Unverified Commit 2e8bf9f3 authored by Justin Bedő's avatar Justin Bedő Committed by GitHub
Browse files

rPackages: CRAN and BioC update (#434138)

parents 5d2bd32a 30cddbf9

pkgs/development/r-modules/bioc-experiment-packages.json

+4 −4
Original line number Diff line number Diff line
@@ -899,8 +899,8 @@ 
    },

    "PhyloProfileData": {

      "name": "PhyloProfileData",

      "version": "1.22.0",

      "sha256": "0zbs9aaf8xmz3is9vf54d0iib00ypa6vly5s207dbcj7l1x4h0yc",

      "version": "1.22.3",

      "sha256": "0bc702idbsnqs2fga4jd9qwqphc0hrv3j1hidwz26awkfwb8yv59",

      "depends": ["BiocStyle", "Biostrings", "ExperimentHub"]

    },

    "ProData": {
@@ -911,8 +911,8 @@ 
    },

    "ProteinGymR": {

      "name": "ProteinGymR",

      "version": "1.2.1",

      "sha256": "1xwva9gnfldgx2bw62zwz3wlc84k4jlnybq81nr0xqa6xdr9fycl",

      "version": "1.2.4",

      "sha256": "0czlxm1z5bpb096alwb96a3gwpv9244h0b8isbbfdiy70rcd21rm",

      "depends": ["AnnotationHub", "ComplexHeatmap", "ExperimentHub", "bio3d", "circlize", "dplyr", "forcats", "ggExtra", "ggdist", "gghalves", "ggplot2", "htmltools", "lifecycle", "pals", "purrr", "queryup", "r3dmol", "rlang", "spdl", "stringr", "tidyr", "tidyselect"]

    },

    "PtH2O2lipids": {

pkgs/development/r-modules/bioc-packages.json

+206 −207

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pkgs/development/r-modules/cran-packages.json

+6815 −4884

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pkgs/development/r-modules/default.nix

+57 −13
Original line number Diff line number Diff line
@@ -451,7 +451,10 @@ let 
      libjpeg

    ];

    bnpmr = [ pkgs.gsl ];

    caviarpd = [ pkgs.cargo ];

    caviarpd = with pkgs; [

      cargo

      rustc

    ];

    cairoDevice = [ pkgs.gtk2.dev ];

    Cairo = with pkgs; [

      libtiff
@@ -569,6 +572,11 @@ let 
    ];

    Rigraphlib = [ pkgs.cmake ];

    HiCseg = [ pkgs.gsl ];

    hypergeo2 = with pkgs; [

      gmp.dev

      mpfr.dev

      pkg-config

    ];

    imager = [ pkgs.xorg.libX11.dev ];

    imbibe = [ pkgs.zlib.dev ];

    image_CannyEdges = with pkgs; [
@@ -586,7 +594,10 @@ let 
    leidenAlg = [ pkgs.gmp.dev ];

    Libra = [ pkgs.gsl ];

    libstable4u = [ pkgs.gsl ];

    heck = [ pkgs.cargo ];

    heck = with pkgs; [

      cargo

      rustc

    ];

    LOMAR = [ pkgs.gmp.dev ];

    littler = [ pkgs.libdeflate ];

    lpsymphony = with pkgs; [
@@ -678,6 +689,11 @@ let 
    gdalcubes = [ pkgs.pkg-config ];

    rgeos = [ pkgs.geos ];

    Rglpk = [ pkgs.glpk ];

    RcppPlanc = with pkgs; [

      which

      cmake

      pkg-config

    ];

    RGtk2 = [ pkgs.gtk2.dev ];

    rhdf5 = [ pkgs.zlib ];

    Rhdf5lib = with pkgs; [ zlib.dev ];
@@ -1106,7 +1122,10 @@ let 
      fftw.dev

    ];

    specklestar = [ pkgs.fftw.dev ];

    cartogramR = [ pkgs.fftw.dev ];

    cartogramR = with pkgs; [

      fftw.dev

      pkg-config

    ];

    jqr = [ pkgs.jq.out ];

    kza = [ pkgs.pkg-config ];

    igraph = with pkgs; [
@@ -1114,7 +1133,10 @@ let 
      libxml2.dev

      glpk

    ];

    interpolation = [ pkgs.gmp ];

    interpolation = with pkgs; [

      gmp

      mpfr

    ];

    image_textlinedetector = with pkgs; [

      pkg-config

      opencv
@@ -1364,6 +1386,10 @@ let 
    crandep = [ pkgs.gsl ];

    catSurv = [ pkgs.gsl ];

    ccfindR = [ pkgs.gsl ];

    RcppPlanc = with pkgs; [

      hwloc

      hdf5.dev

    ];

    screenCounter = [ pkgs.zlib.dev ];

    SPARSEMODr = [ pkgs.gsl ];

    RKHSMetaMod = [ pkgs.gsl ];
@@ -1424,7 +1450,11 @@ let 
    ];

    DropletUtils = [ pkgs.zlib.dev ];

    RMariaDB = [ pkgs.libmysqlclient.dev ];

    ijtiff = [ pkgs.libtiff ];

    ijtiff = with pkgs; [

      libtiff

      libjpeg

      zlib

    ];

    ragg =

      with pkgs;

      [
@@ -1644,6 +1674,7 @@ let 
    "minired" # deprecated on CRAN



    # Impure network access during build

    "BulkSignalR"

    "waddR"

    "tiledb"

    "switchr"
@@ -1753,6 +1784,14 @@ let 
      postPatch = "patchShebangs configure";

    });



    arcgisplaces = old.arcgisplaces.overrideAttrs (attrs: {

      postPatch = "patchShebangs configure";

    });



    cartogramR = old.cartogramR.overrideAttrs (attrs: {

      postPatch = "patchShebangs configure";

    });



    rshift = old.rshift.overrideAttrs (attrs: {

      postPatch = "patchShebangs configure";

    });
@@ -1790,6 +1829,10 @@ let 
      '';

    });



    fcl = old.fcl.overrideAttrs (attrs: {

      postPatch = "patchShebangs configure";

    });



    fio = old.fio.overrideAttrs (attrs: {

      postPatch = "patchShebangs configure";

    });
@@ -1976,7 +2019,11 @@ let 
    });



    zoomerjoin = old.zoomerjoin.overrideAttrs (attrs: {

      nativeBuildInputs = [ pkgs.cargo ] ++ attrs.nativeBuildInputs;

      nativeBuildInputs = [

        pkgs.cargo

        pkgs.rustc

      ]

      ++ attrs.nativeBuildInputs;

      postPatch = "patchShebangs configure";

    });
@@ -1999,13 +2046,6 @@ let 
      postPatch = "patchShebangs configure";

    });



    graper = old.graper.overrideAttrs (attrs: {

      postPatch = ''

        substituteInPlace "src/Makevars" \

          --replace-fail "CXX_STD=CXX11" "CXX_STD=CXX14"

      '';

    });



    ocf = old.ocf.overrideAttrs (attrs: {

      postPatch = "patchShebangs configure";

    });
@@ -2705,6 +2745,10 @@ let 
      '';

    });



    webfakes = old.webfakes.overrideAttrs (_: {

      postPatch = "patchShebangs configure";

    });



    redland = old.redland.overrideAttrs (_: {

      PKGCONFIG_CFLAGS = "-I${pkgs.redland}/include -I${pkgs.librdf_raptor2}/include/raptor2 -I${pkgs.librdf_rasqal}/include/rasqal";

      PKGCONFIG_LIBS = "-L${pkgs.redland}/lib -L${pkgs.librdf_raptor2}/lib -L${pkgs.librdf_rasqal}/lib -lrdf -lraptor2 -lrasqal";