diff options
Diffstat (limited to 'pkgs/development/r-modules/default.nix')
| -rw-r--r-- | pkgs/development/r-modules/default.nix | 38 |
1 files changed, 35 insertions, 3 deletions
diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index 8db5242f455a..e20077db6020 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 ]; @@ -321,6 +322,7 @@ let 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 ]; @@ -351,6 +353,7 @@ let 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 ]; @@ -360,6 +363,7 @@ 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 ]; @@ -381,6 +385,7 @@ 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 ]; @@ -406,7 +411,7 @@ 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 ]; @@ -427,6 +432,7 @@ 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 ]; @@ -453,6 +459,7 @@ let topicmodels = [ pkgs.gsl ]; udunits2 = with pkgs; [ udunits expat ]; units = [ pkgs.udunits ]; + vdiffr = [ pkgs.libpng.dev ]; V8 = [ pkgs.v8 ]; XBRL = with pkgs; [ zlib libxml2.dev ]; XLConnect = [ pkgs.jdk ]; @@ -501,9 +508,10 @@ let RDieHarder = [ pkgs.gsl ]; QF = [ pkgs.gsl ]; PICS = [ pkgs.gsl ]; - RcppCWB = [ pkgs.pkg-config ]; + RcppCWB = [ pkgs.pkg-config pkgs.pcre2 ]; redux = [ pkgs.pkg-config ]; rrd = [ pkgs.pkg-config ]; + Rbwa = [ pkgs.zlib.dev ]; trackViewer = [ pkgs.zlib.dev ]; themetagenomics = [ pkgs.zlib.dev ]; NanoMethViz = [ pkgs.zlib.dev ]; @@ -512,16 +520,20 @@ 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 ]; @@ -585,6 +597,7 @@ 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 ]; @@ -594,6 +607,7 @@ let Signac = [ pkgs.zlib.dev ]; TransView = [ pkgs.zlib.dev ]; bigsnpr = [ pkgs.zlib.dev ]; + zlib = [ pkgs.zlib.dev ]; divest = [ pkgs.zlib.dev ]; hipread = [ pkgs.zlib.dev ]; jackalope = with pkgs; [ zlib.dev xz.dev ]; @@ -653,6 +667,7 @@ 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 = [ @@ -831,6 +846,7 @@ let "svWidgets" "SYNCSA" "SyNet" + "switchboard" "tcltk2" "TestScorer" "TIMP" @@ -863,10 +879,12 @@ let "R_filesets" "RKorAPClient" "R_rsp" + "salso" "scholar" "stepR" "styler" "TreeTools" + "TreeSearch" "ACNE" "APAlyzer" "EstMix" @@ -892,6 +910,7 @@ let "fixest" "paxtoolsr" "systemPipeShiny" + "matlab2r" ]; packagesToSkipCheck = [ @@ -944,7 +963,7 @@ let cargoDeps = pkgs.rustPlatform.fetchCargoTarball { src = attrs.src; sourceRoot = "gifski/src/myrustlib"; - hash = "sha256-vBrTQ+5JZA8554Aasbqw7mbaOfJNQjrOpG00IXAcamI="; + hash = "sha256-e6nuiQU22GiO2I+bu0muyICGrdkCLSZUDHDz2mM2hz0="; }; cargoRoot = "src/myrustlib"; @@ -1001,6 +1020,10 @@ let preConfigure = "patchShebangs configure"; }); + gmailr = old.gmailr.overrideAttrs (attrs: { + postPatch = "patchShebangs configure"; + }); + purrr = old.purrr.overrideAttrs (attrs: { patchPhase = "patchShebangs configure"; }); @@ -1046,6 +1069,15 @@ 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 |