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

3 files changed, 66 insertions, 51 deletions

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..cc8a840eda25 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; [pkgs.proj.dev proj pkg-config geos sqlite 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)