diff options
Diffstat (limited to 'nixpkgs/pkgs/development/r-modules/default.nix')
| -rw-r--r-- | nixpkgs/pkgs/development/r-modules/default.nix | 101 |
1 files changed, 58 insertions, 43 deletions
diff --git a/nixpkgs/pkgs/development/r-modules/default.nix b/nixpkgs/pkgs/development/r-modules/default.nix index 292653d75e51..e827c9b807fd 100644 --- a/nixpkgs/pkgs/development/r-modules/default.nix +++ b/nixpkgs/pkgs/development/r-modules/default.nix @@ -237,7 +237,7 @@ let BayesSAE = [ pkgs.gsl_1 ]; BayesVarSel = [ pkgs.gsl_1 ]; BayesXsrc = [ pkgs.readline.dev pkgs.ncurses ]; - bigGP = [ pkgs.openmpi ]; + bigGP = [ pkgs.mpi ]; bio3d = [ pkgs.zlib ]; BiocCheck = [ pkgs.which ]; Biostrings = [ pkgs.zlib ]; @@ -246,7 +246,7 @@ let Cairo = [ pkgs.libtiff pkgs.libjpeg pkgs.cairo.dev pkgs.x11 pkgs.fontconfig.lib ]; Cardinal = [ pkgs.which ]; chebpol = [ pkgs.fftw ]; - ChemmineOB = [ pkgs.openbabel pkgs.pkgconfig ]; + ChemmineOB = [ pkgs.openbabel pkgs.pkg-config ]; cit = [ pkgs.gsl_1 ]; curl = [ pkgs.curl.dev ]; data_table = [pkgs.zlib.dev] ++ lib.optional stdenv.isDarwin pkgs.llvmPackages.openmp; @@ -257,12 +257,13 @@ let fftwtools = [ pkgs.fftw.dev ]; 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.pkgconfig ]; + git2r = [ pkgs.zlib.dev pkgs.openssl.dev pkgs.libssh2.dev pkgs.libgit2 pkgs.pkg-config ]; GLAD = [ pkgs.gsl_1 ]; glpkAPI = [ pkgs.gmp pkgs.glpk ]; gmp = [ pkgs.gmp.dev ]; graphscan = [ pkgs.gsl_1 ]; gsl = [ pkgs.gsl_1 ]; + gert = [ pkgs.libgit2 ]; haven = [ pkgs.libiconv pkgs.zlib.dev ]; h5vc = [ pkgs.zlib.dev ]; HiCseg = [ pkgs.gsl_1 ]; @@ -279,12 +280,12 @@ let mvabund = [ pkgs.gsl_1 ]; mwaved = [ pkgs.fftw.dev ]; ncdf4 = [ pkgs.netcdf ]; - nloptr = [ pkgs.nlopt pkgs.pkgconfig ]; + nloptr = [ pkgs.nlopt pkgs.pkg-config ]; + n1qn1 = [ pkgs.gfortran ]; odbc = [ pkgs.unixODBC ]; pander = [ pkgs.pandoc pkgs.which ]; - pbdMPI = [ pkgs.openmpi ]; - pbdNCDF4 = [ pkgs.netcdf ]; - pbdPROF = [ pkgs.openmpi ]; + pbdMPI = [ pkgs.mpi ]; + pbdPROF = [ pkgs.mpi ]; pbdZMQ = lib.optionals stdenv.isDarwin [ pkgs.which ]; pdftools = [ pkgs.poppler.dev ]; phytools = [ pkgs.which ]; @@ -308,14 +309,14 @@ let RGtk2 = [ pkgs.gtk2.dev ]; rhdf5 = [ pkgs.zlib ]; Rhdf5lib = [ pkgs.zlib ]; - Rhpc = [ pkgs.zlib pkgs.bzip2.dev pkgs.icu pkgs.lzma.dev pkgs.openmpi pkgs.pcre.dev ]; + Rhpc = [ pkgs.zlib pkgs.bzip2.dev pkgs.icu pkgs.lzma.dev pkgs.mpi pkgs.pcre.dev ]; Rhtslib = [ pkgs.zlib.dev pkgs.automake pkgs.autoconf pkgs.bzip2.dev pkgs.lzma.dev pkgs.curl.dev ]; rjags = [ pkgs.jags ]; 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.dev ]; Rmpfr = [ pkgs.gmp pkgs.mpfr.dev ]; - Rmpi = [ pkgs.openmpi ]; + Rmpi = [ pkgs.mpi ]; RMySQL = [ pkgs.zlib pkgs.libmysqlclient pkgs.openssl.dev ]; RNetCDF = [ pkgs.netcdf pkgs.udunits ]; RODBC = [ pkgs.libiodbc ]; @@ -330,7 +331,8 @@ let rtiff = [ pkgs.libtiff.dev ]; runjags = [ pkgs.jags ]; RVowpalWabbit = [ pkgs.zlib.dev pkgs.boost ]; - rzmq = [ pkgs.zeromq ]; + rzmq = [ pkgs.zeromq pkgs.pkg-config ]; + clustermq = [ pkgs.zeromq ]; SAVE = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre ]; sdcTable = [ pkgs.gmp pkgs.glpk ]; seewave = [ pkgs.fftw.dev pkgs.libsndfile.dev ]; @@ -380,40 +382,47 @@ let rmutil = lib.optionals stdenv.isDarwin [ pkgs.libiconv ]; robustbase = lib.optionals stdenv.isDarwin [ pkgs.libiconv ]; SparseM = lib.optionals stdenv.isDarwin [ pkgs.libiconv ]; + hexbin = lib.optionals stdenv.isDarwin [ pkgs.libiconv ]; svKomodo = [ pkgs.which ]; nat = [ pkgs.which ]; nat_templatebrains = [ pkgs.which ]; pbdZMQ = lib.optionals stdenv.isDarwin [ pkgs.darwin.binutils ]; + clustermq = [ pkgs.pkg-config ]; RMark = [ pkgs.which ]; RPushbullet = [ pkgs.which ]; RcppEigen = [ pkgs.libiconv ]; RCurl = [ pkgs.curl.dev ]; - R2SWF = [ pkgs.pkgconfig ]; + R2SWF = [ pkgs.pkg-config ]; rgl = [ pkgs.libGLU pkgs.libGLU.dev pkgs.libGL pkgs.xlibsWrapper ]; - RGtk2 = [ pkgs.pkgconfig ]; - RProtoBuf = [ pkgs.pkgconfig ]; - Rpoppler = [ pkgs.pkgconfig ]; - XML = [ pkgs.pkgconfig ]; - cairoDevice = [ pkgs.pkgconfig ]; - chebpol = [ pkgs.pkgconfig ]; - fftw = [ pkgs.pkgconfig ]; - gdtools = [ pkgs.pkgconfig ]; + RGtk2 = [ pkgs.pkg-config ]; + RProtoBuf = [ pkgs.pkg-config ]; + Rpoppler = [ pkgs.pkg-config ]; + XML = [ pkgs.pkg-config ]; + cairoDevice = [ pkgs.pkg-config ]; + chebpol = [ pkgs.pkg-config ]; + fftw = [ pkgs.pkg-config ]; + gdtools = [ pkgs.pkg-config ]; jqr = [ pkgs.jq.lib ]; - kza = [ pkgs.pkgconfig ]; - magick = [ pkgs.pkgconfig ]; - mwaved = [ pkgs.pkgconfig ]; - odbc = [ pkgs.pkgconfig ]; - openssl = [ pkgs.pkgconfig ]; - pdftools = [ pkgs.pkgconfig ]; - sf = [ pkgs.pkgconfig pkgs.sqlite.dev pkgs.proj.dev ]; - showtext = [ pkgs.pkgconfig ]; - spate = [ pkgs.pkgconfig ]; - stringi = [ pkgs.pkgconfig ]; - sysfonts = [ pkgs.pkgconfig ]; - systemfonts = [ pkgs.pkgconfig ]; - tesseract = [ pkgs.pkgconfig ]; - Cairo = [ pkgs.pkgconfig ]; - Rsymphony = [ pkgs.pkgconfig pkgs.doxygen pkgs.graphviz pkgs.subversion ]; + kza = [ pkgs.pkg-config ]; + 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 ]; + showtext = [ pkgs.pkg-config ]; + spate = [ pkgs.pkg-config ]; + stringi = [ pkgs.pkg-config ]; + sysfonts = [ pkgs.pkg-config ]; + systemfonts = [ pkgs.pkg-config ]; + tesseract = [ pkgs.pkg-config ]; + Cairo = [ pkgs.pkg-config ]; + CLVTools = [ pkgs.gsl ]; + JMcmprsk = [ pkgs.gsl ]; + 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 ]; gridGraphics = [ pkgs.which ]; @@ -478,7 +487,6 @@ let "Demerelate" "detrendeR" "dgmb" - "DivMelt" "dpa" "DSpat" "dynamicGraph" @@ -498,14 +506,12 @@ let "forensim" "FreeSortR" "fscaret" - "fSRM" "gcmr" "geomorph" "geoR" "georob" "GGEBiplotGUI" "gnm" - "GPCSIV" "GrapheR" "GroupSeq" "gsubfn" @@ -580,7 +586,6 @@ let "RcmdrPlugin_orloca" "RcmdrPlugin_plotByGroup" "RcmdrPlugin_pointG" - "RcmdrPlugin_qual" "RcmdrPlugin_ROC" "RcmdrPlugin_sampling" "RcmdrPlugin_SCDA" @@ -606,7 +611,6 @@ let "soundecology" "spatsurv" "sqldf" - "SRRS" "SSDforR" "statcheck" "StatDA" @@ -623,8 +627,6 @@ let "tcltk2" "TestScorer" "TIMP" - "titan" - "tkrgl" "tkrplot" "tmap" "tspmeta" @@ -670,6 +672,14 @@ let ''; }); + rzmq = old.rzmq.overrideDerivation (attrs: { + preConfigure = "patchShebangs configure"; + }); + + clustermq = old.clustermq.overrideDerivation (attrs: { + preConfigure = "patchShebangs configure"; + }); + Cairo = old.Cairo.overrideDerivation (attrs: { NIX_LDFLAGS = "-lfontconfig"; }); @@ -698,7 +708,6 @@ let data_table = old.data_table.overrideDerivation (attrs: { NIX_CFLAGS_COMPILE = attrs.NIX_CFLAGS_COMPILE + " -fopenmp"; patchPhase = "patchShebangs configure"; - postInstall = "mv $out/library/data.table/libs/{data.table,datatable}.so"; }); ModelMetrics = old.ModelMetrics.overrideDerivation (attrs: { @@ -800,7 +809,7 @@ let openssl = old.openssl.overrideDerivation (attrs: { preConfigure = '' patchShebangs configure - ''; + ''; PKGCONFIG_CFLAGS = "-I${pkgs.openssl.dev}/include"; PKGCONFIG_LIBS = "-Wl,-rpath,${pkgs.openssl.out}/lib -L${pkgs.openssl.out}/lib -lssl -lcrypto"; }); @@ -855,6 +864,12 @@ let ''; }); + libgeos = old.libgeos.overrideDerivation (attrs: { + preConfigure = '' + patchShebangs configure + ''; + }); + protolite = old.protolite.overrideDerivation (attrs: { preConfigure = '' patchShebangs configure |