* Package: dev-haskell/biosff-0.3.7.1 * Repository: gentoo * Maintainer: haskell@gentoo.org * USE: abi_x86_64 amd64 elibc_glibc fclip frecover kernel_linux userland_GNU * FEATURES: network-sandbox preserve-libs sandbox userpriv usersandbox >>> Unpacking source... >>> Unpacking biosff-0.3.7.1.tar.gz to /var/tmp/portage/dev-haskell/biosff-0.3.7.1/work >>> Source unpacked in /var/tmp/portage/dev-haskell/biosff-0.3.7.1/work >>> Preparing source in /var/tmp/portage/dev-haskell/biosff-0.3.7.1/work/biosff-0.3.7.1 ... * Applying biosff-0.3.7.1-ghc-7.10.patch ... [ ok ] >>> Source prepared. >>> Configuring source in /var/tmp/portage/dev-haskell/biosff-0.3.7.1/work/biosff-0.3.7.1 ... * Using cabal-1.24.2.0. * Prepending /usr/lib64/ghc-8.0.2 to LD_LIBRARY_PATH /usr/bin/ghc -package Cabal-1.24.2.0 --make /var/tmp/portage/dev-haskell/biosff-0.3.7.1/work/biosff-0.3.7.1/Setup.hs -j1 +RTS -A256M -qb0 -RTS -threaded -dynamic -o setup [1 of 1] Compiling Main ( /var/tmp/portage/dev-haskell/biosff-0.3.7.1/work/biosff-0.3.7.1/Setup.hs, /var/tmp/portage/dev-haskell/biosff-0.3.7.1/work/biosff-0.3.7.1/Setup.o ) Linking setup ... ./setup configure --ghc --prefix=/usr --with-compiler=/usr/bin/ghc --with-hc-pkg=/usr/bin/ghc-pkg --prefix=/usr --libdir=/usr/lib64 --libsubdir=biosff-0.3.7.1/ghc-8.0.2 --datadir=/usr/share/ --datasubdir=biosff-0.3.7.1/ghc-8.0.2 --ghc-options=-j1 +RTS -A256M -qb0 -RTS --with-ar=x86_64-pc-linux-gnu-ar --ghc-option=-optc-O2 --ghc-option=-optc-pipe --ghc-option=-optc-march=native --ghc-option=-optc-falign-functions=32:25:16 --ghc-option=-optl-Wl,-O1 --ghc-option=-optl-Wl,--as-needed --ghc-option=-optl-Wl,--defsym=__gentoo_check_ldflags__=0 --disable-executable-stripping --docdir=/usr/share/doc/biosff-0.3.7.1 --verbose --enable-shared --enable-executable-dynamic --sysconfdir=/etc --disable-library-stripping --flags=fclip --flags=-flower --flags=frecover Configuring biosff-0.3.7.1... Flags chosen: fclip=True, frecover=True, flower=False Dependency array -any: using array-0.5.1.1 Dependency base >=3 && <5: using base-4.9.1.0 Dependency binary -any: using binary-0.8.3.0 Dependency biocore >=0.3: using biocore-0.3.1 Dependency bytestring -any: using bytestring-0.10.8.1 Using Cabal-1.24.2.0 compiled by ghc-8.0 Using compiler: ghc-8.0.2 Using install prefix: /usr Binaries installed in: /usr/bin Libraries installed in: /usr/lib64/biosff-0.3.7.1/ghc-8.0.2 Dynamic libraries installed in: /usr/lib64/x86_64-linux-ghc-8.0.2 Private binaries installed in: /usr/libexec Data files installed in: /usr/share/biosff-0.3.7.1/ghc-8.0.2 Documentation installed in: /usr/share/doc/biosff-0.3.7.1 Configuration files installed in: /etc Using alex version 3.2.4 found on system at: /usr/bin/alex Using ar given by user at: /usr/bin/x86_64-pc-linux-gnu-ar Using c2hs version 0.28.3 found on system at: /usr/bin/c2hs Using cpphs version 1.20.8 found on system at: /usr/bin/cpphs Using gcc version 9.3.0 found on system at: /usr/bin/x86_64-pc-linux-gnu-gcc Using ghc version 8.0.2 given by user at: /usr/bin/ghc Using ghc-pkg version 8.0.2 given by user at: /usr/bin/ghc-pkg No ghcjs found No ghcjs-pkg found No greencard found Using haddock version 2.17.3 found on system at: /usr/bin/haddock Using happy version 1.19.12 found on system at: /usr/bin/happy Using haskell-suite found on system at: haskell-suite-dummy-location Using haskell-suite-pkg found on system at: haskell-suite-pkg-dummy-location No hmake found Using hpc version 0.67 found on system at: /usr/bin/hpc Using hsc2hs version 0.68.1 found on system at: /usr/bin/hsc2hs No hscolour found No jhc found Using ld found on system at: /usr/bin/x86_64-pc-linux-gnu-ld No lhc found No lhc-pkg found Using pkg-config version 0.29.2 found on system at: /usr/bin/pkg-config Using strip version 2.34 found on system at: /usr/bin/strip Using tar found on system at: /bin/tar No uhc found >>> Source configured. >>> Compiling source in /var/tmp/portage/dev-haskell/biosff-0.3.7.1/work/biosff-0.3.7.1 ... ./setup build Building biosff-0.3.7.1... Preprocessing library biosff-0.3.7.1... [1 of 3] Compiling Bio.Sequence.SFF_name ( src/Bio/Sequence/SFF_name.hs, dist/build/Bio/Sequence/SFF_name.o ) [2 of 3] Compiling Bio.Sequence.SFF ( src/Bio/Sequence/SFF.hs, dist/build/Bio/Sequence/SFF.o ) src/Bio/Sequence/SFF.hs:68:32: warning: [-Wdeprecations] In the use of ‘runGetState’ (imported from Data.Binary.Get): Deprecated: "Use runGetIncremental instead. This function will be removed." src/Bio/Sequence/SFF.hs:75:22: warning: [-Wdeprecations] In the use of ‘runGetState’ (imported from Data.Binary.Get): Deprecated: "Use runGetIncremental instead. This function will be removed." [3 of 3] Compiling Bio.Sequence.SFF_filters ( src/Bio/Sequence/SFF_filters.hs, dist/build/Bio/Sequence/SFF_filters.o ) Preprocessing executable 'frecover' for biosff-0.3.7.1... [1 of 3] Compiling Bio.Sequence.SFF_name ( src/Bio/Sequence/SFF_name.hs, dist/build/frecover/frecover-tmp/Bio/Sequence/SFF_name.dyn_o ) [2 of 3] Compiling Bio.Sequence.SFF ( src/Bio/Sequence/SFF.hs, dist/build/frecover/frecover-tmp/Bio/Sequence/SFF.dyn_o ) src/Bio/Sequence/SFF.hs:68:32: warning: [-Wdeprecations] In the use of ‘runGetState’ (imported from Data.Binary.Get): Deprecated: "Use runGetIncremental instead. This function will be removed." src/Bio/Sequence/SFF.hs:75:22: warning: [-Wdeprecations] In the use of ‘runGetState’ (imported from Data.Binary.Get): Deprecated: "Use runGetIncremental instead. This function will be removed." [3 of 3] Compiling Main ( src/FRecover/Main.hs, dist/build/frecover/frecover-tmp/Main.dyn_o ) Linking dist/build/frecover/frecover ... Preprocessing executable 'fclip' for biosff-0.3.7.1... [1 of 4] Compiling Options ( src/FClip/Options.hs, dist/build/fclip/fclip-tmp/Options.dyn_o ) src/FClip/Options.hs:5:1: error: Failed to load interface for ‘System.Console.CmdArgs’ It is a member of the hidden package ‘cmdargs-0.10.20’. Perhaps you need to add ‘cmdargs’ to the build-depends in your .cabal file. Use -v to see a list of the files searched for. * ERROR: dev-haskell/biosff-0.3.7.1::gentoo failed (compile phase): * setup build failed * * Call stack: * ebuild.sh, line 125: Called src_compile * environment, line 2647: Called haskell-cabal_src_compile * environment, line 1881: Called cabal_src_compile * environment, line 767: Called cabal-build * environment, line 525: Called die * The specific snippet of code: * ./setup "$@" || die "setup build failed" * * If you need support, post the output of `emerge --info '=dev-haskell/biosff-0.3.7.1::gentoo'`, * the complete build log and the output of `emerge -pqv '=dev-haskell/biosff-0.3.7.1::gentoo'`. * The complete build log is located at '/var/log/portage/dev-haskell:biosff-0.3.7.1:20200504-075915.log'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/dev-haskell/biosff-0.3.7.1/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/dev-haskell/biosff-0.3.7.1/temp/environment'. * Working directory: '/var/tmp/portage/dev-haskell/biosff-0.3.7.1/work/biosff-0.3.7.1' * S: '/var/tmp/portage/dev-haskell/biosff-0.3.7.1/work/biosff-0.3.7.1'