pkgs/development/r-modules/default.nix at 15.09-beta

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nixpkgs / pkgs / development / r-modules / default.nix
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Peter Simons R: fix Hydra build & evaluation errors 10 years ago
5d1bcf2f
   1/* This file defines the composition for CRAN (R) packages. */
   2
   3{ R, pkgs, overrides }:
   4
   5let
   6  inherit (pkgs) fetchurl stdenv lib;
   7
   8  buildRPackage = pkgs.callPackage ./generic-builder.nix { inherit R; };
   9
  10  # Generates package templates given per-repository settings
  11  #
  12  # some packages, e.g. cncaGUI, require X running while installation,
  13  # so that we use xvfb-run if requireX is true.
  14  mkDerive = {mkHomepage, mkUrls}: lib.makeOverridable ({
  15        name, version, sha256,
  16        depends ? [],
  17        doCheck ? true,
  18        requireX ? false,
  19        broken ? false,
  20        hydraPlatforms ? R.meta.hydraPlatforms
  21      }: buildRPackage {
  22    name = "${name}-${version}";
  23    src = fetchurl {
  24      inherit sha256;
  25      urls = mkUrls { inherit name version; };
  26    };
  27    inherit doCheck requireX;
  28    propagatedBuildInputs = depends;
  29    nativeBuildInputs = depends;
  30    meta.homepage = mkHomepage name;
  31    meta.platforms = R.meta.platforms;
  32    meta.hydraPlatforms = hydraPlatforms;
  33    meta.broken = broken;
  34  });
  35
  36  # Templates for generating Bioconductor and CRAN packages
  37  # from the name, version, sha256, and optional per-package arguments above
  38  #
  39  deriveBioc = mkDerive {
  40    mkHomepage = name: "http://cran.r-project.org/web/packages/${name}/";
  41    mkUrls = {name, version}: [ "mirror://bioc/src/contrib/${name}_${version}.tar.gz" ];
  42  };
  43  deriveCran = mkDerive {
  44    mkHomepage = name: "http://bioconductor.org/packages/release/bioc/html/${name}.html";
  45    mkUrls = {name, version}: [
  46      "mirror://cran/src/contrib/${name}_${version}.tar.gz"
  47      "mirror://cran/src/contrib/00Archive/${name}/${name}_${version}.tar.gz"
  48    ];
  49  };
  50
  51  # Overrides package definitions with nativeBuildInputs.
  52  # For example,
  53  #
  54  # overrideNativeBuildInputs {
  55  #   foo = [ pkgs.bar ]
  56  # } old
  57  #
  58  # results in
  59  #
  60  # {
  61  #   foo = old.foo.overrideDerivation (attrs: {
  62  #     nativeBuildInputs = attrs.nativeBuildInputs ++ [ pkgs.bar ];
  63  #   });
  64  # }
  65  overrideNativeBuildInputs = overrides: old:
  66    lib.mapAttrs (name: value:
  67      (builtins.getAttr name old).overrideDerivation (attrs: {
  68        nativeBuildInputs = attrs.nativeBuildInputs ++ value;
  69      })
  70    ) overrides;
  71
  72  # Overrides package definitions with buildInputs.
  73  # For example,
  74  #
  75  # overrideBuildInputs {
  76  #   foo = [ pkgs.bar ]
  77  # } old
  78  #
  79  # results in
  80  #
  81  # {
  82  #   foo = old.foo.overrideDerivation (attrs: {
  83  #     buildInputs = attrs.buildInputs ++ [ pkgs.bar ];
  84  #   });
  85  # }
  86  overrideBuildInputs = overrides: old:
  87    lib.mapAttrs (name: value:
  88      (builtins.getAttr name old).overrideDerivation (attrs: {
  89        buildInputs = attrs.buildInputs ++ value;
  90      })
  91    ) overrides;
  92
  93  # Overrides package definitions with new R dependencies.
  94  # For example,
  95  #
  96  # overrideRDepends {
  97  #   foo = [ self.bar ]
  98  # } old
  99  #
 100  # results in
 101  #
 102  # {
 103  #   foo = old.foo.overrideDerivation (attrs: {
 104  #     nativeBuildInputs = attrs.nativeBuildInputs ++ [ self.bar ];
 105  #     propagatedNativeBuildInputs = attrs.propagatedNativeBuildInputs ++ [ self.bar ];
 106  #   });
 107  # }
 108  overrideRDepends = overrides: old:
 109    lib.mapAttrs (name: value:
 110      (builtins.getAttr name old).overrideDerivation (attrs: {
 111        nativeBuildInputs = attrs.nativeBuildInputs ++ value;
 112        propagatedNativeBuildInputs = attrs.propagatedNativeBuildInputs ++ value;
 113      })
 114    ) overrides;
 115
 116  # Overrides package definition requiring X running to install.
 117  # For example,
 118  #
 119  # overrideRequireX [
 120  #   "foo"
 121  # ] old
 122  #
 123  # results in
 124  #
 125  # {
 126  #   foo = old.foo.override {
 127  #     requireX = true;
 128  #   };
 129  # }
 130  overrideRequireX = packageNames: old:
 131    let
 132      nameValuePairs = map (name: {
 133        inherit name;
 134        value = (builtins.getAttr name old).override {
 135          requireX = true;
 136        };
 137      }) packageNames;
 138    in
 139      builtins.listToAttrs nameValuePairs;
 140
 141  # Overrides package definition to skip check.
 142  # For example,
 143  #
 144  # overrideSkipCheck [
 145  #   "foo"
 146  # ] old
 147  #
 148  # results in
 149  #
 150  # {
 151  #   foo = old.foo.override {
 152  #     doCheck = false;
 153  #   };
 154  # }
 155  overrideSkipCheck = packageNames: old:
 156    let
 157      nameValuePairs = map (name: {
 158        inherit name;
 159        value = (builtins.getAttr name old).override {
 160          doCheck = false;
 161        };
 162      }) packageNames;
 163    in
 164      builtins.listToAttrs nameValuePairs;
 165
 166  # Overrides package definition to mark it broken.
 167  # For example,
 168  #
 169  # overrideBroken [
 170  #   "foo"
 171  # ] old
 172  #
 173  # results in
 174  #
 175  # {
 176  #   foo = old.foo.override {
 177  #     broken = true;
 178  #   };
 179  # }
 180  overrideBroken = packageNames: old:
 181    let
 182      nameValuePairs = map (name: {
 183        inherit name;
 184        value = (builtins.getAttr name old).override {
 185          broken = true;
 186        };
 187      }) packageNames;
 188    in
 189      builtins.listToAttrs nameValuePairs;
 190
 191  defaultOverrides = old: new:
 192    let old0 = old; in
 193    let
 194      old1 = old0 // (overrideRequireX packagesRequireingX old0);
 195      old2 = old1 // (overrideSkipCheck packagesToSkipCheck old1);
 196      old3 = old2 // (overrideRDepends packagesWithRDepends old2);
 197      old4 = old3 // (overrideNativeBuildInputs packagesWithNativeBuildInputs old3);
 198      old5 = old4 // (overrideBuildInputs packagesWithBuildInputs old4);
 199      old6 = old5 // (overrideBroken brokenPackages old5);
 200      old = old6;
 201    in old // (otherOverrides old new);
 202
 203  # Recursive override pattern.
 204  # `_self` is a collection of packages;
 205  # `self` is `_self` with overridden packages;
 206  # packages in `_self` may depends on overridden packages.
 207  self = (defaultOverrides _self self) // overrides;
 208  _self = import ./bioc-packages.nix { inherit self; derive = deriveBioc; } //
 209          import ./cran-packages.nix { inherit self; derive = deriveCran; };
 210
 211  # tweaks for the individual packages and "in self" follow
 212
 213  packagesWithRDepends = {
 214    FactoMineR = [ self.car ];
 215    pander = [ self.codetools ];
 216  };
 217
 218  packagesWithNativeBuildInputs = {
 219    abn = [ pkgs.gsl ];
 220    adimpro = [ pkgs.imagemagick ];
 221    audio = [ pkgs.portaudio ];
 222    BayesSAE = [ pkgs.gsl ];
 223    BayesVarSel = [ pkgs.gsl ];
 224    BayesXsrc = [ pkgs.readline pkgs.ncurses ];
 225    bigGP = [ pkgs.openmpi ];
 226    BiocCheck = [ pkgs.which ];
 227    Biostrings = [ pkgs.zlib ];
 228    bnpmr = [ pkgs.gsl ];
 229    BNSP = [ pkgs.gsl ];
 230    cairoDevice = [ pkgs.gtk2 ];
 231    Cairo = [ pkgs.libtiff pkgs.libjpeg pkgs.cairo ];
 232    Cardinal = [ pkgs.which ];
 233    CARramps = [ pkgs.linuxPackages.nvidia_x11 pkgs.liblapack ];
 234    chebpol = [ pkgs.fftw ];
 235    ChemmineOB = [ pkgs.openbabel pkgs.pkgconfig ];
 236    cit = [ pkgs.gsl ];
 237    curl = [ pkgs.curl ];
 238    devEMF = [ pkgs.xlibs.libXft ];
 239    diversitree = [ pkgs.gsl pkgs.fftw ];
 240    EMCluster = [ pkgs.liblapack ];
 241    fftw = [ pkgs.fftw ];
 242    fftwtools = [ pkgs.fftw ];
 243    Formula = [ pkgs.gmp ];
 244    geoCount = [ pkgs.gsl ];
 245    git2r = [ pkgs.zlib pkgs.openssl ];
 246    GLAD = [ pkgs.gsl ];
 247    glpkAPI = [ pkgs.gmp pkgs.glpk ];
 248    gmp = [ pkgs.gmp ];
 249    graphscan = [ pkgs.gsl ];
 250    gsl = [ pkgs.gsl ];
 251    HiCseg = [ pkgs.gsl ];
 252    iBMQ = [ pkgs.gsl ];
 253    igraph = [ pkgs.gmp ];
 254    JavaGD = [ pkgs.jdk ];
 255    jpeg = [ pkgs.libjpeg ];
 256    KFKSDS = [ pkgs.gsl ];
 257    kza = [ pkgs.fftw ];
 258    libamtrack = [ pkgs.gsl ];
 259    mixcat = [ pkgs.gsl ];
 260    mvabund = [ pkgs.gsl ];
 261    mwaved = [ pkgs.fftw ];
 262    ncdf4 = [ pkgs.netcdf ];
 263    ncdf = [ pkgs.netcdf ];
 264    nloptr = [ pkgs.nlopt ];
 265    openssl = [ pkgs.openssl ];
 266    outbreaker = [ pkgs.gsl ];
 267    pander = [ pkgs.pandoc pkgs.which ];
 268    pbdMPI = [ pkgs.openmpi ];
 269    pbdNCDF4 = [ pkgs.netcdf ];
 270    pbdPROF = [ pkgs.openmpi ];
 271    PKI = [ pkgs.openssl ];
 272    png = [ pkgs.libpng ];
 273    PopGenome = [ pkgs.zlib ];
 274    proj4 = [ pkgs.proj ];
 275    qtbase = [ pkgs.qt4 ];
 276    qtpaint = [ pkgs.qt4 ];
 277    R2GUESS = [ pkgs.gsl ];
 278    R2SWF = [ pkgs.zlib pkgs.libpng pkgs.freetype ];
 279    RAppArmor = [ pkgs.libapparmor ];
 280    rapportools = [ pkgs.which ];
 281    rapport = [ pkgs.which ];
 282    rbamtools = [ pkgs.zlib ];
 283    RCA = [ pkgs.gmp ];
 284    rcdd = [ pkgs.gmp ];
 285    RcppCNPy = [ pkgs.zlib ];
 286    RcppGSL = [ pkgs.gsl ];
 287    RcppOctave = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre pkgs.octave ];
 288    RcppZiggurat = [ pkgs.gsl ];
 289    rgdal = [ pkgs.proj pkgs.gdal ];
 290    rgeos = [ pkgs.geos ];
 291    rggobi = [ pkgs.ggobi pkgs.gtk2 pkgs.libxml2 ];
 292    rgl = [ pkgs.mesa pkgs.x11 ];
 293    Rglpk = [ pkgs.glpk ];
 294    RGtk2 = [ pkgs.gtk2 ];
 295    Rhpc = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.openmpi pkgs.pcre ];
 296    Rhtslib = [ pkgs.zlib ];
 297    ridge = [ pkgs.gsl ];
 298    RJaCGH = [ pkgs.zlib ];
 299    rjags = [ pkgs.jags ];
 300    rJava = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre pkgs.jdk pkgs.libzip ];
 301    Rlibeemd = [ pkgs.gsl ];
 302    rmatio = [ pkgs.zlib ];
 303    Rmpfr = [ pkgs.gmp pkgs.mpfr ];
 304    Rmpi = [ pkgs.openmpi ];
 305    RMySQL = [ pkgs.zlib pkgs.mysql.lib ];
 306    RNetCDF = [ pkgs.netcdf pkgs.udunits ];
 307    RODBCext = [ pkgs.libiodbc ];
 308    RODBC = [ pkgs.libiodbc ];
 309    rpg = [ pkgs.postgresql ];
 310    rphast = [ pkgs.pcre pkgs.zlib pkgs.bzip2 pkgs.gzip pkgs.readline ];
 311    Rpoppler = [ pkgs.poppler ];
 312    RPostgreSQL = [ pkgs.postgresql ];
 313    RProtoBuf = [ pkgs.protobuf ];
 314    rpud = [ pkgs.linuxPackages.nvidia_x11 ];
 315    rPython = [ pkgs.python ];
 316    RSclient = [ pkgs.openssl ];
 317    Rserve = [ pkgs.openssl ];
 318    Rssa = [ pkgs.fftw ];
 319    rtfbs = [ pkgs.zlib pkgs.pcre pkgs.bzip2 pkgs.gzip pkgs.readline ];
 320    rtiff = [ pkgs.libtiff ];
 321    runjags = [ pkgs.jags ];
 322    RVowpalWabbit = [ pkgs.zlib pkgs.boost ];
 323    rzmq = [ pkgs.zeromq3 ];
 324    SAVE = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre ];
 325    sdcTable = [ pkgs.gmp pkgs.glpk ];
 326    seewave = [ pkgs.fftw pkgs.libsndfile ];
 327    SemiCompRisks = [ pkgs.gsl ];
 328    seqinr = [ pkgs.zlib ];
 329    seqminer = [ pkgs.zlib pkgs.bzip2 ];
 330    showtext = [ pkgs.zlib pkgs.libpng pkgs.icu pkgs.freetype ];
 331    simplexreg = [ pkgs.gsl ];
 332    SOD = [ pkgs.cudatoolkit ]; # requres CL/cl.h
 333    spate = [ pkgs.fftw ];
 334    sprint = [ pkgs.openmpi ];
 335    ssanv = [ pkgs.proj ];
 336    stsm = [ pkgs.gsl ];
 337    stringi = [ pkgs.icu ];
 338    survSNP = [ pkgs.gsl ];
 339    sysfonts = [ pkgs.zlib pkgs.libpng pkgs.freetype ];
 340    TAQMNGR = [ pkgs.zlib ];
 341    tiff = [ pkgs.libtiff ];
 342    TKF = [ pkgs.gsl ];
 343    tkrplot = [ pkgs.xlibs.libX11 ];
 344    topicmodels = [ pkgs.gsl ];
 345    udunits2 = [ pkgs.udunits pkgs.expat ];
 346    V8 = [ pkgs.v8 ];
 347    VBLPCM = [ pkgs.gsl ];
 348    VBmix = [ pkgs.gsl pkgs.fftw pkgs.qt4 ];
 349    WhopGenome = [ pkgs.zlib ];
 350    XBRL = [ pkgs.zlib pkgs.libxml2 ];
 351    xml2 = [ pkgs.libxml2 ];
 352    XML = [ pkgs.libtool pkgs.libxml2 pkgs.xmlsec pkgs.libxslt ];
 353  };
 354
 355  packagesWithBuildInputs = {
 356    # sort -t '=' -k 2
 357    svKomodo = [ pkgs.which ];
 358    nat = [ pkgs.which ];
 359    nat_nblast = [ pkgs.which ];
 360    nat_templatebrains = [ pkgs.which ];
 361    RMark = [ pkgs.which ];
 362    RPushbullet = [ pkgs.which ];
 363    qtpaint = [ pkgs.cmake ];
 364    qtbase = [ pkgs.cmake pkgs.perl ];
 365    gmatrix = [ pkgs.cudatoolkit ];
 366    WideLM = [ pkgs.cudatoolkit ];
 367    RCurl = [ pkgs.curl ];
 368    R2SWF = [ pkgs.pkgconfig ];
 369    rggobi = [ pkgs.pkgconfig ];
 370    RGtk2 = [ pkgs.pkgconfig ];
 371    RProtoBuf = [ pkgs.pkgconfig ];
 372    Rpoppler = [ pkgs.pkgconfig ];
 373    VBmix = [ pkgs.pkgconfig ];
 374    XML = [ pkgs.pkgconfig ];
 375    cairoDevice = [ pkgs.pkgconfig ];
 376    chebpol = [ pkgs.pkgconfig ];
 377    fftw = [ pkgs.pkgconfig ];
 378    geoCount = [ pkgs.pkgconfig ];
 379    kza = [ pkgs.pkgconfig ];
 380    mwaved = [ pkgs.pkgconfig ];
 381    showtext = [ pkgs.pkgconfig ];
 382    spate = [ pkgs.pkgconfig ];
 383    stringi = [ pkgs.pkgconfig ];
 384    sysfonts = [ pkgs.pkgconfig ];
 385    Cairo = [ pkgs.pkgconfig ];
 386    Rsymphony = [ pkgs.pkgconfig pkgs.doxygen pkgs.graphviz pkgs.subversion ];
 387    qtutils = [ pkgs.qt4 ];
 388    ecoretriever = [ pkgs.which ];
 389    tcltk2 = [ pkgs.tcl pkgs.tk ];
 390    tikzDevice = [ pkgs.which pkgs.texLive ];
 391    rPython = [ pkgs.which ];
 392    CARramps = [ pkgs.which pkgs.cudatoolkit ];
 393    gridGraphics = [ pkgs.which ];
 394    gputools = [ pkgs.which pkgs.cudatoolkit ];
 395    rpud = [ pkgs.which pkgs.cudatoolkit ];
 396    adimpro = [ pkgs.which pkgs.xorg.xdpyinfo ];
 397    PET = [ pkgs.which pkgs.xorg.xdpyinfo pkgs.imagemagick ];
 398    dti = [ pkgs.which pkgs.xorg.xdpyinfo pkgs.imagemagick ];
 399  };
 400
 401  packagesRequireingX = [
 402    "accrual"
 403    "ade4TkGUI"
 404    "adehabitat"
 405    "analogue"
 406    "analogueExtra"
 407    "AnalyzeFMRI"
 408    "AnnotLists"
 409    "AnthropMMD"
 410    "aplpack"
 411    "aqfig"
 412    "arf3DS4"
 413    "asbio"
 414    "AtelieR"
 415    "BAT"
 416    "bayesDem"
 417    "BCA"
 418    "BEQI2"
 419    "betapart"
 420    "betaper"
 421    "BiodiversityR"
 422    "BioGeoBEARS"
 423    "bio_infer"
 424    "bipartite"
 425    "biplotbootGUI"
 426    "blender"
 427    "cairoDevice"
 428    "CCTpack"
 429    "cncaGUI"
 430    "cocorresp"
 431    "CommunityCorrelogram"
 432    "confidence"
 433    "constrainedKriging"
 434    "ConvergenceConcepts"
 435    "cpa"
 436    "DALY"
 437    "dave"
 438    "debug"
 439    "Deducer"
 440    "DeducerExtras"
 441    "DeducerPlugInExample"
 442    "DeducerPlugInScaling"
 443    "DeducerSpatial"
 444    "DeducerSurvival"
 445    "DeducerText"
 446    "Demerelate"
 447    "DescTools"
 448    "detrendeR"
 449    "dgmb"
 450    "DivMelt"
 451    "dpa"
 452    "DSpat"
 453    "dynamicGraph"
 454    "dynBiplotGUI"
 455    "EasyqpcR"
 456    "EcoVirtual"
 457    "ENiRG"
 458    "EnQuireR"
 459    "eVenn"
 460    "exactLoglinTest"
 461    "FAiR"
 462    "fat2Lpoly"
 463    "fbati"
 464    "FD"
 465    "feature"
 466    "FeedbackTS"
 467    "FFD"
 468    "fgui"
 469    "fisheyeR"
 470    "fit4NM"
 471    "forams"
 472    "forensim"
 473    "FreeSortR"
 474    "fscaret"
 475    "fSRM"
 476    "gcmr"
 477    "Geneland"
 478    "GeoGenetix"
 479    "geomorph"
 480    "geoR"
 481    "geoRglm"
 482    "georob"
 483    "GeoXp"
 484    "GGEBiplotGUI"
 485    "gnm"
 486    "GPCSIV"
 487    "GrammR"
 488    "GrapheR"
 489    "GroupSeq"
 490    "gsubfn"
 491    "GUniFrac"
 492    "gWidgets2RGtk2"
 493    "gWidgets2tcltk"
 494    "gWidgetsRGtk2"
 495    "gWidgetstcltk"
 496    "HH"
 497    "HiveR"
 498    "HomoPolymer"
 499    "iBUGS"
 500    "ic50"
 501    "iDynoR"
 502    "in2extRemes"
 503    "iplots"
 504    "isopam"
 505    "IsotopeR"
 506    "JGR"
 507    "KappaGUI"
 508    "likeLTD"
 509    "loe"
 510    "logmult"
 511    "LS2Wstat"
 512    "MAR1"
 513    "MareyMap"
 514    "memgene"
 515    "MergeGUI"
 516    "metacom"
 517    "Meth27QC"
 518    "MetSizeR"
 519    "MicroStrategyR"
 520    "migui"
 521    "miniGUI"
 522    "MissingDataGUI"
 523    "mixsep"
 524    "mlDNA"
 525    "MplusAutomation"
 526    "mpmcorrelogram"
 527    "mritc"
 528    "MTurkR"
 529    "multgee"
 530    "multibiplotGUI"
 531    "nodiv"
 532    "OligoSpecificitySystem"
 533    "onemap"
 534    "OpenRepGrid"
 535    "palaeoSig"
 536    "paleoMAS"
 537    "pbatR"
 538    "PBSadmb"
 539    "PBSmodelling"
 540    "PCPS"
 541    "pez"
 542    "phylotools"
 543    "picante"
 544    "PKgraph"
 545    "playwith"
 546    "plotSEMM"
 547    "plsRbeta"
 548    "plsRglm"
 549    "pmg"
 550    "PopGenReport"
 551    "poppr"
 552    "powerpkg"
 553    "PredictABEL"
 554    "prefmod"
 555    "PrevMap"
 556    "ProbForecastGOP"
 557    "QCAGUI"
 558    "qtbase"
 559    "qtpaint"
 560    "qtutils"
 561    "R2STATS"
 562    "r4ss"
 563    "RandomFields"
 564    "rareNMtests"
 565    "rAverage"
 566    "Rcmdr"
 567    "RcmdrPlugin_BCA"
 568    "RcmdrPlugin_coin"
 569    "RcmdrPlugin_depthTools"
 570    "RcmdrPlugin_DoE"
 571    "RcmdrPlugin_doex"
 572    "RcmdrPlugin_EACSPIR"
 573    "RcmdrPlugin_EBM"
 574    "RcmdrPlugin_EcoVirtual"
 575    "RcmdrPlugin_epack"
 576    "RcmdrPlugin_EZR"
 577    "RcmdrPlugin_FactoMineR"
 578    "RcmdrPlugin_HH"
 579    "RcmdrPlugin_IPSUR"
 580    "RcmdrPlugin_KMggplot2"
 581    "RcmdrPlugin_lfstat"
 582    "RcmdrPlugin_MA"
 583    "RcmdrPlugin_mosaic"
 584    "RcmdrPlugin_MPAStats"
 585    "RcmdrPlugin_orloca"
 586    "RcmdrPlugin_plotByGroup"
 587    "RcmdrPlugin_pointG"
 588    "RcmdrPlugin_qual"
 589    "RcmdrPlugin_ROC"
 590    "RcmdrPlugin_sampling"
 591    "RcmdrPlugin_SCDA"
 592    "RcmdrPlugin_SLC"
 593    "RcmdrPlugin_SM"
 594    "RcmdrPlugin_sos"
 595    "RcmdrPlugin_StatisticalURV"
 596    "RcmdrPlugin_steepness"
 597    "RcmdrPlugin_survival"
 598    "RcmdrPlugin_TeachingDemos"
 599    "RcmdrPlugin_temis"
 600    "RcmdrPlugin_UCA"
 601    "recluster"
 602    "relax"
 603    "relimp"
 604    "RenextGUI"
 605    "reportRx"
 606    "reshapeGUI"
 607    "rgl"
 608    "RHRV"
 609    "rich"
 610    "rioja"
 611    "ripa"
 612    "rite"
 613    "rnbn"
 614    "RNCEP"
 615    "RQDA"
 616    "RSDA"
 617    "rsgcc"
 618    "RSurvey"
 619    "RunuranGUI"
 620    "sdcMicroGUI"
 621    "sharpshootR"
 622    "simba"
 623    "Simile"
 624    "SimpleTable"
 625    "SOLOMON"
 626    "soundecology"
 627    "SPACECAP"
 628    "spacodiR"
 629    "spatsurv"
 630    "sqldf"
 631    "SRRS"
 632    "SSDforR"
 633    "statcheck"
 634    "StatDA"
 635    "STEPCAM"
 636    "stosim"
 637    "strvalidator"
 638    "stylo"
 639    "svDialogstcltk"
 640    "svIDE"
 641    "svSocket"
 642    "svWidgets"
 643    "SYNCSA"
 644    "SyNet"
 645    "tcltk2"
 646    "TDMR"
 647    "TED"
 648    "TestScorer"
 649    "TIMP"
 650    "titan"
 651    "tkrgl"
 652    "tkrplot"
 653    "tmap"
 654    "tspmeta"
 655    "TTAinterfaceTrendAnalysis"
 656    "twiddler"
 657    "vcdExtra"
 658    "VecStatGraphs3D"
 659    "vegan"
 660    "vegan3d"
 661    "vegclust"
 662    "VIMGUI"
 663    "WMCapacity"
 664    "x12GUI"
 665    "xergm"
 666  ];
 667
 668  packagesToSkipCheck = [
 669    "Rmpi" # tries to run MPI processes
 670    "gmatrix" # requires CUDA runtime
 671    "sprint" # tries to run MPI processes
 672    "pbdMPI" # tries to run MPI processes
 673  ];
 674
 675  # Packages which cannot be installed due to lack of dependencies or other reasons.
 676  brokenPackages = [
 677    "a4Base" # depends on broken package annaffy-1.41.1
 678    "a4" # depends on broken package annaffy-1.41.1
 679    "a4Reporting" # depends on broken package annaffy-1.41.1
 680    "abd" # depends on broken package nlopt-2.4.2
 681    "Actigraphy" # Build Is Broken
 682    "adabag" # depends on broken package nlopt-2.4.2
 683    "ADaCGH2" # depends on broken package tilingArray-1.47.0
 684    "adSplit" # build is broken
 685    "AER" # depends on broken package nlopt-2.4.2
 686    "afex" # depends on broken package nlopt-2.4.2
 687    "affyContam" # depends on broken package affyio-1.37.0
 688    "affycoretools" # depends on broken package affyio-1.37.0
 689    "affy" # depends on broken package affyio-1.37.0
 690    "AffyExpress" # depends on broken package affyio-1.37.0
 691    "affyILM" # depends on broken package affyio-1.37.0
 692    "affyio" # build is broken
 693    "affylmGUI" # depends on broken package affyio-1.37.0
 694    "affyPara" # depends on broken package affyio-1.37.0
 695    "affypdnn" # depends on broken package affyio-1.37.0
 696    "affyPLM" # depends on broken package affyio-1.37.0
 697    "affyQCReport" # depends on broken package affyio-1.37.0
 698    "AffyRNADegradation" # depends on broken package affyio-1.37.0
 699    "AffyTiling" # depends on broken package affyio-1.37.0
 700    "AgiMicroRna" # depends on broken package affyio-1.37.0
 701    "agRee" # depends on broken package nlopt-2.4.2
 702    "aLFQ" # depends on broken package nlopt-2.4.2
 703    "AllelicImbalance" # depends on broken package Rsamtools-1.21.8
 704    "alr3" # depends on broken package nlopt-2.4.2
 705    "alr4" # depends on broken package nlopt-2.4.2
 706    "alsace" # depends on broken nloptr-1.0.4
 707    "altcdfenvs" # depends on broken package affyio-1.37.0
 708    "ampliQueso" # depends on broken package Rsamtools-1.21.8
 709    "anacor" # depends on broken package nlopt-2.4.2
 710    "annaffy" # build is broken
 711    "annmap" # depends on broken package Rsamtools-1.21.8
 712    "AnnotationForge" # Build Is Broken
 713    "AnnotationHub" # depends on broken package interactiveDisplayBase-1.7.0
 714    "aods3" # depends on broken package nlopt-2.4.2
 715    "apComplex" # build is broken
 716    "apt" # depends on broken package nlopt-2.4.2
 717    "ArfimaMLM" # depends on broken package nlopt-2.4.2
 718    "arm" # depends on broken package nlopt-2.4.2
 719    "ArrayExpress" # depends on broken package affyio-1.37.0
 720    "ArrayExpressHTS" # depends on broken package Rsamtools-1.21.8
 721    "arrayMvout" # depends on broken package affyio-1.37.0
 722    "arrayQualityMetrics" # depends on broken package affyio-1.37.0
 723    "ArrayTools" # depends on broken package affyio-1.37.0
 724    "ArrayTV" # depends on broken package affyio-1.37.0
 725    "ARRmNormalization" # Build Is Broken
 726    "ARTool" # depends on broken package nlopt-2.4.2
 727    "attract" # depends on broken package AnnotationForge-1.11.3
 728    "BACA" # depends on broken package Category-2.35.1
 729    "BAGS" # build is broken
 730    "ballgown" # depends on broken package Rsamtools-1.21.8
 731    "bamsignals" # build is broken
 732    "bartMachine" # depends on broken package nlopt-2.4.2
 733    "Basic4Cseq" # depends on broken package Rsamtools-1.21.8
 734    "bayesDem" # depends on broken package nlopt-2.4.2
 735    "bayesLife" # depends on broken package nlopt-2.4.2
 736    "bayesPop" # depends on broken package nlopt-2.4.2
 737    "Bayesthresh" # depends on broken package nlopt-2.4.2
 738    "BBRecapture" # depends on broken package nlopt-2.4.2
 739    "BCA" # depends on broken package nlopt-2.4.2
 740    "BEAT" # depends on broken package Rsamtools-1.21.8
 741    "bgmm" # depends on broken package nlopt-2.4.2
 742    "bgx" # depends on broken package affyio-1.37.0
 743    "BIFIEsurvey" # depends on broken package nlopt-2.4.2
 744    "bigGP" # build is broken
 745    "BiGGR" # depends on broken package rsbml-2.27.0
 746    "BiodiversityR" # depends on broken package nlopt-2.4.2
 747    "biomvRCNS" # depends on broken package Rsamtools-1.21.8
 748    "biotools" # depends on broken package rpanel-1.1-3
 749    "biovizBase" # depends on broken package Rsamtools-1.21.8
 750    "birte" # build is broken
 751    "BiSEp" # depends on broken package GOSemSim-1.27.3
 752    "BiSeq" # depends on broken package Rsamtools-1.21.8
 753    "BitSeq" # depends on broken package Rsamtools-1.21.8
 754    "BLCOP" # depends on broken package Rsymphony-0.1-20
 755    "blmeco" # depends on broken package nlopt-2.4.2
 756    "blme" # depends on broken package nlopt-2.4.2
 757    "bmd" # depends on broken package nlopt-2.4.2
 758    "bmem" # depends on broken package nlopt-2.4.2
 759    "bootnet" # depends on broken package nlopt-2.4.2
 760    "boss" # depends on broken package nlopt-2.4.2
 761    "BradleyTerry2" # depends on broken package nlopt-2.4.2
 762    "BRugs" # build is broken
 763    "BSgenome" # depends on broken package Rsamtools-1.21.8
 764    "bumphunter" # depends on broken package Rsamtools-1.21.8
 765    "CADFtest" # depends on broken package nlopt-2.4.2
 766    "CAFE" # depends on broken package affyio-1.37.0
 767    "CAGEr" # depends on broken package Rsamtools-1.21.8
 768    "cAIC4" # depends on broken package nlopt-2.4.2
 769    "CAMERA" # depends on broken package mzR-2.3.1
 770    "canceR" # depends on broken package Category-2.35.1
 771    "candisc" # depends on broken package nlopt-2.4.2
 772    "carcass" # depends on broken package nlopt-2.4.2
 773    "car" # depends on broken package nlopt-2.4.2
 774    "caret" # depends on broken package nlopt-2.4.2
 775    "caretEnsemble" # depends on broken package nlopt-2.4.2
 776    "CARrampsOcl" # depends on broken package OpenCL-0.1-3
 777    "casper" # depends on broken package Rsamtools-1.21.8
 778    "Category" # Build Is Broken
 779    "categoryCompare" # depends on broken package Category-2.35.1
 780    "CCpop" # depends on broken package nlopt-2.4.2
 781    "cellHTS2" # depends on broken package Category-2.35.1
 782    "CexoR" # depends on broken package Rsamtools-1.21.8
 783    "ChainLadder" # depends on broken package nlopt-2.4.2
 784    "ChAMP" # depends on broken package affyio-1.37.0
 785    "charm" # depends on broken package affyio-1.37.0
 786    "ChemmineR" # Build Is Broken
 787    "chimera" # depends on broken package Rsamtools-1.21.8
 788    "chipenrich" # build is broken
 789    "chipPCR" # depends on broken nloptr-1.0.4
 790    "ChIPpeakAnno" # depends on broken package Rsamtools-1.21.8
 791    "ChIPQC" # depends on broken package AnnotationForge-1.11.3
 792    "ChIPseeker" # depends on broken package Rsamtools-1.21.8
 793    "chipseq" # depends on broken package Rsamtools-1.21.8
 794    "ChIPseqR" # depends on broken package Rsamtools-1.21.8
 795    "ChIPsim" # depends on broken package Rsamtools-1.21.8
 796    "ChIPXpress" # depends on broken package affyio-1.37.0
 797    "ChromHeatMap" # depends on broken package Rsamtools-1.21.8
 798    "cleanUpdTSeq" # depends on broken package Rsamtools-1.21.8
 799    "climwin" # depends on broken package nlopt-2.4.2
 800    "clipper" # depends on broken package Rsamtools-1.21.8
 801    "CLME" # depends on broken package nlopt-2.4.2
 802    "clpAPI" # build is broken
 803    "clusterPower" # depends on broken package nlopt-2.4.2
 804    "clusterProfiler" # depends on broken package GOSemSim-1.27.3
 805    "clusterSEs" # depends on broken AER-1.2-4
 806    "ClustGeo" # depends on broken FactoMineR-1.31.3
 807    "CNEr" # depends on broken package Rsamtools-1.21.8
 808    "cn_farms" # depends on broken package affyio-1.37.0
 809    "cn_mops" # depends on broken package Rsamtools-1.21.8
 810    "CNORfuzzy" # depends on broken package nlopt-2.4.2
 811    "CNVPanelizer" # depends on broken cn.mops-1.15.1
 812    "CNVrd2" # depends on broken package Rsamtools-1.21.8
 813    "cobindR" # depends on broken package Rsamtools-1.21.8
 814    "CoCiteStats" # Build Is Broken
 815    "CODEX" # depends on broken package Rsamtools-1.21.8
 816    "COHCAP" # build is broken
 817    "colorscience"
 818    "coMET" # depends on broken package Rsamtools-1.21.8
 819    "compEpiTools" # depends on broken package topGO-2.21.0
 820    "CompGO" # depends on broken package Category-2.35.1
 821    "conformal" # depends on broken package nlopt-2.4.2
 822    "ConsensusClusterPlus" # Build Is Broken
 823    "conumee" # depends on broken package Rsamtools-1.21.8
 824    "CopyNumber450k" # depends on broken package Rsamtools-1.21.8
 825    "CopywriteR" # depends on broken package Rsamtools-1.21.8
 826    "corHMM" # depends on broken package nlopt-2.4.2
 827    "Cormotif" # depends on broken package affyio-1.37.0
 828    "coRNAi" # depends on broken package Category-2.35.1
 829    "cosmiq" # depends on broken package mzR-2.3.1
 830    "CosmoPhotoz" # depends on broken package nlopt-2.4.2
 831    "CoverageView" # depends on broken package Rsamtools-1.21.8
 832    "cplexAPI" # build is broken
 833    "cpvSNP" # depends on broken package Rsamtools-1.21.8
 834    "CRISPRseek" # depends on broken package Rsamtools-1.21.8
 835    "crlmm" # depends on broken package affyio-1.37.0
 836    "Crossover" # Build Is Broken
 837    "CrypticIBDcheck" # depends on broken package nlopt-2.4.2
 838    "csaw" # depends on broken package Rsamtools-1.21.8
 839    "cudaBayesreg" # build is broken
 840    "cummeRbund" # depends on broken package Rsamtools-1.21.8
 841    "customProDB" # depends on broken package Rsamtools-1.21.8
 842    "daff" # depends on broken package V8-0.6
 843    "dagbag" # build is broken
 844    "dagLogo" # depends on broken package Rsamtools-1.21.8
 845    "DAMisc" # depends on broken package nlopt-2.4.2
 846    "DBKGrad" # depends on broken package rpanel-1.1-3
 847    "Deducer" # depends on broken package nlopt-2.4.2
 848    "DeducerExtras" # depends on broken package nlopt-2.4.2
 849    "DeducerPlugInExample" # depends on broken package nlopt-2.4.2
 850    "DeducerPlugInScaling" # depends on broken package nlopt-2.4.2
 851    "DeducerSpatial" # depends on broken package nlopt-2.4.2
 852    "DeducerSurvival" # depends on broken package nlopt-2.4.2
 853    "DeducerText" # depends on broken package nlopt-2.4.2
 854    "deepSNV" # depends on broken package Rsamtools-1.21.8
 855    "DEGraph" # depends on broken package RCytoscape-1.19.0
 856    "demi" # depends on broken package affyio-1.37.0
 857    "derfinder" # depends on broken package Rsamtools-1.21.8
 858    "derfinderPlot" # depends on broken package Rsamtools-1.21.8
 859    "destiny" # depends on broken package VIM-4.3.0
 860    "DEXSeq" # depends on broken package Rsamtools-1.21.8
 861    "DiagTest3Grp" # depends on broken package nlopt-2.4.2
 862    "DiffBind" # depends on broken package AnnotationForge-1.11.3
 863    "diffHic" # depends on broken package rhdf5-2.13.1
 864    "difR" # depends on broken package nlopt-2.4.2
 865    "DirichletMultinomial" # Build Is Broken
 866    "discSurv" # depends on broken package nlopt-2.4.2
 867    "DistatisR" # depends on broken package nlopt-2.4.2
 868    "diveRsity" # depends on broken package nlopt-2.4.2
 869    "DMRcate" # depends on broken package Rsamtools-1.21.8
 870    "DMRforPairs" # depends on broken package Rsamtools-1.21.8
 871    "domainsignatures" # build is broken
 872    "doMPI" # build is broken
 873    "DOQTL" # depends on broken package Rsamtools-1.21.8
 874    "DOSE" # depends on broken package GOSemSim-1.27.3
 875    "dpa" # depends on broken package nlopt-2.4.2
 876    "dpcR" # depends on broken nloptr-1.0.4
 877    "drc" # depends on broken package nlopt-2.4.2
 878    "drfit" # depends on broken package nlopt-2.4.2
 879    "drsmooth" # depends on broken package nlopt-2.4.2
 880    "DrugVsDisease" # depends on broken package affyio-1.37.0
 881    "dualKS" # depends on broken package affyio-1.37.0
 882    "dynlm" # depends on broken package nlopt-2.4.2
 883    "easyanova" # depends on broken package nlopt-2.4.2
 884    "easyRNASeq" # depends on broken package Rsamtools-1.21.8
 885    "EDASeq" # depends on broken package Rsamtools-1.21.8
 886    "edge" # depends on broken package nlopt-2.4.2
 887    "eeptools" # depends on broken package nlopt-2.4.2
 888    "EffectLiteR" # depends on broken package nlopt-2.4.2
 889    "effects" # depends on broken package nlopt-2.4.2
 890    "eiR" # depends on broken package ChemmineR-2.21.7
 891    "eisa" # depends on broken package Category-2.35.1
 892    "ELMER" # depends on broken package Rsamtools-1.21.8
 893    "EMA" # depends on broken package nlopt-2.4.2
 894    "ENmix" # depends on broken package affyio-1.37.0
 895    "EnQuireR" # depends on broken package nlopt-2.4.2
 896    "EnrichmentBrowser" # depends on broken package r-EDASeq-2.3.2
 897    "ensembldb" # depends on broken package interactiveDisplayBase-1.7.0
 898    "ensemblVEP" # depends on broken package Rsamtools-1.21.8
 899    "epigenomix" # depends on broken package Rsamtools-1.21.8
 900    "episplineDensity" # depends on broken package nlopt-2.4.2
 901    "epivizr" # depends on broken package Rsamtools-1.21.8
 902    "epr" # depends on broken package nlopt-2.4.2
 903    "erer" # depends on broken package nlopt-2.4.2
 904    "erma" # depends on broken GenomicFiles-1.5.4
 905    "erpR" # depends on broken package rpanel-1.1-3
 906    "ExiMiR" # depends on broken package affyio-1.37.0
 907    "exomeCopy" # depends on broken package Rsamtools-1.21.8
 908    "ExomeDepth" # depends on broken package Rsamtools-1.21.8
 909    "exomePeak" # depends on broken package Rsamtools-1.21.8
 910    "ExpressionView" # depends on broken package Category-2.35.1
 911    "extRemes" # depends on broken package nlopt-2.4.2
 912    "ez" # depends on broken package nlopt-2.4.2
 913    "facopy" # depends on broken package nlopt-2.4.2
 914    "FactoMineR" # depends on broken package nlopt-2.4.2
 915    "Factoshiny" # depends on broken package nlopt-2.4.2
 916    "faoutlier" # depends on broken package nlopt-2.4.2
 917    "farms" # depends on broken package affyio-1.37.0
 918    "fastLiquidAssociation" # depends on broken package LiquidAssociation-1.23.0
 919    "fastR" # depends on broken package nlopt-2.4.2
 920    "FDRreg" # depends on broken package nlopt-2.4.2
 921    "FEM" # build is broken
 922    "ffpe" # depends on broken package affyio-1.37.0
 923    "flagme" # depends on broken package mzR-2.3.1
 924    "flowDensity" # depends on broken package nlopt-2.4.2
 925    "flowPeaks" # build is broken
 926    "flowQ" # build is broken
 927    "FlowSOM" # depends on broken package ConsensusClusterPlus-1.23.0
 928    "flowStats" # depends on broken package ncdfFlow-2.15.2
 929    "flowVS" # depends on broken package ncdfFlow-2.15.2
 930    "flowWorkspace" # depends on broken package ncdfFlow-2.15.2
 931    "fmcsR" # depends on broken package ChemmineR-2.21.7
 932    "FourCSeq" # depends on broken package Rsamtools-1.21.8
 933    "fPortfolio" # depends on broken package Rsymphony-0.1-20
 934    "freqweights" # depends on broken package nlopt-2.4.2
 935    "frma" # depends on broken package affyio-1.37.0
 936    "frmaTools" # depends on broken package affyio-1.37.0
 937    "fscaret" # depends on broken package nlopt-2.4.2
 938    "FunciSNP" # depends on broken package snpStats-1.19.0
 939    "FunctionalNetworks" # Build Is Broken
 940    "fxregime" # depends on broken package nlopt-2.4.2
 941    "gamclass" # depends on broken package nlopt-2.4.2
 942    "gamlss_demo" # depends on broken package rpanel-1.1-3
 943    "gamm4" # depends on broken package nlopt-2.4.2
 944    "gCMAP" # depends on broken package Category-2.35.1
 945    "gCMAPWeb" # depends on broken package Category-2.35.1
 946    "gcmr" # depends on broken package nlopt-2.4.2
 947    "gcrma" # depends on broken package affyio-1.37.0
 948    "GDAtools" # depends on broken package nlopt-2.4.2
 949    "GENE_E" # depends on broken package rhdf5-2.13.1
 950    "GeneExpressionSignature" # depends on broken package annaffy-1.41.1
 951    "GeneticTools" # depends on broken package snpStats-1.19.0
 952    "genomation" # depends on broken package Rsamtools-1.21.8
 953    "GenomicAlignments" # depends on broken package Rsamtools-1.21.8
 954    "GenomicFeatures" # depends on broken package Rsamtools-1.21.8
 955    "GenomicFiles" # depends on broken package Rsamtools-1.21.8
 956    "GenomicInteractions" # depends on broken package Rsamtools-1.21.8
 957    "genotypeeval" # depends on broken package r-rtracklayer-1.29.12
 958    "GenoView" # depends on broken package Rsamtools-1.21.8
 959    "genridge" # depends on broken package nlopt-2.4.2
 960    "geojsonio" # depends on broken package V8-0.6
 961    "GEOsubmission" # depends on broken package affyio-1.37.0
 962    "gespeR" # depends on broken package Category-2.35.1
 963    "GEWIST" # depends on broken package nlopt-2.4.2
 964    "GGBase" # depends on broken package snpStats-1.19.0
 965    "ggbio" # depends on broken package Rsamtools-1.21.8
 966    "GGtools" # depends on broken package snpStats-1.19.0
 967    "gimme" # depends on broken package nlopt-2.4.2
 968    "girafe" # depends on broken package Rsamtools-1.21.8
 969    "gmapR" # depends on broken package Rsamtools-1.21.8
 970    "gmatrix" # depends on broken package cudatoolkit-5.5.22
 971    "gMCP" # build is broken
 972    "GOFunction" # build is broken
 973    "GOGANPA" # depends on broken package WGCNA-1.47
 974    "GoogleGenomics" # depends on broken package Rsamtools-1.21.8
 975    "goProfiles" # build is broken
 976    "GOSemSim" # Build Is Broken
 977    "goseq" # build is broken
 978    "GOSim" # depends on broken package topGO-2.21.0
 979    "GOstats" # depends on broken package AnnotationForge-1.11.3
 980    "GOTHiC" # depends on broken package Rsamtools-1.21.8
 981    "goTools" # build is broken
 982    "gplm" # depends on broken package nlopt-2.4.2
 983    "gputools" # depends on broken package cudatoolkit-5.5.22
 984    "gQTLstats" # depends on broken package snpStats-1.19.0
 985    "granova" # depends on broken package nlopt-2.4.2
 986    "graphicalVAR" # depends on broken package nlopt-2.4.2
 987    "GraphPCA" # depends on broken package nlopt-2.4.2
 988    "GreyListChIP" # depends on broken package Rsamtools-1.21.8
 989    "groHMM" # depends on broken package Rsamtools-1.21.8
 990    "GSCA" # depends on broken package rhdf5-2.13.1
 991    "GUIDE" # depends on broken package rpanel-1.1-3
 992    "Gviz" # depends on broken package Rsamtools-1.21.8
 993    "GWAF" # depends on broken package nlopt-2.4.2
 994    "gwascat" # depends on broken package interactiveDisplayBase-1.7.0
 995    "h2o" # build is broken
 996    "h5" # build is broken
 997    "h5vc" # depends on broken package rhdf5-2.13.1
 998    "Harshlight" # depends on broken package affyio-1.37.0
 999    "hbsae" # depends on broken package nlopt-2.4.2
1000    "heplots" # depends on broken package nlopt-2.4.2
1001    "hiAnnotator" # depends on broken package Rsamtools-1.21.8
1002    "hierGWAS"
1003    "HierO" # Build Is Broken
1004    "highriskzone"
1005    "HilbertVisGUI" # Build Is Broken
1006    "HiPLARM" # Build Is Broken
1007    "hiReadsProcessor" # depends on broken package Rsamtools-1.21.8
1008    "HistDAWass" # depends on broken package nlopt-2.4.2
1009    "HiTC" # depends on broken package Rsamtools-1.21.8
1010    "HLMdiag" # depends on broken package nlopt-2.4.2
1011    "HTqPCR" # depends on broken package affyio-1.37.0
1012    "HTSanalyzeR" # depends on broken package Category-2.35.1
1013    "HTSeqGenie" # depends on broken package Rsamtools-1.21.8
1014    "htSeqTools" # depends on broken package Rsamtools-1.21.8
1015    "hysteresis" # depends on broken package nlopt-2.4.2
1016    "IATscores" # depends on broken package nlopt-2.4.2
1017    "ibd" # depends on broken package nlopt-2.4.2
1018    "ibh" # build is broken
1019    "iccbeta" # depends on broken package nlopt-2.4.2
1020    "IdeoViz" # depends on broken package Rsamtools-1.21.8
1021    "ifaTools" # depends on broken package r-OpenMx-2.2.6
1022    "iFes" # depends on broken package cudatoolkit-5.5.22
1023    "imageHTS" # depends on broken package Category-2.35.1
1024    "immunoClust" # build is broken
1025    "imputeR" # depends on broken package nlopt-2.4.2
1026    "in2extRemes" # depends on broken package nlopt-2.4.2
1027    "inferference" # depends on broken package nlopt-2.4.2
1028    "influence_ME" # depends on broken package nlopt-2.4.2
1029    "InPAS" # depends on broken package Rsamtools-1.21.8
1030    "inSilicoMerging" # build is broken
1031    "INSPEcT" # depends on broken GenomicFeatures-1.21.13
1032    "intansv" # depends on broken package Rsamtools-1.21.8
1033    "interactiveDisplayBase" # build is broken
1034    "interactiveDisplay" # depends on broken package Category-2.35.1
1035    "interplot" # depends on broken arm-1.8-5
1036    "IONiseR" # depends on broken rhdf5-2.13.4
1037    "iptools"
1038    "IsingFit" # depends on broken package nlopt-2.4.2
1039    "IsoGene" # depends on broken package affyio-1.37.0
1040    "IsoGeneGUI" # depends on broken package affyio-1.37.0
1041    "ITALICS" # depends on broken package oligo-1.33.0
1042    "IVAS" # depends on broken package nlopt-2.4.2
1043    "ivpack" # depends on broken package nlopt-2.4.2
1044    "JAGUAR" # depends on broken package nlopt-2.4.2
1045    "jetset"
1046    "joda" # depends on broken package nlopt-2.4.2
1047    "jomo" # build is broken
1048    "js" # depends on broken package V8-0.6
1049    "KANT" # depends on broken package affyio-1.37.0
1050    "keggorthology" # build is broken
1051    "KEGGprofile" # Build Is Broken
1052    "lawn" # depends on broken package V8-0.6
1053    "learnstats" # depends on broken package nlopt-2.4.2
1054    "lefse" # build is broken
1055    "lessR" # depends on broken package nlopt-2.4.2
1056    "lfe" # build is broken
1057    "lgcp" # depends on broken package rpanel-1.1-3
1058    "limmaGUI" # depends on broken package affyio-1.37.0
1059    "LinRegInteractive" # depends on broken package rpanel-1.1-3
1060    "LiquidAssociation" # build is broken
1061    "lmdme" # build is broken
1062    "lme4" # depends on broken package nlopt-2.4.2
1063    "LMERConvenienceFunctions" # depends on broken package nlopt-2.4.2
1064    "lmerTest" # depends on broken package nlopt-2.4.2
1065    "LMGene" # depends on broken package affyio-1.37.0
1066    "lmSupport" # depends on broken package nlopt-2.4.2
1067    "LogisticDx" # depends on broken package nlopt-2.4.2
1068    "logitT" # depends on broken package affyio-1.37.0
1069    "longpower" # depends on broken package nlopt-2.4.2
1070    "LowMACA" # depends on broken package Rsamtools-1.21.8
1071    "lumi" # depends on broken package affyio-1.37.0
1072    "LVSmiRNA" # depends on broken package affyio-1.37.0
1073    "M3D" # depends on broken package Rsamtools-1.21.8
1074    "MAIT" # depends on broken package nlopt-2.4.2
1075    "makecdfenv" # depends on broken package affyio-1.37.0
1076    "mAPKL" # build is broken
1077    "maPredictDSC" # depends on broken package nlopt-2.4.2
1078    "marked" # depends on broken package nlopt-2.4.2
1079    "maskBAD" # depends on broken package affyio-1.37.0
1080    "MatrixRider" # depends on broken package DirichletMultinomial-1.11.1
1081    "MaxPro" # depends on broken package nlopt-2.4.2
1082    "mbest" # depends on broken package nlopt-2.4.2
1083    "MBmca" # depends on broken nloptr-1.0.4
1084    "mBPCR" # depends on broken package affyio-1.37.0
1085    "mcaGUI" # depends on broken package Rsamtools-1.21.8
1086    "MCRestimate" # build is broken
1087    "mdgsa" # build is broken
1088    "meboot" # depends on broken package nlopt-2.4.2
1089    "mediation" # depends on broken package r-lme4-1.1-8
1090    "MEDIPS" # depends on broken package Rsamtools-1.21.8
1091    "MEDME" # depends on broken package nlopt-2.4.2
1092    "MEMSS" # depends on broken package nlopt-2.4.2
1093    "meshr" # depends on broken package Category-2.35.1
1094    "Metab" # depends on broken package mzR-2.3.1
1095    "metagear" # build is broken
1096    "metagene" # depends on broken package Rsamtools-1.21.8
1097    "metaMix" # build is broken
1098    "metaMS" # depends on broken package mzR-2.3.1
1099    "metaplus" # depends on broken package nlopt-2.4.2
1100    "metaSEM" # depends on broken package OpenMx-2.2.4
1101    "metaseqR" # depends on broken package affyio-1.37.0
1102    "Metatron" # depends on broken package nlopt-2.4.2
1103    "methyAnalysis" # depends on broken package affyio-1.37.0
1104    "MethylAid" # depends on broken package Rsamtools-1.21.8
1105    "methylPipe" # depends on broken package Rsamtools-1.21.8
1106    "MethylSeekR" # depends on broken package Rsamtools-1.21.8
1107    "methylumi" # depends on broken package Rsamtools-1.21.8
1108    "miceadds" # depends on broken package nlopt-2.4.2
1109    "micEconAids" # depends on broken package nlopt-2.4.2
1110    "micEconCES" # depends on broken package nlopt-2.4.2
1111    "micEconSNQP" # depends on broken package nlopt-2.4.2
1112    "mi" # depends on broken package nlopt-2.4.2
1113    "MigClim" # Build Is Broken
1114    "migui" # depends on broken package nlopt-2.4.2
1115    "MineICA" # depends on broken package AnnotationForge-1.11.3
1116    "minfi" # depends on broken package Rsamtools-1.21.8
1117    "minimist" # depends on broken package V8-0.6
1118    "MinimumDistance" # depends on broken package affyio-1.37.0
1119    "mirIntegrator" # build is broken
1120    "missDeaths"
1121    "missMDA" # depends on broken package nlopt-2.4.2
1122    "missMethyl" # depends on broken package Rsamtools-1.21.8
1123    "mitoODE" # build is broken
1124    "mixAK" # depends on broken package nlopt-2.4.2
1125    "mixlm" # depends on broken package nlopt-2.4.2
1126    "MixMAP" # depends on broken package nlopt-2.4.2
1127    "mlmRev" # depends on broken package nlopt-2.4.2
1128    "MLP" # depends on broken package affyio-1.37.0
1129    "MLSeq" # depends on broken package nlopt-2.4.2
1130    "mlVAR" # depends on broken package nlopt-2.4.2
1131    "MMDiff" # depends on broken package AnnotationForge-1.11.3
1132    "MmPalateMiRNA" # depends on broken package affyio-1.37.0
1133    "mongolite" # build is broken
1134    "monocle" # build is broken
1135    "mosaic" # depends on broken package nlopt-2.4.2
1136    "MotifDb" # depends on broken package Rsamtools-1.21.8
1137    "motifRG" # depends on broken package Rsamtools-1.21.8
1138    "motifStack" # depends on broken package Rsamtools-1.21.8
1139    "MotIV" # depends on broken package Rsamtools-1.21.8
1140    "MSeasy" # depends on broken package mzR-2.3.1
1141    "MSeasyTkGUI" # depends on broken package mzR-2.3.1
1142    "MSGFgui" # depends on broken package MSGFplus-1.3.0
1143    "MSGFplus" # Build Is Broken
1144    "msmsEDA" # depends on broken package affyio-1.37.0
1145    "msmsTests" # depends on broken package affyio-1.37.0
1146    "MSnbase" # depends on broken package affyio-1.37.0
1147    "MSnID" # depends on broken package affyio-1.37.0
1148    "MSstats" # depends on broken package nlopt-2.4.2
1149    "multiDimBio" # depends on broken package nlopt-2.4.2
1150    "MultiRR" # depends on broken package nlopt-2.4.2
1151    "muma" # depends on broken package nlopt-2.4.2
1152    "munsellinterpol"
1153    "mutossGUI" # build is broken
1154    "mvGST" # depends on broken package AnnotationForge-1.11.3
1155    "mvinfluence" # depends on broken package nlopt-2.4.2
1156    "mygene" # depends on broken package Rsamtools-1.21.8
1157    "mzR" # build is broken
1158    "NanoStringQCPro" # build is broken
1159    "nCal" # depends on broken package nlopt-2.4.2
1160    "ncdfFlow" # build is broken
1161    "NCIgraph" # depends on broken package RCytoscape-1.19.0
1162    "netbenchmark" # build is broken
1163    "nettools" # depends on broken package WGCNA-1.47
1164    "NGScopy"
1165    "NHPoisson" # depends on broken package nlopt-2.4.2
1166    "nloptr" # depends on broken package nlopt-2.4.2
1167    "nondetects" # depends on broken package affyio-1.37.0
1168    "nonrandom" # depends on broken package nlopt-2.4.2
1169    "NormqPCR" # depends on broken package affyio-1.37.0
1170    "NORRRM" # build is broken
1171    "npIntFactRep" # depends on broken package nlopt-2.4.2
1172    "nucleR" # depends on broken package Rsamtools-1.21.8
1173    "oligoClasses" # depends on broken package affyio-1.37.0
1174    "oligo" # depends on broken package affyio-1.37.0
1175    "OmicsMarkeR" # depends on broken package nlopt-2.4.2
1176    "oneChannelGUI" # depends on broken package affyio-1.37.0
1177    "OpenCL" # build is broken
1178    "openCyto" # depends on broken package ncdfFlow-2.15.2
1179    "OpenMx" # build is broken
1180    "OperaMate" # depends on broken package Category-2.35.1
1181    "optBiomarker" # depends on broken package rpanel-1.1-3
1182    "ora" # depends on broken package ROracle-1.1-12
1183    "ordBTL" # depends on broken package nlopt-2.4.2
1184    "OrganismDbi" # depends on broken package Rsamtools-1.21.8
1185    "OTUbase" # depends on broken package Rsamtools-1.21.8
1186    "OUwie" # depends on broken package nlopt-2.4.2
1187    "PADOG" # build is broken
1188    "pamm" # depends on broken package nlopt-2.4.2
1189    "PANDA" # build is broken
1190    "panelAR" # depends on broken package nlopt-2.4.2
1191    "panp" # depends on broken package affyio-1.37.0
1192    "papeR" # depends on broken package nlopt-2.4.2
1193    "parboost" # depends on broken package nlopt-2.4.2
1194    "parma" # depends on broken package nlopt-2.4.2
1195    "Pasha" # depends on broken package GenomicAlignments-1.5.12
1196    "pathClass" # depends on broken package affyio-1.37.0
1197    "pathRender" # build is broken
1198    "pathview" # build is broken
1199    "PatternClass" # build is broken
1200    "Pbase" # depends on broken package affyio-1.37.0
1201    "pbdBASE" # depends on broken package pbdSLAP-0.2-0
1202    "pbdDEMO" # depends on broken package pbdSLAP-0.2-0
1203    "pbdDMAT" # depends on broken package pbdSLAP-0.2-0
1204    "pbdSLAP" # build is broken
1205    "PBImisc" # depends on broken package nlopt-2.4.2
1206    "pbkrtest" # depends on broken package nlopt-2.4.2
1207    "PBSddesolve" # build is broken
1208    "PBSmapping" # build is broken
1209    "pcaBootPlot" # depends on broken FactoMineR-1.31.3
1210    "pcaL1" # build is broken
1211    "PCpheno" # depends on broken package Category-2.35.1
1212    "pdInfoBuilder" # depends on broken package affyio-1.37.0
1213    "pdmclass" # build is broken
1214    "PECA" # depends on broken package affyio-1.37.0
1215    "pedigreemm" # depends on broken package nlopt-2.4.2
1216    "pedometrics" # depends on broken package nlopt-2.4.2
1217    "pequod" # depends on broken package nlopt-2.4.2
1218    "permGPU" # build is broken
1219    "PGA" # depends on broken package Rsamtools-1.21.8
1220    "PGSEA" # depends on broken package annaffy-1.41.1
1221    "PharmacoGx"
1222    "phenoDist" # depends on broken package Category-2.35.1
1223    "phenoTest" # depends on broken package Category-2.35.1
1224    "PhenStat" # depends on broken package nlopt-2.4.2
1225    "phia" # depends on broken package nlopt-2.4.2
1226    "phylocurve" # depends on broken package nlopt-2.4.2
1227    "phyloTop" # depends on broken package nlopt-2.4.2
1228    "PICS" # depends on broken package Rsamtools-1.21.8
1229    "PING" # depends on broken package Rsamtools-1.21.8
1230    "plateCore" # depends on broken package ncdfFlow-2.15.2
1231    "plier" # depends on broken package affyio-1.37.0
1232    "plsRbeta" # depends on broken package nlopt-2.4.2
1233    "plsRcox" # depends on broken package nlopt-2.4.2
1234    "plsRglm" # depends on broken package nlopt-2.4.2
1235    "plw" # depends on broken package affyio-1.37.0
1236    "pmclust" # build is broken
1237    "pmm" # depends on broken package nlopt-2.4.2
1238    "podkat" # depends on broken package Rsamtools-1.21.8
1239    "polytomous" # depends on broken package nlopt-2.4.2
1240    "pomp" # depends on broken package nlopt-2.4.2
1241    "ppiPre" # depends on broken package GOSemSim-1.27.3
1242    "ppiStats" # depends on broken package Category-2.35.1
1243    "prebs" # depends on broken package affyio-1.37.0
1244    "predictmeans" # depends on broken package nlopt-2.4.2
1245    "prLogistic" # depends on broken package nlopt-2.4.2
1246    "proBAMr" # depends on broken package Rsamtools-1.21.8
1247    "ProCoNA" # depends on broken package AnnotationForge-1.11.3
1248    "pRoloc" # depends on broken package nlopt-2.4.2
1249    "pRolocGUI" # depends on broken package nlopt-2.4.2
1250    "proteoQC" # depends on broken package affyio-1.37.0
1251    "PSAboot" # depends on broken package nlopt-2.4.2
1252    "ptw" # depends on broken nloptr-1.0.4
1253    "puma" # depends on broken package affyio-1.37.0
1254    "pvac" # depends on broken package affyio-1.37.0
1255    "pvca" # depends on broken package nlopt-2.4.2
1256    "Pviz" # depends on broken package Rsamtools-1.21.8
1257    "pwOmics" # depends on broken package interactiveDisplayBase-1.7.0
1258    "PythonInR"
1259    "qcmetrics" # build is broken
1260    "QDNAseq" # depends on broken package Rsamtools-1.21.8
1261    "QFRM"
1262    "qgraph" # depends on broken package nlopt-2.4.2
1263    "qpcrNorm" # depends on broken package affyio-1.37.0
1264    "qpgraph" # depends on broken package Rsamtools-1.21.8
1265    "qrqc" # depends on broken package Rsamtools-1.21.8
1266    "qtbase" # build is broken
1267    "qtlnet" # depends on broken package nlopt-2.4.2
1268    "qtpaint" # depends on broken package qtbase-1.0.9
1269    "qtutils" # depends on broken package qtbase-1.0.9
1270    "QUALIFIER" # depends on broken package ncdfFlow-2.15.2
1271    "quantification" # depends on broken package nlopt-2.4.2
1272    "quantro" # depends on broken package Rsamtools-1.21.8
1273    "QuasR" # depends on broken package Rsamtools-1.21.8
1274    "R2STATS" # depends on broken package nlopt-2.4.2
1275    "R3CPET" # depends on broken package Rsamtools-1.21.8
1276    "r3Cseq" # depends on broken package Rsamtools-1.21.8
1277    "R453Plus1Toolbox" # depends on broken package Rsamtools-1.21.8
1278    "radiant" # depends on broken package nlopt-2.4.2
1279    "raincpc" # build is broken
1280    "rainfreq" # build is broken
1281    "RamiGO" # depends on broken package RCytoscape-1.19.0
1282    "RapidPolygonLookup" # depends on broken package PBSmapping-2.69.76
1283    "RAPIDR" # depends on broken package Rsamtools-1.21.8
1284    "RareVariantVis" # depends on broken VariantAnnotation-1.15.19
1285    "Rariant" # depends on broken package Rsamtools-1.21.8
1286    "rasclass" # depends on broken package nlopt-2.4.2
1287    "RBerkeley"
1288    "RbioRXN" # depends on broken package ChemmineR-2.21.7
1289    "Rcade" # depends on broken package Rsamtools-1.21.8
1290    "rCGH" # depends on broken package r-affy-1.47.1
1291    "Rchemcpp" # depends on broken package ChemmineR-2.21.7
1292    "Rcmdr" # depends on broken package nlopt-2.4.2
1293    "RcmdrMisc" # depends on broken package nlopt-2.4.2
1294    "RcmdrPlugin_BCA" # depends on broken package nlopt-2.4.2
1295    "RcmdrPlugin_coin" # depends on broken package nlopt-2.4.2
1296    "RcmdrPlugin_depthTools" # depends on broken package nlopt-2.4.2
1297    "RcmdrPlugin_DoE" # depends on broken package nlopt-2.4.2
1298    "RcmdrPlugin_doex" # depends on broken package nlopt-2.4.2
1299    "RcmdrPlugin_EACSPIR" # depends on broken package nlopt-2.4.2
1300    "RcmdrPlugin_EBM" # depends on broken package nlopt-2.4.2
1301    "RcmdrPlugin_EcoVirtual" # depends on broken package nlopt-2.4.2
1302    "RcmdrPlugin_epack" # depends on broken package nlopt-2.4.2
1303    "RcmdrPlugin_EZR" # depends on broken package nlopt-2.4.2
1304    "RcmdrPlugin_FactoMineR" # depends on broken package nlopt-2.4.2
1305    "RcmdrPlugin_HH" # depends on broken package nlopt-2.4.2
1306    "RcmdrPlugin_IPSUR" # depends on broken package nlopt-2.4.2
1307    "RcmdrPlugin_KMggplot2" # depends on broken package nlopt-2.4.2
1308    "RcmdrPlugin_lfstat" # depends on broken package nlopt-2.4.2
1309    "RcmdrPlugin_MA" # depends on broken package nlopt-2.4.2
1310    "RcmdrPlugin_mosaic" # depends on broken package nlopt-2.4.2
1311    "RcmdrPlugin_MPAStats" # depends on broken package nlopt-2.4.2
1312    "RcmdrPlugin_NMBU" # depends on broken package nlopt-2.4.2
1313    "RcmdrPlugin_orloca" # depends on broken package nlopt-2.4.2
1314    "RcmdrPlugin_plotByGroup" # depends on broken package nlopt-2.4.2
1315    "RcmdrPlugin_pointG" # depends on broken package nlopt-2.4.2
1316    "RcmdrPlugin_qual" # depends on broken package nlopt-2.4.2
1317    "RcmdrPlugin_RMTCJags" # depends on broken package nlopt-2.4.2
1318    "RcmdrPlugin_ROC" # depends on broken package nlopt-2.4.2
1319    "RcmdrPlugin_sampling" # depends on broken package nlopt-2.4.2
1320    "RcmdrPlugin_SCDA" # depends on broken package nlopt-2.4.2
1321    "RcmdrPlugin_seeg" # depends on broken package nlopt-2.4.2
1322    "RcmdrPlugin_SLC" # depends on broken package nlopt-2.4.2
1323    "RcmdrPlugin_SM" # depends on broken package nlopt-2.4.2
1324    "RcmdrPlugin_sos" # depends on broken package nlopt-2.4.2
1325    "RcmdrPlugin_StatisticalURV" # depends on broken package nlopt-2.4.2
1326    "RcmdrPlugin_steepness" # depends on broken package nlopt-2.4.2
1327    "RcmdrPlugin_survival" # depends on broken package nlopt-2.4.2
1328    "RcmdrPlugin_TeachingDemos" # depends on broken package nlopt-2.4.2
1329    "RcmdrPlugin_temis" # depends on broken package nlopt-2.4.2
1330    "RcmdrPlugin_UCA" # depends on broken package nlopt-2.4.2
1331    "Rcpi" # depends on broken package ChemmineR-2.21.7
1332    "Rcplex" # Build Is Broken
1333    "RcppAPT" # Build Is Broken
1334    "RcppOctave" # build is broken
1335    "RcppRedis" # build is broken
1336    "RCytoscape" # Build Is Broken
1337    "RDAVIDWebService" # depends on broken package Category-2.35.1
1338    "rdd" # depends on broken package nlopt-2.4.2
1339    "rddtools" # depends on broken package r-AER-1.2-4
1340    "rDEA" # build is broken
1341    "RDieHarder" # build is broken
1342    "ReactomePA" # depends on broken package GOSemSim-1.27.3
1343    "ReadqPCR" # depends on broken package affyio-1.37.0
1344    "REBayes" # depends on broken package Rmosek-1.2.5.1
1345    "REDseq" # depends on broken package Rsamtools-1.21.8
1346    "referenceIntervals" # depends on broken package nlopt-2.4.2
1347    "RefNet" # depends on broken package interactiveDisplayBase-1.7.0
1348    "RefPlus" # depends on broken package affyio-1.37.0
1349    "refund" # depends on broken package nlopt-2.4.2
1350    "regioneR" # depends on broken package Rsamtools-1.21.8
1351    "regionReport" # depends on broken package Rsamtools-1.21.8
1352    "repijson" # depends on broken package V8-0.6
1353    "Repitools" # depends on broken package affyio-1.37.0
1354    "ReportingTools" # depends on broken package Category-2.35.1
1355    "ReQON" # depends on broken package Rsamtools-1.21.8
1356    "REST" # depends on broken package nlopt-2.4.2
1357    "rfPred" # depends on broken package Rsamtools-1.21.8
1358    "rGADEM" # depends on broken package Rsamtools-1.21.8
1359    "rgbif" # depends on broken package V8-0.6
1360    "Rgnuplot"
1361    "rgp" # build is broken
1362    "rgpui" # depends on broken package rgp-0.4-1
1363    "rgsepd" # depends on broken package goseq-1.21.1
1364    "rhdf5" # build is broken
1365    "rHVDM" # depends on broken package affyio-1.37.0
1366    "Ringo" # depends on broken package affyio-1.37.0
1367    "RIPSeeker" # depends on broken package Rsamtools-1.21.8
1368    "Risa" # depends on broken package affyio-1.37.0
1369    "rjade" # depends on broken package V8-0.6
1370    "rJPSGCS" # build is broken
1371    "rLindo" # build is broken
1372    "RMassBank" # depends on broken package mzR-2.3.1
1373    "rMAT" # build is broken
1374    "rmgarch" # depends on broken package nlopt-2.4.2
1375    "rminer" # depends on broken package nlopt-2.4.2
1376    "RmiR" # Build Is Broken
1377    "Rmosek" # build is broken
1378    "RNAinteract" # depends on broken package Category-2.35.1
1379    "RNAither" # depends on broken package nlopt-2.4.2
1380    "RNAprobR" # depends on broken package Rsamtools-1.21.8
1381    "rnaSeqMap" # depends on broken package Rsamtools-1.21.8
1382    "RnaSeqSampleSize" # Build Is Broken
1383    "RnavGraph" # build is broken
1384    "RnBeads" # depends on broken package Rsamtools-1.21.8
1385    "Rnits" # depends on broken package affyio-1.37.0
1386    "roar" # depends on broken package Rsamtools-1.21.8
1387    "RobLoxBioC" # depends on broken package affyio-1.37.0
1388    "robustlmm" # depends on broken package nlopt-2.4.2
1389    "rockchalk" # depends on broken package nlopt-2.4.2
1390    "ROI_plugin_symphony" # depends on broken package Rsymphony-0.1-20
1391    "Rolexa" # depends on broken package Rsamtools-1.21.8
1392    "rols" # build is broken
1393    "ROracle" # Build Is Broken
1394    "RPA" # depends on broken package affyio-1.37.0
1395    "rpanel" # build is broken
1396    "rpubchem" # depends on broken package nlopt-2.4.2
1397    "Rqc" # depends on broken package Rsamtools-1.21.8
1398    "RQuantLib" # build is broken
1399    "rr" # depends on broken package nlopt-2.4.2
1400    "Rsamtools" # Build Is Broken
1401    "RSAP" # build is broken
1402    "rsbml" # build is broken
1403    "rscala" # build is broken
1404    "RSDA" # depends on broken package nlopt-2.4.2
1405    "rSFFreader" # depends on broken package Rsamtools-1.21.8
1406    "Rsubread" # Build Is Broken
1407    "RSVSim" # depends on broken package Rsamtools-1.21.8
1408    "Rsymphony" # build is broken
1409    "rTANDEM" # build is broken
1410    "RTN" # depends on broken package nlopt-2.4.2
1411    "rtracklayer" # depends on broken package Rsamtools-1.21.8
1412    "rTRMui" # depends on broken package Rsamtools-1.21.8
1413    "rugarch" # depends on broken package nlopt-2.4.2
1414    "RUVcorr" # build is broken
1415    "RUVnormalize" # Build Is Broken
1416    "RUVSeq" # depends on broken package Rsamtools-1.21.8
1417    "RVAideMemoire" # depends on broken package nlopt-2.4.2
1418    "RVFam" # depends on broken package nlopt-2.4.2
1419    "RVideoPoker" # depends on broken package rpanel-1.1-3
1420    "ryouready" # depends on broken package nlopt-2.4.2
1421    "sampleSelection" # depends on broken package nlopt-2.4.2
1422    "sapFinder" # depends on broken package rTANDEM-1.9.0
1423    "SCAN_UPC" # depends on broken package affyio-1.37.0
1424    "ScISI" # depends on broken package apComplex-2.35.0
1425    "sdcMicro" # depends on broken package nlopt-2.4.2
1426    "sdcMicroGUI" # depends on broken package nlopt-2.4.2
1427    "SDD" # depends on broken package rpanel-1.1-3
1428    "seeg" # depends on broken package nlopt-2.4.2
1429    "segmentSeq" # depends on broken package Rsamtools-1.21.8
1430    "sem" # depends on broken package nlopt-2.4.2
1431    "semdiag" # depends on broken package nlopt-2.4.2
1432    "SemDist" # Build Is Broken
1433    "semGOF" # depends on broken package nlopt-2.4.2
1434    "semPlot" # depends on broken package nlopt-2.4.2
1435    "SensoMineR" # depends on broken package nlopt-2.4.2
1436    "SEPA" # depends on broken package topGO-2.21.0
1437    "seq2pathway" # depends on broken package WGCNA-1.47
1438    "SeqArray" # depends on broken package Rsamtools-1.21.8
1439    "seqbias" # depends on broken package Rsamtools-1.21.8
1440    "seqCNA" # build is broken
1441    "SeqGrapheR" # Build Is Broken
1442    "seqplots" # depends on broken package Rsamtools-1.21.8
1443    "seqTools" # build is broken
1444    "SeqVarTools" # depends on broken package Rsamtools-1.21.8
1445    "SGSeq" # depends on broken package Rsamtools-1.21.8
1446    "shinyMethyl" # depends on broken package Rsamtools-1.21.8
1447    "shinyTANDEM" # depends on broken package rTANDEM-1.9.0
1448    "ShortRead" # depends on broken package Rsamtools-1.21.8
1449    "SIMAT" # depends on broken package mzR-2.3.1
1450    "SimBindProfiles" # depends on broken package affyio-1.37.0
1451    "similaRpeak" # depends on broken package Rsamtools-1.21.8
1452    "simpleaffy" # depends on broken package affyio-1.37.0
1453    "SimRAD" # depends on broken package Rsamtools-1.21.8
1454    "sirt" # depends on broken package nlopt-2.4.2
1455    "sjPlot" # depends on broken package nlopt-2.4.2
1456    "skewr" # depends on broken package affyio-1.37.0
1457    "SLGI" # depends on broken package apComplex-2.35.0
1458    "SNAGEE" # build is broken
1459    "snapCGH" # depends on broken package tilingArray-1.47.0
1460    "snm" # depends on broken package nlopt-2.4.2
1461    "SNPchip" # depends on broken package affyio-1.37.0
1462    "snpEnrichment" # depends on broken package snpStats-1.19.0
1463    "snpStats" # build is broken
1464    "snpStatsWriter" # depends on broken package snpStats-1.19.0
1465    "SNPtools" # depends on broken package Rsamtools-1.21.8
1466    "SOD" # depends on broken package cudatoolkit-5.5.22
1467    "soGGi" # depends on broken package Rsamtools-1.21.8
1468    "soilphysics" # depends on broken package rpanel-1.1-3
1469    "SomaticSignatures" # depends on broken package Rsamtools-1.21.8
1470    "SoyNAM" # depends on broken package r-lme4-1.1-8
1471    "spacom" # depends on broken package nlopt-2.4.2
1472    "specificity" # depends on broken package nlopt-2.4.2
1473    "spliceR" # depends on broken package Rsamtools-1.21.8
1474    "SplicingGraphs" # depends on broken package Rsamtools-1.21.8
1475    "spocc" # depends on broken package V8-0.6
1476    "spoccutils" # depends on broken spocc-0.3.0
1477    "spsann" # depends on broken package r-pedometrics-0.6-2
1478    "sscore" # depends on broken package affyio-1.37.0
1479    "ssmrob" # depends on broken package nlopt-2.4.2
1480    "ssviz" # depends on broken package Rsamtools-1.21.8
1481    "stagePop" # depends on broken package PBSddesolve-1.11.29
1482    "staRank" # depends on broken package Category-2.35.1
1483    "Starr" # depends on broken package affyio-1.37.0
1484    "STATegRa" # depends on broken package affyio-1.37.0
1485    "stcm" # depends on broken package nlopt-2.4.2
1486    "stepp" # depends on broken package nlopt-2.4.2
1487    "stringgaussnet" # build is broken
1488    "Surrogate" # depends on broken package nlopt-2.4.2
1489    "SVM2CRM" # depends on broken package Rsamtools-1.21.8
1490    "sybilSBML" # build is broken
1491    "synapter" # depends on broken package affyio-1.37.0
1492    "systemfit" # depends on broken package nlopt-2.4.2
1493    "systemPipeR" # depends on broken package AnnotationForge-1.11.3
1494    "TargetSearch" # depends on broken package mzR-2.3.1
1495    "TcGSA" # depends on broken package nlopt-2.4.2
1496    "TDMR" # depends on broken package nlopt-2.4.2
1497    "TEQC" # depends on broken package Rsamtools-1.21.8
1498    "TFBSTools" # depends on broken package DirichletMultinomial-1.11.1
1499    "tigerstats" # depends on broken package nlopt-2.4.2
1500    "tilingArray" # depends on broken package affyio-1.37.0
1501    "TIN" # depends on broken package WGCNA-1.47
1502    "TitanCNA" # depends on broken package Rsamtools-1.21.8
1503    "ToPASeq" # depends on broken package Rsamtools-1.21.8
1504    "topGO" # build is broken
1505    "topologyGSA" # depends on broken package Rsamtools-1.21.8
1506    "tracktables" # depends on broken package Rsamtools-1.21.8
1507    "trackViewer" # depends on broken package Rsamtools-1.21.8
1508    "translateSPSS2R" # depends on broken car-2.0-25
1509    "tRanslatome" # depends on broken package GOSemSim-1.27.3
1510    "TransView" # depends on broken package Rsamtools-1.21.8
1511    "traseR"
1512    "TriMatch" # depends on broken package nlopt-2.4.2
1513    "TROM" # depends on broken package topGO-2.21.0
1514    "TurboNorm" # depends on broken package affyio-1.37.0
1515    "unifiedWMWqPCR" # depends on broken package affyio-1.37.0
1516    "userfriendlyscience" # depends on broken package nlopt-2.4.2
1517    "V8" # build is broken
1518    "VanillaICE" # depends on broken package affyio-1.37.0
1519    "variancePartition" # depends on broken package lme4-1.1-8
1520    "VariantAnnotation" # depends on broken package Rsamtools-1.21.8
1521    "VariantFiltering" # depends on broken package Rsamtools-1.21.8
1522    "VariantTools" # depends on broken package Rsamtools-1.21.8
1523    "VIM" # depends on broken package nlopt-2.4.2
1524    "VIMGUI" # depends on broken package nlopt-2.4.2
1525    "vmsbase" # depends on broken package PBSmapping-2.69.76
1526    "vows" # depends on broken package nlopt-2.4.2
1527    "vsn" # depends on broken package affyio-1.37.0
1528    "vtpnet" # depends on broken package interactiveDisplayBase-1.7.0
1529    "wateRmelon" # depends on broken package affyio-1.37.0
1530    "wavClusteR" # depends on broken package Rsamtools-1.21.8
1531    "waveTiling" # depends on broken package affyio-1.37.0
1532    "webbioc" # depends on broken package affyio-1.37.0
1533    "wfe" # depends on broken package nlopt-2.4.2
1534    "WGCNA" # build is broken
1535    "wgsea" # depends on broken package snpStats-1.19.0
1536    "WideLM" # depends on broken package cudatoolkit-5.5.22
1537    "xcms" # depends on broken package mzR-2.3.1
1538    "xergm" # depends on broken package nlopt-2.4.2
1539    "xps" # build is broken
1540    "yaqcaffy" # depends on broken package affyio-1.37.0
1541    "ZeligMultilevel" # depends on broken package nlopt-2.4.2
1542    "zetadiv" # depends on broken package nlopt-2.4.2
1543  ];
1544
1545  otherOverrides = old: new: {
1546    stringi = old.stringi.overrideDerivation (attrs: {
1547      postInstall = let
1548        icuName = "icudt52l";
1549        icuSrc = pkgs.fetchzip {
1550          url = "http://static.rexamine.com/packages/${icuName}.zip";
1551          sha256 = "0hvazpizziq5ibc9017i1bb45yryfl26wzfsv05vk9mc1575r6xj";
1552          stripRoot = false;
1553        };
1554        in ''
1555          ${attrs.postInstall or ""}
1556          cp ${icuSrc}/${icuName}.dat $out/library/stringi/libs
1557        '';
1558    });
1559
1560    xml2 = old.xml2.overrideDerivation (attrs: {
1561      preConfigure = "export LIBXML_INCDIR=${pkgs.libxml2}/include/libxml2";
1562    });
1563
1564    curl = old.curl.overrideDerivation (attrs: {
1565      preConfigure = "export CURL_INCLUDES=${pkgs.curl}/include";
1566    });
1567
1568    iFes = old.iFes.overrideDerivation (attrs: {
1569      patches = [ ./patches/iFes.patch ];
1570      CUDA_HOME = "${pkgs.cudatoolkit}";
1571    });
1572
1573    RcppArmadillo = old.RcppArmadillo.overrideDerivation (attrs: {
1574      patchPhase = "patchShebangs configure";
1575    });
1576
1577    rpf = old.rpf.overrideDerivation (attrs: {
1578      patchPhase = "patchShebangs configure";
1579    });
1580
1581    BayesXsrc = old.BayesXsrc.overrideDerivation (attrs: {
1582      patches = [ ./patches/BayesXsrc.patch ];
1583    });
1584
1585    rJava = old.rJava.overrideDerivation (attrs: {
1586      preConfigure = ''
1587        export JAVA_CPPFLAGS=-I${pkgs.jdk}/include/
1588        export JAVA_HOME=${pkgs.jdk}
1589      '';
1590    });
1591
1592    JavaGD = old.JavaGD.overrideDerivation (attrs: {
1593      preConfigure = ''
1594        export JAVA_CPPFLAGS=-I${pkgs.jdk}/include/
1595        export JAVA_HOME=${pkgs.jdk}
1596      '';
1597    });
1598
1599    Mposterior = old.Mposterior.overrideDerivation (attrs: {
1600      PKG_LIBS = "-L${pkgs.openblasCompat}/lib -lopenblas";
1601    });
1602
1603    qtbase = old.qtbase.overrideDerivation (attrs: {
1604      patches = [ ./patches/qtbase.patch ];
1605    });
1606
1607    Rmpi = old.Rmpi.overrideDerivation (attrs: {
1608      configureFlags = [
1609        "--with-Rmpi-type=OPENMPI"
1610      ];
1611    });
1612
1613    Rmpfr = old.Rmpfr.overrideDerivation (attrs: {
1614      configureFlags = [
1615        "--with-mpfr-include=${pkgs.mpfr}/include"
1616      ];
1617    });
1618
1619    RVowpalWabbit = old.RVowpalWabbit.overrideDerivation (attrs: {
1620      configureFlags = [
1621        "--with-boost=${pkgs.boost.dev}" "--with-boost-libdir=${pkgs.boost.lib}/lib"
1622      ];
1623    });
1624
1625    RAppArmor = old.RAppArmor.overrideDerivation (attrs: {
1626      patches = [ ./patches/RAppArmor.patch ];
1627      LIBAPPARMOR_HOME = "${pkgs.libapparmor}";
1628    });
1629
1630    RMySQL = old.RMySQL.overrideDerivation (attrs: {
1631      patches = [ ./patches/RMySQL.patch ];
1632      MYSQL_DIR="${pkgs.mysql.lib}";
1633    });
1634
1635    devEMF = old.devEMF.overrideDerivation (attrs: {
1636      NIX_CFLAGS_LINK = "-L${pkgs.xlibs.libXft}/lib -lXft";
1637    });
1638
1639    slfm = old.slfm.overrideDerivation (attrs: {
1640      PKG_LIBS = "-L${pkgs.openblasCompat}/lib -lopenblas";
1641    });
1642
1643    SamplerCompare = old.SamplerCompare.overrideDerivation (attrs: {
1644      PKG_LIBS = "-L${pkgs.openblasCompat}/lib -lopenblas";
1645    });
1646
1647    gputools = old.gputools.overrideDerivation (attrs: {
1648      patches = [ ./patches/gputools.patch ];
1649      CUDA_HOME = "${pkgs.cudatoolkit}";
1650    });
1651
1652    # It seems that we cannot override meta attributes with overrideDerivation.
1653    CARramps = (old.CARramps.override { hydraPlatforms = stdenv.lib.platforms.none; }).overrideDerivation (attrs: {
1654      patches = [ ./patches/CARramps.patch ];
1655      configureFlags = [
1656        "--with-cuda-home=${pkgs.cudatoolkit}"
1657      ];
1658    });
1659
1660    gmatrix = old.gmatrix.overrideDerivation (attrs: {
1661      patches = [ ./patches/gmatrix.patch ];
1662      CUDA_LIB_PATH = "${pkgs.cudatoolkit}/lib64";
1663      R_INC_PATH = "${pkgs.R}/lib/R/include";
1664      CUDA_INC_PATH = "${pkgs.cudatoolkit}/usr_include";
1665    });
1666
1667    # It seems that we cannot override meta attributes with overrideDerivation.
1668    rpud = (old.rpud.override { hydraPlatforms = stdenv.lib.platforms.none; }).overrideDerivation (attrs: {
1669      patches = [ ./patches/rpud.patch ];
1670      CUDA_HOME = "${pkgs.cudatoolkit}";
1671    });
1672
1673    WideLM = old.WideLM.overrideDerivation (attrs: {
1674      patches = [ ./patches/WideLM.patch ];
1675      configureFlags = [
1676        "--with-cuda-home=${pkgs.cudatoolkit}"
1677      ];
1678    });
1679
1680    EMCluster = old.EMCluster.overrideDerivation (attrs: {
1681      patches = [ ./patches/EMCluster.patch ];
1682    });
1683
1684    spMC = old.spMC.overrideDerivation (attrs: {
1685      patches = [ ./patches/spMC.patch ];
1686    });
1687
1688    BayesLogit = old.BayesLogit.overrideDerivation (attrs: {
1689      patches = [ ./patches/BayesLogit.patch ];
1690      buildInputs = (attrs.buildInputs or []) ++ [ pkgs.openblasCompat ];
1691    });
1692
1693    BayesBridge = old.BayesBridge.overrideDerivation (attrs: {
1694      patches = [ ./patches/BayesBridge.patch ];
1695    });
1696
1697    openssl = old.openssl.overrideDerivation (attrs: {
1698      OPENSSL_INCLUDES = "${pkgs.openssl}/include";
1699    });
1700
1701    Rserve = old.Rserve.overrideDerivation (attrs: {
1702      patches = [ ./patches/Rserve.patch ];
1703      configureFlags = [
1704        "--with-server" "--with-client"
1705      ];
1706    });
1707
1708    nloptr = old.nloptr.overrideDerivation (attrs: {
1709      configureFlags = [
1710        "--with-nlopt-cflags=-I${pkgs.nlopt}/include"
1711        "--with-nlopt-libs='-L${pkgs.nlopt}/lib -lnlopt_cxx -lm'"
1712      ];
1713    });
1714
1715    V8 = old.V8.overrideDerivation (attrs: {
1716      preConfigure = "export V8_INCLUDES=${pkgs.v8}/include";
1717    });
1718
1719  };
1720in
1721  self