Nixpkgs: hmatrix: broken libgfortran linkage

[akru]

Issue description

I compile self little package with hmatrix in dependencies and get troubles with linkage:

.../lts-9.10/8.0.2/bin/robodist: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory

$ ldd executable
        linux-vdso.so.1 (0x00007ffe9feea000)
        libblas.so => /nix/store/wgryyb0rx955fimy9qk2k74cw0092m44-blas-3.5.0/lib/libblas.so (0x00007fd9f29bb000)
        libm.so.6 => /nix/store/xzx1bv1d7z4mgg6sg6ly0jx609qvka4x-glibc-2.25-49/lib/libm.so.6 (0x00007fd9f26a8000)
        libgmp.so.10 => /nix/store/h4hz48cvx05f1gw6mcqrdkxvq8b2s2d5-gmp-6.1.2/lib/libgmp.so.10 (0x00007fd9f2415000)
        librt.so.1 => /nix/store/xzx1bv1d7z4mgg6sg6ly0jx609qvka4x-glibc-2.25-49/lib/librt.so.1 (0x00007fd9f220d000)
        libdl.so.2 => /nix/store/xzx1bv1d7z4mgg6sg6ly0jx609qvka4x-glibc-2.25-49/lib/libdl.so.2 (0x00007fd9f2009000)
        libpthread.so.0 => /nix/store/xzx1bv1d7z4mgg6sg6ly0jx609qvka4x-glibc-2.25-49/lib/libpthread.so.0 (0x00007fd9f1deb000)
        libc.so.6 => /nix/store/xzx1bv1d7z4mgg6sg6ly0jx609qvka4x-glibc-2.25-49/lib/libc.so.6 (0x00007fd9f1a4c000)
        /nix/store/xzx1bv1d7z4mgg6sg6ly0jx609qvka4x-glibc-2.25-49/lib/ld-linux-x86-64.so.2 (0x00007fd9f2c11000)
        libgfortran.so.3 => not found
        libgfortran.so.3 => /nix/store/b2dny33b8sdx6rw2l1gfa00a244nm37s-gfortran-6.4.0-lib/lib/libgfortran.so.3 (0x00007fd9f1727000)
        libgcc_s.so.1 => /nix/store/xzx1bv1d7z4mgg6sg6ly0jx609qvka4x-glibc-2.25-49/lib/libgcc_s.so.1 (0x00007fd9f1511000)
        libquadmath.so.0 => /nix/store/b2dny33b8sdx6rw2l1gfa00a244nm37s-gfortran-6.4.0-lib/lib/libquadmath.so.0 (0x00007fd9f12d2000)

In my opinion linkage broken in

       libgfortran.so.3 => not found
       libgfortran.so.3 => /nix/store/b2dny33b8sdx6rw2l1gfa00a244nm37s-gfortran-6.4.0-lib/lib/libgfortran.so.3 (0x00007fd9f1727000)

Steps to reproduce

Compile haskell executable with hmatrix as dependency.

Technical details

• System: 17.09.1869.cd9ce6dd60 (Hummingbird)
• Nix version: nix-env (Nix) 1.11.15
• Nixpkgs version: 17.09.1869.cd9ce6dd60
• Sandboxing enabled: build-use-sandbox = false

[vaibhavsagar]

Can you provide more details about the expression you're evaluating to get this output?

[volhovm]

I experience the same problem using stack/nix setup. My project is minimal, it depends on base and hmatrix only and doesn't contain any (almost) logic at all. Though stack build works, but stack ghci fails with the same as PR author had shared. Adding gfortran to packages section of stack.yaml doesn't help.

[akru]

1. stack new foo

stack.yaml

+nix:
+  packages: [ blas liblapack ]

foo.cabal

+     hmatrix

1. stack build

akru@krakov ~/devel/foo $ ldd .stack-work/install/x86_64-linux-nix/lts-10.2/8.2.2/lib/x86_64-linux-ghc-8.2.2/libHSfoo-0.1.0.0-CTCRiTYOB3j81v1wLDBJbt-ghc8.2.2.so                                                                                                     

        libHSstorable-complex-0.2.2-4WEqCO29MfMHlD0g6H5VIw-ghc8.2.2.so => /home/akru/.stack/snapshots/x86_64-linux-nix/lts-10.2/8.2.2/lib/x86_64-linux-ghc-8.2.2/libHSstorable-complex-0.2.2-4WEqCO29MfMHlD0g6H5VIw-ghc8.2.2.so (0x00007f2479fe6000)
        libHSsplit-0.2.3.2-7cayvoeRj5XIrIBUB58mMy-ghc8.2.2.so => /home/akru/.stack/snapshots/x86_64-linux-nix/lts-10.2/8.2.2/lib/x86_64-linux-ghc-8.2.2/libHSsplit-0.2.3.2-7cayvoeRj5XIrIBUB58mMy-ghc8.2.2.so (0x00007f2479dcd000)
        libHSrandom-1.1-LLUGZ7T9DqQ5vN0Jbcd0We-ghc8.2.2.so => /home/akru/.stack/snapshots/x86_64-linux-nix/lts-10.2/8.2.2/lib/x86_64-linux-ghc-8.2.2/libHSrandom-1.1-LLUGZ7T9DqQ5vN0Jbcd0We-ghc8.2.2.so (0x00007f2479b6b000)
        libHStime-1.8.0.2-ghc8.2.2.so => /nix/store/sr6pskh0xl1xm035p473scq2ac0bggci-ghc-8.2.2/lib/ghc-8.2.2/time-1.8.0.2/libHStime-1.8.0.2-ghc8.2.2.so (0x00007f247986e000)
        libHSbinary-0.8.5.1-ghc8.2.2.so => /nix/store/sr6pskh0xl1xm035p473scq2ac0bggci-ghc-8.2.2/lib/ghc-8.2.2/binary-0.8.5.1/libHSbinary-0.8.5.1-ghc8.2.2.so (0x00007f24795ca000)
        libHScontainers-0.5.10.2-ghc8.2.2.so => /nix/store/sr6pskh0xl1xm035p473scq2ac0bggci-ghc-8.2.2/lib/ghc-8.2.2/containers-0.5.10.2/libHScontainers-0.5.10.2-ghc8.2.2.so (0x00007f24790ec000)
        libHSbytestring-0.10.8.2-ghc8.2.2.so => /nix/store/sr6pskh0xl1xm035p473scq2ac0bggci-ghc-8.2.2/lib/ghc-8.2.2/bytestring-0.10.8.2/libHSbytestring-0.10.8.2-ghc8.2.2.so (0x00007f2478df8000)
        libHSdeepseq-1.4.3.0-ghc8.2.2.so => /nix/store/sr6pskh0xl1xm035p473scq2ac0bggci-ghc-8.2.2/lib/ghc-8.2.2/deepseq-1.4.3.0/libHSdeepseq-1.4.3.0-ghc8.2.2.so (0x00007f2478bdf000)
        libHSarray-0.5.2.0-ghc8.2.2.so => /nix/store/sr6pskh0xl1xm035p473scq2ac0bggci-ghc-8.2.2/lib/ghc-8.2.2/array-0.5.2.0/libHSarray-0.5.2.0-ghc8.2.2.so (0x00007f247895b000)
        libHSbase-4.10.1.0-ghc8.2.2.so => /nix/store/sr6pskh0xl1xm035p473scq2ac0bggci-ghc-8.2.2/lib/ghc-8.2.2/base-4.10.1.0/libHSbase-4.10.1.0-ghc8.2.2.so (0x00007f2477d94000)
        libHSinteger-gmp-1.0.1.0-ghc8.2.2.so => /nix/store/sr6pskh0xl1xm035p473scq2ac0bggci-ghc-8.2.2/lib/ghc-8.2.2/integer-gmp-1.0.1.0/libHSinteger-gmp-1.0.1.0-ghc8.2.2.so (0x00007f2477b59000)
        libHSghc-prim-0.5.1.1-ghc8.2.2.so => /nix/store/sr6pskh0xl1xm035p473scq2ac0bggci-ghc-8.2.2/lib/ghc-8.2.2/ghc-prim-0.5.1.1/libHSghc-prim-0.5.1.1-ghc8.2.2.so (0x00007f24774bd000)
        libblas.so => /nix/store/d86l8zyls7immy3hq9sydjxl28b797v4-blas-3.7.1/lib/libblas.so (0x00007f2477267000)
        libgmp.so.10 => /nix/store/2p7a3yb6hilmjch90p3bw56shn76a0h5-gmp-6.1.2/lib/libgmp.so.10 (0x00007f2476fd4000)
        libc.so.6 => /nix/store/glb7dzs11di2cl66rsi8f49wraaj0pqd-glibc-2.26-75/lib/libc.so.6 (0x00007f2476c21000)
        /nix/store/glb7dzs11di2cl66rsi8f49wraaj0pqd-glibc-2.26-75/lib64/ld-linux-x86-64.so.2 (0x00007f247baec000)
        libgfortran.so.3 => not found
        libgfortran.so.3 => /nix/store/bk86fm18kp3c0mr89vvjls9r3v0g0irz-gfortran-6.4.0-lib/lib/libgfortran.so.3 (0x00007f24768fc000)
        libgcc_s.so.1 => /nix/store/glb7dzs11di2cl66rsi8f49wraaj0pqd-glibc-2.26-75/lib/libgcc_s.so.1 (0x00007f24766e6000)
        libquadmath.so.0 => /nix/store/bk86fm18kp3c0mr89vvjls9r3v0g0irz-gfortran-6.4.0-lib/lib/libquadmath.so.0 (0x00007f24764a7000) 

[Fuuzetsu]

It will work if you add gfortran.cc.lib to your packages.

[Fuuzetsu]

cc @peti probably hmatrix should link out of the box

[cdepillabout]

I ran into this problem as well. I was able to fix it by using the suggestion by @Fuuzetsu. I am using a relatively recent version of nixpkgs unstable.

[dmjio]

I'm running into this as well (calling stack ghci with hmatrix). It appears liblapack in nixpkgs no longer has shared objects (if it ever did)? See below.

@Fuuzetsu, adding gfortran.cc.lib works well, but then this error arises

$ stack ghci
<command line>: can't load .so/.DLL for: liblapack.so 
  (liblapack.so: cannot open shared object file: No such file or directory)

tree /nix/store/pk0qn3xg3awg1354lm4xjl5nhxyi0dll-liblapack-3.8.0
`-- lib
    |-- cmake
    |   `-- lapack-3.8.0
    |       |-- lapack-config-version.cmake
    |       |-- lapack-config.cmake
    |       |-- lapack-targets-release.cmake
    |       `-- lapack-targets.cmake
    |-- libblas.a
    |-- liblapack.a
    `-- pkgconfig
        |-- blas.pc
        `-- lapack.pc

EDIT: Upon further inspection into the derivation, I see I can override and add shared libs.

{ config ? {                                                                                                                                   
    allowUnfree = true;                                                                                                                        
    packageOverrides = pkgs: {                                                                                                                 
      liblapack = pkgs.liblapack.override { shared = true; };                                                                                  
    };                                                                                                                                         
  }                                                                                                                                            
, json ? builtins.fromJSON (builtins.readFile ./nixpkgs.json)                                                                                  
, pkgs ? with json; import (builtins.fetchTarball {                                                                                            
    url = "https://github.com/NixOS/nixpkgs/archive/${rev}.tar.gz";                                                                            
    inherit sha256;                                                                                                                            
  }) { inherit config; }                                                                                                                       
, compiler ? "ghc844"                                                                                                                          
}:                  

cc @Fuuzetsu disregard please :)

[stale[bot]]

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[Fuuzetsu]

I think it's still broken.