diff --git a/pkgs/development/r-modules/cran-packages.nix b/pkgs/development/r-modules/cran-packages.nix index 25c945c29f72..a09fa4af80a6 100644 --- a/pkgs/development/r-modules/cran-packages.nix +++ b/pkgs/development/r-modules/cran-packages.nix @@ -10268,7 +10268,7 @@ in with self; { implicitMeasures = derive2 { name="implicitMeasures"; version="0.2.0"; sha256="0w0dwnzfhw5v5j7q3zpfsca4ydmq7b9fzspvyf9sibyh587isb9c"; depends=[ggplot2 stringr tidyr xtable]; }; implied = derive2 { name="implied"; version="0.3.1"; sha256="11mrvpsh9qc5a5s5mpbsksri6vx36ij1gvpli6lyz6dkg48a9kdn"; depends=[]; }; implyr = derive2 { name="implyr"; version="0.4.0"; sha256="0rblsmx1z2n4g3fims5wa3wyf5znr0gkwd2yfz3130bcm6346da0"; depends=[assertthat DBI dbplyr dplyr rlang tidyselect]; }; - r_import = derive2 { name="r_import"; version="1.2.0"; sha256="018s0x224gqnv4cjfh0fwliyfg6ma9vslmwybrlizfsmqcc5wp37"; depends=[]; }; + r_import = derive2 { name="import"; version="1.2.0"; sha256="018s0x224gqnv4cjfh0fwliyfg6ma9vslmwybrlizfsmqcc5wp37"; depends=[]; }; importar = derive2 { name="importar"; version="0.1.1"; sha256="0xv445fmjhsbdlsq03k2rlycnggn3rcyq5a49zrg4jvjamzr0rgr"; depends=[]; }; importinegi = derive2 { name="importinegi"; version="1.1.3"; sha256="1r0p01mc9wb24ifldn3dmi0fqxwkp0290h0qrgr72grd34v2xszc"; depends=[data_table dplyr foreign haven rgdal]; }; impressionist_colors = derive2 { name="impressionist.colors"; version="1.0"; sha256="03z5w7y7vbvlnn30r9y3ip93h364f87nhwdb9hcki26csiq2bnlv"; depends=[]; }; diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index eb244ae91df8..4341e659bed0 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -237,54 +237,56 @@ let audio = [ pkgs.portaudio ]; BayesSAE = [ pkgs.gsl_1 ]; BayesVarSel = [ pkgs.gsl_1 ]; - BayesXsrc = [ pkgs.readline.dev pkgs.ncurses ]; + BayesXsrc = with pkgs; [ readline.dev ncurses ]; bigGP = [ pkgs.mpi ]; bio3d = [ pkgs.zlib ]; BiocCheck = [ pkgs.which ]; Biostrings = [ pkgs.zlib ]; bnpmr = [ pkgs.gsl_1 ]; cairoDevice = [ pkgs.gtk2.dev ]; - Cairo = [ pkgs.libtiff pkgs.libjpeg pkgs.cairo.dev pkgs.x11 pkgs.fontconfig.lib ]; + Cairo = with pkgs; [ libtiff libjpeg cairo.dev x11 fontconfig.lib ]; Cardinal = [ pkgs.which ]; chebpol = [ pkgs.fftw ]; - ChemmineOB = [ pkgs.openbabel pkgs.pkg-config ]; + ChemmineOB = with pkgs; [ openbabel pkg-config ]; curl = [ pkgs.curl.dev ]; - data_table = [pkgs.zlib.dev] ++ lib.optional stdenv.isDarwin pkgs.llvmPackages.openmp; - devEMF = [ pkgs.xorg.libXft.dev pkgs.x11 ]; - diversitree = [ pkgs.gsl_1 pkgs.fftw ]; + data_table = [ pkgs.zlib.dev ] ++ lib.optional stdenv.isDarwin pkgs.llvmPackages.openmp; + devEMF = with pkgs; [ xorg.libXft.dev x11 ]; + diversitree = with pkgs; [ gsl_1 fftw ]; + exactextractr = [ pkgs.geos ]; EMCluster = [ pkgs.lapack ]; fftw = [ pkgs.fftw.dev ]; - fftwtools = [ pkgs.fftw.dev ]; + fftwtools = with pkgs; [ fftw.dev pkg-config ]; Formula = [ pkgs.gmp ]; - gdtools = [ pkgs.cairo.dev pkgs.fontconfig.lib pkgs.freetype.dev ]; - git2r = [ pkgs.zlib.dev pkgs.openssl.dev pkgs.libssh2.dev pkgs.libgit2 pkgs.pkg-config ]; + gdtools = with pkgs; [ cairo.dev fontconfig.lib freetype.dev ]; + git2r = with pkgs; [ zlib.dev openssl.dev libssh2.dev libgit2 pkg-config ]; GLAD = [ pkgs.gsl_1 ]; - glpkAPI = [ pkgs.gmp pkgs.glpk ]; + glpkAPI = with pkgs; [ gmp glpk ]; gmp = [ pkgs.gmp.dev ]; graphscan = [ pkgs.gsl_1 ]; gsl = [ pkgs.gsl_1 ]; gert = [ pkgs.libgit2 ]; - haven = [ pkgs.libiconv pkgs.zlib.dev ]; + haven = with pkgs; [ libiconv zlib.dev ]; h5vc = [ pkgs.zlib.dev ]; HiCseg = [ pkgs.gsl_1 ]; imager = [ pkgs.x11 ]; iBMQ = [ pkgs.gsl_1 ]; - igraph = [ pkgs.gmp pkgs.libxml2.dev ]; + igraph = with pkgs; [ gmp libxml2.dev ]; JavaGD = [ pkgs.jdk ]; jpeg = [ pkgs.libjpeg.dev ]; jqr = [ pkgs.jq.dev ]; KFKSDS = [ pkgs.gsl_1 ]; kza = [ pkgs.fftw.dev ]; - lwgeom = [ pkgs.gdal pkgs.geos pkgs.proj ]; + lpsymphony = with pkgs; [ pkg-config gfortran gettext ]; + lwgeom = with pkgs; [ proj geos gdal ]; magick = [ pkgs.imagemagick.dev ]; ModelMetrics = lib.optional stdenv.isDarwin pkgs.llvmPackages.openmp; mvabund = [ pkgs.gsl_1 ]; mwaved = [ pkgs.fftw.dev ]; ncdf4 = [ pkgs.netcdf ]; - nloptr = [ pkgs.nlopt pkgs.pkg-config ]; + nloptr = with pkgs; [ nlopt pkg-config ]; n1qn1 = [ pkgs.gfortran ]; odbc = [ pkgs.unixODBC ]; - pander = [ pkgs.pandoc pkgs.which ]; + pander = with pkgs; [ pandoc which ]; pbdMPI = [ pkgs.mpi ]; pbdPROF = [ pkgs.mpi ]; pbdZMQ = lib.optionals stdenv.isDarwin [ pkgs.which ]; @@ -294,7 +296,7 @@ let png = [ pkgs.libpng.dev ]; proj4 = [ pkgs.proj ]; protolite = [ pkgs.protobuf ]; - R2SWF = [ pkgs.zlib pkgs.libpng pkgs.freetype.dev ]; + R2SWF = with pkgs; [ zlib libpng freetype.dev ]; RAppArmor = [ pkgs.libapparmor ]; rapportools = [ pkgs.which ]; rapport = [ pkgs.which ]; @@ -304,42 +306,43 @@ let RcppGSL = [ pkgs.gsl_1 ]; RcppZiggurat = [ pkgs.gsl_1 ]; reprex = [ pkgs.which ]; - rgdal = [ pkgs.proj.dev pkgs.gdal ]; + rgdal = with pkgs; [ proj.dev gdal ]; rgeos = [ pkgs.geos ]; Rglpk = [ pkgs.glpk ]; RGtk2 = [ pkgs.gtk2.dev ]; rhdf5 = [ pkgs.zlib ]; Rhdf5lib = [ pkgs.zlib.dev ]; - Rhpc = [ pkgs.zlib pkgs.bzip2.dev pkgs.icu pkgs.xz.dev pkgs.mpi pkgs.pcre.dev ]; - Rhtslib = [ pkgs.zlib.dev pkgs.automake pkgs.autoconf pkgs.bzip2.dev pkgs.xz.dev pkgs.curl.dev ]; + Rhpc = with pkgs; [ zlib bzip2.dev icu xz.dev mpi pcre.dev ]; + Rhtslib = with pkgs; [ zlib.dev automake autoconf bzip2.dev xz.dev curl.dev ]; rjags = [ pkgs.jags ]; - rJava = [ pkgs.zlib pkgs.bzip2.dev pkgs.icu pkgs.xz.dev pkgs.pcre.dev pkgs.jdk pkgs.libzip ]; + rJava = with pkgs; [ zlib bzip2.dev icu xz.dev pcre.dev jdk libzip ]; Rlibeemd = [ pkgs.gsl_1 ]; rmatio = [ pkgs.zlib.dev ]; - Rmpfr = [ pkgs.gmp pkgs.mpfr.dev ]; + Rmpfr = with pkgs; [ gmp mpfr.dev ]; Rmpi = [ pkgs.mpi ]; - RMySQL = [ pkgs.zlib pkgs.libmysqlclient pkgs.openssl.dev ]; - RNetCDF = [ pkgs.netcdf pkgs.udunits ]; + RMySQL = with pkgs; [ zlib libmysqlclient openssl.dev ]; + RNetCDF = with pkgs; [ netcdf udunits ]; RODBC = [ pkgs.libiodbc ]; rpanel = [ pkgs.bwidget ]; Rpoppler = [ pkgs.poppler ]; - RPostgreSQL = [ pkgs.postgresql pkgs.postgresql ]; + RPostgreSQL = with pkgs; [ postgresql postgresql ]; RProtoBuf = [ pkgs.protobuf ]; RSclient = [ pkgs.openssl.dev ]; Rserve = [ pkgs.openssl ]; Rssa = [ pkgs.fftw.dev ]; rsvg = [ pkgs.pkg-config ]; runjags = [ pkgs.jags ]; - RVowpalWabbit = [ pkgs.zlib.dev pkgs.boost ]; - rzmq = [ pkgs.zeromq pkgs.pkg-config ]; + RVowpalWabbit = with pkgs; [ zlib.dev boost ]; + rzmq = with pkgs; [ zeromq pkg-config ]; clustermq = [ pkgs.zeromq ]; - SAVE = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.xz pkgs.pcre ]; - sdcTable = [ pkgs.gmp pkgs.glpk ]; - seewave = [ pkgs.fftw.dev pkgs.libsndfile.dev ]; + SAVE = with pkgs; [ zlib bzip2 icu xz pcre ]; + sdcTable = with pkgs; [ gmp glpk ]; + seewave = with pkgs; [ fftw.dev libsndfile.dev ]; seqinr = [ pkgs.zlib.dev ]; - seqminer = [ pkgs.zlib.dev pkgs.bzip2 ]; - sf = [ pkgs.gdal pkgs.proj pkgs.geos ]; - showtext = [ pkgs.zlib pkgs.libpng pkgs.icu pkgs.freetype.dev ]; + seqminer = with pkgs; [ zlib.dev bzip2 ]; + sf = with pkgs; [ gdal proj geos ]; + terra = with pkgs; [ gdal proj geos ]; + showtext = with pkgs; [ zlib libpng icu freetype.dev ]; simplexreg = [ pkgs.gsl_1 ]; spate = [ pkgs.fftw.dev ]; ssanv = [ pkgs.proj ]; @@ -347,19 +350,19 @@ let stringi = [ pkgs.icu.dev ]; survSNP = [ pkgs.gsl_1 ]; svglite = [ pkgs.libpng.dev ]; - sysfonts = [ pkgs.zlib pkgs.libpng pkgs.freetype.dev ]; - systemfonts = [ pkgs.fontconfig.dev pkgs.freetype.dev ]; + sysfonts = with pkgs; [ zlib libpng freetype.dev ]; + systemfonts = with pkgs; [ fontconfig.dev freetype.dev ]; TAQMNGR = [ pkgs.zlib.dev ]; - tesseract = [ pkgs.tesseract pkgs.leptonica ]; + tesseract = with pkgs; [ tesseract leptonica ]; tiff = [ pkgs.libtiff.dev ]; - tkrplot = [ pkgs.xorg.libX11 pkgs.tk.dev ]; + tkrplot = with pkgs; [ xorg.libX11 tk.dev ]; topicmodels = [ pkgs.gsl_1 ]; - udunits2 = [ pkgs.udunits pkgs.expat ]; + udunits2 = with pkgs; [ udunits expat ]; units = [ pkgs.udunits ]; V8 = [ pkgs.v8 ]; - XBRL = [ pkgs.zlib pkgs.libxml2.dev ]; + XBRL = with pkgs; [ zlib libxml2.dev ]; xml2 = [ pkgs.libxml2.dev ] ++ lib.optionals stdenv.isDarwin [ pkgs.perl ]; - XML = [ pkgs.libtool pkgs.libxml2.dev pkgs.xmlsec pkgs.libxslt ]; + XML = with pkgs; [ libtool libxml2.dev xmlsec libxslt ]; affyPLM = [ pkgs.zlib.dev ]; bamsignals = [ pkgs.zlib.dev ]; BitSeq = [ pkgs.zlib.dev ]; @@ -369,10 +372,10 @@ let gmapR = [ pkgs.zlib.dev ]; Rsubread = [ pkgs.zlib.dev ]; XVector = [ pkgs.zlib.dev ]; - Rsamtools = [ pkgs.zlib.dev pkgs.curl.dev ]; + Rsamtools = with pkgs; [ zlib.dev curl.dev ]; rtracklayer = [ pkgs.zlib.dev ]; affyio = [ pkgs.zlib.dev ]; - VariantAnnotation = [ pkgs.zlib.dev pkgs.curl.dev ]; + VariantAnnotation = with pkgs; [ zlib.dev curl.dev ]; snpStats = [ pkgs.zlib.dev ]; hdf5r = [ pkgs.hdf5.dev ]; }; @@ -396,7 +399,7 @@ let RcppEigen = [ pkgs.libiconv ]; RCurl = [ pkgs.curl.dev ]; R2SWF = [ pkgs.pkg-config ]; - rgl = [ pkgs.libGLU pkgs.libGLU.dev pkgs.libGL pkgs.xlibsWrapper ]; + rgl = with pkgs; [ libGLU libGLU.dev libGL xlibsWrapper ]; RGtk2 = [ pkgs.pkg-config ]; RProtoBuf = [ pkgs.pkg-config ]; Rpoppler = [ pkgs.pkg-config ]; @@ -407,13 +410,14 @@ let gdtools = [ pkgs.pkg-config ]; jqr = [ pkgs.jq.lib ]; kza = [ pkgs.pkg-config ]; - lwgeom = [ pkgs.pkg-config pkgs.proj.dev pkgs.sqlite.dev ]; + lwgeom = with pkgs; [ pkg-config proj.dev sqlite.dev ]; magick = [ pkgs.pkg-config ]; mwaved = [ pkgs.pkg-config ]; odbc = [ pkgs.pkg-config ]; openssl = [ pkgs.pkg-config ]; pdftools = [ pkgs.pkg-config ]; - sf = [ pkgs.pkg-config pkgs.sqlite.dev pkgs.proj.dev ]; + sf = with pkgs; [ pkg-config sqlite.dev proj.dev ]; + terra = with pkgs; [ pkg-config sqlite.dev proj.dev ]; showtext = [ pkgs.pkg-config ]; spate = [ pkgs.pkg-config ]; stringi = [ pkgs.pkg-config ]; @@ -426,11 +430,11 @@ let mashr = [ pkgs.gsl ]; hadron = [ pkgs.gsl ]; AMOUNTAIN = [ pkgs.gsl ]; - Rsymphony = [ pkgs.pkg-config pkgs.doxygen pkgs.graphviz pkgs.subversion ]; - tcltk2 = [ pkgs.tcl pkgs.tk ]; - tikzDevice = [ pkgs.which pkgs.texlive.combined.scheme-medium ]; + Rsymphony = with pkgs; [ pkg-config doxygen graphviz subversion ]; + tcltk2 = with pkgs; [ tcl tk ]; + tikzDevice = with pkgs; [ which texlive.combined.scheme-medium ]; gridGraphics = [ pkgs.which ]; - adimpro = [ pkgs.which pkgs.xorg.xdpyinfo ]; + adimpro = with pkgs; [ which xorg.xdpyinfo ]; mzR = [ pkgs.netcdf ]; cluster = [ pkgs.libiconv ]; KernSmooth = [ pkgs.libiconv ]; @@ -951,6 +955,18 @@ let ''; }); + R_cache = old.R_cache.overrideDerivation (attrs: { + preConfigure = '' + export R_CACHE_ROOTPATH=$TMP + ''; + }); + + lpsymphony = old.lpsymphony.overrideDerivation (attrs: { + preConfigure = '' + patchShebangs configure + ''; + }); + }; in self diff --git a/pkgs/development/r-modules/generate-r-packages.R b/pkgs/development/r-modules/generate-r-packages.R index da9e0970b0f4..1ac15ef79e79 100755 --- a/pkgs/development/r-modules/generate-r-packages.R +++ b/pkgs/development/r-modules/generate-r-packages.R @@ -48,8 +48,7 @@ escapeName <- function(name) { } formatPackage <- function(name, version, sha256, depends, imports, linkingTo) { - name <- escapeName(name) - attr <- gsub(".", "_", name, fixed=TRUE) + attr <- gsub(".", "_", escapeName(name), fixed=TRUE) options(warn=5) depends <- paste( if (is.na(depends)) "" else gsub("[ \t\n]+", "", depends) , if (is.na(imports)) "" else gsub("[ \t\n]+", "", imports)