diff options
author | Justin Bedő <cu@cua0.org> | 2024-05-12 08:43:54 +1000 |
---|---|---|
committer | GitHub <noreply@github.com> | 2024-05-12 08:43:54 +1000 |
commit | 0d3377a696f110f746142176c4c5d79b2c1f7028 (patch) | |
tree | 07835ce9f9704aeccd563eaba047cecd70e73aac /pkgs | |
parent | 78c337ecc1de6ce8420c4860656a722c60441360 (diff) | |
parent | ffb6ffa430df38b9c867910b07421182f544288e (diff) |
Merge pull request #305638 from Kupac/fix_rsbml
rPackages.rsbml: fix build
Diffstat (limited to 'pkgs')
-rw-r--r-- | pkgs/by-name/li/libsbml/package.nix | 58 | ||||
-rw-r--r-- | pkgs/development/r-modules/default.nix | 2 |
2 files changed, 60 insertions, 0 deletions
diff --git a/pkgs/by-name/li/libsbml/package.nix b/pkgs/by-name/li/libsbml/package.nix new file mode 100644 index 0000000000000..ce895beee0060 --- /dev/null +++ b/pkgs/by-name/li/libsbml/package.nix @@ -0,0 +1,58 @@ +{ + 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; + }; +}) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index 2565d1004fb3f..8d4004d7580f3 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -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 ]; |