tjh.dev / nixpkgs
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nixpkgs / pkgs / development / r-modules / default.nix
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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 { 9 inherit R; 10 inherit (pkgs.darwin.apple_sdk.frameworks) Cocoa Foundation; 11 inherit (pkgs) gettext gfortran; 12 }; 13 14 # Generates package templates given per-repository settings 15 # 16 # some packages, e.g. cncaGUI, require X running while installation, 17 # so that we use xvfb-run if requireX is true. 18 mkDerive = {mkHomepage, mkUrls}: args: 19 # XXX: not ideal ("2.2" would match "2.22") but sufficient 20 assert (!(args ? rVersion) || lib.hasPrefix args.rVersion (lib.getVersion R)); 21 lib.makeOverridable ({ 22 name, version, sha256, 23 depends ? [], 24 doCheck ? true, 25 requireX ? false, 26 broken ? false, 27 hydraPlatforms ? R.meta.hydraPlatforms 28 }: buildRPackage { 29 name = "${name}-${version}"; 30 src = fetchurl { 31 inherit sha256; 32 urls = mkUrls (args // { inherit name version; }); 33 }; 34 inherit doCheck requireX; 35 propagatedBuildInputs = depends; 36 nativeBuildInputs = depends; 37 meta.homepage = mkHomepage (args // { inherit name; }); 38 meta.platforms = R.meta.platforms; 39 meta.hydraPlatforms = hydraPlatforms; 40 meta.broken = broken; 41 }); 42 43 # Templates for generating Bioconductor, CRAN and IRkernel packages 44 # from the name, version, sha256, and optional per-package arguments above 45 # 46 deriveBioc = mkDerive { 47 mkHomepage = {name, rVersion}: "https://bioconductor.org/packages/${rVersion}/bioc/html/${name}.html"; 48 mkUrls = {name, version, rVersion}: [ "mirror://bioc/${rVersion}/bioc/src/contrib/${name}_${version}.tar.gz" ]; 49 }; 50 deriveBiocAnn = mkDerive { 51 mkHomepage = {name, rVersion}: "http://www.bioconductor.org/packages/${name}.html"; 52 mkUrls = {name, version, rVersion}: [ "mirror://bioc/${rVersion}/data/annotation/src/contrib/${name}_${version}.tar.gz" ]; 53 }; 54 deriveBiocExp = mkDerive { 55 mkHomepage = {name, rVersion}: "http://www.bioconductor.org/packages/${name}.html"; 56 mkUrls = {name, version, rVersion}: [ "mirror://bioc/${rVersion}/data/experiment/src/contrib/${name}_${version}.tar.gz" ]; 57 }; 58 deriveCran = mkDerive { 59 mkHomepage = {name, snapshot}: "http://mran.revolutionanalytics.com/snapshot/${snapshot}/web/packages/${name}/"; 60 mkUrls = {name, version, snapshot}: [ "http://mran.revolutionanalytics.com/snapshot/${snapshot}/src/contrib/${name}_${version}.tar.gz" ]; 61 }; 62 deriveIRkernel = mkDerive { 63 mkHomepage = {name}: "https://irkernel.github.io/"; 64 mkUrls = {name, version}: [ "http://irkernel.github.io/src/contrib/${name}_${version}.tar.gz" ]; 65 }; 66 67 # Overrides package definitions with nativeBuildInputs. 68 # For example, 69 # 70 # overrideNativeBuildInputs { 71 # foo = [ pkgs.bar ] 72 # } old 73 # 74 # results in 75 # 76 # { 77 # foo = old.foo.overrideDerivation (attrs: { 78 # nativeBuildInputs = attrs.nativeBuildInputs ++ [ pkgs.bar ]; 79 # }); 80 # } 81 overrideNativeBuildInputs = overrides: old: 82 lib.mapAttrs (name: value: 83 (builtins.getAttr name old).overrideDerivation (attrs: { 84 nativeBuildInputs = attrs.nativeBuildInputs ++ value; 85 }) 86 ) overrides; 87 88 # Overrides package definitions with buildInputs. 89 # For example, 90 # 91 # overrideBuildInputs { 92 # foo = [ pkgs.bar ] 93 # } old 94 # 95 # results in 96 # 97 # { 98 # foo = old.foo.overrideDerivation (attrs: { 99 # buildInputs = attrs.buildInputs ++ [ pkgs.bar ]; 100 # }); 101 # } 102 overrideBuildInputs = overrides: old: 103 lib.mapAttrs (name: value: 104 (builtins.getAttr name old).overrideDerivation (attrs: { 105 buildInputs = attrs.buildInputs ++ value; 106 }) 107 ) overrides; 108 109 # Overrides package definitions with new R dependencies. 110 # For example, 111 # 112 # overrideRDepends { 113 # foo = [ self.bar ] 114 # } old 115 # 116 # results in 117 # 118 # { 119 # foo = old.foo.overrideDerivation (attrs: { 120 # nativeBuildInputs = attrs.nativeBuildInputs ++ [ self.bar ]; 121 # propagatedNativeBuildInputs = attrs.propagatedNativeBuildInputs ++ [ self.bar ]; 122 # }); 123 # } 124 overrideRDepends = overrides: old: 125 lib.mapAttrs (name: value: 126 (builtins.getAttr name old).overrideDerivation (attrs: { 127 nativeBuildInputs = attrs.nativeBuildInputs ++ value; 128 propagatedNativeBuildInputs = attrs.propagatedNativeBuildInputs ++ value; 129 }) 130 ) overrides; 131 132 # Overrides package definition requiring X running to install. 133 # For example, 134 # 135 # overrideRequireX [ 136 # "foo" 137 # ] old 138 # 139 # results in 140 # 141 # { 142 # foo = old.foo.override { 143 # requireX = true; 144 # }; 145 # } 146 overrideRequireX = packageNames: old: 147 let 148 nameValuePairs = map (name: { 149 inherit name; 150 value = (builtins.getAttr name old).override { 151 requireX = true; 152 }; 153 }) packageNames; 154 in 155 builtins.listToAttrs nameValuePairs; 156 157 # Overrides package definition to skip check. 158 # For example, 159 # 160 # overrideSkipCheck [ 161 # "foo" 162 # ] old 163 # 164 # results in 165 # 166 # { 167 # foo = old.foo.override { 168 # doCheck = false; 169 # }; 170 # } 171 overrideSkipCheck = packageNames: old: 172 let 173 nameValuePairs = map (name: { 174 inherit name; 175 value = (builtins.getAttr name old).override { 176 doCheck = false; 177 }; 178 }) packageNames; 179 in 180 builtins.listToAttrs nameValuePairs; 181 182 # Overrides package definition to mark it broken. 183 # For example, 184 # 185 # overrideBroken [ 186 # "foo" 187 # ] old 188 # 189 # results in 190 # 191 # { 192 # foo = old.foo.override { 193 # broken = true; 194 # }; 195 # } 196 overrideBroken = packageNames: old: 197 let 198 nameValuePairs = map (name: { 199 inherit name; 200 value = (builtins.getAttr name old).override { 201 broken = true; 202 }; 203 }) packageNames; 204 in 205 builtins.listToAttrs nameValuePairs; 206 207 defaultOverrides = old: new: 208 let old0 = old; in 209 let 210 old1 = old0 // (overrideRequireX packagesRequireingX old0); 211 old2 = old1 // (overrideSkipCheck packagesToSkipCheck old1); 212 old3 = old2 // (overrideRDepends packagesWithRDepends old2); 213 old4 = old3 // (overrideNativeBuildInputs packagesWithNativeBuildInputs old3); 214 old5 = old4 // (overrideBuildInputs packagesWithBuildInputs old4); 215 old6 = old5 // (overrideBroken brokenPackages old5); 216 old = old6; 217 in old // (otherOverrides old new); 218 219 # Recursive override pattern. 220 # `_self` is a collection of packages; 221 # `self` is `_self` with overridden packages; 222 # packages in `_self` may depends on overridden packages. 223 self = (defaultOverrides _self self) // overrides; 224 _self = import ./bioc-packages.nix { inherit self; derive = deriveBioc; } // 225 import ./bioc-annotation-packages.nix { inherit self; derive = deriveBiocAnn; } // 226 import ./bioc-experiment-packages.nix { inherit self; derive = deriveBiocExp; } // 227 import ./cran-packages.nix { inherit self; derive = deriveCran; } // 228 import ./irkernel-packages.nix { inherit self; derive = deriveIRkernel; }; 229 230 # tweaks for the individual packages and "in self" follow 231 232 packagesWithRDepends = { 233 FactoMineR = [ self.car ]; 234 pander = [ self.codetools ]; 235 }; 236 237 packagesWithNativeBuildInputs = { 238 abn = [ pkgs.gsl_1 ]; 239 adimpro = [ pkgs.imagemagick ]; 240 audio = [ pkgs.portaudio ]; 241 BayesSAE = [ pkgs.gsl_1 ]; 242 BayesVarSel = [ pkgs.gsl_1 ]; 243 BayesXsrc = [ pkgs.readline pkgs.ncurses ]; 244 bigGP = [ pkgs.openmpi ]; 245 BiocCheck = [ pkgs.which ]; 246 Biostrings = [ pkgs.zlib ]; 247 bnpmr = [ pkgs.gsl_1 ]; 248 BNSP = [ pkgs.gsl_1 ]; 249 cairoDevice = [ pkgs.gtk2 ]; 250 Cairo = [ pkgs.libtiff pkgs.libjpeg pkgs.cairo ]; 251 Cardinal = [ pkgs.which ]; 252 chebpol = [ pkgs.fftw ]; 253 ChemmineOB = [ pkgs.openbabel pkgs.pkgconfig ]; 254 cit = [ pkgs.gsl_1 ]; 255 curl = [ pkgs.curl ]; 256 devEMF = [ pkgs.xorg.libXft ]; 257 diversitree = [ pkgs.gsl_1 pkgs.fftw ]; 258 EMCluster = [ pkgs.liblapack ]; 259 fftw = [ pkgs.fftw ]; 260 fftwtools = [ pkgs.fftw ]; 261 Formula = [ pkgs.gmp ]; 262 geoCount = [ pkgs.gsl_1 ]; 263 git2r = [ pkgs.zlib pkgs.openssl ]; 264 GLAD = [ pkgs.gsl_1 ]; 265 glpkAPI = [ pkgs.gmp pkgs.glpk ]; 266 gmp = [ pkgs.gmp ]; 267 graphscan = [ pkgs.gsl_1 ]; 268 gsl = [ pkgs.gsl_1 ]; 269 HiCseg = [ pkgs.gsl_1 ]; 270 iBMQ = [ pkgs.gsl_1 ]; 271 igraph = [ pkgs.gmp ]; 272 JavaGD = [ pkgs.jdk ]; 273 jpeg = [ pkgs.libjpeg ]; 274 KFKSDS = [ pkgs.gsl_1 ]; 275 kza = [ pkgs.fftw ]; 276 libamtrack = [ pkgs.gsl_1 ]; 277 mixcat = [ pkgs.gsl_1 ]; 278 mvabund = [ pkgs.gsl_1 ]; 279 mwaved = [ pkgs.fftw ]; 280 ncdf4 = [ pkgs.netcdf ]; 281 nloptr = [ pkgs.nlopt ]; 282 openssl = [ pkgs.openssl ]; 283 outbreaker = [ pkgs.gsl_1 ]; 284 pander = [ pkgs.pandoc pkgs.which ]; 285 pbdMPI = [ pkgs.openmpi ]; 286 pbdNCDF4 = [ pkgs.netcdf ]; 287 pbdPROF = [ pkgs.openmpi ]; 288 PKI = [ pkgs.openssl ]; 289 png = [ pkgs.libpng ]; 290 PopGenome = [ pkgs.zlib ]; 291 proj4 = [ pkgs.proj ]; 292 qtbase = [ pkgs.qt4 ]; 293 qtpaint = [ pkgs.qt4 ]; 294 R2GUESS = [ pkgs.gsl_1 ]; 295 R2SWF = [ pkgs.zlib pkgs.libpng pkgs.freetype ]; 296 RAppArmor = [ pkgs.libapparmor ]; 297 rapportools = [ pkgs.which ]; 298 rapport = [ pkgs.which ]; 299 rbamtools = [ pkgs.zlib ]; 300 rcdd = [ pkgs.gmp ]; 301 RcppCNPy = [ pkgs.zlib ]; 302 RcppGSL = [ pkgs.gsl_1 ]; 303 RcppOctave = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre pkgs.octave ]; 304 RcppZiggurat = [ pkgs.gsl_1 ]; 305 rgdal = [ pkgs.proj pkgs.gdal ]; 306 rgeos = [ pkgs.geos ]; 307 rggobi = [ pkgs.ggobi pkgs.gtk2 pkgs.libxml2 ]; 308 rgl = [ pkgs.mesa pkgs.xlibsWrapper ]; 309 Rglpk = [ pkgs.glpk ]; 310 RGtk2 = [ pkgs.gtk2 ]; 311 Rhpc = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.openmpi pkgs.pcre ]; 312 Rhtslib = [ pkgs.zlib ]; 313 RJaCGH = [ pkgs.zlib ]; 314 rjags = [ pkgs.jags ]; 315 rJava = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre pkgs.jdk pkgs.libzip ]; 316 Rlibeemd = [ pkgs.gsl_1 ]; 317 rmatio = [ pkgs.zlib ]; 318 Rmpfr = [ pkgs.gmp pkgs.mpfr ]; 319 Rmpi = [ pkgs.openmpi ]; 320 RMySQL = [ pkgs.zlib pkgs.mysql.lib ]; 321 RNetCDF = [ pkgs.netcdf pkgs.udunits ]; 322 RODBCext = [ pkgs.libiodbc ]; 323 RODBC = [ pkgs.libiodbc ]; 324 rpg = [ pkgs.postgresql ]; 325 rphast = [ pkgs.pcre pkgs.zlib pkgs.bzip2 pkgs.gzip pkgs.readline ]; 326 Rpoppler = [ pkgs.poppler ]; 327 RPostgreSQL = [ pkgs.postgresql ]; 328 RProtoBuf = [ pkgs.protobuf ]; 329 rPython = [ pkgs.python ]; 330 RSclient = [ pkgs.openssl ]; 331 Rserve = [ pkgs.openssl ]; 332 Rssa = [ pkgs.fftw ]; 333 rtfbs = [ pkgs.zlib pkgs.pcre pkgs.bzip2 pkgs.gzip pkgs.readline ]; 334 rtiff = [ pkgs.libtiff ]; 335 runjags = [ pkgs.jags ]; 336 RVowpalWabbit = [ pkgs.zlib pkgs.boost ]; 337 rzmq = [ pkgs.zeromq3 ]; 338 SAVE = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre ]; 339 sdcTable = [ pkgs.gmp pkgs.glpk ]; 340 seewave = [ pkgs.fftw pkgs.libsndfile ]; 341 seqinr = [ pkgs.zlib ]; 342 seqminer = [ pkgs.zlib pkgs.bzip2 ]; 343 showtext = [ pkgs.zlib pkgs.libpng pkgs.icu pkgs.freetype ]; 344 simplexreg = [ pkgs.gsl_1 ]; 345 SOD = [ pkgs.cudatoolkit ]; # requres CL/cl.h 346 spate = [ pkgs.fftw ]; 347 sprint = [ pkgs.openmpi ]; 348 ssanv = [ pkgs.proj ]; 349 stsm = [ pkgs.gsl_1 ]; 350 stringi = [ pkgs.icu.dev ]; 351 survSNP = [ pkgs.gsl_1 ]; 352 sysfonts = [ pkgs.zlib pkgs.libpng pkgs.freetype ]; 353 TAQMNGR = [ pkgs.zlib ]; 354 tiff = [ pkgs.libtiff ]; 355 TKF = [ pkgs.gsl_1 ]; 356 tkrplot = [ pkgs.xorg.libX11 ]; 357 topicmodels = [ pkgs.gsl_1 ]; 358 udunits2 = [ pkgs.udunits pkgs.expat ]; 359 V8 = [ pkgs.v8 ]; 360 VBLPCM = [ pkgs.gsl_1 ]; 361 VBmix = [ pkgs.gsl_1 pkgs.fftw pkgs.qt4 ]; 362 WhopGenome = [ pkgs.zlib ]; 363 XBRL = [ pkgs.zlib pkgs.libxml2 ]; 364 xml2 = [ pkgs.libxml2 ]; 365 XML = [ pkgs.libtool pkgs.libxml2 pkgs.xmlsec pkgs.libxslt ]; 366 affyPLM = [ pkgs.zlib ]; 367 bamsignals = [ pkgs.zlib ]; 368 BitSeq = [ pkgs.zlib ]; 369 DiffBind = [ pkgs.zlib ]; 370 ShortRead = [ pkgs.zlib ]; 371 oligo = [ pkgs.zlib ]; 372 gmapR = [ pkgs.zlib ]; 373 Rsubread = [ pkgs.zlib ]; 374 XVector = [ pkgs.zlib ]; 375 Rsamtools = [ pkgs.zlib ]; 376 rtracklayer = [ pkgs.zlib ]; 377 affyio = [ pkgs.zlib ]; 378 VariantAnnotation = [ pkgs.zlib ]; 379 snpStats = [ pkgs.zlib ]; 380 }; 381 382 packagesWithBuildInputs = { 383 # sort -t '=' -k 2 384 svKomodo = [ pkgs.which ]; 385 nat = [ pkgs.which ]; 386 nat_nblast = [ pkgs.which ]; 387 nat_templatebrains = [ pkgs.which ]; 388 RMark = [ pkgs.which ]; 389 RPushbullet = [ pkgs.which ]; 390 qtpaint = [ pkgs.cmake ]; 391 qtbase = [ pkgs.cmake pkgs.perl ]; 392 gmatrix = [ pkgs.cudatoolkit ]; 393 RCurl = [ pkgs.curl ]; 394 R2SWF = [ pkgs.pkgconfig ]; 395 rggobi = [ pkgs.pkgconfig ]; 396 RGtk2 = [ pkgs.pkgconfig ]; 397 RProtoBuf = [ pkgs.pkgconfig ]; 398 Rpoppler = [ pkgs.pkgconfig ]; 399 VBmix = [ pkgs.pkgconfig ]; 400 XML = [ pkgs.pkgconfig ]; 401 cairoDevice = [ pkgs.pkgconfig ]; 402 chebpol = [ pkgs.pkgconfig ]; 403 fftw = [ pkgs.pkgconfig ]; 404 geoCount = [ pkgs.pkgconfig ]; 405 kza = [ pkgs.pkgconfig ]; 406 mwaved = [ pkgs.pkgconfig ]; 407 showtext = [ pkgs.pkgconfig ]; 408 spate = [ pkgs.pkgconfig ]; 409 stringi = [ pkgs.pkgconfig ]; 410 sysfonts = [ pkgs.pkgconfig ]; 411 Cairo = [ pkgs.pkgconfig ]; 412 Rsymphony = [ pkgs.pkgconfig pkgs.doxygen pkgs.graphviz pkgs.subversion ]; 413 qtutils = [ pkgs.qt4 ]; 414 ecoretriever = [ pkgs.which ]; 415 tcltk2 = [ pkgs.tcl pkgs.tk ]; 416 tikzDevice = [ pkgs.which pkgs.texlive.combined.scheme-medium ]; 417 rPython = [ pkgs.which ]; 418 gridGraphics = [ pkgs.which ]; 419 gputools = [ pkgs.which pkgs.cudatoolkit ]; 420 adimpro = [ pkgs.which pkgs.xorg.xdpyinfo ]; 421 PET = [ pkgs.which pkgs.xorg.xdpyinfo pkgs.imagemagick ]; 422 dti = [ pkgs.which pkgs.xorg.xdpyinfo pkgs.imagemagick ]; 423 mzR = [ pkgs.netcdf ]; 424 }; 425 426 packagesRequireingX = [ 427 "accrual" 428 "ade4TkGUI" 429 "adehabitat" 430 "analogue" 431 "analogueExtra" 432 "AnalyzeFMRI" 433 "AnnotLists" 434 "AnthropMMD" 435 "aplpack" 436 "aqfig" 437 "arf3DS4" 438 "asbio" 439 "AtelieR" 440 "BAT" 441 "bayesDem" 442 "BCA" 443 "BEQI2" 444 "betapart" 445 "betaper" 446 "BiodiversityR" 447 "BioGeoBEARS" 448 "bio_infer" 449 "bipartite" 450 "biplotbootGUI" 451 "blender" 452 "cairoDevice" 453 "CCTpack" 454 "cncaGUI" 455 "cocorresp" 456 "CommunityCorrelogram" 457 "confidence" 458 "constrainedKriging" 459 "ConvergenceConcepts" 460 "cpa" 461 "DALY" 462 "dave" 463 "debug" 464 "Deducer" 465 "DeducerExtras" 466 "DeducerPlugInExample" 467 "DeducerPlugInScaling" 468 "DeducerSpatial" 469 "DeducerSurvival" 470 "DeducerText" 471 "Demerelate" 472 "DescTools" 473 "detrendeR" 474 "dgmb" 475 "DivMelt" 476 "dpa" 477 "DSpat" 478 "dynamicGraph" 479 "dynBiplotGUI" 480 "EasyqpcR" 481 "EcoVirtual" 482 "ENiRG" 483 "EnQuireR" 484 "eVenn" 485 "exactLoglinTest" 486 "FAiR" 487 "fat2Lpoly" 488 "fbati" 489 "FD" 490 "feature" 491 "FeedbackTS" 492 "FFD" 493 "fgui" 494 "fisheyeR" 495 "fit4NM" 496 "forams" 497 "forensim" 498 "FreeSortR" 499 "fscaret" 500 "fSRM" 501 "gcmr" 502 "Geneland" 503 "GeoGenetix" 504 "geomorph" 505 "geoR" 506 "geoRglm" 507 "georob" 508 "GeoXp" 509 "GGEBiplotGUI" 510 "gnm" 511 "GPCSIV" 512 "GrammR" 513 "GrapheR" 514 "GroupSeq" 515 "gsubfn" 516 "GUniFrac" 517 "gWidgets2RGtk2" 518 "gWidgets2tcltk" 519 "gWidgetsRGtk2" 520 "gWidgetstcltk" 521 "HH" 522 "HiveR" 523 "HomoPolymer" 524 "iBUGS" 525 "ic50" 526 "iDynoR" 527 "in2extRemes" 528 "iplots" 529 "isopam" 530 "IsotopeR" 531 "JGR" 532 "KappaGUI" 533 "likeLTD" 534 "logmult" 535 "LS2Wstat" 536 "MAR1" 537 "MareyMap" 538 "memgene" 539 "MergeGUI" 540 "metacom" 541 "Meth27QC" 542 "MetSizeR" 543 "MicroStrategyR" 544 "migui" 545 "miniGUI" 546 "MissingDataGUI" 547 "mixsep" 548 "mlDNA" 549 "MplusAutomation" 550 "mpmcorrelogram" 551 "mritc" 552 "MTurkR" 553 "multgee" 554 "multibiplotGUI" 555 "nodiv" 556 "OligoSpecificitySystem" 557 "onemap" 558 "OpenRepGrid" 559 "palaeoSig" 560 "paleoMAS" 561 "pbatR" 562 "PBSadmb" 563 "PBSmodelling" 564 "PCPS" 565 "pez" 566 "phylotools" 567 "picante" 568 "PKgraph" 569 "playwith" 570 "plotSEMM" 571 "plsRbeta" 572 "plsRglm" 573 "pmg" 574 "PopGenReport" 575 "poppr" 576 "powerpkg" 577 "PredictABEL" 578 "prefmod" 579 "PrevMap" 580 "ProbForecastGOP" 581 "QCAGUI" 582 "qtbase" 583 "qtpaint" 584 "qtutils" 585 "R2STATS" 586 "r4ss" 587 "RandomFields" 588 "rareNMtests" 589 "rAverage" 590 "Rcmdr" 591 "RcmdrPlugin_BCA" 592 "RcmdrPlugin_coin" 593 "RcmdrPlugin_depthTools" 594 "RcmdrPlugin_DoE" 595 "RcmdrPlugin_doex" 596 "RcmdrPlugin_EACSPIR" 597 "RcmdrPlugin_EBM" 598 "RcmdrPlugin_EcoVirtual" 599 "RcmdrPlugin_epack" 600 "RcmdrPlugin_EZR" 601 "RcmdrPlugin_FactoMineR" 602 "RcmdrPlugin_HH" 603 "RcmdrPlugin_IPSUR" 604 "RcmdrPlugin_KMggplot2" 605 "RcmdrPlugin_lfstat" 606 "RcmdrPlugin_MA" 607 "RcmdrPlugin_mosaic" 608 "RcmdrPlugin_MPAStats" 609 "RcmdrPlugin_orloca" 610 "RcmdrPlugin_plotByGroup" 611 "RcmdrPlugin_pointG" 612 "RcmdrPlugin_qual" 613 "RcmdrPlugin_ROC" 614 "RcmdrPlugin_sampling" 615 "RcmdrPlugin_SCDA" 616 "RcmdrPlugin_SLC" 617 "RcmdrPlugin_SM" 618 "RcmdrPlugin_sos" 619 "RcmdrPlugin_steepness" 620 "RcmdrPlugin_survival" 621 "RcmdrPlugin_TeachingDemos" 622 "RcmdrPlugin_temis" 623 "RcmdrPlugin_UCA" 624 "recluster" 625 "relax" 626 "relimp" 627 "RenextGUI" 628 "reportRx" 629 "reshapeGUI" 630 "rgl" 631 "RHRV" 632 "rich" 633 "rioja" 634 "ripa" 635 "rite" 636 "rnbn" 637 "RNCEP" 638 "RQDA" 639 "RSDA" 640 "rsgcc" 641 "RSurvey" 642 "RunuranGUI" 643 "sdcMicroGUI" 644 "sharpshootR" 645 "simba" 646 "Simile" 647 "SimpleTable" 648 "SOLOMON" 649 "soundecology" 650 "SPACECAP" 651 "spacodiR" 652 "spatsurv" 653 "sqldf" 654 "SRRS" 655 "SSDforR" 656 "statcheck" 657 "StatDA" 658 "STEPCAM" 659 "stosim" 660 "strvalidator" 661 "stylo" 662 "svDialogstcltk" 663 "svIDE" 664 "svSocket" 665 "svWidgets" 666 "SYNCSA" 667 "SyNet" 668 "tcltk2" 669 "TDMR" 670 "TED" 671 "TestScorer" 672 "TIMP" 673 "titan" 674 "tkrgl" 675 "tkrplot" 676 "tmap" 677 "tspmeta" 678 "TTAinterfaceTrendAnalysis" 679 "twiddler" 680 "vcdExtra" 681 "VecStatGraphs3D" 682 "vegan" 683 "vegan3d" 684 "vegclust" 685 "VIMGUI" 686 "WMCapacity" 687 "x12GUI" 688 "xergm" 689 ]; 690 691 packagesToSkipCheck = [ 692 "Rmpi" # tries to run MPI processes 693 "gmatrix" # requires CUDA runtime 694 "sprint" # tries to run MPI processes 695 "pbdMPI" # tries to run MPI processes 696 ]; 697 698 # Packages which cannot be installed due to lack of dependencies or other reasons. 699 brokenPackages = [ 700 "TED" # depends on broken package animation 701 "streamMOA" # depends on broken package animation 702 "stream" # depends on broken package animation 703 "spdynmod" # depends on broken package animation 704 "treeplyr" # depends on broken package animation 705 "recluster" # depends on broken package animation 706 "geomorph" # depends on broken package animation 707 "phytools" # depends on broken package animation 708 "animation" # broken build 709 "srd" # broken build 710 "paleotree" # broken build 711 "ndtv" # broken build 712 "mvMORPH" # broken build 713 "mptools" # broken build 714 "monogeneaGM" # broken build 715 "molaR" # broken build 716 "idm" # broken build 717 "hisse" # broken build 718 "gfcanalysis" # broken build 719 "evolqg" # broken build 720 "evobiR" # broken build 721 "convevol" # broken build 722 "bayou" # broken build 723 "anim_plots" # broken build 724 "TKF" # broken build 725 "Rphylopars" # broken build 726 "RAM" # broken build 727 "PhySortR" # broken build 728 "MonoPhy" # broken build 729 "Momocs" # broken build 730 "Evomorph" # broken build 731 "PBD" # depends on broken package DDD 732 "DDD" # broken build 733 "BMhyd" # broken build 734 "rscala" # broken build 735 "rgpui" # depends on broken package rgp 736 "rgp" # broken build 737 "qcmetrics" # broken build 738 "lfe" # broken build 739 "interactiveDisplay" # depends on broken package interactiveDisplayBase 740 "RefNet" # depends on broken package interactiveDisplayBase 741 "pwOmics" # depends on broken package interactiveDisplayBase 742 "grasp2db" # depends on broken package interactiveDisplayBase 743 "EnsDb_Rnorvegicus_v79" # depends on broken package interactiveDisplayBase 744 "EnsDb_Rnorvegicus_v75" # depends on broken package interactiveDisplayBase 745 "EnsDb_Mmusculus_v79" # depends on broken package interactiveDisplayBase 746 "EnsDb_Mmusculus_v75" # depends on broken package interactiveDisplayBase 747 "EnsDb_Hsapiens_v79" # depends on broken package interactiveDisplayBase 748 "EnsDb_Hsapiens_v75" # depends on broken package interactiveDisplayBase 749 "ensembldb" # depends on broken package interactiveDisplayBase 750 "AnnotationHubData" # depends on broken package interactiveDisplayBase 751 "AnnotationHub" # depends on broken package interactiveDisplayBase 752 "interactiveDisplayBase" # broken build 753 "h2o" # broken build 754 "funModeling" # broken build 755 "brr" # broken build 756 "bedr" # broken build 757 "Sabermetrics" # broken build 758 "RKEEL" # depends on broken package RKEELjars 759 "RKEELjars" # broken build 760 "RapidPolygonLookup" # depends on broken package PBSmapping 761 "PBSmapping" # broken build 762 "stagePop" # depends on broken package PBSddesolve 763 "PBSddesolve" # broken build 764 "Metab" # broken build 765 "Crossover" # broken build 766 "CardinalWorkflows" # broken build 767 "spoccutils" # depends on broken package spocc 768 "mapr" # depends on broken package spocc 769 "vmsbase" # broken build 770 "vcfR" # broken build 771 "strataG" # broken build 772 "SSDM" # broken build 773 "SimInf" # broken build 774 "shazam" # broken build 775 "rsvg" # broken build 776 "Rothermel" # broken build 777 "rfPermute" # broken build 778 "redland" # broken build 779 "RAppArmor" # broken build 780 "permGPU" # broken build 781 "pdftools" # broken build 782 "OceanView" # broken build 783 "MSeasyTkGUI" # broken build 784 "mrMLM" # broken build 785 "MonetDBLite" # broken build 786 "MixGHD" # broken build 787 "LCMCR" # broken build 788 "hunspell" # broken build 789 "googleformr" # broken build 790 "ggseas" # depends on broken package x13binary 791 "seasonal" # depends on broken package x13binary 792 "gunsales" # depends on broken package x13binary 793 "x13binary" # broken build 794 "fds" # broken build 795 "exifr" # broken build 796 "rite" # depends on broken package euroMix 797 "MBCB" # depends on broken package euroMix 798 "forensim" # depends on broken package euroMix 799 "dynBiplotGUI" # depends on broken package euroMix 800 "cncaGUI" # depends on broken package euroMix 801 "biplotbootGUI" # depends on broken package euroMix 802 "AnthropMMD" # depends on broken package euroMix 803 "ilc" # depends on broken package demography 804 "demography" # broken build 805 "webbioc" # depends on broken package limma 806 "davidTiling" # depends on broken package limma 807 "tilingArray" # depends on broken package limma 808 "NAPPA" # depends on broken package limma 809 "NanoStringNorm" # depends on broken package limma 810 "synapterdata" # depends on broken package limma 811 "synapter" # depends on broken package limma 812 "RforProteomics" # depends on broken package limma 813 "pRolocdata" # depends on broken package limma 814 "ProCoNA" # depends on broken package limma 815 "Pbase" # depends on broken package limma 816 "MSnID" # depends on broken package limma 817 "msmsEDA" # depends on broken package limma 818 "MSnbase" # depends on broken package limma 819 "staRank" # depends on broken package limma 820 "phenoDist" # depends on broken package limma 821 "imageHTS" # depends on broken package limma 822 "Mulder2012" # depends on broken package limma 823 "HTSanalyzeR" # depends on broken package limma 824 "gespeR" # depends on broken package limma 825 "cellHTS2" # depends on broken package limma 826 "affyPara" # depends on broken package limma 827 "vsn" # depends on broken package limma 828 "ttScreening" # depends on broken package limma 829 "metaX" # depends on broken package limma 830 "SSPA" # depends on broken package limma 831 "SQDA" # depends on broken package limma 832 "ADaCGH2" # depends on broken package limma 833 "snapCGH" # depends on broken package limma 834 "Shrinkage" # depends on broken package limma 835 "SafeQuant" # depends on broken package limma 836 "RTopper" # depends on broken package limma 837 "RTCGAToolbox" # depends on broken package limma 838 "RPPanalyzer" # depends on broken package limma 839 "Rnits" # depends on broken package limma 840 "RNAinteractMAPK" # depends on broken package limma 841 "RNAinteract" # depends on broken package limma 842 "SimBindProfiles" # depends on broken package limma 843 "ccTutorial" # depends on broken package limma 844 "Ringo" # depends on broken package limma 845 "rCGH" # depends on broken package limma 846 "qusage" # depends on broken package limma 847 "qpcrNorm" # depends on broken package limma 848 "prot2D" # depends on broken package limma 849 "polyester" # depends on broken package limma 850 "plmDE" # depends on broken package limma 851 "phenoTest" # depends on broken package limma 852 "RANKS" # depends on broken package limma 853 "PerfMeas" # depends on broken package limma 854 "pepStat" # depends on broken package limma 855 "PECA" # depends on broken package limma 856 "PADOG" # depends on broken package limma 857 "OGSA" # depends on broken package limma 858 "nethet" # depends on broken package limma 859 "lpNet" # depends on broken package limma 860 "nem" # depends on broken package limma 861 "monocle" # depends on broken package limma 862 "MmPalateMiRNA" # depends on broken package limma 863 "miRtest" # depends on broken package limma 864 "miRLAB" # depends on broken package limma 865 "mGSZ" # depends on broken package limma 866 "MAMA" # depends on broken package limma 867 "metaMA" # depends on broken package limma 868 "msd16s" # depends on broken package limma 869 "metagenomeSeq" # depends on broken package limma 870 "metabolomics" # depends on broken package limma 871 "maSigPro" # depends on broken package limma 872 "timecourse" # depends on broken package limma 873 "stepNorm" # depends on broken package limma 874 "RBM" # depends on broken package limma 875 "saps" # depends on broken package limma 876 "PharmacoGx" # depends on broken package limma 877 "piano" # depends on broken package limma 878 "OLINgui" # depends on broken package limma 879 "OLIN" # depends on broken package limma 880 "nnNorm" # depends on broken package limma 881 "ListerEtAlBSseq" # depends on broken package limma 882 "compEpiTools" # depends on broken package limma 883 "methylPipe" # depends on broken package limma 884 "dyebiasexamples" # depends on broken package limma 885 "dyebias" # depends on broken package limma 886 "CluMix" # depends on broken package limma 887 "HCsnip" # depends on broken package limma 888 "sigaR" # depends on broken package limma 889 "plrs" # depends on broken package limma 890 "CGHregions" # depends on broken package limma 891 "QDNAseq_mm10" # depends on broken package limma 892 "QDNAseq_hg19" # depends on broken package limma 893 "QDNAseq" # depends on broken package limma 894 "GeneBreak" # depends on broken package limma 895 "focalCall" # depends on broken package limma 896 "CGHnormaliter" # depends on broken package limma 897 "CGHcall" # depends on broken package limma 898 "CGHbase" # depends on broken package limma 899 "beta7" # depends on broken package limma 900 "marray" # depends on broken package limma 901 "LVSmiRNA" # depends on broken package limma 902 "lmdme" # depends on broken package limma 903 "limmaGUI" # depends on broken package limma 904 "InPAS" # depends on broken package limma 905 "iChip" # depends on broken package limma 906 "unifiedWMWqPCR" # depends on broken package limma 907 "nondetects" # depends on broken package limma 908 "HTqPCR" # depends on broken package limma 909 "HD2013SGI" # depends on broken package limma 910 "vtpnet" # depends on broken package limma 911 "gwascat" # depends on broken package limma 912 "gQTLstats" # depends on broken package limma 913 "GOsummaries" # depends on broken package limma 914 "yri1kgv" # depends on broken package limma 915 "hmyriB36" # depends on broken package limma 916 "cheung2010" # depends on broken package limma 917 "GGtools" # depends on broken package limma 918 "GGdata" # depends on broken package limma 919 "encoDnaseI" # depends on broken package limma 920 "dsQTL" # depends on broken package limma 921 "ceuhm3" # depends on broken package limma 922 "ceu1kgv" # depends on broken package limma 923 "ceu1kg" # depends on broken package limma 924 "GGBase" # depends on broken package limma 925 "GeneSelector" # depends on broken package limma 926 "GeneSelectMMD" # depends on broken package limma 927 "gCMAPWeb" # depends on broken package limma 928 "gCMAP" # depends on broken package limma 929 "flowBin" # depends on broken package limma 930 "Fletcher2013a" # depends on broken package limma 931 "FEM" # depends on broken package limma 932 "explorase" # depends on broken package limma 933 "ExiMiR" # depends on broken package limma 934 "tweeDEseq" # depends on broken package limma 935 "tRanslatome" # depends on broken package limma 936 "ToPASeq" # depends on broken package limma 937 "timeSeq" # depends on broken package limma 938 "TCGAbiolinks" # depends on broken package limma 939 "TCC" # depends on broken package limma 940 "systemPipeR" # depends on broken package limma 941 "STATegRa" # depends on broken package limma 942 "ssizeRNA" # depends on broken package limma 943 "RUVSeq" # depends on broken package limma 944 "RnaSeqSampleSizeData" # depends on broken package limma 945 "RnaSeqSampleSize" # depends on broken package limma 946 "rnaSeqMap" # depends on broken package limma 947 "ReportingTools" # depends on broken package limma 948 "QuasiSeq" # depends on broken package limma 949 "PROPER" # depends on broken package limma 950 "myTAI" # depends on broken package limma 951 "msmsTests" # depends on broken package limma 952 "methylMnM" # depends on broken package limma 953 "metaseqR" # depends on broken package limma 954 "MEDIPS" # depends on broken package limma 955 "manta" # depends on broken package limma 956 "HTSFilter" # depends on broken package limma 957 "HTSCluster" # depends on broken package limma 958 "GSAgm" # depends on broken package limma 959 "fdrDiscreteNull" # depends on broken package limma 960 "erccdashboard" # depends on broken package limma 961 "EnrichmentBrowser" # depends on broken package limma 962 "edgeRun" # depends on broken package limma 963 "EDDA" # depends on broken package limma 964 "RnaSeqTutorial" # depends on broken package limma 965 "easyRNASeq" # depends on broken package limma 966 "DEGreport" # depends on broken package limma 967 "Imetagene" # depends on broken package limma 968 "metagene" # depends on broken package limma 969 "DBChIP" # depends on broken package limma 970 "babel" # depends on broken package limma 971 "apmsWAPP" # depends on broken package limma 972 "ampliQueso" # depends on broken package limma 973 "edgeR" # depends on broken package limma 974 "MMDiff" # depends on broken package limma 975 "ChIPQC" # depends on broken package limma 976 "DiffBind" # depends on broken package limma 977 "DCGL" # depends on broken package limma 978 "Prostar" # depends on broken package limma 979 "DAPAR" # depends on broken package limma 980 "DAAGbio" # depends on broken package limma 981 "csaw" # depends on broken package limma 982 "cp4p" # depends on broken package limma 983 "coRNAi" # depends on broken package limma 984 "Cormotif" # depends on broken package limma 985 "CORM" # depends on broken package limma 986 "TurboNorm" # depends on broken package limma 987 "maigesPack" # depends on broken package limma 988 "convert" # depends on broken package limma 989 "compcodeR" # depends on broken package limma 990 "codelink" # depends on broken package limma 991 "clippda" # depends on broken package limma 992 "REDseq" # depends on broken package limma 993 "GUIDEseq" # depends on broken package limma 994 "ggtut" # depends on broken package limma 995 "FunciSNP" # depends on broken package limma 996 "ChIPpeakAnno" # depends on broken package limma 997 "ChIPComp" # depends on broken package limma 998 "ChimpHumanBrainData" # depends on broken package limma 999 "charmData" # depends on broken package limma 1000 "charm" # depends on broken package limma 1001 "cghMCR" # depends on broken package limma 1002 "CCl4" # depends on broken package limma 1003 "casper" # depends on broken package limma 1004 "CancerMutationAnalysis" # depends on broken package limma 1005 "CALIB" # depends on broken package limma 1006 "quantro" # depends on broken package limma 1007 "RnBeads" # depends on broken package limma 1008 "mvoutData" # depends on broken package limma 1009 "MineICA" # depends on broken package limma 1010 "methyAnalysis" # depends on broken package limma 1011 "MAQCsubsetILM" # depends on broken package limma 1012 "MAQCsubset" # depends on broken package limma 1013 "lumiRatIDMapping" # depends on broken package limma 1014 "lumiMouseIDMapping" # depends on broken package limma 1015 "lumiHumanIDMapping" # depends on broken package limma 1016 "lumiBarnes" # depends on broken package limma 1017 "iCheck" # depends on broken package limma 1018 "ffpeExampleData" # depends on broken package limma 1019 "arrayMvout" # depends on broken package limma 1020 "lumi" # depends on broken package limma 1021 "ffpe" # depends on broken package limma 1022 "methylumi" # depends on broken package limma 1023 "shinyMethyl" # depends on broken package limma 1024 "MethylAidData" # depends on broken package limma 1025 "MethylAid" # depends on broken package limma 1026 "IlluminaHumanMethylation450kmanifest" # depends on broken package limma 1027 "skewr" # depends on broken package limma 1028 "wateRmelon" # depends on broken package limma 1029 "missMethyl" # depends on broken package limma 1030 "minfiData" # depends on broken package limma 1031 "IlluminaHumanMethylation450kanno_ilmn12_hg19" # depends on broken package limma 1032 "IlluminaHumanMethylation27kmanifest" # depends on broken package limma 1033 "FlowSorted_DLPFC_450k" # depends on broken package limma 1034 "FlowSorted_Blood_450k" # depends on broken package limma 1035 "ENmix" # depends on broken package limma 1036 "ELMER" # depends on broken package limma 1037 "MEAL" # depends on broken package limma 1038 "DMRcate" # depends on broken package limma 1039 "CopyNumber450kData" # depends on broken package limma 1040 "CopyNumber450k" # depends on broken package limma 1041 "conumee" # depends on broken package limma 1042 "ChAMP" # depends on broken package limma 1043 "minfi" # depends on broken package limma 1044 "regionReport" # depends on broken package limma 1045 "derfinderPlot" # depends on broken package limma 1046 "derfinder" # depends on broken package limma 1047 "bumphunter" # depends on broken package limma 1048 "birta" # depends on broken package limma 1049 "betr" # depends on broken package limma 1050 "beadarrayMSV" # depends on broken package limma 1051 "RobLoxBioC" # depends on broken package limma 1052 "maGUI" # depends on broken package limma 1053 "epigenomix" # depends on broken package limma 1054 "blima" # depends on broken package limma 1055 "BeadArrayUseCases" # depends on broken package limma 1056 "beadarrayFilter" # depends on broken package limma 1057 "beadarrayExampleData" # depends on broken package limma 1058 "beadarray" # depends on broken package limma 1059 "ballgown" # depends on broken package limma 1060 "attract" # depends on broken package limma 1061 "ArrayTools" # depends on broken package limma 1062 "arrayQuality" # depends on broken package limma 1063 "DrugVsDisease" # depends on broken package limma 1064 "ArrayExpress" # depends on broken package limma 1065 "oneChannelGUI" # depends on broken package limma 1066 "affylmGUI" # depends on broken package limma 1067 "AffyExpress" # depends on broken package limma 1068 "AgiMicroRna" # depends on broken package limma 1069 "affycoretools" # depends on broken package limma 1070 "ABSSeq" # depends on broken package limma 1071 "a4" # depends on broken package limma 1072 "a4Base" # depends on broken package limma 1073 "limma" # broken build 1074 "TransView" # broken build 1075 "Starr" # broken build 1076 "SICtools" # broken build 1077 "ReQON" # depends on broken package seqbias 1078 "seqbias" # broken build 1079 "Repitools" # broken build 1080 "QuasR" # broken build 1081 "qrqc" # broken build 1082 "ProteomicsAnnotationHubData" # broken build 1083 "podkat" # broken build 1084 "PING" # depends on broken package PICS 1085 "PICS" # broken build 1086 "mcaGUI" # broken build 1087 "deepSNV" # broken build 1088 "motifbreakR" # depends on broken package MotIV 1089 "LowMACA" # depends on broken package MotIV 1090 "dagLogo" # depends on broken package MotIV 1091 "motifStack" # depends on broken package MotIV 1092 "MotIV" # broken build 1093 "CNEr" # broken build 1094 "canceR" # broken build 1095 "BubbleTree" # broken build 1096 "arrayQualityMetrics" # broken build 1097 "ArrayExpressHTS" # broken build 1098 "TargetSearchData" # depends on broken package TargetSearch 1099 "TargetSearch" # broken build 1100 "ptw" # depends on broken package nloptr 1101 "gpuR" # broken build 1102 "erma" # broken build 1103 "MBmca" # depends on broken package chipPCR 1104 "dpcR" # depends on broken package chipPCR 1105 "chipPCR" # broken build 1106 "alsace" # broken build 1107 "rrlda" # depends on broken package VIM 1108 "qrfactor" # depends on broken package VIM 1109 "MVN" # depends on broken package VIM 1110 "mvoutlier" # depends on broken package VIM 1111 "robCompositions" # depends on broken package VIM 1112 "DiagrammeRsvg" # depends on broken package V8 1113 "dagitty" # depends on broken package V8 1114 "remoter" # depends on broken package sodium 1115 "Fletcher2013b" # depends on broken package RTN 1116 "apaStyle" # depends on broken package ReporteRs 1117 "categoryCompare" # depends on broken package RCytoscape 1118 "preseqR" # depends on broken package polynom 1119 "permutations" # depends on broken package partitions 1120 "GLMMRR" # depends on broken package lme4 1121 "replicationInterval" # depends on broken package lme4 1122 "GWASdata" # depends on broken package GWASTools 1123 "EnsemblePCReg" # depends on broken package EnsembleBase 1124 "EnsembleCV" # depends on broken package EnsembleBase 1125 "cpgen" # depends on broken package pedigreemm 1126 "mitml" # depends on broken package jomo 1127 "IlluminaHumanMethylation450k_db" # broken build 1128 "gahgu95ecdf" # broken build 1129 "gahgu95dcdf" # broken build 1130 "gahgu95ccdf" # broken build 1131 "gahgu95bcdf" # broken build 1132 "gahgu95av2cdf" # broken build 1133 "PREDAsampledata" # depends on broken package gahgu133plus2cdf 1134 "gahgu133plus2cdf" # broken build 1135 "gahgu133bcdf" # broken build 1136 "gahgu133acdf" # broken build 1137 "annmap" # depends on broken package RMySQL 1138 "choroplethr" # depends on broken package acs 1139 "acs" # broken build 1140 "spray" # depends on broken package partitions 1141 "CNVrd2" # broken build 1142 "proteoQC" # depends on broken package rTANDEM 1143 "PGA" # depends on broken package rTANDEM 1144 "MBESS" # depends on broken package OpenMx 1145 "IONiseR" # depends on broken package rhdf5 1146 "DOQTL" # depends on broken package rhdf5 1147 "DmelSGI" # depends on broken package rhdf5 1148 "flowDiv" # depends on broken package ncdfFlow 1149 "ChemmineDrugs" # depends on broken package ChemmineR 1150 "stpm" # depends on broken package nloptr 1151 "sjmisc" # depends on broken package nloptr 1152 "rstanarm" # depends on broken package nloptr 1153 "glmmsr" # depends on broken package nloptr 1154 "FDboost" # depends on broken package nloptr 1155 "faraway" # depends on broken package nloptr 1156 "interplot" # depends on broken package nloptr 1157 "VSE" # depends on broken package car 1158 "VARSEDIG" # depends on broken package car 1159 "translateSPSS2R" # depends on broken package car 1160 "tadaatoolbox" # depends on broken package car 1161 "lavaan_shiny" # depends on broken package car 1162 "RcmdrPlugin_GWRM" # depends on broken package car 1163 "TextoMineR" # depends on broken package car 1164 "pcaBootPlot" # depends on broken package car 1165 "ClustGeo" # depends on broken package car 1166 "preproviz" # depends on broken package car 1167 "hsdar" # depends on broken package car 1168 "DecisionCurve" # depends on broken package car 1169 "CONDOP" # depends on broken package car 1170 "EnsemblePenReg" # depends on broken package car 1171 "EnsembleBase" # depends on broken package car 1172 "fullfact" # depends on broken package car 1173 "clusterSEs" # depends on broken package car 1174 "ggiraph" # depends on broken package gdtools 1175 "rvg" # depends on broken package gdtools 1176 "ggpmisc" # depends on broken package polynom 1177 "mlt_docreg" # depends on broken package polynom 1178 "mlt" # depends on broken package polynom 1179 "basefun" # depends on broken package polynom 1180 "rtable" # depends on broken package ReporteRs 1181 "Mediana" # depends on broken package ReporteRs 1182 "ReporteRs" # broken build 1183 "abd" # depends on broken package nlopt 1184 "adabag" # depends on broken package nlopt 1185 "adhoc" # broken build 1186 "AER" # depends on broken package nlopt 1187 "afex" # depends on broken package nlopt 1188 "agRee" # depends on broken package nlopt 1189 "aLFQ" # depends on broken package nlopt 1190 "algstat" # broken build 1191 "alr3" # depends on broken package nlopt 1192 "alr4" # depends on broken package nlopt 1193 "alsace" # depends on broken nloptr 1194 "anacor" # depends on broken package nlopt 1195 "aods3" # depends on broken package nlopt 1196 "apaTables" # depends on broken package car 1197 "apt" # depends on broken package nlopt 1198 "ArfimaMLM" # depends on broken package nlopt 1199 "arm" # depends on broken package nlopt 1200 "ART" # depends on broken package car 1201 "ARTool" # depends on broken package nlopt 1202 "AssetPricing" # broken build 1203 "AtelieR" # broken build 1204 "auRoc" # depends on broken package MBESS 1205 "AutoModel" # depends on broken package car 1206 "bamdit" # broken build 1207 "bapred" # depends on broken package lme4 1208 "bartMachine" # depends on broken package nlopt 1209 "bayesDem" # depends on broken package nlopt 1210 "bayesLife" # depends on broken package nlopt 1211 "BayesMed" # broken build 1212 "bayesmix" # broken build 1213 "bayesPop" # depends on broken package nlopt 1214 "Bayesthresh" # depends on broken package nlopt 1215 "BaySIC" # broken build 1216 "BBRecapture" # depends on broken package nlopt 1217 "BCA" # depends on broken package nlopt 1218 "bdynsys" # depends on broken package car 1219 "BEST" # broken build 1220 "bgmm" # depends on broken package nlopt 1221 "BIFIEsurvey" # depends on broken package nlopt 1222 "BiGGR" # depends on broken package rsbml 1223 "bioassayR" # broken build 1224 "BiodiversityR" # depends on broken package nlopt 1225 "biotools" # depends on broken package rpanel 1226 "birte" # build is broken 1227 "BLCOP" # depends on broken package Rsymphony 1228 "blmeco" # depends on broken package nlopt 1229 "blme" # depends on broken package nlopt 1230 "bmd" # depends on broken package nlopt 1231 "bmem" # depends on broken package nlopt 1232 "bmeta" # depends on broken package R2jags 1233 "bootnet" # depends on broken package nlopt 1234 "boral" # broken build 1235 "BradleyTerry2" # depends on broken package nlopt 1236 "BrailleR" # broken build 1237 "brainGraph" # build is broken 1238 "brms" # build is broken 1239 "BRugs" # build is broken 1240 "BTSPAS" # broken build 1241 "CADFtest" # depends on broken package nlopt 1242 "cAIC4" # depends on broken package nlopt 1243 "candisc" # depends on broken package nlopt 1244 "carcass" # depends on broken package nlopt 1245 "car" # depends on broken package nlopt 1246 "caret" # depends on broken package nlopt 1247 "caretEnsemble" # depends on broken package nlopt 1248 "CARrampsOcl" # depends on broken package OpenCL 1249 "Causata" # broken build 1250 "CCpop" # depends on broken package nlopt 1251 "CCTpack" # broken build 1252 "ChainLadder" # depends on broken package nlopt 1253 "ChemmineR" # Build Is Broken 1254 "chipenrich" # build is broken 1255 "chipPCR" # depends on broken nloptr 1256 "classify" # broken build 1257 "climwin" # depends on broken package nlopt 1258 "CLME" # depends on broken package nlopt 1259 "clpAPI" # build is broken 1260 "clusterPower" # depends on broken package nlopt 1261 "clusterSEs" # depends on broken AER 1262 "ClustGeo" # depends on broken FactoMineR 1263 "CNORfuzzy" # depends on broken package nlopt 1264 "CNVPanelizer" # depends on broken cn.mops 1265 "COHCAP" # build is broken 1266 "colorscience" # broken build 1267 "compendiumdb" # broken build 1268 "conformal" # depends on broken package nlopt 1269 "corHMM" # depends on broken package nlopt 1270 "CosmoPhotoz" # depends on broken package nlopt 1271 "covmat" # depends on broken package VIM 1272 "cplexAPI" # build is broken 1273 "cquad" # depends on broken package car 1274 "CrypticIBDcheck" # depends on broken package nlopt 1275 "ctsem" # depends on broken package OpenMx 1276 "cudaBayesreg" # build is broken 1277 "daff" # depends on broken package V8 1278 "dagbag" # build is broken 1279 "DAMisc" # depends on broken package nlopt 1280 "datafsm" # depends on broken package caret 1281 "dbConnect" # broken build 1282 "DBKGrad" # depends on broken package rpanel 1283 #"dcmle" # broken build 1284 "ddst" # broken build 1285 "Deducer" # depends on broken package nlopt 1286 "DeducerExtras" # depends on broken package nlopt 1287 "DeducerPlugInExample" # depends on broken package nlopt 1288 "DeducerPlugInScaling" # depends on broken package nlopt 1289 "DeducerSpatial" # depends on broken package nlopt 1290 "DeducerSurvival" # depends on broken package nlopt 1291 "DeducerText" # depends on broken package nlopt 1292 "DEGraph" # depends on broken package RCytoscape 1293 "destiny" # depends on broken package VIM 1294 "DiagTest3Grp" # depends on broken package nlopt 1295 "diffHic" # depends on broken package rhdf5 1296 "difR" # depends on broken package nlopt 1297 "DirichletMultinomial" # Build Is Broken 1298 "DistatisR" # depends on broken package nlopt 1299 "diveRsity" # depends on broken package nlopt 1300 "DJL" # depends on broken package car 1301 "dpa" # depends on broken package nlopt 1302 "dpcR" # depends on broken nloptr 1303 "drc" # depends on broken package nlopt 1304 "drfit" # depends on broken package nlopt 1305 "drsmooth" # depends on broken package nlopt 1306 "dynlm" # depends on broken package nlopt 1307 "easyanova" # depends on broken package nlopt 1308 "ecd" # depends on broken package polynom 1309 "edge" # depends on broken package nlopt 1310 "eeptools" # depends on broken package nlopt 1311 "EffectLiteR" # depends on broken package nlopt 1312 "effects" # depends on broken package nlopt 1313 "eiR" # depends on broken package ChemmineR 1314 "EMA" # depends on broken package nlopt 1315 "embryogrowth" # broken build 1316 "emg" # broken build 1317 "EnQuireR" # depends on broken package nlopt 1318 "episplineDensity" # depends on broken package nlopt 1319 "epr" # depends on broken package nlopt 1320 "erer" # depends on broken package nlopt 1321 "erma" # depends on broken GenomicFiles 1322 "erpR" # depends on broken package rpanel 1323 "ESKNN" # depends on broken package caret 1324 "euroMix" # build is broken 1325 "extRemes" # depends on broken package nlopt 1326 "ez" # depends on broken package nlopt 1327 "ezec" # depends on broken package drc 1328 "facopy" # depends on broken package nlopt 1329 "FactoMineR" # depends on broken package nlopt 1330 "Factoshiny" # depends on broken package nlopt 1331 "faoutlier" # depends on broken package nlopt 1332 "fastR" # depends on broken package nlopt 1333 "FDRreg" # depends on broken package nlopt 1334 "fishmethods" # depends on broken package lme4 1335 "flipflop" # broken build 1336 "flowDensity" # depends on broken package nlopt 1337 "flowPeaks" # build is broken 1338 "flowQ" # build is broken 1339 "flowStats" # depends on broken package ncdfFlow 1340 "flowVS" # depends on broken package ncdfFlow 1341 "flowWorkspace" # depends on broken package ncdfFlow 1342 "fmcsR" # depends on broken package ChemmineR 1343 "fPortfolio" # depends on broken package Rsymphony 1344 "fracprolif" # broken build 1345 "FreeSortR" # broken build 1346 "freqweights" # depends on broken package nlopt 1347 "frmqa" # broken build 1348 "FSA" # depends on broken package car 1349 "fscaret" # depends on broken package nlopt 1350 "funcy" # depends on broken package car 1351 "fxregime" # depends on broken package nlopt 1352 "gamclass" # depends on broken package nlopt 1353 "gamlss_demo" # depends on broken package rpanel 1354 "gamm4" # depends on broken package nlopt 1355 "gaussquad" # broken build 1356 "gcmr" # depends on broken package nlopt 1357 "GDAtools" # depends on broken package nlopt 1358 "gdtools" # broken build 1359 "GENE_E" # depends on broken package rhdf5 1360 "GENESIS" # broken build 1361 "genridge" # depends on broken package nlopt 1362 "geojsonio" # depends on broken package V8 1363 "GEWIST" # depends on broken package nlopt 1364 "ggtree" # broken build 1365 "gimme" # depends on broken package nlopt 1366 "gmatrix" # depends on broken package cudatoolkit 1367 "gMCP" # build is broken 1368 "gmum_r" # broken build 1369 "Goslate" # depends on broken package PythonInR 1370 "GPC" # broken build 1371 "gplm" # depends on broken package nlopt 1372 "gpuR" # depends on GPU-specific header files 1373 "gputools" # depends on broken package cudatoolkit 1374 "granova" # depends on broken package nlopt 1375 "graphicalVAR" # depends on broken package nlopt 1376 "GraphPAC" # broken build 1377 "gridGraphics" # build is broken 1378 "GSCA" # depends on broken package rhdf5 1379 "GUIDE" # depends on broken package rpanel 1380 "GWAF" # depends on broken package nlopt 1381 "GWASTools" # broken build 1382 "h5" # build is broken 1383 "h5vc" # depends on broken package rhdf5 1384 "hbsae" # depends on broken package nlopt 1385 "heplots" # depends on broken package nlopt 1386 "HiDimMaxStable" # broken build 1387 "HierO" # Build Is Broken 1388 "HilbertVisGUI" # Build Is Broken 1389 "HiPLARM" # Build Is Broken 1390 "HistDAWass" # depends on broken package nlopt 1391 "HLMdiag" # depends on broken package nlopt 1392 "homomorpheR" # broken build 1393 "hpcwld" # broken build 1394 "hwwntest" # broken build 1395 "HydeNet" # broken build 1396 "hysteresis" # depends on broken package nlopt 1397 "IATscores" # depends on broken package nlopt 1398 "ibd" # depends on broken package nlopt 1399 "iccbeta" # depends on broken package nlopt 1400 "iClick" # depends on broken package rugarch 1401 "ifaTools" # depends on broken package OpenMx 1402 "imager" # broken build 1403 "immunoClust" # build is broken 1404 "in2extRemes" # depends on broken package nlopt 1405 "inferference" # depends on broken package nlopt 1406 "influence_ME" # depends on broken package nlopt 1407 "inSilicoMerging" # build is broken 1408 "INSPEcT" # depends on broken GenomicFeatures 1409 "interplot" # depends on broken arm 1410 "IONiseR" # depends on broken rhdf5 1411 "IsingFit" # depends on broken package nlopt 1412 "ITEMAN" # depends on broken package car 1413 "iteRates" # broken build 1414 "iterpc" # broken build 1415 "IUPS" # broken build 1416 "IVAS" # depends on broken package nlopt 1417 "ivpack" # depends on broken package nlopt 1418 "jagsUI" # broken build 1419 "JAGUAR" # depends on broken package nlopt 1420 "joda" # depends on broken package nlopt 1421 "jomo" # build is broken 1422 "js" # depends on broken package V8 1423 "KoNLP" # broken build 1424 "kzft" # broken build 1425 "LaplaceDeconv" # depends on broken package orthopolynom 1426 "lawn" # depends on broken package V8 1427 "ldamatch" # broken build 1428 "learnstats" # depends on broken package nlopt 1429 "lefse" # build is broken 1430 "lessR" # depends on broken package nlopt 1431 "lgcp" # depends on broken package rpanel 1432 "Libra" # broken build 1433 "LinRegInteractive" # depends on broken package rpanel 1434 "lira" # broken build 1435 "littler" # broken build 1436 "lme4" # depends on broken package nlopt 1437 "LMERConvenienceFunctions" # depends on broken package nlopt 1438 "lmerTest" # depends on broken package nlopt 1439 "lmSupport" # depends on broken package nlopt 1440 "LOGIT" # depends on broken package caret 1441 "longpower" # depends on broken package nlopt 1442 "LPTime" # broken build 1443 "MAIT" # depends on broken package nlopt 1444 "mAPKL" # build is broken 1445 "maPredictDSC" # depends on broken package nlopt 1446 "mar1s" # broken build 1447 "marked" # depends on broken package nlopt 1448 "matchingMarkets" # broken build 1449 "MatrixRider" # depends on broken package DirichletMultinomial 1450 "MaxPro" # depends on broken package nlopt 1451 "mbest" # depends on broken package nlopt 1452 "MBmca" # depends on broken nloptr 1453 "mBvs" # build is broken 1454 "meboot" # depends on broken package nlopt 1455 "medflex" # depends on broken package car 1456 "mediation" # depends on broken package lme4 1457 "MEDME" # depends on broken package nlopt 1458 "MEMSS" # depends on broken package nlopt 1459 "merTools" # depends on broken package arm 1460 "meta4diag" # broken build 1461 "metagear" # build is broken 1462 "metaheur" # depends on broken package preprocomb 1463 "metamisc" # broken build 1464 "metaplus" # depends on broken package nlopt 1465 "metaSEM" # depends on broken package OpenMx 1466 "Metatron" # depends on broken package nlopt 1467 "miceadds" # depends on broken package nlopt 1468 "micEconAids" # depends on broken package nlopt 1469 "micEconCES" # depends on broken package nlopt 1470 "micEconSNQP" # depends on broken package nlopt 1471 "mi" # depends on broken package nlopt 1472 "MigClim" # Build Is Broken 1473 "migui" # depends on broken package nlopt 1474 "minimist" # depends on broken package V8 1475 "missMDA" # depends on broken package nlopt 1476 "mitoODE" # build is broken 1477 "mixAK" # depends on broken package nlopt 1478 "MixedPoisson" # broken build 1479 "mixlm" # depends on broken package nlopt 1480 "MixMAP" # depends on broken package nlopt 1481 "mlma" # depends on broken package lme4 1482 "mlmRev" # depends on broken package nlopt 1483 "MLSeq" # depends on broken package nlopt 1484 "mlVAR" # depends on broken package nlopt 1485 "MM" # broken build 1486 "mongolite" # build is broken 1487 "mosaic" # depends on broken package nlopt 1488 "mpoly" # broken build 1489 "mRMRe" # broken build 1490 "msa" # broken build 1491 "MSGFgui" # depends on broken package MSGFplus 1492 "MSGFplus" # Build Is Broken 1493 "MSstats" # depends on broken package nlopt 1494 "MultiRR" # depends on broken package nlopt 1495 "muma" # depends on broken package nlopt 1496 "munsellinterpol" # broken build 1497 "mutossGUI" # build is broken 1498 "mvinfluence" # depends on broken package nlopt 1499 "MXM" # broken build 1500 "NanoStringDiff" # broken build 1501 "NanoStringQCPro" # build is broken 1502 "nCal" # depends on broken package nlopt 1503 "ncdfFlow" # build is broken 1504 "NCIgraph" # depends on broken package RCytoscape 1505 "NHPoisson" # depends on broken package nlopt 1506 "nloptr" # depends on broken package nlopt 1507 "nlsem" # broken build 1508 "nlts" # broken build 1509 "nonrandom" # depends on broken package nlopt 1510 "NORRRM" # build is broken 1511 "npIntFactRep" # depends on broken package nlopt 1512 "NSM3" # broken build 1513 "omics" # depends on broken package lme4 1514 "OmicsMarkeR" # depends on broken package nlopt 1515 "OPDOE" # broken build 1516 "OpenCL" # build is broken 1517 "openCyto" # depends on broken package ncdfFlow 1518 "OpenMx" # build is broken 1519 "optBiomarker" # depends on broken package rpanel 1520 "ora" # depends on broken package ROracle 1521 "ordBTL" # depends on broken package nlopt 1522 "ordPens" # depends on broken package lme4 1523 "orthopolynom" # broken build 1524 "OUwie" # depends on broken package nlopt 1525 "oz" # broken build 1526 "PAA" # broken build 1527 "pamm" # depends on broken package nlopt 1528 "panelAR" # depends on broken package nlopt 1529 "papeR" # depends on broken package nlopt 1530 "parboost" # depends on broken package nlopt 1531 "parma" # depends on broken package nlopt 1532 "partitions" # broken build 1533 "PatternClass" # build is broken 1534 "PBImisc" # depends on broken package nlopt 1535 "pcaBootPlot" # depends on broken FactoMineR 1536 "pcaL1" # build is broken 1537 "pcnetmeta" # broken build 1538 "PDQutils" # broken build 1539 "pedigreemm" # depends on broken package nlopt 1540 "pequod" # depends on broken package nlopt 1541 "pglm" # depends on broken package car 1542 "PhenStat" # depends on broken package nlopt 1543 "phia" # depends on broken package nlopt 1544 "phylocurve" # depends on broken package nlopt 1545 "piecewiseSEM" # depends on broken package lme4 1546 "plateCore" # depends on broken package ncdfFlow 1547 "plfMA" # broken build 1548 "plm" # depends on broken package car 1549 "plsRbeta" # depends on broken package nlopt 1550 "plsRcox" # depends on broken package nlopt 1551 "plsRglm" # depends on broken package nlopt 1552 "pmm" # depends on broken package nlopt 1553 "polynom" # broken build 1554 "pomp" # depends on broken package nlopt 1555 "predictmeans" # depends on broken package nlopt 1556 "preprocomb" # depends on broken package caret 1557 "prevalence" # broken build 1558 "prLogistic" # depends on broken package nlopt 1559 "pRoloc" # depends on broken package nlopt 1560 "pRolocGUI" # depends on broken package nlopt 1561 "PSAboot" # depends on broken package nlopt 1562 "ptw" # depends on broken nloptr 1563 "PurBayes" # broken build 1564 "pvca" # depends on broken package nlopt 1565 "PythonInR" # broken build 1566 "QFRM" # broken build 1567 "qgraph" # depends on broken package nlopt 1568 "qtbase" # build is broken 1569 "qtlnet" # depends on broken package nlopt 1570 "qtpaint" # depends on broken package qtbase 1571 "qtutils" # depends on broken package qtbase 1572 "QUALIFIER" # depends on broken package ncdfFlow 1573 "quantification" # depends on broken package nlopt 1574 "QuartPAC" # broken build 1575 "R2jags" # broken build 1576 "R2STATS" # depends on broken package nlopt 1577 "rain" # broken build 1578 "raincpc" # build is broken 1579 "rainfreq" # build is broken 1580 "RamiGO" # depends on broken package RCytoscape 1581 "RareVariantVis" # depends on broken VariantAnnotation 1582 "rasclass" # depends on broken package nlopt 1583 "rationalfun" # broken build 1584 "RBerkeley" # broken build 1585 "RbioRXN" # depends on broken package ChemmineR 1586 "Rblpapi" # broken build 1587 "Rchemcpp" # depends on broken package ChemmineR 1588 "rchess" # depends on broken package V8 1589 "Rchoice" # depends on broken package car 1590 "Rcmdr" # depends on broken package nlopt 1591 "RcmdrMisc" # depends on broken package nlopt 1592 "RcmdrPlugin_BCA" # depends on broken package nlopt 1593 "RcmdrPlugin_coin" # depends on broken package nlopt 1594 "RcmdrPlugin_depthTools" # depends on broken package nlopt 1595 "RcmdrPlugin_DoE" # depends on broken package nlopt 1596 "RcmdrPlugin_doex" # depends on broken package nlopt 1597 "RcmdrPlugin_EACSPIR" # depends on broken package nlopt 1598 "RcmdrPlugin_EBM" # depends on broken package nlopt 1599 "RcmdrPlugin_EcoVirtual" # depends on broken package nlopt 1600 "RcmdrPlugin_epack" # depends on broken package nlopt 1601 "RcmdrPlugin_Export" # depends on broken package Rcmdr 1602 "RcmdrPlugin_EZR" # depends on broken package nlopt 1603 "RcmdrPlugin_FactoMineR" # depends on broken package nlopt 1604 "RcmdrPlugin_HH" # depends on broken package nlopt 1605 "RcmdrPlugin_IPSUR" # depends on broken package nlopt 1606 "RcmdrPlugin_KMggplot2" # depends on broken package nlopt 1607 "RcmdrPlugin_lfstat" # depends on broken package nlopt 1608 "RcmdrPlugin_MA" # depends on broken package nlopt 1609 "RcmdrPlugin_mosaic" # depends on broken package nlopt 1610 "RcmdrPlugin_MPAStats" # depends on broken package nlopt 1611 "RcmdrPlugin_NMBU" # depends on broken package nlopt 1612 "RcmdrPlugin_orloca" # depends on broken package nlopt 1613 "RcmdrPlugin_plotByGroup" # depends on broken package nlopt 1614 "RcmdrPlugin_pointG" # depends on broken package nlopt 1615 "RcmdrPlugin_qual" # depends on broken package nlopt 1616 "RcmdrPlugin_RMTCJags" # depends on broken package nlopt 1617 "RcmdrPlugin_ROC" # depends on broken package nlopt 1618 "RcmdrPlugin_sampling" # depends on broken package nlopt 1619 "RcmdrPlugin_SCDA" # depends on broken package nlopt 1620 "RcmdrPlugin_seeg" # depends on broken package nlopt 1621 "RcmdrPlugin_SLC" # depends on broken package nlopt 1622 "RcmdrPlugin_SM" # depends on broken package nlopt 1623 "RcmdrPlugin_sos" # depends on broken package nlopt 1624 "RcmdrPlugin_steepness" # depends on broken package nlopt 1625 "RcmdrPlugin_survival" # depends on broken package nlopt 1626 "RcmdrPlugin_TeachingDemos" # depends on broken package nlopt 1627 "RcmdrPlugin_temis" # depends on broken package nlopt 1628 "RcmdrPlugin_UCA" # depends on broken package nlopt 1629 "Rcpi" # depends on broken package ChemmineR 1630 "Rcplex" # Build Is Broken 1631 "RcppAPT" # Build Is Broken 1632 "RcppRedis" # build is broken 1633 "rcrypt" # broken build 1634 "RCytoscape" # Build Is Broken 1635 "rdd" # depends on broken package nlopt 1636 "rddtools" # depends on broken package AER 1637 "rDEA" # build is broken 1638 "RDieHarder" # build is broken 1639 "REBayes" # depends on broken package Rmosek 1640 "referenceIntervals" # depends on broken package nlopt 1641 "refund" # depends on broken package nlopt 1642 "refund_shiny" # depends on broken package refund 1643 "REndo" # depends on broken package AER 1644 "repijson" # depends on broken package V8 1645 "REST" # depends on broken package nlopt 1646 "rgbif" # depends on broken package V8 1647 "Rgnuplot" # broken build 1648 "rhdf5" # build is broken 1649 "rjade" # depends on broken package V8 1650 "rJPSGCS" # build is broken 1651 "rLindo" # build is broken 1652 "RLRsim" # depends on broken package lme4 1653 "RMallow" # broken build 1654 "rMAT" # build is broken 1655 "rmgarch" # depends on broken package nlopt 1656 "rminer" # depends on broken package nlopt 1657 "Rmosek" # build is broken 1658 "RMySQL" # broken build 1659 "RNAither" # depends on broken package nlopt 1660 "RnavGraph" # build is broken 1661 "rnetcarto" # broken build 1662 "robustlmm" # depends on broken package nlopt 1663 "rockchalk" # depends on broken package nlopt 1664 "ROI_plugin_symphony" # depends on broken package Rsymphony 1665 "rols" # build is broken 1666 "ROracle" # Build Is Broken 1667 "rpanel" # build is broken 1668 "Rpoppler" # broken build 1669 "rpubchem" # depends on broken package nlopt 1670 "RQuantLib" # build is broken 1671 "rr" # depends on broken package nlopt 1672 "RRreg" # depends on broken package lme4 1673 "RSAP" # build is broken 1674 "rsbml" # build is broken 1675 "RSDA" # depends on broken package nlopt 1676 "Rsomoclu" # broken build 1677 "RStoolbox" # depends on broken package caret 1678 "Rsymphony" # build is broken 1679 "rTableICC" # broken build 1680 "rTANDEM" # build is broken 1681 "RTN" # depends on broken package nlopt 1682 "rugarch" # depends on broken package nlopt 1683 "rUnemploymentData" # broken build 1684 "RVAideMemoire" # depends on broken package nlopt 1685 "RVFam" # depends on broken package nlopt 1686 "RVideoPoker" # depends on broken package rpanel 1687 "RWebServices" # broken build 1688 "ryouready" # depends on broken package nlopt 1689 "sadists" # broken build 1690 "sampleSelection" # depends on broken package nlopt 1691 "sapFinder" # depends on broken package rTANDEM 1692 "sdcMicro" # depends on broken package nlopt 1693 "sdcMicroGUI" # depends on broken package nlopt 1694 "SDD" # depends on broken package rpanel 1695 "seeg" # depends on broken package nlopt 1696 "Sejong" # broken build 1697 "sem" # depends on broken package nlopt 1698 "semdiag" # depends on broken package nlopt 1699 "semGOF" # depends on broken package nlopt 1700 "semPlot" # depends on broken package nlopt 1701 "SensMixed" # depends on broken package lme4 1702 "SensoMineR" # depends on broken package nlopt 1703 "seqCNA" # build is broken 1704 "SeqFeatR" # broken build 1705 "SeqGrapheR" # Build Is Broken 1706 "seqHMM" # depends on broken package nloptr 1707 "seqTools" # build is broken 1708 "SharpeR" # broken build 1709 "shinyTANDEM" # depends on broken package rTANDEM 1710 "SIBER" # broken build 1711 "simPop" # depends on broken package VIM 1712 "simr" # depends on broken package lme4 1713 "SJava" # broken build 1714 "sjPlot" # depends on broken package nlopt 1715 "smacof" # broken build 1716 "SNAGEE" # build is broken 1717 "snm" # depends on broken package nlopt 1718 "SOD" # depends on broken package cudatoolkit 1719 "sodium" # broken build 1720 "soilphysics" # depends on broken package rpanel 1721 "sortinghat" # broken build 1722 "SoyNAM" # depends on broken package lme4 1723 "spacom" # depends on broken package nlopt 1724 "SparseLearner" # depends on broken package qgraph 1725 "specificity" # depends on broken package nlopt 1726 "specmine" # depends on broken package caret 1727 "splm" # depends on broken package car 1728 "spocc" # depends on broken package V8 1729 "spoccutils" # depends on broken spocc 1730 "ssmrob" # depends on broken package nlopt 1731 "StatMethRank" # broken build 1732 "stepp" # depends on broken package nlopt 1733 "stringgaussnet" # build is broken 1734 "Surrogate" # depends on broken package nlopt 1735 "svglite" # depends on broken package gdtools 1736 "sybilSBML" # build is broken 1737 "systemfit" # depends on broken package nlopt 1738 "TcGSA" # depends on broken package nlopt 1739 "TDMR" # depends on broken package nlopt 1740 "TextoMineR" # depends on broken package FactoMineR 1741 "TFBSTools" # depends on broken package DirichletMultinomial 1742 "tigerstats" # depends on broken package nlopt 1743 "TLBC" # depends on broken package caret 1744 "tmle" # broken build 1745 "tnam" # depends on broken package lme4 1746 "tolBasis" # depends on broken package polynom 1747 "translateSPSS2R" # depends on broken car 1748 "TriMatch" # depends on broken package nlopt 1749 "TSMySQL" # broken build 1750 "tsoutliers" # broken build 1751 "UBCRM" # broken build 1752 "umx" # depends on broken package OpenMx 1753 "uniftest" # broken build 1754 "untb" # broken build 1755 "userfriendlyscience" # depends on broken package nlopt 1756 "V8" # build is broken 1757 "varComp" # depends on broken package lme4 1758 "varian" # build is broken 1759 "variancePartition" # depends on broken package lme4 1760 "VBmix" # broken build 1761 "VIM" # depends on broken package nlopt 1762 "VIMGUI" # depends on broken package nlopt 1763 "vows" # depends on broken package nlopt 1764 "webp" # build is broken 1765 "wfe" # depends on broken package nlopt 1766 "wordbankr" # depends on broken package RMySQL 1767 "xergm" # depends on broken package nlopt 1768 "xps" # build is broken 1769 "ZeligChoice" # depends on broken package AER 1770 "Zelig" # depends on broken package AER 1771 "zetadiv" # depends on broken package nlopt 1772 "zoib" # broken build 1773 ]; 1774 1775 otherOverrides = old: new: { 1776 stringi = old.stringi.overrideDerivation (attrs: { 1777 postInstall = let 1778 icuName = "icudt52l"; 1779 icuSrc = pkgs.fetchzip { 1780 url = "http://static.rexamine.com/packages/${icuName}.zip"; 1781 sha256 = "0hvazpizziq5ibc9017i1bb45yryfl26wzfsv05vk9mc1575r6xj"; 1782 stripRoot = false; 1783 }; 1784 in '' 1785 ${attrs.postInstall or ""} 1786 cp ${icuSrc}/${icuName}.dat $out/library/stringi/libs 1787 ''; 1788 }); 1789 1790 xml2 = old.xml2.overrideDerivation (attrs: { 1791 preConfigure = '' 1792 export LIBXML_INCDIR=${pkgs.libxml2.dev}/include/libxml2 1793 patchShebangs configure 1794 ''; 1795 }); 1796 1797 curl = old.curl.overrideDerivation (attrs: { 1798 preConfigure = "patchShebangs configure"; 1799 }); 1800 1801 RcppArmadillo = old.RcppArmadillo.overrideDerivation (attrs: { 1802 patchPhase = "patchShebangs configure"; 1803 }); 1804 1805 rpf = old.rpf.overrideDerivation (attrs: { 1806 patchPhase = "patchShebangs configure"; 1807 }); 1808 1809 BayesXsrc = old.BayesXsrc.overrideDerivation (attrs: { 1810 patches = [ ./patches/BayesXsrc.patch ]; 1811 }); 1812 1813 rJava = old.rJava.overrideDerivation (attrs: { 1814 preConfigure = '' 1815 export JAVA_CPPFLAGS=-I${pkgs.jdk}/include/ 1816 export JAVA_HOME=${pkgs.jdk} 1817 ''; 1818 }); 1819 1820 JavaGD = old.JavaGD.overrideDerivation (attrs: { 1821 preConfigure = '' 1822 export JAVA_CPPFLAGS=-I${pkgs.jdk}/include/ 1823 export JAVA_HOME=${pkgs.jdk} 1824 ''; 1825 }); 1826 1827 Mposterior = old.Mposterior.overrideDerivation (attrs: { 1828 PKG_LIBS = "-L${pkgs.openblasCompat}/lib -lopenblas"; 1829 }); 1830 1831 qtbase = old.qtbase.overrideDerivation (attrs: { 1832 patches = [ ./patches/qtbase.patch ]; 1833 }); 1834 1835 Rmpi = old.Rmpi.overrideDerivation (attrs: { 1836 configureFlags = [ 1837 "--with-Rmpi-type=OPENMPI" 1838 ]; 1839 }); 1840 1841 Rmpfr = old.Rmpfr.overrideDerivation (attrs: { 1842 configureFlags = [ 1843 "--with-mpfr-include=${pkgs.mpfr.dev}/include" 1844 ]; 1845 }); 1846 1847 RVowpalWabbit = old.RVowpalWabbit.overrideDerivation (attrs: { 1848 configureFlags = [ 1849 "--with-boost=${pkgs.boost.dev}" "--with-boost-libdir=${pkgs.boost.out}/lib" 1850 ]; 1851 }); 1852 1853 RAppArmor = old.RAppArmor.overrideDerivation (attrs: { 1854 patches = [ ./patches/RAppArmor.patch ]; 1855 LIBAPPARMOR_HOME = "${pkgs.libapparmor}"; 1856 }); 1857 1858 RMySQL = old.RMySQL.overrideDerivation (attrs: { 1859 patches = [ ./patches/RMySQL.patch ]; 1860 MYSQL_DIR="${pkgs.mysql.lib}"; 1861 }); 1862 1863 devEMF = old.devEMF.overrideDerivation (attrs: { 1864 NIX_CFLAGS_LINK = "-L${pkgs.xorg.libXft.out}/lib -lXft"; 1865 }); 1866 1867 slfm = old.slfm.overrideDerivation (attrs: { 1868 PKG_LIBS = "-L${pkgs.openblasCompat}/lib -lopenblas"; 1869 }); 1870 1871 SamplerCompare = old.SamplerCompare.overrideDerivation (attrs: { 1872 PKG_LIBS = "-L${pkgs.openblasCompat}/lib -lopenblas"; 1873 }); 1874 1875 gputools = old.gputools.overrideDerivation (attrs: { 1876 patches = [ ./patches/gputools.patch ]; 1877 CUDA_HOME = "${pkgs.cudatoolkit}"; 1878 }); 1879 1880 gmatrix = old.gmatrix.overrideDerivation (attrs: { 1881 patches = [ ./patches/gmatrix.patch ]; 1882 CUDA_LIB_PATH = "${pkgs.cudatoolkit}/lib64"; 1883 R_INC_PATH = "${pkgs.R}/lib/R/include"; 1884 CUDA_INC_PATH = "${pkgs.cudatoolkit}/include"; 1885 }); 1886 1887 EMCluster = old.EMCluster.overrideDerivation (attrs: { 1888 patches = [ ./patches/EMCluster.patch ]; 1889 }); 1890 1891 spMC = old.spMC.overrideDerivation (attrs: { 1892 patches = [ ./patches/spMC.patch ]; 1893 }); 1894 1895 BayesLogit = old.BayesLogit.overrideDerivation (attrs: { 1896 patches = [ ./patches/BayesLogit.patch ]; 1897 buildInputs = (attrs.buildInputs or []) ++ [ pkgs.openblasCompat ]; 1898 }); 1899 1900 BayesBridge = old.BayesBridge.overrideDerivation (attrs: { 1901 patches = [ ./patches/BayesBridge.patch ]; 1902 }); 1903 1904 openssl = old.openssl.overrideDerivation (attrs: { 1905 OPENSSL_INCLUDES = "${pkgs.openssl.dev}/include"; 1906 }); 1907 1908 Rserve = old.Rserve.overrideDerivation (attrs: { 1909 patches = [ ./patches/Rserve.patch ]; 1910 configureFlags = [ 1911 "--with-server" "--with-client" 1912 ]; 1913 }); 1914 1915 nloptr = old.nloptr.overrideDerivation (attrs: { 1916 configureFlags = [ 1917 "--with-nlopt-cflags=-I${pkgs.nlopt}/include" 1918 "--with-nlopt-libs='-L${pkgs.nlopt}/lib -lnlopt_cxx -lm'" 1919 ]; 1920 }); 1921 1922 V8 = old.V8.overrideDerivation (attrs: { 1923 preConfigure = "export V8_INCLUDES=${pkgs.v8}/include"; 1924 }); 1925 1926 }; 1927in 1928 self