diff options
Diffstat (limited to 'pkgs/development/r-modules/default.nix')
| -rw-r--r-- | pkgs/development/r-modules/default.nix | 39 |
1 files changed, 37 insertions, 2 deletions
diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index de3cde2425cd..36302ccaa087 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -309,6 +309,7 @@ let }; packagesWithNativeBuildInputs = { + adbcpostgresql = [ pkgs.postgresql ]; arrow = [ pkgs.pkg-config pkgs.arrow-cpp ]; adimpro = [ pkgs.imagemagick ]; animation = [ pkgs.which ]; @@ -316,11 +317,13 @@ let BayesSAE = [ pkgs.gsl ]; BayesVarSel = [ pkgs.gsl ]; BayesXsrc = with pkgs; [ readline.dev ncurses gsl ]; + bioacoustics = [ pkgs.fftw.dev pkgs.cmake ]; bigGP = [ pkgs.mpi ]; bio3d = [ pkgs.zlib ]; BiocCheck = [ pkgs.which ]; Biostrings = [ pkgs.zlib ]; CellBarcode = [ pkgs.zlib ]; + cld3 = [ pkgs.protobuf ]; bnpmr = [ pkgs.gsl ]; cairoDevice = [ pkgs.gtk2.dev ]; Cairo = with pkgs; [ libtiff libjpeg cairo.dev xorg.libXt.dev fontconfig.lib ]; @@ -338,6 +341,7 @@ let fftwtools = with pkgs; [ fftw.dev pkg-config ]; Formula = [ pkgs.gmp ]; gdtools = with pkgs; [ cairo.dev fontconfig.lib freetype.dev ]; + GeneralizedWendland = [ pkgs.gsl ]; ggiraph = with pkgs; [ pkgs.libpng.dev ]; git2r = with pkgs; [ zlib.dev openssl.dev libssh2.dev libgit2 pkg-config ]; GLAD = [ pkgs.gsl ]; @@ -346,10 +350,12 @@ let GPBayes = [ pkgs.gsl ]; graphscan = [ pkgs.gsl ]; gsl = [ pkgs.gsl ]; + gslnls = [ pkgs.gsl ]; gert = [ pkgs.libgit2 ]; haven = with pkgs; [ zlib.dev ]; h5vc = [ pkgs.zlib.dev ]; highs = [ pkgs.which pkgs.cmake ]; + rbedrock = [ pkgs.zlib.dev pkgs.which pkgs.cmake ]; HiCseg = [ pkgs.gsl ]; imager = [ pkgs.xorg.libX11.dev ]; iBMQ = [ pkgs.gsl ]; @@ -359,6 +365,7 @@ let jqr = [ pkgs.jq.dev ]; KFKSDS = [ pkgs.gsl ]; kza = [ pkgs.fftw.dev ]; + leidenAlg = [ pkgs.gmp.dev ]; Libra = [ pkgs.gsl ]; LOMAR = [ pkgs.gmp.dev ]; lpsymphony = with pkgs; [ pkg-config gfortran gettext ]; @@ -380,6 +387,7 @@ let pbdMPI = [ pkgs.mpi ]; pbdPROF = [ pkgs.mpi ]; pbdZMQ = [ pkgs.pkg-config ] ++ lib.optionals stdenv.isDarwin [ pkgs.which ]; + pcaL1 = [ pkgs.pkg-config pkgs.clp ]; pdftools = [ pkgs.poppler.dev ]; phytools = [ pkgs.which ]; PKI = [ pkgs.openssl.dev ]; @@ -405,7 +413,7 @@ let rjags = [ pkgs.jags ]; rJava = with pkgs; [ zlib bzip2.dev icu xz.dev pcre.dev jdk libzip ]; Rlibeemd = [ pkgs.gsl ]; - rmatio = [ pkgs.zlib.dev ]; + rmatio = [ pkgs.zlib.dev pkgs.pkg-config ]; Rmpfr = with pkgs; [ gmp mpfr.dev ]; Rmpi = [ pkgs.mpi ]; RMySQL = with pkgs; [ zlib libmysqlclient openssl.dev ]; @@ -426,6 +434,7 @@ let httpuv = [ pkgs.zlib.dev ]; clustermq = [ pkgs.zeromq ]; SAVE = with pkgs; [ zlib bzip2 icu xz pcre ]; + salso = [ pkgs.cargo ]; sdcTable = with pkgs; [ gmp glpk ]; seewave = with pkgs; [ fftw.dev libsndfile.dev ]; seqinr = [ pkgs.zlib.dev ]; @@ -435,6 +444,7 @@ let strawr = with pkgs; [ curl.dev ]; terra = with pkgs; [ gdal proj geos ]; apcf = with pkgs; [ geos ]; + SemiCompRisks = [ pkgs.gsl ]; showtext = with pkgs; [ zlib libpng icu freetype.dev ]; simplexreg = [ pkgs.gsl ]; spate = [ pkgs.fftw.dev ]; @@ -446,6 +456,7 @@ let sysfonts = with pkgs; [ zlib libpng freetype.dev ]; systemfonts = with pkgs; [ fontconfig.dev freetype.dev ]; TAQMNGR = [ pkgs.zlib.dev ]; + TDA = [ pkgs.gmp ]; tesseract = with pkgs; [ tesseract leptonica ]; tiff = [ pkgs.libtiff.dev ]; tkrplot = with pkgs; [ xorg.libX11 tk.dev ]; @@ -514,16 +525,20 @@ let textshaping = [ pkgs.pkg-config ]; ragg = [ pkgs.pkg-config ]; qqconf = [ pkgs.pkg-config ]; + vapour = [ pkgs.pkg-config ]; }; packagesWithBuildInputs = { # sort -t '=' -k 2 + asciicast = with pkgs; [ xz.dev bzip2.dev zlib.dev icu.dev ]; svKomodo = [ pkgs.which ]; 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 ]; + bayesWatch = [ pkgs.boost.dev ]; clustermq = [ pkgs.pkg-config ]; + coga = [ pkgs.gsl.dev ]; webp = [ pkgs.libwebp ]; RMark = [ pkgs.which ]; RPushbullet = [ pkgs.which ]; @@ -587,6 +602,7 @@ let DiffBind = with pkgs; [ zlib.dev ]; CNEr = with pkgs; [ zlib ]; GMMAT = with pkgs; [ zlib.dev bzip2.dev ]; + rmumps = with pkgs; [ zlib.dev ]; HiCDCPlus = [ pkgs.zlib.dev ]; PopGenome = [ pkgs.zlib.dev ]; QuasR = [ pkgs.zlib.dev ]; @@ -641,6 +657,7 @@ let redux = [ pkgs.hiredis ]; RmecabKo = [ pkgs.mecab ]; PoissonBinomial = [ pkgs.fftw.dev ]; + poisbinom = [ pkgs.fftw.dev ]; PoissonMultinomial = [ pkgs.fftw.dev ]; rrd = [ pkgs.rrdtool ]; flowWorkspace = [ pkgs.zlib.dev ]; @@ -656,6 +673,7 @@ let ijtiff = [ pkgs.libtiff ]; ragg = with pkgs; [ freetype.dev libpng.dev libtiff.dev zlib.dev libjpeg.dev bzip2.dev ]; qqconf = [ pkgs.fftw.dev ]; + vapour = with pkgs; [ proj.dev gdal ]; }; packagesRequiringX = [ @@ -834,6 +852,7 @@ let "svWidgets" "SYNCSA" "SyNet" + "switchboard" "tcltk2" "TestScorer" "TIMP" @@ -866,10 +885,12 @@ let "R_filesets" "RKorAPClient" "R_rsp" + "salso" "scholar" "stepR" "styler" "TreeTools" + "TreeSearch" "ACNE" "APAlyzer" "EstMix" @@ -895,6 +916,7 @@ let "fixest" "paxtoolsr" "systemPipeShiny" + "matlab2r" ]; packagesToSkipCheck = [ @@ -947,7 +969,7 @@ let cargoDeps = pkgs.rustPlatform.fetchCargoTarball { src = attrs.src; sourceRoot = "gifski/src/myrustlib"; - hash = "sha256-vBrTQ+5JZA8554Aasbqw7mbaOfJNQjrOpG00IXAcamI="; + hash = "sha256-e6nuiQU22GiO2I+bu0muyICGrdkCLSZUDHDz2mM2hz0="; }; cargoRoot = "src/myrustlib"; @@ -1004,6 +1026,10 @@ let preConfigure = "patchShebangs configure"; }); + gmailr = old.gmailr.overrideAttrs (attrs: { + postPatch = "patchShebangs configure"; + }); + purrr = old.purrr.overrideAttrs (attrs: { patchPhase = "patchShebangs configure"; }); @@ -1049,6 +1075,15 @@ let ''; }); + pathfindR = old.pathfindR.overrideAttrs (attrs: { + postPatch = '' + substituteInPlace "R/zzz.R" \ + --replace-fail " check_java_version()" " Sys.setenv(JAVA_HOME = \"${lib.getBin pkgs.jre_minimal}\"); check_java_version()" + substituteInPlace "R/active_snw_search.R" \ + --replace-fail "system(paste0(\"java" "system(paste0(\"${lib.getBin pkgs.jre_minimal}/bin/java" + ''; + }); + pbdZMQ = old.pbdZMQ.overrideAttrs (attrs: { postPatch = lib.optionalString stdenv.isDarwin '' for file in R/*.{r,r.in}; do |