diff options
Diffstat (limited to 'pkgs/development/r-modules/default.nix')
| -rw-r--r-- | pkgs/development/r-modules/default.nix | 96 |
1 files changed, 65 insertions, 31 deletions
diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index 43aacdddb6e6..37930d4c67b0 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -339,7 +339,8 @@ let adimpro = [ pkgs.imagemagick ]; animation = [ pkgs.which ]; Apollonius = with pkgs; [ pkg-config gmp.dev mpfr.dev ]; - arrow = with pkgs; [ pkg-config cmake ] ++ lib.optionals stdenv.isDarwin [ intltool ]; + arrow = with pkgs; [ pkg-config cmake ] ++ lib.optionals stdenv.hostPlatform.isDarwin [ intltool ]; + alcyon = with pkgs; [ cmake which ]; audio = [ pkgs.portaudio ]; BayesSAE = [ pkgs.gsl ]; BayesVarSel = [ pkgs.gsl ]; @@ -363,7 +364,7 @@ let clarabel = [ pkgs.cargo ]; curl = [ pkgs.curl.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.hostPlatform.isDarwin pkgs.llvmPackages.openmp; devEMF = with pkgs; [ xorg.libXft.dev ]; diversitree = with pkgs; [ gsl fftw ]; exactextractr = [ pkgs.geos ]; @@ -423,8 +424,9 @@ let rvg = [ pkgs.libpng.dev ]; MAGEE = [ pkgs.zlib.dev pkgs.bzip2.dev ]; magick = [ pkgs.imagemagick.dev ]; - ModelMetrics = lib.optional stdenv.isDarwin pkgs.llvmPackages.openmp; + ModelMetrics = lib.optional stdenv.hostPlatform.isDarwin pkgs.llvmPackages.openmp; mvabund = [ pkgs.gsl ]; + mcrPioda = [ pkgs.gsl ]; mwaved = [ pkgs.fftw.dev ]; mzR = with pkgs; [ zlib netcdf ]; nanonext = with pkgs; [ mbedtls nng ]; @@ -438,7 +440,7 @@ let pander = with pkgs; [ pandoc which ]; pbdMPI = [ pkgs.mpi ]; pbdPROF = [ pkgs.mpi ]; - pbdZMQ = [ pkgs.pkg-config ] ++ lib.optionals stdenv.isDarwin [ pkgs.which ]; + pbdZMQ = [ pkgs.pkg-config ] ++ lib.optionals stdenv.hostPlatform.isDarwin [ pkgs.which ]; pcaL1 = [ pkgs.pkg-config pkgs.clp ]; pdftools = [ pkgs.poppler.dev ]; PEPBVS = [ pkgs.gsl ]; @@ -455,6 +457,7 @@ let RcppGSL = [ pkgs.gsl ]; RcppZiggurat = [ pkgs.gsl ]; reprex = [ pkgs.which ]; + resultant = with pkgs; [ gmp.dev mpfr.dev pkg-config ]; rgdal = with pkgs; [ proj.dev gdal ]; Rhisat2 = [ pkgs.which pkgs.hostname ]; gdalcubes = [ pkgs.pkg-config ]; @@ -474,7 +477,7 @@ let RMySQL = with pkgs; [ zlib libmysqlclient openssl.dev ]; RNetCDF = with pkgs; [ netcdf udunits ]; RODBC = [ pkgs.libiodbc ]; - rpanel = [ pkgs.bwidget ]; + rpanel = [ pkgs.tclPackages.bwidget ]; Rpoppler = [ pkgs.poppler ]; RPostgres = with pkgs; [ postgresql ]; RPostgreSQL = with pkgs; [ postgresql postgresql ]; @@ -533,7 +536,7 @@ let V8 = [ pkgs.nodejs.libv8 ]; XBRL = with pkgs; [ zlib libxml2.dev ]; XLConnect = [ pkgs.jdk ]; - xml2 = [ pkgs.libxml2.dev ] ++ lib.optionals stdenv.isDarwin [ pkgs.perl ]; + xml2 = [ pkgs.libxml2.dev ] ++ lib.optionals stdenv.hostPlatform.isDarwin [ pkgs.perl ]; XML = with pkgs; [ libtool libxml2.dev xmlsec libxslt ]; affyPLM = [ pkgs.zlib.dev ]; BitSeq = [ pkgs.zlib.dev ]; @@ -579,6 +582,7 @@ let RcppCWB = [ pkgs.pkg-config pkgs.pcre2 ]; redux = [ pkgs.pkg-config ]; rswipl = with pkgs; [ cmake pkg-config ]; + scorematchingad = [ pkgs.cmake ]; rrd = [ pkgs.pkg-config ]; surveyvoi = [ pkgs.pkg-config ]; Rbwa = [ pkgs.zlib.dev ]; @@ -607,8 +611,8 @@ let unrtf = with pkgs; [ xz.dev bzip2.dev zlib.dev icu.dev libdeflate ]; nat = [ pkgs.which ]; nat_templatebrains = [ pkgs.which ]; - pbdZMQ = [ pkgs.zeromq ] ++ lib.optionals stdenv.isDarwin [ pkgs.darwin.binutils ]; - bigmemory = lib.optionals stdenv.isLinux [ pkgs.libuuid.dev ]; + pbdZMQ = [ pkgs.zeromq ] ++ lib.optionals stdenv.hostPlatform.isDarwin [ pkgs.darwin.binutils ]; + bigmemory = lib.optionals stdenv.hostPlatform.isLinux [ pkgs.libuuid.dev ]; bayesWatch = [ pkgs.boost.dev ]; clustermq = [ pkgs.pkg-config ]; coga = [ pkgs.gsl.dev ]; @@ -643,9 +647,10 @@ let gdalcubes = with pkgs; [ proj.dev gdal sqlite.dev netcdf ]; rsbml = [ pkgs.libsbml ]; SuperGauss = [ pkgs.pkg-config pkgs.fftw.dev]; + ravetools = with pkgs; [ pkg-config fftw.dev]; specklestar = [ pkgs.fftw.dev ]; cartogramR = [ pkgs.fftw.dev ]; - jqr = [ pkgs.jq.lib ]; + jqr = [ pkgs.jq.out ]; kza = [ pkgs.pkg-config ]; igraph = with pkgs; [ gmp libxml2.dev glpk ]; interpolation = [ pkgs.gmp ]; @@ -670,6 +675,7 @@ let Cairo = [ pkgs.pkg-config ]; CLVTools = [ pkgs.gsl ]; excursions = [ pkgs.gsl ]; + OpenCL = with pkgs; [ opencl-clhpp ocl-icd ]; gpuMagic = [ pkgs.ocl-icd ]; JMcmprsk = [ pkgs.gsl ]; KSgeneral = [ pkgs.fftw.dev ]; @@ -792,7 +798,7 @@ let DropletUtils = [ pkgs.zlib.dev ]; RMariaDB = [ pkgs.libmysqlclient.dev ]; ijtiff = [ pkgs.libtiff ]; - 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.hostPlatform.isDarwin lerc.dev; qqconf = [ pkgs.fftw.dev ]; spFW = [ pkgs.fftw.dev ]; qspray = with pkgs; [ gmp.dev mpfr.dev ]; @@ -801,7 +807,7 @@ let sphereTessellation = with pkgs; [ gmp.dev mpfr.dev ]; vapour = with pkgs; [ proj.dev gdal ]; MedianaDesigner = [ pkgs.zlib.dev ]; - ChemmineOB = [ pkgs.eigen ]; + ChemmineOB = with pkgs; [ eigen openbabel ]; DGP4LCF = [ pkgs.lapack pkgs.blas ]; }; @@ -1049,10 +1055,11 @@ let }); timeless = old.timeless.overrideAttrs (attrs: { + preConfigure = "patchShebangs configure"; cargoDeps = pkgs.rustPlatform.fetchCargoTarball { src = attrs.src; sourceRoot = "timeless/src/rust"; - hash = "sha256-n0/52CV3NzWe7T3N6VoaURMxWrnqeYaUMPKkUy+LRQs="; + hash = "sha256-AccuRY3lfTXzaMnaYieKCEJErKo5132oSXgILbFhePI="; }; cargoRoot = "src/rust"; @@ -1084,6 +1091,36 @@ let ''; }); + alcyon = old.alcyon.overrideAttrs (attrs: { + configureFlags = [ + "--enable-force-openmp" + ]; + }); + + lwgeom = old.lwgeom.overrideAttrs (attrs: { + configureFlags = [ + "--with-proj-lib=${pkgs.lib.getLib pkgs.proj}/lib" + ]; + }); + + sf = old.sf.overrideAttrs (attrs: { + configureFlags = [ + "--with-proj-lib=${pkgs.lib.getLib pkgs.proj}/lib" + ]; + }); + + terra = old.terra.overrideAttrs (attrs: { + configureFlags = [ + "--with-proj-lib=${pkgs.lib.getLib pkgs.proj}/lib" + ]; + }); + + vapour = old.vapour.overrideAttrs (attrs: { + configureFlags = [ + "--with-proj-lib=${pkgs.lib.getLib pkgs.proj}/lib" + ]; + }); + rzmq = old.rzmq.overrideAttrs (attrs: { preConfigure = "patchShebangs configure"; }); @@ -1220,7 +1257,7 @@ let ModelMetrics = old.ModelMetrics.overrideAttrs (attrs: { env = (attrs.env or { }) // { - NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE + lib.optionalString stdenv.isDarwin " -fopenmp"; + NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE + lib.optionalString stdenv.hostPlatform.isDarwin " -fopenmp"; }; }); @@ -1275,7 +1312,7 @@ let }); pbdZMQ = old.pbdZMQ.overrideAttrs (attrs: { - postPatch = lib.optionalString stdenv.isDarwin '' + postPatch = lib.optionalString stdenv.hostPlatform.isDarwin '' for file in R/*.{r,r.in}; do sed -i 's#system("which \(\w\+\)"[^)]*)#"${pkgs.cctools}/bin/\1"#g' $file done @@ -1442,9 +1479,9 @@ let rpanel = old.rpanel.overrideAttrs (attrs: { preConfigure = '' - export TCLLIBPATH="${pkgs.bwidget}/lib/bwidget${pkgs.bwidget.version}" + export TCLLIBPATH="${pkgs.tclPackages.bwidget}/lib/bwidget${pkgs.tclPackages.bwidget.version}" ''; - TCLLIBPATH = "${pkgs.bwidget}/lib/bwidget${pkgs.bwidget.version}"; + TCLLIBPATH = "${pkgs.tclPackages.bwidget}/lib/bwidget${pkgs.tclPackages.bwidget.version}"; }); networkscaleup = old.networkscaleup.overrideAttrs (attrs: { @@ -1564,29 +1601,26 @@ let PKGCONFIG_LIBS = "-Wl,-rpath,${lib.getLib pkgs.openssl}/lib -L${lib.getLib pkgs.openssl}/lib -L${pkgs.cyrus_sasl.out}/lib -L${pkgs.zlib.out}/lib -lssl -lcrypto -lsasl2 -lz"; }); - ChemmineOB = let - # R package doesn't compile with the latest (unstable) version. - # Override from nixpkgs-23.11 - openbabel3 = pkgs.openbabel.overrideAttrs (attrs: { - version = "3.1.1"; - src = pkgs.fetchFromGitHub { - owner = "openbabel"; - repo = "openbabel"; - rev = "openbabel-${lib.replaceStrings ["."] ["-"] attrs.version}"; - sha256 = "sha256-wQpgdfCyBAoh4pmj9j7wPTlMtraJ62w/EShxi/olVMY="; - }; - }); - in - old.ChemmineOB.overrideAttrs (attrs: { + ChemmineOB = old.ChemmineOB.overrideAttrs (attrs: { # pkg-config knows openbabel-3 without the .0 # Eigen3 is also looked for in the wrong location + # pointer was changed in newer version of openbabel: + # https://github.com/openbabel/openbabel/commit/305a6fd3183540e4a8ae1d79d10bf1860e6aa373 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" + substituteInPlace src/ChemmineOB.cpp \ + --replace-fail "obsharedptr<" "std::shared_ptr<" ''; - buildInputs = attrs.buildInputs ++ [openbabel3]; + + # copied from fastnlo-toolkit: + # None of our currently packaged versions of swig are C++17-friendly + # Use a workaround from https://github.com/swig/swig/issues/1538 + env = (attrs.env or { }) // { + NIX_CFLAGS_COMPILE = (attrs.env.NIX_CFLAGS_COMPILE or "") + lib.optionalString stdenv.hostPlatform.isDarwin " -D_LIBCPP_ENABLE_CXX17_REMOVED_FEATURES"; + }; }); ps = old.ps.overrideAttrs (attrs: { |