Merge pull request #21722 from mimadrid/fix/r-modules

Fix a lot of rPackages

1 files changed, 58 insertions, 53 deletions

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index 093bc2f7884..49273e34c7e 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -240,30 +240,30 @@ let
     audio = [ pkgs.portaudio ];
     BayesSAE = [ pkgs.gsl_1 ];
     BayesVarSel = [ pkgs.gsl_1 ];
-    BayesXsrc = [ pkgs.readline pkgs.ncurses ];
+    BayesXsrc = [ pkgs.readline.dev pkgs.ncurses ];
     bigGP = [ pkgs.openmpi ];
     BiocCheck = [ pkgs.which ];
     Biostrings = [ pkgs.zlib ];
     bnpmr = [ pkgs.gsl_1 ];
     BNSP = [ pkgs.gsl_1 ];
-    cairoDevice = [ pkgs.gtk2 ];
-    Cairo = [ pkgs.libtiff pkgs.libjpeg pkgs.cairo ];
+    cairoDevice = [ pkgs.gtk2.dev ];
+    Cairo = [ pkgs.libtiff pkgs.libjpeg pkgs.cairo.dev pkgs.x11 pkgs.fontconfig.lib ];
     Cardinal = [ pkgs.which ];
     chebpol = [ pkgs.fftw ];
     ChemmineOB = [ pkgs.openbabel pkgs.pkgconfig ];
     cit = [ pkgs.gsl_1 ];
     curl = [ pkgs.curl.dev ];
-    devEMF = [ pkgs.xorg.libXft ];
+    devEMF = [ pkgs.xorg.libXft.dev pkgs.x11 ];
     diversitree = [ pkgs.gsl_1 pkgs.fftw ];
     EMCluster = [ pkgs.liblapack ];
-    fftw = [ pkgs.fftw ];
-    fftwtools = [ pkgs.fftw ];
+    fftw = [ pkgs.fftw.dev ];
+    fftwtools = [ pkgs.fftw.dev ];
     Formula = [ pkgs.gmp ];
     geoCount = [ pkgs.gsl_1 ];
-    git2r = [ pkgs.zlib pkgs.openssl ];
+    git2r = [ pkgs.zlib.dev pkgs.openssl.dev ];
     GLAD = [ pkgs.gsl_1 ];
     glpkAPI = [ pkgs.gmp pkgs.glpk ];
-    gmp = [ pkgs.gmp ];
+    gmp = [ pkgs.gmp.dev ];
     graphscan = [ pkgs.gsl_1 ];
     gsl = [ pkgs.gsl_1 ];
     h5 = [ pkgs.hdf5-cpp pkgs.which ];
@@ -272,13 +272,13 @@ let
     iBMQ = [ pkgs.gsl_1 ];
     igraph = [ pkgs.gmp ];
     JavaGD = [ pkgs.jdk ];
-    jpeg = [ pkgs.libjpeg ];
+    jpeg = [ pkgs.libjpeg.dev ];
     KFKSDS = [ pkgs.gsl_1 ];
-    kza = [ pkgs.fftw ];
+    kza = [ pkgs.fftw.dev ];
     libamtrack = [ pkgs.gsl_1 ];
     mixcat = [ pkgs.gsl_1 ];
     mvabund = [ pkgs.gsl_1 ];
-    mwaved = [ pkgs.fftw ];
+    mwaved = [ pkgs.fftw.dev ];
     ncdf4 = [ pkgs.netcdf ];
     nloptr = [ pkgs.nlopt ];
     openssl = [ pkgs.openssl.dev ];
@@ -287,99 +287,99 @@ let
     pbdMPI = [ pkgs.openmpi ];
     pbdNCDF4 = [ pkgs.netcdf ];
     pbdPROF = [ pkgs.openmpi ];
-    PKI = [ pkgs.openssl ];
+    PKI = [ pkgs.openssl.dev ];
     png = [ pkgs.libpng.dev ];
-    PopGenome = [ pkgs.zlib ];
+    PopGenome = [ pkgs.zlib.dev ];
     proj4 = [ pkgs.proj ];
     qtbase = [ pkgs.qt4 ];
     qtpaint = [ pkgs.qt4 ];
     R2GUESS = [ pkgs.gsl_1 ];
-    R2SWF = [ pkgs.zlib pkgs.libpng pkgs.freetype ];
+    R2SWF = [ pkgs.zlib pkgs.libpng pkgs.freetype.dev ];
     RAppArmor = [ pkgs.libapparmor ];
     rapportools = [ pkgs.which ];
     rapport = [ pkgs.which ];
-    rbamtools = [ pkgs.zlib ];
-    rcdd = [ pkgs.gmp ];
-    RcppCNPy = [ pkgs.zlib ];
+    rbamtools = [ pkgs.zlib.dev ];
+    rcdd = [ pkgs.gmp.dev ];
+    RcppCNPy = [ pkgs.zlib.dev ];
     RcppGSL = [ pkgs.gsl_1 ];
-    RcppOctave = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre pkgs.octave ];
+    RcppOctave = [ pkgs.zlib pkgs.bzip2.dev pkgs.icu pkgs.lzma.dev pkgs.pcre.dev pkgs.octave ];
     RcppZiggurat = [ pkgs.gsl_1 ];
     rgdal = [ pkgs.proj pkgs.gdal ];
     rgeos = [ pkgs.geos ];
-    rggobi = [ pkgs.ggobi pkgs.gtk2 pkgs.libxml2 ];
+    rggobi = [ pkgs.ggobi pkgs.gtk2.dev pkgs.libxml2.dev ];
     rgl = [ pkgs.mesa pkgs.xlibsWrapper ];
     Rglpk = [ pkgs.glpk ];
-    RGtk2 = [ pkgs.gtk2 ];
+    RGtk2 = [ pkgs.gtk2.dev ];
     rhdf5 = [ pkgs.zlib ];
-    Rhpc = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.openmpi pkgs.pcre ];
-    Rhtslib = [ pkgs.zlib ];
-    RJaCGH = [ pkgs.zlib ];
+    Rhpc = [ pkgs.zlib pkgs.bzip2.dev pkgs.icu pkgs.lzma.dev pkgs.openmpi pkgs.pcre.dev ];
+    Rhtslib = [ pkgs.zlib.dev ];
+    RJaCGH = [ pkgs.zlib.dev ];
     rjags = [ pkgs.jags ];
-    rJava = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre pkgs.jdk pkgs.libzip ];
+    rJava = [ pkgs.zlib pkgs.bzip2.dev pkgs.icu pkgs.lzma.dev pkgs.pcre.dev pkgs.jdk pkgs.libzip ];
     Rlibeemd = [ pkgs.gsl_1 ];
-    rmatio = [ pkgs.zlib ];
-    Rmpfr = [ pkgs.gmp pkgs.mpfr ];
+    rmatio = [ pkgs.zlib.dev ];
+    Rmpfr = [ pkgs.gmp pkgs.mpfr.dev ];
     Rmpi = [ pkgs.openmpi ];
     RMySQL = [ pkgs.zlib pkgs.mysql.lib ];
     RNetCDF = [ pkgs.netcdf pkgs.udunits ];
     RODBCext = [ pkgs.libiodbc ];
     RODBC = [ pkgs.libiodbc ];
     rpg = [ pkgs.postgresql ];
-    rphast = [ pkgs.pcre pkgs.zlib pkgs.bzip2 pkgs.gzip pkgs.readline ];
+    rphast = [ pkgs.pcre.dev pkgs.zlib pkgs.bzip2 pkgs.gzip pkgs.readline ];
     Rpoppler = [ pkgs.poppler ];
     RPostgreSQL = [ pkgs.postgresql ];
     RProtoBuf = [ pkgs.protobuf ];
     rPython = [ pkgs.python ];
-    RSclient = [ pkgs.openssl ];
+    RSclient = [ pkgs.openssl.dev ];
     Rserve = [ pkgs.openssl ];
-    Rssa = [ pkgs.fftw ];
-    rtfbs = [ pkgs.zlib pkgs.pcre pkgs.bzip2 pkgs.gzip pkgs.readline ];
-    rtiff = [ pkgs.libtiff ];
+    Rssa = [ pkgs.fftw.dev ];
+    rtfbs = [ pkgs.zlib pkgs.pcre.dev pkgs.bzip2 pkgs.gzip pkgs.readline ];
+    rtiff = [ pkgs.libtiff.dev ];
     runjags = [ pkgs.jags ];
-    RVowpalWabbit = [ pkgs.zlib pkgs.boost ];
+    RVowpalWabbit = [ pkgs.zlib.dev pkgs.boost ];
     rzmq = [ pkgs.zeromq3 ];
     SAVE = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre ];
     sdcTable = [ pkgs.gmp pkgs.glpk ];
     seewave = [ pkgs.fftw.dev pkgs.libsndfile.dev ];
-    seqinr = [ pkgs.zlib ];
-    seqminer = [ pkgs.zlib pkgs.bzip2 ];
-    showtext = [ pkgs.zlib pkgs.libpng pkgs.icu pkgs.freetype ];
+    seqinr = [ pkgs.zlib.dev ];
+    seqminer = [ pkgs.zlib.dev pkgs.bzip2 ];
+    showtext = [ pkgs.zlib pkgs.libpng pkgs.icu pkgs.freetype.dev ];
     simplexreg = [ pkgs.gsl_1 ];
     SOD = [ pkgs.cudatoolkit ]; # requres CL/cl.h
-    spate = [ pkgs.fftw ];
+    spate = [ pkgs.fftw.dev ];
     sprint = [ pkgs.openmpi ];
     ssanv = [ pkgs.proj ];
     stsm = [ pkgs.gsl_1 ];
     stringi = [ pkgs.icu.dev ];
     survSNP = [ pkgs.gsl_1 ];
-    sysfonts = [ pkgs.zlib pkgs.libpng pkgs.freetype ];
-    TAQMNGR = [ pkgs.zlib ];
-    tiff = [ pkgs.libtiff ];
+    sysfonts = [ pkgs.zlib pkgs.libpng pkgs.freetype.dev ];
+    TAQMNGR = [ pkgs.zlib.dev ];
+    tiff = [ pkgs.libtiff.dev ];
     TKF = [ pkgs.gsl_1 ];
-    tkrplot = [ pkgs.xorg.libX11 ];
+    tkrplot = [ pkgs.xorg.libX11 pkgs.tk.dev ];
     topicmodels = [ pkgs.gsl_1 ];
     udunits2 = [ pkgs.udunits pkgs.expat ];
     V8 = [ pkgs.v8 ];
     VBLPCM = [ pkgs.gsl_1 ];
     VBmix = [ pkgs.gsl_1 pkgs.fftw pkgs.qt4 ];
-    WhopGenome = [ pkgs.zlib ];
-    XBRL = [ pkgs.zlib pkgs.libxml2 ];
-    xml2 = [ pkgs.libxml2 ];
+    WhopGenome = [ pkgs.zlib.dev ];
+    XBRL = [ pkgs.zlib pkgs.libxml2.dev ];
+    xml2 = [ pkgs.libxml2.dev ];
     XML = [ pkgs.libtool pkgs.libxml2.dev pkgs.xmlsec pkgs.libxslt ];
-    affyPLM = [ pkgs.zlib ];
-    bamsignals = [ pkgs.zlib ];
-    BitSeq = [ pkgs.zlib ];
+    affyPLM = [ pkgs.zlib.dev ];
+    bamsignals = [ pkgs.zlib.dev ];
+    BitSeq = [ pkgs.zlib.dev ];
     DiffBind = [ pkgs.zlib ];
     ShortRead = [ pkgs.zlib.dev ];
-    oligo = [ pkgs.zlib ];
-    gmapR = [ pkgs.zlib ];
-    Rsubread = [ pkgs.zlib ];
+    oligo = [ pkgs.zlib.dev ];
+    gmapR = [ pkgs.zlib.dev ];
+    Rsubread = [ pkgs.zlib.dev ];
     XVector = [ pkgs.zlib.dev ];
     Rsamtools = [ pkgs.zlib.dev ];
-    rtracklayer = [ pkgs.zlib ];
-    affyio = [ pkgs.zlib ];
-    VariantAnnotation = [ pkgs.zlib ];
-    snpStats = [ pkgs.zlib ];
+    rtracklayer = [ pkgs.zlib.dev ];
+    affyio = [ pkgs.zlib.dev ];
+    VariantAnnotation = [ pkgs.zlib.dev ];
+    snpStats = [ pkgs.zlib.dev ];
   };
 
   packagesWithBuildInputs = {
@@ -1791,6 +1791,10 @@ let
         '';
     });
 
+    Cairo = old.Cairo.overrideDerivation (attrs: {
+      NIX_LDFLAGS = "-lfontconfig";
+    });
+
     curl = old.curl.overrideDerivation (attrs: {
       preConfigure = "patchShebangs configure";
     });
@@ -1859,6 +1863,7 @@ let
 
     devEMF = old.devEMF.overrideDerivation (attrs: {
       NIX_CFLAGS_LINK = "-L${pkgs.xorg.libXft.out}/lib -lXft";
+      NIX_LDFLAGS = "-lX11";
     });
 
     slfm = old.slfm.overrideDerivation (attrs: {