r-modules: fix git2r, TAQMNGR, and WhopGenome

1 files changed, 99 insertions, 97 deletions

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index 0e92dcb6202..3dc8b0874ed 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -198,131 +198,132 @@ let
   # tweaks for the individual packages and "in self" follow
 
   packagesWithRDepends = {
-    # sort -t '=' -k 2
     FactoMineR = [ self.car ];
   };
 
   packagesWithNativeBuildInputs = {
-    # sort -t '=' -k 2
-    graphscan = [ pkgs.gsl ];
-    RAppArmor = [ pkgs.apparmor ];
+    abn = [ pkgs.gsl ];
+    adimpro = [ pkgs.imagemagick ];
+    audio = [ pkgs.portaudio ];
+    BayesSAE = [ pkgs.gsl ];
+    BayesVarSel = [ pkgs.gsl ];
+    BayesXsrc = [ pkgs.readline pkgs.ncurses ];
+    bigGP = [ pkgs.openmpi ];
+    bnpmr = [ pkgs.gsl ];
     BNSP = [ pkgs.gsl ];
-    SOD = [ pkgs.cudatoolkit ]; # requres CL/cl.h
+    cairoDevice = [ pkgs.gtk2 ];
+    Cairo = [ pkgs.libtiff pkgs.libjpeg pkgs.cairo ];
+    CARramps = [ pkgs.linuxPackages.nvidia_x11 pkgs.liblapack ];
+    chebpol = [ pkgs.fftw ];
+    cit = [ pkgs.gsl ];
     curl = [ pkgs.curl pkgs.openldap ];
-    Rssa = [ pkgs.fftw ];
+    devEMF = [ pkgs.xlibs.libXft ];
+    diversitree = [ pkgs.gsl pkgs.fftw ];
+    EMCluster = [ pkgs.liblapack ];
     fftw = [ pkgs.fftw ];
     fftwtools = [ pkgs.fftw ];
-    kza = [ pkgs.fftw ];
-    mwaved = [ pkgs.fftw ];
-    spate = [ pkgs.fftw ];
-    chebpol = [ pkgs.fftw ];
-    seewave = [ pkgs.fftw pkgs.libsndfile ];
-    rgeos = [ pkgs.geos ];
-    Rglpk = [ pkgs.glpk ];
-    RCA = [ pkgs.gmp ];
-    gmp = [ pkgs.gmp ];
-    rcdd = [ pkgs.gmp ];
-    Rlibeemd = [ pkgs.gsl ];
-    igraph = [ pkgs.gmp ];
-    glpkAPI = [ pkgs.gmp pkgs.glpk ];
-    sdcTable = [ pkgs.gmp pkgs.glpk ];
-    Rmpfr = [ pkgs.gmp pkgs.mpfr ];
     Formula = [ pkgs.gmp ];
-    BayesSAE = [ pkgs.gsl ];
-    BayesVarSel = [ pkgs.gsl ];
+    geoCount = [ pkgs.gsl ];
+    git2r = [ pkgs.zlib ];
+    glpkAPI = [ pkgs.gmp pkgs.glpk ];
+    gmp = [ pkgs.gmp ];
+    graphscan = [ pkgs.gsl ];
+    gsl = [ pkgs.gsl ];
     HiCseg = [ pkgs.gsl ];
+    igraph = [ pkgs.gmp ];
+    JavaGD = [ pkgs.jdk ];
+    jpeg = [ pkgs.libjpeg ];
     KFKSDS = [ pkgs.gsl ];
-    R2GUESS = [ pkgs.gsl ];
-    RcppZiggurat = [ pkgs.gsl ];
-    SemiCompRisks = [ pkgs.gsl ];
-    VBLPCM = [ pkgs.gsl ];
-    abn = [ pkgs.gsl ];
-    cit = [ pkgs.gsl ];
+    kza = [ pkgs.fftw ];
     libamtrack = [ pkgs.gsl ];
     mixcat = [ pkgs.gsl ];
-    outbreaker = [ pkgs.gsl ];
-    ridge = [ pkgs.gsl ];
-    simplexreg = [ pkgs.gsl ];
-    stsm = [ pkgs.gsl ];
-    survSNP = [ pkgs.gsl ];
-    topicmodels = [ pkgs.gsl ];
-    RcppGSL = [ pkgs.gsl ];
-    bnpmr = [ pkgs.gsl ];
-    V8 = [ pkgs.v8 ];
-    geoCount = [ pkgs.gsl ];
-    devEMF = [ pkgs.xlibs.libXft ];
-    gsl = [ pkgs.gsl ];
     mvabund = [ pkgs.gsl ];
-    diversitree = [ pkgs.gsl pkgs.fftw ];
-    TKF = [ pkgs.gsl ];
-    VBmix = [ pkgs.gsl pkgs.fftw pkgs.qt4 ];
-    RGtk2 = [ pkgs.gtk2 ];
-    cairoDevice = [ pkgs.gtk2 ];
-    adimpro = [ pkgs.imagemagick ];
-    rjags = [ pkgs.jags ];
-    runjags = [ pkgs.jags ];
-    JavaGD = [ pkgs.jdk ];
-    RODBC = [ pkgs.libiodbc ];
-    RODBCext = [ pkgs.libiodbc ];
-    jpeg = [ pkgs.libjpeg ];
-    EMCluster = [ pkgs.liblapack ];
-    png = [ pkgs.libpng ];
-    pbdMPI = [ pkgs.openmpi ];
-    bigGP = [ pkgs.openmpi ];
-    rtiff = [ pkgs.libtiff ];
-    tiff = [ pkgs.libtiff ];
-    Cairo = [ pkgs.libtiff pkgs.libjpeg pkgs.cairo ];
-    XML = [ pkgs.libtool pkgs.libxml2 pkgs.xmlsec pkgs.libxslt ];
-    rpud = [ pkgs.linuxPackages.nvidia_x11 ];
-    CARramps = [ pkgs.linuxPackages.nvidia_x11 pkgs.liblapack ];
-    rgl = [ pkgs.mesa pkgs.x11 ];
-    ncdf = [ pkgs.netcdf ];
+    mwaved = [ pkgs.fftw ];
     ncdf4 = [ pkgs.netcdf ];
-    pbdNCDF4 = [ pkgs.netcdf ];
-    RNetCDF = [ pkgs.netcdf pkgs.udunits ];
+    ncdf = [ pkgs.netcdf ];
     nloptr = [ pkgs.nlopt ];
     npRmpi = [ pkgs.openmpi ];
-    pbdPROF = [ pkgs.openmpi ];
-    sprint = [ pkgs.openmpi ];
-    Rmpi = [ pkgs.openmpi ];
     openssl = [ pkgs.openssl ];
+    outbreaker = [ pkgs.gsl ];
+    pbdMPI = [ pkgs.openmpi ];
+    pbdNCDF4 = [ pkgs.netcdf ];
+    pbdPROF = [ pkgs.openmpi ];
     PKI = [ pkgs.openssl ];
-    RSclient = [ pkgs.openssl ];
-    Rserve = [ pkgs.openssl ];
-    Rpoppler = [ pkgs.poppler ];
-    audio = [ pkgs.portaudio ];
-    rpg = [ pkgs.postgresql ];
-    RPostgreSQL = [ pkgs.postgresql ];
-    ssanv = [ pkgs.proj ];
+    png = [ pkgs.libpng ];
+    PopGenome = [ pkgs.zlib ];
     proj4 = [ pkgs.proj ];
-    rgdal = [ pkgs.proj pkgs.gdal ];
-    RProtoBuf = [ pkgs.protobuf ];
-    rPython = [ pkgs.python ];
-    qtpaint = [ pkgs.qt4 ];
     qtbase = [ pkgs.qt4 ];
-    BayesXsrc = [ pkgs.readline pkgs.ncurses ];
-    udunits2 = [ pkgs.udunits pkgs.expat ];
-    tkrplot = [ pkgs.xlibs.libX11 ];
-    rzmq = [ pkgs.zeromq3 ];
-    PopGenome = [ pkgs.zlib ];
-    RJaCGH = [ pkgs.zlib ];
-    RcppCNPy = [ pkgs.zlib ];
+    qtpaint = [ pkgs.qt4 ];
+    R2GUESS = [ pkgs.gsl ];
+    R2SWF = [ pkgs.zlib pkgs.libpng pkgs.freetype ];
+    RAppArmor = [ pkgs.apparmor ];
     rbamtools = [ pkgs.zlib ];
+    RCA = [ pkgs.gmp ];
+    rcdd = [ pkgs.gmp ];
+    RcppCNPy = [ pkgs.zlib ];
+    RcppGSL = [ pkgs.gsl ];
+    RcppOctave = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre pkgs.octave ];
+    RcppZiggurat = [ pkgs.gsl ];
+    rgdal = [ pkgs.proj pkgs.gdal ];
+    rgeos = [ pkgs.geos ];
+    rgl = [ pkgs.mesa pkgs.x11 ];
+    Rglpk = [ pkgs.glpk ];
+    RGtk2 = [ pkgs.gtk2 ];
+    Rhpc = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.openmpi pkgs.pcre ];
+    ridge = [ pkgs.gsl ];
+    RJaCGH = [ pkgs.zlib ];
+    rjags = [ pkgs.jags ];
+    rJava = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre pkgs.jdk pkgs.libzip ];
+    Rlibeemd = [ pkgs.gsl ];
     rmatio = [ pkgs.zlib ];
-    RVowpalWabbit = [ pkgs.zlib pkgs.boost ];
-    seqminer = [ pkgs.zlib pkgs.bzip2 ];
-    seqinr = [ pkgs.zlib ];
+    Rmpfr = [ pkgs.gmp pkgs.mpfr ];
+    Rmpi = [ pkgs.openmpi ];
+    RMySQL = [ pkgs.zlib pkgs.mysql ];
+    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 ];
+    Rpoppler = [ pkgs.poppler ];
+    RPostgreSQL = [ pkgs.postgresql ];
+    RProtoBuf = [ pkgs.protobuf ];
+    rpud = [ pkgs.linuxPackages.nvidia_x11 ];
+    rPython = [ pkgs.python ];
+    RSclient = [ pkgs.openssl ];
+    Rserve = [ pkgs.openssl ];
+    Rssa = [ pkgs.fftw ];
     rtfbs = [ pkgs.zlib pkgs.pcre pkgs.bzip2 pkgs.gzip pkgs.readline ];
-    Rhpc = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.openmpi pkgs.pcre ];
+    rtiff = [ pkgs.libtiff ];
+    runjags = [ pkgs.jags ];
+    RVowpalWabbit = [ pkgs.zlib pkgs.boost ];
+    rzmq = [ pkgs.zeromq3 ];
     SAVE = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre ];
-    RcppOctave = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre pkgs.octave ];
-    rJava = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre pkgs.jdk pkgs.libzip ];
-    R2SWF = [ pkgs.zlib pkgs.libpng pkgs.freetype ];
-    sysfonts = [ pkgs.zlib pkgs.libpng pkgs.freetype ];
+    sdcTable = [ pkgs.gmp pkgs.glpk ];
+    seewave = [ pkgs.fftw pkgs.libsndfile ];
+    SemiCompRisks = [ pkgs.gsl ];
+    seqinr = [ pkgs.zlib ];
+    seqminer = [ pkgs.zlib pkgs.bzip2 ];
     showtext = [ pkgs.zlib pkgs.libpng pkgs.icu pkgs.freetype ];
+    simplexreg = [ pkgs.gsl ];
+    SOD = [ pkgs.cudatoolkit ]; # requres CL/cl.h
+    spate = [ pkgs.fftw ];
+    sprint = [ pkgs.openmpi ];
+    ssanv = [ pkgs.proj ];
+    stsm = [ pkgs.gsl ];
+    survSNP = [ pkgs.gsl ];
+    sysfonts = [ pkgs.zlib pkgs.libpng pkgs.freetype ];
+    TAQMNGR = [ pkgs.zlib ];
+    tiff = [ pkgs.libtiff ];
+    TKF = [ pkgs.gsl ];
+    tkrplot = [ pkgs.xlibs.libX11 ];
+    topicmodels = [ pkgs.gsl ];
+    udunits2 = [ pkgs.udunits pkgs.expat ];
+    V8 = [ pkgs.v8 ];
+    VBLPCM = [ pkgs.gsl ];
+    VBmix = [ pkgs.gsl pkgs.fftw pkgs.qt4 ];
+    WhopGenome = [ pkgs.zlib ];
     XBRL = [ pkgs.zlib pkgs.libxml2 ];
-    RMySQL = [ pkgs.zlib pkgs.mysql ];
+    XML = [ pkgs.libtool pkgs.libxml2 pkgs.xmlsec pkgs.libxslt ];
   };
 
   packagesWithBuildInputs = {
@@ -847,6 +848,7 @@ let
     "RAM" # requires Heatplus
     "RAPIDR" # requires Biostrings, Rsamtools, and GenomicRanges
     "RbioRXN" # requires fmcsR, and KEGGREST
+    "RcppAPT" # configure script depends on /bin/sh
     "Rcell" # requires EBImage
     "RcmdrPlugin_seeg" # requires seeg
     "Rcplex" # requires cplexAPI