4.1.nix

{ stdenv, fetchurl, bzip2, gfortran, libX11, libXmu, libXt, libjpeg, libpng
, libtiff, ncurses, pango, pcre2, perl, readline, tcl, texLive, tk, xz, zlib
, less, texinfo, graphviz, icu, pkgconfig, bison, imake, which, jdk, blas, lapack
, curl, Cocoa, Foundation, libobjc, libcxx, tzdata, fetchpatch, lib
, withRecommendedPackages ? true
, enableStrictBarrier ? 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
, mkl
}:

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

stdenv.mkDerivation rec {
  name = "R-4.1.0";

  src = fetchurl {
    url = "https://cran.r-project.org/src/base/R-4/${name}.tar.gz";
    sha256 = "109732arm6dq6d6v3fl1nyx63lcvv9569j8g6r3s2b18sxcqkrp8";
  };

  dontUseImakeConfigure = true;

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

  patches = [
    ./no-usr-local-search-paths.patch
    # ./fix-failing-test.patch
  ];

  prePatch = lib.optionalString stdenv.isDarwin ''
    substituteInPlace configure --replace "-install_name libR.dylib" "-install_name $out/lib/R/lib/libR.dylib"
  '';

  dontDisableStatic = static;

  preConfigure = ''
    configureFlagsArray=(
      --disable-lto
      --with${lib.optionalString (!withRecommendedPackages) "out"}-recommended-packages
      # --with-blas="-L${blas}/lib -lblas -lmkl_gf_lp64 -lmkl_gnu_thread -lmkl_core "
      --with-blas="-L${mkl}/lib -Wl,--no-as-needed -lmkl_gf_lp64 -Wl,--start-group -lmkl_gnu_thread  -lmkl_core  -Wl,--end-group -fopenmp  -ldl -lpthread -lm"
      --with-lapack
      --with-readline
      --with-tcltk --with-tcl-config="${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"}
      ${if static then "--enable-R-static-lib" else "--enable-R-shlib"}
      AR=$(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=$(type -p ranlib)
      R_SHELL="${stdenv.shell}"
  '' + lib.optionalString stdenv.isDarwin ''
      --disable-R-framework
      OBJC="clang"
      CPPFLAGS="-isystem ${libcxx}/include/c++/v1"
      LDFLAGS="-L${libcxx}/lib"
  '' + ''
    )
    echo >>etc/Renviron.in "TCLLIBPATH=${tk}/lib"
    echo >>etc/Renviron.in "TZDIR=${tzdata}/share/zoneinfo"
  '';

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

  # 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 TZ=CET; bin/Rscript -e 'sessionInfo()'";

  enableParallelBuilding = true;

  setupHook = ./setup-hook.sh;

  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.
    '';

    platforms = platforms.all;
    hydraPlatforms = platforms.linux;

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