Unverified Commit 0d3377a6 authored by Justin Bedő's avatar Justin Bedő Committed by GitHub
Browse files

Merge pull request #305638 from Kupac/fix_rsbml 

rPackages.rsbml: fix build
parents 78c337ec ffb6ffa4

pkgs/by-name/li/libsbml/package.nix

0 → 100644
+58 −0
Original line number Diff line number Diff line 
{

  lib,

  stdenv,

  fetchFromGitHub,

  fetchpatch,

  cmake,

  pkg-config,

  bzip2,

  libxml2,

  swig,

}:

stdenv.mkDerivation (attrs: {

  pname = "libsbml";

  version = "5.20.2";



  src = fetchFromGitHub {

    owner = "sbmlteam";

    repo = "libsbml";

    rev = "v${attrs.version}";

    hash = "sha256-8JT2r0zuf61VewtZaOAccaOUmDlQPnllA0fXE9rT5X8=";

  };



  patches = [

    # This should be in next release, remember to remove fetchpatch

    (fetchpatch {

      name = "fix-xmlerror-conversion.patch";

      url = "https://github.com/sbmlteam/libsbml/pull/358.patch";

      hash = "sha256-uirG6XJ+w0hqBUEAGDnzhHoVtJVRdN1eqBYeneKMBao=";

    })

  ];



  nativeBuildInputs = [

    cmake

    pkg-config

    swig

  ];



  buildInputs = [

    bzip2.dev

    libxml2

  ];



  # libSBML doesn't always make use of pkg-config

  cmakeFlags = [

    "-DLIBXML_INCLUDE_DIR=${lib.getDev libxml2}/include/libxml2"

    "-DLIBXML_LIBRARY=${lib.getLib libxml2}/lib/libxml2${stdenv.hostPlatform.extensions.sharedLibrary}"

    "-DPKG_CONFIG_EXECUTABLE=${lib.getBin pkg-config}/bin/pkg-config"

    "-DSWIG_EXECUTABLE=${lib.getBin swig}/bin/swig"

  ];



  meta = with lib; {

    description = "Library for manipulating Systems Biology Markup Language (SBML)";

    homepage = "https://github.com/sbmlteam/libsbml";

    license = licenses.lgpl21Only;

    maintainers = [maintainers.kupac];

    platforms = platforms.all;

  };

})

pkgs/development/r-modules/default.nix

+2 −0
Original line number Diff line number Diff line
@@ -380,6 +380,7 @@ let 
    LOMAR = [ pkgs.gmp.dev ];

    lpsymphony = with pkgs; [ pkg-config gfortran gettext ];

    lwgeom = with pkgs; [ proj geos gdal ];

    rsbml = [ pkgs.pkg-config ];

    rvg = [ pkgs.libpng.dev ];

    MAGEE = [ pkgs.zlib.dev pkgs.bzip2.dev ];

    magick = [ pkgs.imagemagick.dev ];
@@ -589,6 +590,7 @@ let 
    gdtools = [ pkgs.pkg-config ];

    archive = [ pkgs.libarchive];

    gdalcubes = with pkgs; [ proj.dev gdal sqlite.dev netcdf ];

    rsbml = [ pkgs.libsbml ];

    SuperGauss = [ pkgs.pkg-config pkgs.fftw.dev];

    specklestar = [ pkgs.fftw.dev ];

    cartogramR = [ pkgs.fftw.dev ];