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Merge pull request #302189 from Kupac/fix_ChemmineOB

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rPackages.ChemmineOB: fix build
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Nick Cao 2024-04-13 11:14:19 -04:00 committed by GitHub
commit a14f05ccbc
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1 changed files with 27 additions and 1 deletions
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28
pkgs/development/r-modules/default.nix
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@ -332,7 +332,7 @@ let
Cairo = with pkgs; [ libtiff libjpeg cairo.dev xorg.libXt.dev fontconfig.lib ]; Cairo = with pkgs; [ libtiff libjpeg cairo.dev xorg.libXt.dev fontconfig.lib ];
Cardinal = [ pkgs.which ]; Cardinal = [ pkgs.which ];
chebpol = [ pkgs.fftw.dev ]; chebpol = [ pkgs.fftw.dev ];
ChemmineOB = with pkgs; [ openbabel pkg-config ]; ChemmineOB = [ pkgs.pkg-config ];
curl = [ pkgs.curl.dev ]; curl = [ pkgs.curl.dev ];
CytoML = [ pkgs.libxml2.dev ]; CytoML = [ pkgs.libxml2.dev ];
data_table = with pkgs; [ pkg-config zlib.dev ] ++ lib.optional stdenv.isDarwin pkgs.llvmPackages.openmp; data_table = with pkgs; [ pkg-config zlib.dev ] ++ lib.optional stdenv.isDarwin pkgs.llvmPackages.openmp;
@ -706,6 +706,7 @@ let
ragg = with pkgs; [ freetype.dev libpng.dev libtiff.dev zlib.dev libjpeg.dev bzip2.dev ] ++ lib.optional stdenv.isDarwin lerc.dev; ragg = with pkgs; [ freetype.dev libpng.dev libtiff.dev zlib.dev libjpeg.dev bzip2.dev ] ++ lib.optional stdenv.isDarwin lerc.dev;
qqconf = [ pkgs.fftw.dev ]; qqconf = [ pkgs.fftw.dev ];
vapour = with pkgs; [ proj.dev gdal ]; vapour = with pkgs; [ proj.dev gdal ];
ChemmineOB = [ pkgs.eigen ];
}; };
packagesRequiringX = [ packagesRequiringX = [
@ -1370,6 +1371,31 @@ let
PKGCONFIG_LIBS = "-Wl,-rpath,${lib.getLib pkgs.openssl}/lib -L${lib.getLib pkgs.openssl}/lib -L${pkgs.cyrus_sasl.out}/lib -L${pkgs.zlib.out}/lib -lssl -lcrypto -lsasl2 -lz"; PKGCONFIG_LIBS = "-Wl,-rpath,${lib.getLib pkgs.openssl}/lib -L${lib.getLib pkgs.openssl}/lib -L${pkgs.cyrus_sasl.out}/lib -L${pkgs.zlib.out}/lib -lssl -lcrypto -lsasl2 -lz";
}); });
ChemmineOB = let
# R package doesn't compile with the latest (unstable) version.
# Override from nixpkgs-23.11
openbabel3 = pkgs.openbabel.overrideAttrs (attrs: {
version = "3.1.1";
src = pkgs.fetchFromGitHub {
owner = "openbabel";
repo = "openbabel";
rev = "openbabel-${lib.replaceStrings ["."] ["-"] attrs.version}";
sha256 = "sha256-wQpgdfCyBAoh4pmj9j7wPTlMtraJ62w/EShxi/olVMY=";
};
});
in
old.ChemmineOB.overrideAttrs (attrs: {
# pkg-config knows openbabel-3 without the .0
# Eigen3 is also looked for in the wrong location
postPatch = ''
substituteInPlace configure \
--replace-fail openbabel-3.0 openbabel-3
substituteInPlace src/Makevars.in \
--replace-fail "-I/usr/include/eigen3" "-I${pkgs.eigen}/include/eigen3"
'';
buildInputs = attrs.buildInputs ++ [openbabel3];
});
ps = old.ps.overrideAttrs (attrs: { ps = old.ps.overrideAttrs (attrs: {
preConfigure = "patchShebangs configure"; preConfigure = "patchShebangs configure";
}); });