r-modules: fix r package build failures
r-modules: fix r package system dependencies r-modules: fix terra package dependencies r-modules: fix edge case for R package import The R package "import" has a name that clashes with the nix function "import". The package name in nixpkgs is correctly modified to avoid the clash, but the name of the R package was also being changed in cran-packages.nix, which broke downloading of the package. cran-packages.nix has been manually patched, and genreate-r-packages.R has been fixed so future automatic updates will succeed. r-modules: fix repeated `pkgs.` and svglite
This commit is contained in:
Phil Dyer
parent
99967a54d8
commit
d7ac07cdbb
2
pkgs/development/r-modules/cran-packages.nix
generated
2
pkgs/development/r-modules/cran-packages.nix
generated
@ -10268,7 +10268,7 @@ in with self; {
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implicitMeasures = derive2 { name="implicitMeasures"; version="0.2.0"; sha256="0w0dwnzfhw5v5j7q3zpfsca4ydmq7b9fzspvyf9sibyh587isb9c"; depends=[ggplot2 stringr tidyr xtable]; };
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implied = derive2 { name="implied"; version="0.3.1"; sha256="11mrvpsh9qc5a5s5mpbsksri6vx36ij1gvpli6lyz6dkg48a9kdn"; depends=[]; };
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implyr = derive2 { name="implyr"; version="0.4.0"; sha256="0rblsmx1z2n4g3fims5wa3wyf5znr0gkwd2yfz3130bcm6346da0"; depends=[assertthat DBI dbplyr dplyr rlang tidyselect]; };
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r_import = derive2 { name="r_import"; version="1.2.0"; sha256="018s0x224gqnv4cjfh0fwliyfg6ma9vslmwybrlizfsmqcc5wp37"; depends=[]; };
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r_import = derive2 { name="import"; version="1.2.0"; sha256="018s0x224gqnv4cjfh0fwliyfg6ma9vslmwybrlizfsmqcc5wp37"; depends=[]; };
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importar = derive2 { name="importar"; version="0.1.1"; sha256="0xv445fmjhsbdlsq03k2rlycnggn3rcyq5a49zrg4jvjamzr0rgr"; depends=[]; };
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importinegi = derive2 { name="importinegi"; version="1.1.3"; sha256="1r0p01mc9wb24ifldn3dmi0fqxwkp0290h0qrgr72grd34v2xszc"; depends=[data_table dplyr foreign haven rgdal]; };
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impressionist_colors = derive2 { name="impressionist.colors"; version="1.0"; sha256="03z5w7y7vbvlnn30r9y3ip93h364f87nhwdb9hcki26csiq2bnlv"; depends=[]; };
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@ -237,54 +237,56 @@ let
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audio = [ pkgs.portaudio ];
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BayesSAE = [ pkgs.gsl_1 ];
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BayesVarSel = [ pkgs.gsl_1 ];
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BayesXsrc = [ pkgs.readline.dev pkgs.ncurses ];
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BayesXsrc = with pkgs; [ readline.dev ncurses ];
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bigGP = [ pkgs.mpi ];
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bio3d = [ pkgs.zlib ];
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BiocCheck = [ pkgs.which ];
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Biostrings = [ pkgs.zlib ];
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bnpmr = [ pkgs.gsl_1 ];
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cairoDevice = [ pkgs.gtk2.dev ];
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Cairo = [ pkgs.libtiff pkgs.libjpeg pkgs.cairo.dev pkgs.x11 pkgs.fontconfig.lib ];
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Cairo = with pkgs; [ libtiff libjpeg cairo.dev x11 fontconfig.lib ];
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Cardinal = [ pkgs.which ];
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chebpol = [ pkgs.fftw ];
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ChemmineOB = [ pkgs.openbabel pkgs.pkg-config ];
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ChemmineOB = with pkgs; [ openbabel pkg-config ];
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curl = [ pkgs.curl.dev ];
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data_table = [pkgs.zlib.dev] ++ lib.optional stdenv.isDarwin pkgs.llvmPackages.openmp;
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devEMF = [ pkgs.xorg.libXft.dev pkgs.x11 ];
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diversitree = [ pkgs.gsl_1 pkgs.fftw ];
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data_table = [ pkgs.zlib.dev ] ++ lib.optional stdenv.isDarwin pkgs.llvmPackages.openmp;
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devEMF = with pkgs; [ xorg.libXft.dev x11 ];
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diversitree = with pkgs; [ gsl_1 fftw ];
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exactextractr = [ pkgs.geos ];
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EMCluster = [ pkgs.lapack ];
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fftw = [ pkgs.fftw.dev ];
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fftwtools = [ pkgs.fftw.dev ];
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fftwtools = with pkgs; [ fftw.dev pkg-config ];
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Formula = [ pkgs.gmp ];
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gdtools = [ pkgs.cairo.dev pkgs.fontconfig.lib pkgs.freetype.dev ];
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git2r = [ pkgs.zlib.dev pkgs.openssl.dev pkgs.libssh2.dev pkgs.libgit2 pkgs.pkg-config ];
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gdtools = with pkgs; [ cairo.dev fontconfig.lib freetype.dev ];
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git2r = with pkgs; [ zlib.dev openssl.dev libssh2.dev libgit2 pkg-config ];
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GLAD = [ pkgs.gsl_1 ];
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glpkAPI = [ pkgs.gmp pkgs.glpk ];
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glpkAPI = with pkgs; [ gmp glpk ];
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gmp = [ pkgs.gmp.dev ];
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graphscan = [ pkgs.gsl_1 ];
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gsl = [ pkgs.gsl_1 ];
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gert = [ pkgs.libgit2 ];
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haven = [ pkgs.libiconv pkgs.zlib.dev ];
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haven = with pkgs; [ libiconv zlib.dev ];
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h5vc = [ pkgs.zlib.dev ];
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HiCseg = [ pkgs.gsl_1 ];
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imager = [ pkgs.x11 ];
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iBMQ = [ pkgs.gsl_1 ];
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igraph = [ pkgs.gmp pkgs.libxml2.dev ];
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igraph = with pkgs; [ gmp libxml2.dev ];
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JavaGD = [ pkgs.jdk ];
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jpeg = [ pkgs.libjpeg.dev ];
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jqr = [ pkgs.jq.dev ];
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KFKSDS = [ pkgs.gsl_1 ];
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kza = [ pkgs.fftw.dev ];
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lwgeom = [ pkgs.gdal pkgs.geos pkgs.proj ];
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lpsymphony = with pkgs; [ pkg-config gfortran gettext ];
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lwgeom = with pkgs; [pkgs.proj.dev proj pkg-config geos sqlite gdal ];
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magick = [ pkgs.imagemagick.dev ];
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ModelMetrics = lib.optional stdenv.isDarwin pkgs.llvmPackages.openmp;
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mvabund = [ pkgs.gsl_1 ];
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mwaved = [ pkgs.fftw.dev ];
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ncdf4 = [ pkgs.netcdf ];
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nloptr = [ pkgs.nlopt pkgs.pkg-config ];
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nloptr = with pkgs; [ nlopt pkg-config ];
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n1qn1 = [ pkgs.gfortran ];
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odbc = [ pkgs.unixODBC ];
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pander = [ pkgs.pandoc pkgs.which ];
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pander = with pkgs; [ pandoc which ];
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pbdMPI = [ pkgs.mpi ];
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pbdPROF = [ pkgs.mpi ];
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pbdZMQ = lib.optionals stdenv.isDarwin [ pkgs.which ];
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@ -294,7 +296,7 @@ let
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png = [ pkgs.libpng.dev ];
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proj4 = [ pkgs.proj ];
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protolite = [ pkgs.protobuf ];
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R2SWF = [ pkgs.zlib pkgs.libpng pkgs.freetype.dev ];
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R2SWF = with pkgs; [ zlib libpng freetype.dev ];
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RAppArmor = [ pkgs.libapparmor ];
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rapportools = [ pkgs.which ];
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rapport = [ pkgs.which ];
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@ -304,42 +306,43 @@ let
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RcppGSL = [ pkgs.gsl_1 ];
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RcppZiggurat = [ pkgs.gsl_1 ];
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reprex = [ pkgs.which ];
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rgdal = [ pkgs.proj.dev pkgs.gdal ];
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rgdal = with pkgs; [ proj.dev gdal ];
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rgeos = [ pkgs.geos ];
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Rglpk = [ pkgs.glpk ];
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RGtk2 = [ pkgs.gtk2.dev ];
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rhdf5 = [ pkgs.zlib ];
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Rhdf5lib = [ pkgs.zlib.dev ];
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Rhpc = [ pkgs.zlib pkgs.bzip2.dev pkgs.icu pkgs.xz.dev pkgs.mpi pkgs.pcre.dev ];
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Rhtslib = [ pkgs.zlib.dev pkgs.automake pkgs.autoconf pkgs.bzip2.dev pkgs.xz.dev pkgs.curl.dev ];
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Rhpc = with pkgs; [ zlib bzip2.dev icu xz.dev mpi pcre.dev ];
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Rhtslib = with pkgs; [ zlib.dev automake autoconf bzip2.dev xz.dev curl.dev ];
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rjags = [ pkgs.jags ];
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rJava = [ pkgs.zlib pkgs.bzip2.dev pkgs.icu pkgs.xz.dev pkgs.pcre.dev pkgs.jdk pkgs.libzip ];
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rJava = with pkgs; [ zlib bzip2.dev icu xz.dev pcre.dev jdk libzip ];
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Rlibeemd = [ pkgs.gsl_1 ];
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rmatio = [ pkgs.zlib.dev ];
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Rmpfr = [ pkgs.gmp pkgs.mpfr.dev ];
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Rmpfr = with pkgs; [ gmp mpfr.dev ];
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Rmpi = [ pkgs.mpi ];
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RMySQL = [ pkgs.zlib pkgs.libmysqlclient pkgs.openssl.dev ];
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RNetCDF = [ pkgs.netcdf pkgs.udunits ];
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RMySQL = with pkgs; [ zlib libmysqlclient openssl.dev ];
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RNetCDF = with pkgs; [ netcdf udunits ];
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RODBC = [ pkgs.libiodbc ];
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rpanel = [ pkgs.bwidget ];
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Rpoppler = [ pkgs.poppler ];
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RPostgreSQL = [ pkgs.postgresql pkgs.postgresql ];
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RPostgreSQL = with pkgs; [ postgresql postgresql ];
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RProtoBuf = [ pkgs.protobuf ];
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RSclient = [ pkgs.openssl.dev ];
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Rserve = [ pkgs.openssl ];
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Rssa = [ pkgs.fftw.dev ];
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rsvg = [ pkgs.pkg-config ];
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runjags = [ pkgs.jags ];
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RVowpalWabbit = [ pkgs.zlib.dev pkgs.boost ];
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rzmq = [ pkgs.zeromq pkgs.pkg-config ];
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RVowpalWabbit = with pkgs; [ zlib.dev boost ];
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rzmq = with pkgs; [ zeromq pkg-config ];
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clustermq = [ pkgs.zeromq ];
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SAVE = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.xz pkgs.pcre ];
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sdcTable = [ pkgs.gmp pkgs.glpk ];
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seewave = [ pkgs.fftw.dev pkgs.libsndfile.dev ];
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SAVE = with pkgs; [ zlib bzip2 icu xz pcre ];
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sdcTable = with pkgs; [ gmp glpk ];
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seewave = with pkgs; [ fftw.dev libsndfile.dev ];
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seqinr = [ pkgs.zlib.dev ];
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seqminer = [ pkgs.zlib.dev pkgs.bzip2 ];
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sf = [ pkgs.gdal pkgs.proj pkgs.geos ];
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showtext = [ pkgs.zlib pkgs.libpng pkgs.icu pkgs.freetype.dev ];
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seqminer = with pkgs; [ zlib.dev bzip2 ];
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sf = with pkgs; [ gdal proj geos ];
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terra = with pkgs; [ gdal proj geos ];
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showtext = with pkgs; [ zlib libpng icu freetype.dev ];
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simplexreg = [ pkgs.gsl_1 ];
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spate = [ pkgs.fftw.dev ];
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ssanv = [ pkgs.proj ];
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@ -347,19 +350,19 @@ let
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stringi = [ pkgs.icu.dev ];
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survSNP = [ pkgs.gsl_1 ];
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svglite = [ pkgs.libpng.dev ];
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sysfonts = [ pkgs.zlib pkgs.libpng pkgs.freetype.dev ];
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systemfonts = [ pkgs.fontconfig.dev pkgs.freetype.dev ];
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sysfonts = with pkgs; [ zlib libpng freetype.dev ];
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systemfonts = with pkgs; [ fontconfig.dev freetype.dev ];
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TAQMNGR = [ pkgs.zlib.dev ];
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tesseract = [ pkgs.tesseract pkgs.leptonica ];
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tesseract = with pkgs; [ tesseract leptonica ];
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tiff = [ pkgs.libtiff.dev ];
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tkrplot = [ pkgs.xorg.libX11 pkgs.tk.dev ];
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tkrplot = with pkgs; [ xorg.libX11 tk.dev ];
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topicmodels = [ pkgs.gsl_1 ];
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udunits2 = [ pkgs.udunits pkgs.expat ];
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udunits2 = with pkgs; [ udunits expat ];
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units = [ pkgs.udunits ];
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V8 = [ pkgs.v8 ];
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XBRL = [ pkgs.zlib pkgs.libxml2.dev ];
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XBRL = with pkgs; [ zlib libxml2.dev ];
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xml2 = [ pkgs.libxml2.dev ] ++ lib.optionals stdenv.isDarwin [ pkgs.perl ];
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XML = [ pkgs.libtool pkgs.libxml2.dev pkgs.xmlsec pkgs.libxslt ];
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XML = with pkgs; [ libtool libxml2.dev xmlsec libxslt ];
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affyPLM = [ pkgs.zlib.dev ];
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bamsignals = [ pkgs.zlib.dev ];
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BitSeq = [ pkgs.zlib.dev ];
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@ -369,10 +372,10 @@ let
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gmapR = [ pkgs.zlib.dev ];
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Rsubread = [ pkgs.zlib.dev ];
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XVector = [ pkgs.zlib.dev ];
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Rsamtools = [ pkgs.zlib.dev pkgs.curl.dev ];
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Rsamtools = with pkgs; [ zlib.dev curl.dev ];
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rtracklayer = [ pkgs.zlib.dev ];
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affyio = [ pkgs.zlib.dev ];
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VariantAnnotation = [ pkgs.zlib.dev pkgs.curl.dev ];
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VariantAnnotation = with pkgs; [ zlib.dev curl.dev ];
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snpStats = [ pkgs.zlib.dev ];
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hdf5r = [ pkgs.hdf5.dev ];
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};
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@ -396,7 +399,7 @@ let
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RcppEigen = [ pkgs.libiconv ];
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RCurl = [ pkgs.curl.dev ];
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R2SWF = [ pkgs.pkg-config ];
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rgl = [ pkgs.libGLU pkgs.libGLU.dev pkgs.libGL pkgs.xlibsWrapper ];
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rgl = with pkgs; [ libGLU libGLU.dev libGL xlibsWrapper ];
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RGtk2 = [ pkgs.pkg-config ];
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RProtoBuf = [ pkgs.pkg-config ];
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Rpoppler = [ pkgs.pkg-config ];
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@ -407,13 +410,14 @@ let
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gdtools = [ pkgs.pkg-config ];
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jqr = [ pkgs.jq.lib ];
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kza = [ pkgs.pkg-config ];
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lwgeom = [ pkgs.pkg-config pkgs.proj.dev pkgs.sqlite.dev ];
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lwgeom = with pkgs; [ pkg-config proj.dev sqlite.dev ];
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magick = [ pkgs.pkg-config ];
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mwaved = [ pkgs.pkg-config ];
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odbc = [ pkgs.pkg-config ];
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openssl = [ pkgs.pkg-config ];
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pdftools = [ pkgs.pkg-config ];
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sf = [ pkgs.pkg-config pkgs.sqlite.dev pkgs.proj.dev ];
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sf = with pkgs; [ pkg-config sqlite.dev proj.dev ];
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terra = with pkgs; [ pkg-config sqlite.dev proj.dev ];
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showtext = [ pkgs.pkg-config ];
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spate = [ pkgs.pkg-config ];
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stringi = [ pkgs.pkg-config ];
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@ -426,11 +430,11 @@ let
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mashr = [ pkgs.gsl ];
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hadron = [ pkgs.gsl ];
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AMOUNTAIN = [ pkgs.gsl ];
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Rsymphony = [ pkgs.pkg-config pkgs.doxygen pkgs.graphviz pkgs.subversion ];
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tcltk2 = [ pkgs.tcl pkgs.tk ];
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tikzDevice = [ pkgs.which pkgs.texlive.combined.scheme-medium ];
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Rsymphony = with pkgs; [ pkg-config doxygen graphviz subversion ];
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tcltk2 = with pkgs; [ tcl tk ];
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tikzDevice = with pkgs; [ which texlive.combined.scheme-medium ];
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gridGraphics = [ pkgs.which ];
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adimpro = [ pkgs.which pkgs.xorg.xdpyinfo ];
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adimpro = with pkgs; [ which xorg.xdpyinfo ];
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mzR = [ pkgs.netcdf ];
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cluster = [ pkgs.libiconv ];
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KernSmooth = [ pkgs.libiconv ];
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@ -951,6 +955,18 @@ let
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'';
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});
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R_cache = old.R_cache.overrideDerivation (attrs: {
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preConfigure = ''
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export R_CACHE_ROOTPATH=$TMP
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'';
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});
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lpsymphony = old.lpsymphony.overrideDerivation (attrs: {
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preConfigure = ''
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patchShebangs configure
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'';
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});
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};
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in
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self
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@ -48,8 +48,7 @@ escapeName <- function(name) {
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}
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formatPackage <- function(name, version, sha256, depends, imports, linkingTo) {
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name <- escapeName(name)
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attr <- gsub(".", "_", name, fixed=TRUE)
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attr <- gsub(".", "_", escapeName(name), fixed=TRUE)
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options(warn=5)
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depends <- paste( if (is.na(depends)) "" else gsub("[ \t\n]+", "", depends)
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, if (is.na(imports)) "" else gsub("[ \t\n]+", "", imports)
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