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tweag / HaskellR

The full power of R in Haskell.
https://tweag.github.io/HaskellR
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Missing (or bad) C library: R on Manjaro Linux #427

Closed nevrome closed 1 month ago

nevrome commented 1 month ago

Thank you for the work on this amazing package. I stumbled over the 2014 paper, realized that inline-r may allow me to use R's brilliant plotting features from within some of my Haskell projects and decided to give it a try. Unfortunately I failed to install inline-r as a dependency. Maybe you could give me some ideas how to overcome this.

Describe the bug I can not install inline-r as a dependency for my Haskell project.

$ stack install --pedantic
inline-r> configure
inline-r> Configuring inline-r-1.0.1...
inline-r> Error: Cabal-simple_DY68M0FN_3.8.1.0_ghc-9.4.7: Missing dependency on a
inline-r> foreign library:
inline-r> * Missing (or bad) C library: R
inline-r> This problem can usually be solved by installing the system package that
inline-r> provides this library (you may need the "-dev" version). If the library is
inline-r> already installed but in a non-standard location then you can use the flags
inline-r> --extra-include-dirs= and --extra-lib-dirs= to specify where it is.If the
inline-r> library file does exist, it may contain errors that are caught by the C
inline-r> compiler at the preprocessing stage. In this case you can re-run configure
inline-r> with the verbosity flag -v3 to see the error messages.
inline-r>

R is installed and I tried setting the paths manually on the command line:

stack install --extra-include-dirs=/usr/include/R/ --extra-lib-dirs=/usr/lib/R/lib/

This gives me the same result.

Here is the (slightly reduced, see [...]) output with `--cabal-verbosity 3` ``` $ stack install --extra-include-dirs=/usr/include/R/ --extra-lib-dirs=/usr/lib/R/lib/ --cabal-verbosity 3 inline-r> configure inline-r> Using Parsec parser inline-r> Configuring inline-r-1.0.1... inline-r> creating .stack-work/dist/x86_64-linux/ghc-9.4.7/build inline-r> creating .stack-work/dist/x86_64-linux/ghc-9.4.7 inline-r> creating .stack-work/dist/x86_64-linux inline-r> creating .stack-work/dist inline-r> creating .stack-work inline-r> creating .stack-work/dist inline-r> creating .stack-work/dist/x86_64-linux inline-r> creating .stack-work/dist/x86_64-linux/ghc-9.4.7 inline-r> creating .stack-work/dist/x86_64-linux/ghc-9.4.7/build inline-r> /home/clemens/.ghcup/ghc/9.4.7/bin/ghc --numeric-version inline-r> /home/clemens/.ghcup/ghc/9.4.7/bin/ghc is version 9.4.7 inline-r> /home/clemens/.ghcup/ghc/9.4.7/bin/ghc-pkg-9.4.7 --version inline-r> /home/clemens/.ghcup/ghc/9.4.7/bin/ghc-pkg-9.4.7 is version 9.4.7 inline-r> /home/clemens/.ghcup/ghc/9.4.7/bin/ghc --supported-languages inline-r> /home/clemens/.ghcup/ghc/9.4.7/bin/ghc --info inline-r> Reading installed packages... inline-r> /home/clemens/.ghcup/ghc/9.4.7/bin/ghc-pkg-9.4.7 dump --global -v0 inline-r> /home/clemens/.ghcup/ghc/9.4.7/bin/ghc-pkg-9.4.7 dump '--package-db=/home/clemens/.stack/snapshots/x86_64-linux/5d821f30b14d16ba2e81b52fb5ffd9cf016e56f09c93b51a16c4430a19698947/9.4.7/pkgdb' -v0 inline-r> /home/clemens/.ghcup/ghc/9.4.7/bin/ghc --print-libdir -fhide-source-paths inline-r> Finalized package description: inline-r> cabal-version: 2.2 inline-r> name: inline-r inline-r> version: 1.0.1 inline-r> license: BSD-3-Clause inline-r> license-file: LICENSE inline-r> maintainer: Mathieu Boespflug inline-r> author: Mathieu Boespflug, Facundo Dominguez, Alexander Vershilov inline-r> homepage: https://tweag.github.io/HaskellR inline-r> synopsis: inline-r> Seamlessly call R from Haskell and vice versa. No FFI required. inline-r> [..] inline-r> Dependency aeson ==2.1.2.1: using aeson-2.1.2.1 inline-r> Dependency base ==4.17.2.0: using base-4.17.2.0 inline-r> Dependency bytestring ==0.11.5.2: using bytestring-0.11.5.2 inline-r> Dependency containers ==0.6.7: using containers-0.6.7 inline-r> Dependency data-default-class ==0.1.2.0: using data-default-class-0.1.2.0 inline-r> Dependency deepseq ==1.4.8.0: using deepseq-1.4.8.0 inline-r> Dependency exceptions ==0.10.5: using exceptions-0.10.5 inline-r> Dependency heredoc ==0.2.0.0: using heredoc-0.2.0.0 inline-r> Dependency inline-c ==0.9.1.10: using inline-c-0.9.1.10 inline-r> Dependency mtl ==2.2.2: using mtl-2.2.2 inline-r> Dependency pretty ==1.1.3.6: using pretty-1.1.3.6 inline-r> Dependency primitive ==0.8.0.0: using primitive-0.8.0.0 inline-r> Dependency process ==1.6.17.0: using process-1.6.17.0 inline-r> Dependency reflection ==2.1.7: using reflection-2.1.7 inline-r> Dependency setenv ==0.1.1.3: using setenv-0.1.1.3 inline-r> Dependency singletons ==3.0.2: using singletons-3.0.2 inline-r> Dependency singletons-th ==3.1.1: using singletons-th-3.1.1 inline-r> Dependency template-haskell ==2.19.0.0: using template-haskell-2.19.0.0 inline-r> Dependency temporary ==1.3: using temporary-1.3 inline-r> Dependency text ==2.0.2: using text-2.0.2 inline-r> Dependency th-lift ==0.8.4: using th-lift-0.8.4 inline-r> Dependency th-orphans ==0.13.14: using th-orphans-0.13.14 inline-r> Dependency transformers ==0.5.6.2: using transformers-0.5.6.2 inline-r> Dependency unix ==2.7.3: using unix-2.7.3 inline-r> Dependency vector ==0.13.1.0: using vector-0.13.1.0 inline-r> Searching for alex in path. inline-r> Cannot find alex on the path inline-r> Searching for ar in path. inline-r> Found ar at /usr/bin/ar inline-r> Searching for c2hs in path. inline-r> Cannot find c2hs on the path inline-r> Searching for cpphs in path. inline-r> Cannot find cpphs on the path inline-r> Searching for doctest in path. inline-r> Cannot find doctest on the path inline-r> Searching for gcc in path. inline-r> Found gcc at /usr/bin/gcc inline-r> /usr/bin/gcc -dumpversion inline-r> /usr/bin/gcc is version 14.2.1 inline-r> Searching for ghcjs in path. inline-r> Cannot find ghcjs on the path inline-r> Searching for ghcjs-pkg in path. inline-r> Cannot find ghcjs-pkg on the path inline-r> Searching for greencard in path. inline-r> Cannot find greencard on the path inline-r> looking for tool haddock near compiler in /home/clemens/.ghcup/ghc/9.4.7/bin inline-r> candidate locations: inline-r> ["/home/clemens/.ghcup/ghc/9.4.7/bin/haddock-ghc-9.4.7","/home/clemens/.ghcup/ghc/9.4.7/bin/haddock-9.4.7","/home/clemens/.ghcup/ghc/9.4.7/bin/haddock","/home/clemens/.ghcup/ghc/9.4.7/bin/haddock"] inline-r> found haddock in /home/clemens/.ghcup/ghc/9.4.7/bin/haddock-ghc-9.4.7 inline-r> /home/clemens/.ghcup/ghc/9.4.7/bin/haddock-ghc-9.4.7 --version inline-r> /home/clemens/.ghcup/ghc/9.4.7/bin/haddock-ghc-9.4.7 is version 2.27.0 inline-r> Searching for happy in path. inline-r> Cannot find happy on the path inline-r> Searching for hmake in path. inline-r> Cannot find hmake on the path inline-r> looking for tool hpc near compiler in /home/clemens/.ghcup/ghc/9.4.7/bin inline-r> candidate locations: inline-r> ["/home/clemens/.ghcup/ghc/9.4.7/bin/hpc-ghc-9.4.7","/home/clemens/.ghcup/ghc/9.4.7/bin/hpc-9.4.7","/home/clemens/.ghcup/ghc/9.4.7/bin/hpc","/home/clemens/.ghcup/ghc/9.4.7/bin/hpc"] inline-r> found hpc in /home/clemens/.ghcup/ghc/9.4.7/bin/hpc-ghc-9.4.7 inline-r> /home/clemens/.ghcup/ghc/9.4.7/bin/hpc-ghc-9.4.7 version inline-r> /home/clemens/.ghcup/ghc/9.4.7/bin/hpc-ghc-9.4.7 is version 0.68 inline-r> looking for tool hsc2hs near compiler in /home/clemens/.ghcup/ghc/9.4.7/bin inline-r> candidate locations: inline-r> ["/home/clemens/.ghcup/ghc/9.4.7/bin/hsc2hs-ghc-9.4.7","/home/clemens/.ghcup/ghc/9.4.7/bin/hsc2hs-9.4.7","/home/clemens/.ghcup/ghc/9.4.7/bin/hsc2hs","/home/clemens/.ghcup/ghc/9.4.7/bin/hsc2hs"] inline-r> found hsc2hs in /home/clemens/.ghcup/ghc/9.4.7/bin/hsc2hs-ghc-9.4.7 inline-r> /home/clemens/.ghcup/ghc/9.4.7/bin/hsc2hs-ghc-9.4.7 --version inline-r> /home/clemens/.ghcup/ghc/9.4.7/bin/hsc2hs-ghc-9.4.7 is version 0.68.8 inline-r> Searching for HsColour in path. inline-r> Cannot find HsColour on the path inline-r> Searching for jhc in path. inline-r> Cannot find jhc on the path inline-r> Searching for ld.gold in path. inline-r> Found ld.gold at /usr/bin/ld.gold inline-r> Environment: [...] inline-r> /home/clemens/.ghcup/ghc/9.4.7/bin/ghc -hide-all-packages -c /tmp/7115-0.c -o /tmp/7115-1.o -fhide-source-paths inline-r> /usr/bin/ld.gold -x -r /tmp/7115-1.o -o /tmp/7115-2.o inline-r> Searching for pkg-config in path. inline-r> Found pkg-config at /usr/bin/pkg-config inline-r> /usr/bin/pkg-config --version inline-r> /usr/bin/pkg-config is version 2.1.1 inline-r> looking for tool runghc near compiler in /home/clemens/.ghcup/ghc/9.4.7/bin inline-r> candidate locations: inline-r> ["/home/clemens/.ghcup/ghc/9.4.7/bin/runghc-ghc-9.4.7","/home/clemens/.ghcup/ghc/9.4.7/bin/runghc-9.4.7","/home/clemens/.ghcup/ghc/9.4.7/bin/runghc","/home/clemens/.ghcup/ghc/9.4.7/bin/runghc"] inline-r> found runghc in /home/clemens/.ghcup/ghc/9.4.7/bin/runghc-9.4.7 inline-r> /home/clemens/.ghcup/ghc/9.4.7/bin/runghc-9.4.7 --version inline-r> /home/clemens/.ghcup/ghc/9.4.7/bin/runghc-9.4.7 is version 9.4.7 inline-r> Searching for strip in path. inline-r> Found strip at /usr/bin/strip inline-r> /usr/bin/strip --version inline-r> /usr/bin/strip is version 2.43 inline-r> Searching for tar in path. inline-r> Found tar at /usr/bin/tar inline-r> /usr/bin/tar --help inline-r> Searching for uhc in path. inline-r> Cannot find uhc on the path inline-r> /usr/bin/pkg-config --modversion libR inline-r> Dependency libR >=3.0: using version 4.4.1 inline-r> /usr/bin/pkg-config --cflags libR inline-r> /usr/bin/pkg-config --libs libR inline-r> /usr/bin/pkg-config --libs --static libR inline-r> Source component graph: component lib inline-r> Configured component graph: inline-r> component inline-r-1.0.1-D8Cee1Z5GsnGsuPVff7ush inline-r> include aeson-2.1.2.1-HhFysmwCIEh1zDIBJNuaKW inline-r> include base-4.17.2.0 inline-r> include bytestring-0.11.5.2 inline-r> include containers-0.6.7 inline-r> include data-default-class-0.1.2.0-HWomeRk5e2p3WGQsDTnuAN inline-r> include deepseq-1.4.8.0 inline-r> include exceptions-0.10.5 inline-r> include heredoc-0.2.0.0-ycCeR0BdHeLx5jgQD7BWu inline-r> include inline-c-0.9.1.10-B5MMBbOoe8FJ4WsIxMpF1J inline-r> include mtl-2.2.2 inline-r> include pretty-1.1.3.6 inline-r> include primitive-0.8.0.0-LlEyZnmQ2mlGS0nNflVSqQ inline-r> include process-1.6.17.0 inline-r> include reflection-2.1.7-L8rUbOjnHlG7HQ73YOua9e inline-r> include setenv-0.1.1.3-5X2tG8kGRXiEiTQvekWgx7 inline-r> include singletons-3.0.2-3DcR4SWVUp79j2YXjDDaPv inline-r> include singletons-th-3.1.1-IzYwz7x0G623iaZBgQBiIJ inline-r> include template-haskell-2.19.0.0 inline-r> include temporary-1.3-19FjmjtD5KU6XnRnwNXz93 inline-r> include text-2.0.2 inline-r> include th-lift-0.8.4-Hb96g2HGtQyHkKuMt8Wl3a inline-r> include th-orphans-0.13.14-L48kXpANKdOzSkhldMyay inline-r> include transformers-0.5.6.2 inline-r> include unix-2.7.3 inline-r> include vector-0.13.1.0-Evg9D5fxXkeFrKi6ag3zYO inline-r> Linked component graph: inline-r> unit inline-r-1.0.1-D8Cee1Z5GsnGsuPVff7ush inline-r> include aeson-2.1.2.1-HhFysmwCIEh1zDIBJNuaKW inline-r> include base-4.17.2.0 inline-r> include bytestring-0.11.5.2 inline-r> include containers-0.6.7 inline-r> include data-default-class-0.1.2.0-HWomeRk5e2p3WGQsDTnuAN inline-r> include deepseq-1.4.8.0 inline-r> include exceptions-0.10.5 inline-r> include heredoc-0.2.0.0-ycCeR0BdHeLx5jgQD7BWu inline-r> include inline-c-0.9.1.10-B5MMBbOoe8FJ4WsIxMpF1J inline-r> include mtl-2.2.2 inline-r> include pretty-1.1.3.6 inline-r> include primitive-0.8.0.0-LlEyZnmQ2mlGS0nNflVSqQ inline-r> include process-1.6.17.0 inline-r> include reflection-2.1.7-L8rUbOjnHlG7HQ73YOua9e inline-r> include setenv-0.1.1.3-5X2tG8kGRXiEiTQvekWgx7 inline-r> include singletons-3.0.2-3DcR4SWVUp79j2YXjDDaPv inline-r> include singletons-th-3.1.1-IzYwz7x0G623iaZBgQBiIJ inline-r> include template-haskell-2.19.0.0 inline-r> include temporary-1.3-19FjmjtD5KU6XnRnwNXz93 inline-r> include text-2.0.2 inline-r> include th-lift-0.8.4-Hb96g2HGtQyHkKuMt8Wl3a inline-r> include th-orphans-0.13.14-L48kXpANKdOzSkhldMyay inline-r> include transformers-0.5.6.2 inline-r> include unix-2.7.3 inline-r> include vector-0.13.1.0-Evg9D5fxXkeFrKi6ag3zYO inline-r> Control.Memory.Region=inline-r-1.0.1-D8Cee1Z5GsnGsuPVff7ush:Control.Memory.Region,Data.Vector.SEXP=inline-r-1.0.1-D8Cee1Z5GsnGsuPVff7ush:Data.Vector.SEXP,Data.Vector.SEXP.Base=inline-r-1.0.1-D8Cee1Z5GsnGsuPVff7ush:Data.Vector.SEXP.Base,Data.Vector.SEXP.Mutable=inline-r-1.0.1-D8Cee1Z5GsnGsuPVff7ush:Data.Vector.SEXP.Mutable,Foreign.R=inline-r-1.0.1-D8Cee1Z5GsnGsuPVff7ush:Foreign.R,Foreign.R.Constraints=inline-r-1.0.1-D8Cee1Z5GsnGsuPVff7ush:Foreign.R.Constraints,Foreign.R.Context=inline-r-1.0.1-D8Cee1Z5GsnGsuPVff7ush:Foreign.R.Context,Foreign.R.Embedded=inline-r-1.0.1-D8Cee1Z5GsnGsuPVff7ush:Foreign.R.Embedded,Foreign.R.Encoding=inline-r-1.0.1-D8Cee1Z5GsnGsuPVff7ush:Foreign.R.Encoding,Foreign.R.Error=inline-r-1.0.1-D8Cee1Z5GsnGsuPVff7ush:Foreign.R.Error,Foreign.R.EventLoop=inline-r-1.0.1-D8Cee1Z5GsnGsuPVff7ush:Foreign.R.EventLoop,Foreign.R.Internal=inline-r-1.0.1-D8Cee1Z5GsnGsuPVff7ush:Foreign.R.Internal,Foreign.R.Parse=inline-r-1.0.1-D8Cee1Z5GsnGsuPVff7ush:Foreign.R.Parse,Foreign.R.Type=inline-r-1.0.1-D8Cee1Z5GsnGsuPVff7ush:Foreign.R.Type,H.Prelude=inline-r-1.0.1-D8Cee1Z5GsnGsuPVff7ush:H.Prelude,H.Prelude.Interactive=inline-r-1.0.1-D8Cee1Z5GsnGsuPVff7ush:H.Prelude.Interactive,Language.R=inline-r-1.0.1-D8Cee1Z5GsnGsuPVff7ush:Language.R,Language.R.Debug=inline-r-1.0.1-D8Cee1Z5GsnGsuPVff7ush:Language.R.Debug,Language.R.Event=inline-r-1.0.1-D8Cee1Z5GsnGsuPVff7ush:Language.R.Event,Language.R.GC=inline-r-1.0.1-D8Cee1Z5GsnGsuPVff7ush:Language.R.GC,Language.R.Globals=inline-r-1.0.1-D8Cee1Z5GsnGsuPVff7ush:Language.R.Globals,Language.R.HExp=inline-r-1.0.1-D8Cee1Z5GsnGsuPVff7ush:Language.R.HExp,Language.R.Instance=inline-r-1.0.1-D8Cee1Z5GsnGsuPVff7ush:Language.R.Instance,Language.R.Internal=inline-r-1.0.1-D8Cee1Z5GsnGsuPVff7ush:Language.R.Internal,Language.R.Internal.FunWrappers=inline-r-1.0.1-D8Cee1Z5GsnGsuPVff7ush:Language.R.Internal.FunWrappers,Language.R.Internal.FunWrappers.TH=inline-r-1.0.1-D8Cee1Z5GsnGsuPVff7ush:Language.R.Internal.FunWrappers.TH,Language.R.Literal=inline-r-1.0.1-D8Cee1Z5GsnGsuPVff7ush:Language.R.Literal,Language.R.Matcher=inline-r-1.0.1-D8Cee1Z5GsnGsuPVff7ush:Language.R.Matcher,Language.R.QQ=inline-r-1.0.1-D8Cee1Z5GsnGsuPVff7ush:Language.R.QQ inline-r> Ready component graph: inline-r> definite inline-r-1.0.1-D8Cee1Z5GsnGsuPVff7ush inline-r> depends aeson-2.1.2.1-HhFysmwCIEh1zDIBJNuaKW inline-r> depends base-4.17.2.0 inline-r> depends bytestring-0.11.5.2 inline-r> depends containers-0.6.7 inline-r> depends data-default-class-0.1.2.0-HWomeRk5e2p3WGQsDTnuAN inline-r> depends deepseq-1.4.8.0 inline-r> depends exceptions-0.10.5 inline-r> depends heredoc-0.2.0.0-ycCeR0BdHeLx5jgQD7BWu inline-r> depends inline-c-0.9.1.10-B5MMBbOoe8FJ4WsIxMpF1J inline-r> depends mtl-2.2.2 inline-r> depends pretty-1.1.3.6 inline-r> depends primitive-0.8.0.0-LlEyZnmQ2mlGS0nNflVSqQ inline-r> depends process-1.6.17.0 inline-r> depends reflection-2.1.7-L8rUbOjnHlG7HQ73YOua9e inline-r> depends setenv-0.1.1.3-5X2tG8kGRXiEiTQvekWgx7 inline-r> depends singletons-3.0.2-3DcR4SWVUp79j2YXjDDaPv inline-r> depends singletons-th-3.1.1-IzYwz7x0G623iaZBgQBiIJ inline-r> depends template-haskell-2.19.0.0 inline-r> depends temporary-1.3-19FjmjtD5KU6XnRnwNXz93 inline-r> depends text-2.0.2 inline-r> depends th-lift-0.8.4-Hb96g2HGtQyHkKuMt8Wl3a inline-r> depends th-orphans-0.13.14-L48kXpANKdOzSkhldMyay inline-r> depends transformers-0.5.6.2 inline-r> depends unix-2.7.3 inline-r> depends vector-0.13.1.0-Evg9D5fxXkeFrKi6ag3zYO inline-r> Using Cabal-3.8.1.0 compiled by ghc-9.4 inline-r> Using compiler: ghc-9.4.7 inline-r> Using install prefix: /home/clemens/.cabal inline-r> Executables installed in: inline-r> /home/clemens/.stack/snapshots/x86_64-linux/5d821f30b14d16ba2e81b52fb5ffd9cf016e56f09c93b51a16c4430a19698947/9.4.7/bin inline-r> Libraries installed in: inline-r> /home/clemens/.stack/snapshots/x86_64-linux/5d821f30b14d16ba2e81b52fb5ffd9cf016e56f09c93b51a16c4430a19698947/9.4.7/lib/x86_64-linux-ghc-9.4.7/inline-r-1.0.1-D8Cee1Z5GsnGsuPVff7ush inline-r> Dynamic Libraries installed in: inline-r> /home/clemens/.stack/snapshots/x86_64-linux/5d821f30b14d16ba2e81b52fb5ffd9cf016e56f09c93b51a16c4430a19698947/9.4.7/lib/x86_64-linux-ghc-9.4.7 inline-r> Private executables installed in: inline-r> /home/clemens/.stack/snapshots/x86_64-linux/5d821f30b14d16ba2e81b52fb5ffd9cf016e56f09c93b51a16c4430a19698947/9.4.7/libexec/x86_64-linux-ghc-9.4.7/inline-r-1.0.1 inline-r> Data files installed in: inline-r> /home/clemens/.stack/snapshots/x86_64-linux/5d821f30b14d16ba2e81b52fb5ffd9cf016e56f09c93b51a16c4430a19698947/9.4.7/share/x86_64-linux-ghc-9.4.7/inline-r-1.0.1 inline-r> Documentation installed in: inline-r> /home/clemens/.stack/snapshots/x86_64-linux/5d821f30b14d16ba2e81b52fb5ffd9cf016e56f09c93b51a16c4430a19698947/9.4.7/doc/inline-r-1.0.1 inline-r> Configuration files installed in: inline-r> /home/clemens/.stack/snapshots/x86_64-linux/5d821f30b14d16ba2e81b52fb5ffd9cf016e56f09c93b51a16c4430a19698947/9.4.7/etc inline-r> No alex found inline-r> Using ar found on system at: /usr/bin/ar inline-r> No c2hs found inline-r> No cpphs found inline-r> No doctest found inline-r> Using gcc version 14.2.1 found on system at: /usr/bin/gcc inline-r> Using ghc version 9.4.7 given by user at: inline-r> /home/clemens/.ghcup/ghc/9.4.7/bin/ghc inline-r> Using ghc-pkg version 9.4.7 given by user at: inline-r> /home/clemens/.ghcup/ghc/9.4.7/bin/ghc-pkg-9.4.7 inline-r> No ghcjs found inline-r> No ghcjs-pkg found inline-r> No greencard found inline-r> Using haddock version 2.27.0 found on system at: inline-r> /home/clemens/.ghcup/ghc/9.4.7/bin/haddock-ghc-9.4.7 inline-r> No happy found inline-r> Using haskell-suite found on system at: haskell-suite-dummy-location inline-r> Using haskell-suite-pkg found on system at: haskell-suite-pkg-dummy-location inline-r> No hmake found inline-r> Using hpc version 0.68 found on system at: inline-r> /home/clemens/.ghcup/ghc/9.4.7/bin/hpc-ghc-9.4.7 inline-r> Using hsc2hs version 0.68.8 found on system at: inline-r> /home/clemens/.ghcup/ghc/9.4.7/bin/hsc2hs-ghc-9.4.7 inline-r> No hscolour found inline-r> No jhc found inline-r> Using ld found on system at: /usr/bin/ld.gold inline-r> Using pkg-config version 2.1.1 found on system at: /usr/bin/pkg-config inline-r> Using runghc version 9.4.7 found on system at: inline-r> /home/clemens/.ghcup/ghc/9.4.7/bin/runghc-9.4.7 inline-r> Using strip version 2.43 found on system at: /usr/bin/strip inline-r> Using tar found on system at: /usr/bin/tar inline-r> No uhc found inline-r> /usr/bin/gcc '-fuse-ld=gold' /tmp/7115-4.c -o /tmp/7115-5 '-D__GLASGOW_HASKELL__=904' '-Dlinux_BUILD_OS=1' '-Dx86_64_BUILD_ARCH=1' '-Dlinux_HOST_OS=1' '-Dx86_64_HOST_ARCH=1' -I.stack-work/dist/x86_64-linux/ghc-9.4.7/build/autogen -I.stack-work/dist/x86_64-linux/ghc-9.4.7/build/cbits -I./cbits -I/usr/include/R/ -I/usr/include/R -I. -I/home/clemens/.ghcup/ghc/9.4.7/lib/ghc-9.4.7/lib/../lib/x86_64-linux-ghc-9.4.7/process-1.6.17.0/include -I/home/clemens/.stack/snapshots/x86_64-linux/d9458aeeb3d669cf242624ce37488bc8c03689418c89a810484d223c4af7c15e/9.4.7/lib/x86_64-linux-ghc-9.4.7/vector-0.13.1.0-Evg9D5fxXkeFrKi6ag3zYO/include -I/home/clemens/.ghcup/ghc/9.4.7/lib/ghc-9.4.7/lib/../lib/x86_64-linux-ghc-9.4.7/unix-2.7.3/include -I/home/clemens/.ghcup/ghc/9.4.7/lib/ghc-9.4.7/lib/../lib/x86_64-linux-ghc-9.4.7/time-1.12.2/include -I/home/clemens/.stack/snapshots/x86_64-linux/d9458aeeb3d669cf242624ce37488bc8c03689418c89a810484d223c4af7c15e/9.4.7/lib/x86_64-linux-ghc-9.4.7/primitive-0.8.0.0-LlEyZnmQ2mlGS0nNflVSqQ/include -I/home/clemens/.ghcup/ghc/9.4.7/lib/ghc-9.4.7/lib/../lib/x86_64-linux-ghc-9.4.7/bytestring-0.11.5.2/include -I/home/clemens/.ghcup/ghc/9.4.7/lib/ghc-9.4.7/lib/../lib/x86_64-linux-ghc-9.4.7/base-4.17.2.0/include -I/home/clemens/.ghcup/ghc/9.4.7/lib/ghc-9.4.7/lib/../lib/x86_64-linux-ghc-9.4.7/ghc-bignum-1.3/include -I/home/clemens/.ghcup/ghc/9.4.7/lib/ghc-9.4.7/lib/../lib/x86_64-linux-ghc-9.4.7/rts-1.0.2/include -lR -L/usr/lib/R/lib/ -L/usr/lib/R/lib -Wl,--export-dynamic -fopenmp -Wl,-O1 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,-z,pack-relative-relocs '-flto=auto' 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-L/home/clemens/.ghcup/ghc/9.4.7/lib/ghc-9.4.7/lib/../lib/x86_64-linux-ghc-9.4.7/mtl-2.2.2 -L/home/clemens/.ghcup/ghc/9.4.7/lib/ghc-9.4.7/lib/../lib/x86_64-linux-ghc-9.4.7/transformers-0.5.6.2 -L/home/clemens/.ghcup/ghc/9.4.7/lib/ghc-9.4.7/lib/../lib/x86_64-linux-ghc-9.4.7/bytestring-0.11.5.2 -L/home/clemens/.ghcup/ghc/9.4.7/lib/ghc-9.4.7/lib/../lib/x86_64-linux-ghc-9.4.7/containers-0.6.7 -L/home/clemens/.stack/snapshots/x86_64-linux/d9458aeeb3d669cf242624ce37488bc8c03689418c89a810484d223c4af7c15e/9.4.7/lib/x86_64-linux-ghc-9.4.7/OneTuple-0.4.1.1-5m1ALA0bqJEAQoyOrWBAgI -L/home/clemens/.ghcup/ghc/9.4.7/lib/ghc-9.4.7/lib/../lib/x86_64-linux-ghc-9.4.7/template-haskell-2.19.0.0 -L/home/clemens/.ghcup/ghc/9.4.7/lib/ghc-9.4.7/lib/../lib/x86_64-linux-ghc-9.4.7/pretty-1.1.3.6 -L/home/clemens/.ghcup/ghc/9.4.7/lib/ghc-9.4.7/lib/../lib/x86_64-linux-ghc-9.4.7/deepseq-1.4.8.0 -L/home/clemens/.ghcup/ghc/9.4.7/lib/ghc-9.4.7/lib/../lib/x86_64-linux-ghc-9.4.7/array-0.5.4.0 -L/home/clemens/.ghcup/ghc/9.4.7/lib/ghc-9.4.7/lib/../lib/x86_64-linux-ghc-9.4.7/ghc-boot-th-9.4.7 -L/home/clemens/.ghcup/ghc/9.4.7/lib/ghc-9.4.7/lib/../lib/x86_64-linux-ghc-9.4.7/base-4.17.2.0 -L/home/clemens/.ghcup/ghc/9.4.7/lib/ghc-9.4.7/lib/../lib/x86_64-linux-ghc-9.4.7/ghc-bignum-1.3 -L/home/clemens/.ghcup/ghc/9.4.7/lib/ghc-9.4.7/lib/../lib/x86_64-linux-ghc-9.4.7/ghc-prim-0.9.1 -L/home/clemens/.ghcup/ghc/9.4.7/lib/ghc-9.4.7/lib/../lib/x86_64-linux-ghc-9.4.7/rts-1.0.2 inline-r> /usr/bin/gcc returned ExitFailure 1 with error message: inline-r> /usr/bin/ld.gold: pack-relative-relocs: unknown -z option inline-r> /usr/bin/ld.gold: use the --help option for usage information inline-r> collect2: error: ld returned 1 exit status inline-r> [...] inline-r> /usr/bin/gcc returned ExitFailure 1 with error message: inline-r> /usr/bin/ld.gold: pack-relative-relocs: unknown -z option inline-r> /usr/bin/ld.gold: use the --help option for usage information inline-r> collect2: error: ld returned 1 exit status inline-r> [...] inline-r> /usr/bin/gcc returned ExitFailure 1 with error message: inline-r> /usr/bin/ld.gold: pack-relative-relocs: unknown -z option inline-r> /usr/bin/ld.gold: use the --help option for usage information inline-r> collect2: error: ld returned 1 exit status inline-r> /usr/bin/gcc '-fuse-ld=gold' /tmp/7115-10.c -o /tmp/7115-11 -c '-D__GLASGOW_HASKELL__=904' '-Dlinux_BUILD_OS=1' '-Dx86_64_BUILD_ARCH=1' '-Dlinux_HOST_OS=1' '-Dx86_64_HOST_ARCH=1' -I.stack-work/dist/x86_64-linux/ghc-9.4.7/build/autogen -I.stack-work/dist/x86_64-linux/ghc-9.4.7/build/cbits -I./cbits -I/usr/include/R/ -I/usr/include/R -I. -I/home/clemens/.ghcup/ghc/9.4.7/lib/ghc-9.4.7/lib/../lib/x86_64-linux-ghc-9.4.7/process-1.6.17.0/include -I/home/clemens/.stack/snapshots/x86_64-linux/d9458aeeb3d669cf242624ce37488bc8c03689418c89a810484d223c4af7c15e/9.4.7/lib/x86_64-linux-ghc-9.4.7/vector-0.13.1.0-Evg9D5fxXkeFrKi6ag3zYO/include -I/home/clemens/.ghcup/ghc/9.4.7/lib/ghc-9.4.7/lib/../lib/x86_64-linux-ghc-9.4.7/unix-2.7.3/include -I/home/clemens/.ghcup/ghc/9.4.7/lib/ghc-9.4.7/lib/../lib/x86_64-linux-ghc-9.4.7/time-1.12.2/include -I/home/clemens/.stack/snapshots/x86_64-linux/d9458aeeb3d669cf242624ce37488bc8c03689418c89a810484d223c4af7c15e/9.4.7/lib/x86_64-linux-ghc-9.4.7/primitive-0.8.0.0-LlEyZnmQ2mlGS0nNflVSqQ/include -I/home/clemens/.ghcup/ghc/9.4.7/lib/ghc-9.4.7/lib/../lib/x86_64-linux-ghc-9.4.7/bytestring-0.11.5.2/include -I/home/clemens/.ghcup/ghc/9.4.7/lib/ghc-9.4.7/lib/../lib/x86_64-linux-ghc-9.4.7/base-4.17.2.0/include -I/home/clemens/.ghcup/ghc/9.4.7/lib/ghc-9.4.7/lib/../lib/x86_64-linux-ghc-9.4.7/ghc-bignum-1.3/include -I/home/clemens/.ghcup/ghc/9.4.7/lib/ghc-9.4.7/lib/../lib/x86_64-linux-ghc-9.4.7/rts-1.0.2/include inline-r> CallStack (from HasCallStack): inline-r> withMetadata, called at libraries/Cabal/Cabal/src/Distribution/Simple/Utils.hs:370:14 in Cabal-3.8.1.0:Distribution.Simple.Utils inline-r> Error: Cabal-simple_DY68M0FN_3.8.1.0_ghc-9.4.7: Missing dependency on a inline-r> foreign library: inline-r> * Missing (or bad) C library: R inline-r> This problem can usually be solved by installing the system package that inline-r> provides this library (you may need the "-dev" version). If the library is inline-r> already installed but in a non-standard location then you can use the flags inline-r> --extra-include-dirs= and --extra-lib-dirs= to specify where it is.If the inline-r> library file does exist, it may contain errors that are caught by the C inline-r> compiler at the preprocessing stage. In this case you can re-run configure inline-r> with the verbosity flag -v3 to see the error messages. inline-r> Progress 1/2 Error: [S-7282] Stack failed to execute the build plan. While executing the build plan, Stack encountered the error: [S-7011] While building package inline-r-1.0.1 (scroll up to its section to see the error) using: /home/clemens/.stack/setup-exe-cache/x86_64-linux/Cabal-simple_DY68M0FN_3.8.1.0_ghc-9.4.7 --verbose=3 --builddir=.stack-work/dist/x86_64-linux/ghc-9.4.7 configure --with-ghc=/home/clemens/.ghcup/ghc/9.4.7/bin/ghc --with-ghc-pkg=/home/clemens/.ghcup/ghc/9.4.7/bin/ghc-pkg-9.4.7 --user --package-db=clear --package-db=global --package-db=/home/clemens/.stack/snapshots/x86_64-linux/5d821f30b14d16ba2e81b52fb5ffd9cf016e56f09c93b51a16c4430a19698947/9.4.7/pkgdb --libdir=/home/clemens/.stack/snapshots/x86_64-linux/5d821f30b14d16ba2e81b52fb5ffd9cf016e56f09c93b51a16c4430a19698947/9.4.7/lib --bindir=/home/clemens/.stack/snapshots/x86_64-linux/5d821f30b14d16ba2e81b52fb5ffd9cf016e56f09c93b51a16c4430a19698947/9.4.7/bin --datadir=/home/clemens/.stack/snapshots/x86_64-linux/5d821f30b14d16ba2e81b52fb5ffd9cf016e56f09c93b51a16c4430a19698947/9.4.7/share --libexecdir=/home/clemens/.stack/snapshots/x86_64-linux/5d821f30b14d16ba2e81b52fb5ffd9cf016e56f09c93b51a16c4430a19698947/9.4.7/libexec --sysconfdir=/home/clemens/.stack/snapshots/x86_64-linux/5d821f30b14d16ba2e81b52fb5ffd9cf016e56f09c93b51a16c4430a19698947/9.4.7/etc --docdir=/home/clemens/.stack/snapshots/x86_64-linux/5d821f30b14d16ba2e81b52fb5ffd9cf016e56f09c93b51a16c4430a19698947/9.4.7/doc/inline-r-1.0.1 --htmldir=/home/clemens/.stack/snapshots/x86_64-linux/5d821f30b14d16ba2e81b52fb5ffd9cf016e56f09c93b51a16c4430a19698947/9.4.7/doc/inline-r-1.0.1 --haddockdir=/home/clemens/.stack/snapshots/x86_64-linux/5d821f30b14d16ba2e81b52fb5ffd9cf016e56f09c93b51a16c4430a19698947/9.4.7/doc/inline-r-1.0.1 --dependency=aeson=aeson-2.1.2.1-HhFysmwCIEh1zDIBJNuaKW --dependency=base=base-4.17.2.0 --dependency=bytestring=bytestring-0.11.5.2 --dependency=containers=containers-0.6.7 --dependency=data-default-class=data-default-class-0.1.2.0-HWomeRk5e2p3WGQsDTnuAN --dependency=deepseq=deepseq-1.4.8.0 --dependency=exceptions=exceptions-0.10.5 --dependency=heredoc=heredoc-0.2.0.0-ycCeR0BdHeLx5jgQD7BWu --dependency=inline-c=inline-c-0.9.1.10-B5MMBbOoe8FJ4WsIxMpF1J --dependency=mtl=mtl-2.2.2 --dependency=pretty=pretty-1.1.3.6 --dependency=primitive=primitive-0.8.0.0-LlEyZnmQ2mlGS0nNflVSqQ --dependency=process=process-1.6.17.0 --dependency=reflection=reflection-2.1.7-L8rUbOjnHlG7HQ73YOua9e --dependency=setenv=setenv-0.1.1.3-5X2tG8kGRXiEiTQvekWgx7 --dependency=singletons=singletons-3.0.2-3DcR4SWVUp79j2YXjDDaPv --dependency=singletons-th=singletons-th-3.1.1-IzYwz7x0G623iaZBgQBiIJ --dependency=template-haskell=template-haskell-2.19.0.0 --dependency=temporary=temporary-1.3-19FjmjtD5KU6XnRnwNXz93 --dependency=text=text-2.0.2 --dependency=th-lift=th-lift-0.8.4-Hb96g2HGtQyHkKuMt8Wl3a --dependency=th-orphans=th-orphans-0.13.14-L48kXpANKdOzSkhldMyay --dependency=transformers=transformers-0.5.6.2 --dependency=unix=unix-2.7.3 --dependency=vector=vector-0.13.1.0-Evg9D5fxXkeFrKi6ag3zYO --extra-include-dirs=/usr/include/R/ --extra-include-dirs=/usr/include/R --extra-lib-dirs=/usr/lib/R/lib/ --extra-lib-dirs=/usr/lib/R/lib --exact-configuration --ghc-option=-fhide-source-paths Process exited with code: ExitFailure 1 ```

To Reproduce I think this issue may be related to my system configuration or a version mismatch. I don't know how to make this easily reproducible.

Expected behavior The installation should run through and my code should get compiled for great good.

Environment

facundominguez commented 1 month ago

Thanks for the report @nevrome. The following error might indicate some disagreement about flags between Cabal, ghc, pkg-config, and the linker.

inline-r> /usr/bin/ld.gold: pack-relative-relocs: unknown -z option
inline-r> /usr/bin/ld.gold: use the --help option for usage information
inline-r> collect2: error: ld returned 1 exit status

Solving this issue would require investigating the tooling in your setup. If you figure it out, we could work that in the FAQ. Others might be able to help if you can share a docker container or some nix environment to reproduce it.

Also, a workaround could be to provision the environment with Nix.

nevrome commented 1 month ago

OK - thanks for pointing to the linker as the source of the issue. I found this Arch Linux this issue which confirms that there is indeed an issue with ld.gold under certain circumstances.

After a lot of experimenting I managed to change the default linker in the ghc settings file, in my case at ~/.ghcup/ghc/9.4.7/lib/ghc-9.4.7/lib/settings. There I replaced

,("C compiler link flags", "-fuse-ld=gold")

with

,("C compiler link flags", "-fuse-ld=bfd")

and this resolved the issue for me. My code compiles and inline-r seems to be functional (based on a simple print test).

Thanks for the help. Maybe it would indeed be helpful to add a short comment to the FAQ that points to the GHC settings file in case the linker acts up. In fact I struggled most to find out where exactly I can change the default linker after identifying ld.gold as the probable nuisance factor.

facundominguez commented 1 month ago

Thanks @nevrome. I contributed an addition to the FAQ in 30e7fa7.