build/ace2contigs/ace2contigs-tmp -stubdir dist/build/ace2contigs/ace2contigs-tmp -package base-4.1.0.0 -package bio-0.3.5 -package bytestring-0.9.1.4 -package containers-0.2.0.1 -package regex-compat-0.92 -package simpleargs-0.1 -O src/Ace2Contigs.hs [1 of 1] Compiling Main ( src/Ace2Contigs.hs, dist/build/ace2contigs/ace2contigs-tmp/Main.o ) Linking dist/build/ace2contigs/ace2contigs ... Building executable: ace2fasta... Creating dist/build/ace2fasta (and its parents) Creating dist/build/ace2fasta/ace2fasta-tmp (and its parents) /usr/local/bin/ghc -o dist/build/ace2fasta/ace2fasta --make -hide-all-packages -i -idist/build/ace2fasta/ace2fasta-tmp -isrc -idist/build/autogen -Idist/build/autogen -Idist/build/ace2fasta/ace2fasta-tmp -optP-include -optPdist/build/autogen/cabal_macros.h -odir dist/build/ace2fasta/ace2fasta-tmp -hidir dist/build/ace2fasta/ace2fasta-tmp -stubdir dist/build/ace2fasta/ace2fasta-tmp -package base-4.1.0.0 -package bio-0.3.5 -package bytestring-0.9.1.4 -package containers-0.2.0.1 -package regex-compat-0.92 -package simpleargs-0.1 -O src/Ace2Fasta.hs [1 of 1] Compiling Main ( src/Ace2Fasta.hs, dist/build/ace2fasta/ace2fasta-tmp/Main.o ) src/Ace2Fasta.hs:24:27: Not in scope: type constructor or class `Gaps' src/Ace2Fasta.hs:25:109: Not in scope: `insertGaps' *** Trying again with preferred-versions *** setup configure Configuring clustertools-0.1... Dependency base >3 && <4: using base-3.0.3.1 Dependency bio >=0.3.3: using bio-0.3.5 Dependency bytestring -any: using bytestring-0.9.1.4 Dependency containers -any: using containers-0.2.0.1 Dependency regex-compat -any: using regex-compat-0.92 Dependency simpleargs >=0.1: using simpleargs-0.1 Using Cabal-1.6.0.1 compiled by ghc-6.8 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/clustertools-0.1/ghc-6.10.2 Private binaries installed in: /usr/local/tmp/archive/install/libexec Data files installed in: /usr/local/tmp/archive/install/share/clustertools-0.1 Documentation installed in: /usr/local/tmp/archive/install/share/doc/clustertools-0.1 Using alex version 2.2 found on system at: /usr/bin/alex Using ar found on system at: /usr/bin/ar Using c2hs version 0.15.1 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 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 No greencard found 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 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 executables for clustertools-0.1... Building clustertools-0.1... Building executable: filter... Creating dist/build/filter (and its parents) Creating dist/build/filter/filter-tmp (and its parents) /usr/local/bin/ghc -o dist/build/filter/filter --make -hide-all-packages -i -idist/build/filter/filter-tmp -isrc -idist/build/autogen -Idist/build/autogen -Idist/build/filter/filter-tmp -optP-include -optPdist/build/autogen/cabal_macros.h -odir dist/build/filter/filter-tmp -hidir dist/build/filter/filter-tmp -stubdir dist/build/filter/filter-tmp -package base-3.0.3.1 -package bio-0.3.5 -package bytestring-0.9.1.4 -package containers-0.2.0.1 -package regex-compat-0.92 -package simpleargs-0.1 -O -Wall -O2 -funbox-strict-fields src/Filter.hs Building executable: clusc... Creating dist/build/clusc (and its parents) Creating dist/build/clusc/clusc-tmp (and its parents) /usr/local/bin/ghc -o dist/build/clusc/clusc --make -hide-all-packages -i -idist/build/clusc/clusc-tmp -isrc -idist/build/autogen -Idist/build/autogen -Idist/build/clusc/clusc-tmp -optP-include -optPdist/build/autogen/cabal_macros.h -odir dist/build/clusc/clusc-tmp -hidir dist/build/clusc/clusc-tmp -stubdir dist/build/clusc/clusc-tmp -package base-3.0.3.1 -package bio-0.3.5 -package bytestring-0.9.1.4 -package containers-0.2.0.1 -package regex-compat-0.92 -package simpleargs-0.1 -O src/Cluscomp.lhs [1 of 1] Compiling Main ( src/Cluscomp.lhs, dist/build/clusc/clusc-tmp/Main.o ) Linking dist/build/clusc/clusc ... Building executable: add_single... Creating dist/build/add_single (and its parents) Creating dist/build/add_single/add_single-tmp (and its parents) /usr/local/bin/ghc -o dist/build/add_single/add_single --make -hide-all-packages -i -idist/build/add_single/add_single-tmp -isrc -idist/build/autogen -Idist/build/autogen -Idist/build/add_single/add_single-tmp -optP-include -optPdist/build/autogen/cabal_macros.h -odir dist/build/add_single/add_single-tmp -hidir dist/build/add_single/add_single-tmp -stubdir dist/build/add_single/add_single-tmp -package base-3.0.3.1 -package bio-0.3.5 -package bytestring-0.9.1.4 -package containers-0.2.0.1 -package regex-compat-0.92 -package simpleargs-0.1 -O src/AddSingletons.hs [1 of 1] Compiling Main ( src/AddSingletons.hs, dist/build/add_single/add_single-tmp/Main.o ) Linking dist/build/add_single/add_single ... Building executable: ace2contigs... Creating dist/build/ace2contigs (and its parents) Creating dist/build/ace2contigs/ace2contigs-tmp (and its parents) /usr/local/bin/ghc -o dist/build/ace2contigs/ace2contigs --make -hide-all-packages -i -idist/build/ace2contigs/ace2contigs-tmp -isrc -idist/build/autogen -Idist/build/autogen -Idist/build/ace2contigs/ace2contigs-tmp -optP-include -optPdist/build/autogen/cabal_macros.h -odir dist/build/ace2contigs/ace2contigs-tmp -hidir dist/build/ace2contigs/ace2contigs-tmp -stubdir dist/build/ace2contigs/ace2contigs-tmp -package base-3.0.3.1 -package bio-0.3.5 -package bytestring-0.9.1.4 -package containers-0.2.0.1 -package regex-compat-0.92 -package simpleargs-0.1 -O src/Ace2Contigs.hs Building executable: ace2fasta... Creating dist/build/ace2fasta (and its parents) Creating dist/build/ace2fasta/ace2fasta-tmp (and its parents) /usr/local/bin/ghc -o dist/build/ace2fasta/ace2fasta --make -hide-all-packages -i -idist/build/ace2fasta/ace2fasta-tmp -isrc -idist/build/autogen -Idist/build/autogen -Idist/build/ace2fasta/ace2fasta-tmp -optP-include -optPdist/build/autogen/cabal_macros.h -odir dist/build/ace2fasta/ace2fasta-tmp -hidir dist/build/ace2fasta/ace2fasta-tmp -stubdir dist/build/ace2fasta/ace2fasta-tmp -package base-3.0.3.1 -package bio-0.3.5 -package bytestring-0.9.1.4 -package containers-0.2.0.1 -package regex-compat-0.92 -package simpleargs-0.1 -O src/Ace2Fasta.hs [1 of 1] Compiling Main ( src/Ace2Fasta.hs, dist/build/ace2fasta/ace2fasta-tmp/Main.o ) src/Ace2Fasta.hs:24:27: Not in scope: type constructor or class `Gaps' src/Ace2Fasta.hs:25:109: Not in scope: `insertGaps'