depot/third_party/nixpkgs/pkgs/applications/science/math/R/default.nix

{ lib, stdenv, fetchurl, bzip2, gfortran, libX11, libXmu, libXt, libjpeg, libpng
, libtiff, ncurses, pango, pcre2, perl, readline, tcl, texlive, texLive, tk, xz, zlib
, less, texinfo, graphviz, icu, pkg-config, bison, imake, which, jdk, blas, lapack
, curl, Cocoa, Foundation, libobjc, libcxx, tzdata
, withRecommendedPackages ? true
, enableStrictBarrier ? false
, enableMemoryProfiling ? false
# R as of writing does not support outputting both .so and .a files; it outputs:
#     --enable-R-static-lib conflicts with --enable-R-shlib and will be ignored
, static ? false
, testers
}:

assert (!blas.isILP64) && (!lapack.isILP64);

stdenv.mkDerivation (finalAttrs: {
  pname = "R";
  version = "4.3.1";

  src = let
    inherit (finalAttrs) pname version;
  in fetchurl {
    url = "https://cran.r-project.org/src/base/R-${lib.versions.major version}/${pname}-${version}.tar.gz";
    sha256 = "sha256-jdC/JPECPG9hjDsxc4PSkbSklPQNc7mDrCL/6pnkupk=";
  };

  outputs = [ "out" "tex" ];

  dontUseImakeConfigure = true;

  nativeBuildInputs = [ pkg-config ];
  buildInputs = [
    bzip2 gfortran libX11 libXmu libXt libXt libjpeg libpng libtiff ncurses
    pango pcre2 perl readline texLive xz zlib less texinfo graphviz icu
    bison imake which blas lapack curl tcl tk jdk tzdata
  ] ++ lib.optionals stdenv.isDarwin [ Cocoa Foundation libobjc libcxx ];

  patches = [
    ./no-usr-local-search-paths.patch
  ];

  # Test of the examples for package 'tcltk' fails in Darwin sandbox. See:
  # https://github.com/NixOS/nixpkgs/issues/146131
  postPatch = lib.optionalString stdenv.isDarwin ''
    substituteInPlace configure \
      --replace "-install_name libRblas.dylib" "-install_name $out/lib/R/lib/libRblas.dylib" \
      --replace "-install_name libRlapack.dylib" "-install_name $out/lib/R/lib/libRlapack.dylib" \
      --replace "-install_name libR.dylib" "-install_name $out/lib/R/lib/libR.dylib"
    substituteInPlace tests/Examples/Makefile.in \
      --replace "test-Examples: test-Examples-Base" "test-Examples:" # do not test the examples
  '';

  dontDisableStatic = static;

  preConfigure = ''
    configureFlagsArray=(
      --disable-lto
      --with${lib.optionalString (!withRecommendedPackages) "out"}-recommended-packages
      --with-blas="-L${blas}/lib -lblas"
      --with-lapack="-L${lapack}/lib -llapack"
      --with-readline
      --with-tcltk --with-tcl-config="${tcl}/lib/tclConfig.sh" --with-tk-config="${tk}/lib/tkConfig.sh"
      --with-cairo
      --with-libpng
      --with-jpeglib
      --with-libtiff
      --with-ICU
      ${lib.optionalString enableStrictBarrier "--enable-strict-barrier"}
      ${lib.optionalString enableMemoryProfiling "--enable-memory-profiling"}
      ${if static then "--enable-R-static-lib" else "--enable-R-shlib"}
      AR=$(type -p ar)
      AWK=$(type -p gawk)
      CC=$(type -p cc)
      CXX=$(type -p c++)
      FC="${gfortran}/bin/gfortran" F77="${gfortran}/bin/gfortran"
      JAVA_HOME="${jdk}"
      RANLIB=$(type -p ranlib)
      r_cv_have_curl728=yes
      R_SHELL="${stdenv.shell}"
  '' + lib.optionalString stdenv.isDarwin ''
      --disable-R-framework
      --without-x
      OBJC="clang"
      CPPFLAGS="-isystem ${lib.getDev libcxx}/include/c++/v1"
      LDFLAGS="-L${lib.getLib libcxx}/lib"
  '' + ''
    )
    echo >>etc/Renviron.in "TCLLIBPATH=${tk}/lib"
    echo >>etc/Renviron.in "TZDIR=${tzdata}/share/zoneinfo"
  '';

  installTargets = [ "install" "install-info" "install-pdf" ];

  # move tex files to $tex for use with texlive.combine
  # add link in $out since ${R_SHARE_DIR}/texmf is hardcoded in several places
  postInstall = ''
    mv -T "$out/lib/R/share/texmf" "$tex"
    ln -s "$tex" "$out/lib/R/share/texmf"
  '';

  # The store path to "which" is baked into src/library/base/R/unix/system.unix.R,
  # but Nix cannot detect it as a run-time dependency because the installed file
  # is compiled and compressed, which hides the store path.
  postFixup = "echo ${which} > $out/nix-support/undetected-runtime-dependencies";

  doCheck = true;
  preCheck = "export HOME=$TMPDIR; export TZ=CET; bin/Rscript -e 'sessionInfo()'";

  enableParallelBuilding = true;

  setupHook = ./setup-hook.sh;

  passthru.tests.pkg-config = testers.testMetaPkgConfig finalAttrs.finalPackage;

  # make tex output available to texlive.combine
  passthru.pkgs = [ finalAttrs.finalPackage.tex ];
  passthru.tlType = "run";
  # dependencies (based on \RequirePackage in jss.cls, Rd.sty, Sweave.sty)
  passthru.tlDeps = with texlive; [ amsfonts amsmath fancyvrb graphics hyperref iftex jknapltx latex lm tools upquote url ];

  meta = with lib; {
    homepage = "http://www.r-project.org/";
    description = "Free software environment for statistical computing and graphics";
    license = licenses.gpl2Plus;

    longDescription = ''
      GNU R is a language and environment for statistical computing and
      graphics that provides a wide variety of statistical (linear and
      nonlinear modelling, classical statistical tests, time-series
      analysis, classification, clustering, ...) and graphical
      techniques, and is highly extensible. One of R's strengths is the
      ease with which well-designed publication-quality plots can be
      produced, including mathematical symbols and formulae where
      needed. R is an integrated suite of software facilities for data
      manipulation, calculation and graphical display. It includes an
      effective data handling and storage facility, a suite of operators
      for calculations on arrays, in particular matrices, a large,
      coherent, integrated collection of intermediate tools for data
      analysis, graphical facilities for data analysis and display
      either on-screen or on hardcopy, and a well-developed, simple and
      effective programming language which includes conditionals, loops,
      user-defined recursive functions and input and output facilities.
    '';

    pkgConfigModules = [ "libR" ];
    platforms = platforms.all;

    maintainers = with maintainers; [ jbedo ] ++ teams.sage.members;
  };
})