From diggsb at ohsu.edu  Fri Apr 17 20:45:43 2009
From: diggsb at ohsu.edu (Brian Diggs)
Date: Fri, 17 Apr 2009 11:45:43 -0700
Subject: [Rd] suggestion for R >= 3.0: computer-readable CHANGELOG
In-Reply-To: <18920.40641.635120.944317@ron.nulle.part>
References: <49E82D9C.9090402@sciviews.org><49E85C0D.6040809@stats.uwo.ca><49E87A59.2010003@life.ku.dk><49E87E85.4050700@stats.uwo.ca><18920.36404.547796.504974@ron.nulle.part><49E893F1.9000007@stats.uwo.ca>
	<18920.40641.635120.944317@ron.nulle.part>
Message-ID: <D90C24824765F143934E4DE78009D617A1487E@EX-BE05.ohsu.edu>

Dirk Eddelbuettel wrote:
> On 17 April 2009 at 10:36, Duncan Murdoch wrote:
> | Could you take a look at CRAN and Bioconductor, and count how many 
> | packages already have a news/changelog file, and how hard it would be to 
> | convert them to a standard format?
> 
> I can do the count for CRAN using the account we use for cran2deb work.  I'll
> be travelling this weekend (yay, Boston Marathon!) so please ping me next
> week if I forget to aggregate this.

I imagine that Dirk will do a better job than this, but as a point of comparison, I thought I'd look at how many of the CRAN summary pages for each package have a "News/ChangeLog" entry.  Starting from http://cran.r-project.org/web/packages/, the links to the packages were extracted and followed.  302 of the 1754 packages returned a page not found error.  Of the remaining 1452, the summary page was searched for a News/ChangeLog entry.  I don't know how the presence of this entry is determined, but I thought I'd use it as one measure.  389 packages have an entry; 1063 do not.  I didn't look at the variety of formats (or names) of these, but I thought this would be at least a starting point.  R code and output, including a complete list of which packages do and do not have a ChangeLog entry, is below.

I have not used any of the Bioconductor packages, so I don't know if a similar idea would work for them.

> Dirk

--
Brian Diggs, Ph.D.
Senior Research Associate, Department of Surgery, Oregon Health & Science University


library(plyr)

package.page <- readLines("http://cran.r-project.org/web/packages/")
package.lines <- grep("packages/(.*)/index.html",package.page, value=TRUE, perl=TRUE)
package.regexp <- regexpr("packages/(.*)/index.html",package.lines, perl=TRUE)
package.names <- substr(package.lines, package.regexp+9, package.regexp+attr(package.regexp,"match.length")-12)
package.urls <- paste("http://cran.r-project.org/web/packages/",package.names,"/index.html",sep="")
package.summaries <- llply(package.urls, function(x) {try(readLines(x), silent=TRUE)})
names(package.summaries) <- package.names

# packages that the link did not resolve to a page
package.gotsummary <- laply(package.summaries, class)=="character"
names(package.summaries[!package.gotsummary])
  [1] "aaMI"              "abind"             "accuracy"         
  [4] "acepack"           "actuar"            "ada"              
  [7] "adabag"            "adapt"             "ade4"             
 [10] "ade4TkGUI"         "adegenet"          "adehabitat"       
 [13] "adimpro"           "adk"               "adlift"           
 [16] "ads"               "afc"               "agce"             
 [19] "agreement"         "agricolae"         "agsemisc"         
 [22] "akima"             "allelic"           "alphahull"        
 [25] "alr3"              "amap"              "amei"             
 [28] "anacor"            "analogue"          "anapuce"          
 [31] "animation"         "anm"               "aod"              
 [34] "apTreeshape"       "ape"               "aplpack"          
 [37] "apsrtable"         "archetypes"        "argosfilter"      
 [40] "arm"               "arrayImpute"       "arrayMissPattern" 
 [43] "ars"               "arules"            "arulesNBMiner"    
 [46] "arulesSequences"   "ascii"             "ash"              
 [49] "aspace"            "aspect"            "assist"           
 [52] "aster"             "asuR"              "asympTest"        
 [55] "asypow"            "audio"             "automap"          
 [58] "aws"               "aylmer"            "backfitRichards"  
 [61] "backtest"          "bark"              "bayesCGH"         
 [64] "bayesGARCH"        "bayesSurv"         "bayesclust"       
 [67] "bayescount"        "bayesm"            "bayesmix"         
 [70] "bbmle"             "bcp"               "beanplot"         
 [73] "bear"              "benchden"          "bentcableAR"      
 [76] "betaper"           "betareg"           "bethel"           
 [79] "biOps"             "biOpsGUI"          "biclust"          
 [82] "bicreduc"          "bifactorial"       "biglm"            
 [85] "bigmemory"         "bim"               "binGroup"         
 [88] "binMto"            "bindata"           "binom"            
 [91] "bio.infer"         "biopara"           "bipartite"        
 [94] "birch"             "bise"              "bit"              
 [97] "bitops"            "bivpois"           "blighty"          
[100] "blockTools"        "blockmodeling"     "blockrand"        
[103] "bmd"               "bnlearn"           "boa"              
[106] "boolean"           "boost"             "boot"             
[109] "bootStepAIC"       "bootspecdens"      "bootstrap"        
[112] "bpca"              "bqtl"              "brainwaver"       
[115] "brew"              "brglm"             "bs"               
[118] "bspec"             "bvls"              "ca"               
[121] "caMassClass"       "caTools"           "cacheSweave"      
[124] "cacher"            "cairoDevice"       "calib"            
[127] "calibrate"         "candisc"           "canvas"           
[130] "car"               "caret"             "cat"              
[133] "catmap"            "catspec"           "cba"              
[136] "ccems"             "ccgarch"           "cclust"           
[139] "cellVolumeDist"    "celsius"           "cem"              
[142] "cfa"               "cggd"              "cgh"              
[145] "cghFLasso"         "changeLOS"         "cheb"             
[148] "chemCal"           "chemometrics"      "choplump"         
[151] "chplot"            "chron"             "cir"              
[154] "circular"          "clValid"           "clac"             
[157] "classGraph"        "classInt"          "classifly"        
[160] "clim.pact"         "climatol"          "clinfun"          
[163] "clinsig"           "clue"              "clues"            
[166] "clustTool"         "cluster"           "clusterGeneration"
[169] "clusterRepro"      "clusterSim"        "clusterfly"       
[172] "clustvarsel"       "clv"               "cmprsk"           
[175] "cobs"              "cobs99"            "cocorresp"        
[178] "coda"              "codetools"         "coin"             
[181] "colorRamps"        "colorspace"        "combinat"         
[184] "compHclust"        "compOverlapCorr"   "compare"          
[187] "compoisson"        "compositions"      "concor"           
[190] "concord"           "conf.design"       "connectedness"    
[193] "contfrac"          "contrast"          "convexHaz"        
[196] "copas"             "copula"            "corcounts"        
[199] "corpcor"           "corpora"           "corrgram"         
[202] "corrperm"          "covRobust"         "coxphf"           
[205] "coxphw"            "coxrobust"         "cramer"           
[208] "crank"             "crawl"             "crossdes"         
[211] "crosshybDetector"  "crq"               "cslogistic"       
[214] "cts"               "ctv"               "curvetest"        
[217] "cwhmisc"           "cyclones"          "data.table"       
[220] "dataframes2xls"    "date"              "dblcens"          
[223] "ddesolve"          "ddst"              "deSolve"          
[226] "deal"              "debug"             "degreenet"        
[229] "deldir"            "delt"              "demogR"           
[232] "denpro"            "denstrip"          "depmix"           
[235] "depmixS4"          "depth"             "desirability"     
[238] "dfcrm"             "dglm"              "diagram"          
[241] "diamonds"          "dice"              "dichromat"        
[244] "diffractometry"    "digest"            "diptest"          
[247] "dirichlet"         "dispmod"           "distr"            
[250] "distrDoc"          "distrEx"           "distrMod"         
[253] "distrSim"          "distrTEst"         "distrTeach"       
[256] "distributions"     "divagis"           "diveMove"         
[259] "dlm"               "dlmap"             "doBy"             
[262] "dplR"              "dprep"             "dr"               
[265] "drc"               "drfit"             "drm"              
[268] "dse"               "dti"               "dtt"              
[271] "dtw"               "dyad"              "dyn"              
[274] "dynCorr"           "dynamicGraph"      "dynamicTreeCut"   
[277] "dynamo"            "dynlm"             "e1071"            
[280] "eRm"               "earth"             "eba"              
[283] "ecespa"            "eco"               "ecodist"          
[286] "ecolMod"           "effects"           "eha"              
[289] "eiPack"            "eigenmodel"        "elasticnet"       
[292] "ellipse"           "elliptic"          "elrm"             
[295] "emdbook"           "emme2"             "empiricalBayes"   
[298] "emplik"            "emu"               "energy"           
[301] "ensembleBMA"       "entropy"          

package.hasChangeLog <- laply(package.summaries[package.gotsummary],
 function(x) {length(grep("News/ChangeLog", x)) > 0})
names(package.hasChangeLog) <- package.names[package.gotsummary]
 
table(package.hasChangeLog)
package.hasChangeLog
FALSE  TRUE 
 1063   389 

dput(package.hasChangeLog)
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FALSE, FALSE, FALSE, TRUE, FALSE), .Names = c("ADaCGH", "AER", 
"AIGIS", "AIS", "ALS", "AMORE", "ARES", "AcceptanceSampling", 
"AdMit", "AdaptFit", "AlgDesign", "Amelia", "AnalyzeFMRI", "Animal", 
"AquaEnv", "ArDec", "BACCO", "BARD", "BAS", "BAYSTAR", "BB", 
"BCE", "BGSIMD", "BHH2", "BLCOP", "BMA", "BMN", "BPHO", "BSDA", 
"BSagri", "BaM", "BayHaz", "BayesDA", "BayesTree", "BayesValidate", 
"BayesX", "Bchron", "Bhat", "BiasedUrn", "BioIDMapper", "Biodem", 
"BiodiversityR", "BiplotGUI", "Bolstad", "BootCL", "BootPR", 
"BradleyTerry", "Brobdingnag", "BsMD", "CADFtest", "CADStat", 
"CCA", "CDNmoney", "CGIwithR", "CHsharp", "CORREP", "COZIGAM", 
"CPE", "CTFS", "CTT", "CVThresh", "Cairo", "CarbonEL", "CellularAutomaton", 
"ChainLadder", "CircStats", "CoCo", "ComPairWise", "CombMSC", 
"CompetingRiskFrailty", "Containers", "ConvCalendar", "ConvergenceConcepts", 
"CoxBoost", "CreditMetrics", "CvM2SL1Test", "CvM2SL2Test", "DAAG", 
"DAAGbio", "DAAGxtras", "DAKS", "DBI", "DCluster", "DDHFm", "DEA", 
"DEoptim", "DICOM", "DPpackage", "DTK", "Davies", "Defaults", 
"Depela", "DescribeDisplay", "Design", "Devore5", "Devore6", 
"Devore7", "DiagnosisMed", "DierckxSpline", "EDR", "EMC", "EMCC", 
"EMD", "EMJumpDiffusion", "ETC", "EVER", "EbayesThresh", "Ecdat", 
"EffectiveDose", "ElemStatLearn", "EngrExpt", "Epi", "epiR", 
"epibasix", "epicalc", "epitools", "eqtl", "equivalence", "ergm", 
"etm", "evd", "evdbayes", "evir", "exactLoglinTest", "exactRankTests", 
"exactmaxsel", "exams", "experiment", "expert", "extRemes", "FAiR", 
"FBN", "FD", "FGN", "FITSio", "FKBL", "FKF", "FTICRMS", "FactoClass", 
"FactoMineR", "Fahrmeir", "FieldSim", "FinTS", "FitAR", "Flury", 
"Formula", "FrF2", "FracSim", "FunCluster", "FunNet", "fArma", 
"fAsianOptions", "fAssets", "fBasics", "fBonds", "fCalendar", 
"fCopulae", "fEcofin", "fExoticOptions", "fExtremes", "fGarch", 
"fImport", "fMultivar", "fNonlinear", "fOptions", "fPortfolio", 
"fRegression", "fSeries", "fTrading", "fUnitRoots", "fUtilities", 
"fame", "far", "faraway", "fast", "fastICA", "fbati", "fda", 
"fdim", "fdrtool", "feature", "fechner", "ff", "ffmanova", "fgac", 
"fgui", "fields", "filehash", "filehashSQLite", "financial", 
"fingerprint", "fishmethods", "fit4NM", "fitdistrplus", "flashClust", 
"flexclust", "flexmix", "fmri", "foba", "forecasting", "foreign", 
"forensic", "fork", "fortunes", "forward", "fossil", "fpc", "fpca", 
"fpow", "fracdiff", "fractal", "frailtypack", "frontier", "fso", 
"ftnonpar", "fts", "futile", "fuzzyFDR", "fuzzyOP", "fuzzyRankTests", 
"fxregime", "G1DBN", "GAMBoost", "GDD", "GEOmap", "GExMap", "GFMaps", 
"GLDEX", "GOSim", "GPArotation", "GRASS", "GRRGI", "GSA", "GSM", 
"GenABEL", "GenKern", "GeneCycle", "GeneF", "GeneNT", "GeneNet", 
"Geneland", "GeoXp", "GillespieSSA", "GridR", "GroupSeq", "g.data", 
"gRain", "gRbase", "gRc", "gWidgets", "gWidgetsRGtk2", "gWidgetsWWW", 
"gWidgetsrJava", "gWidgetstcltk", "gafit", "gam", "gamair", "gamlss", 
"gamlss.cens", "gamlss.dist", "gamlss.mx", "gamlss.nl", "gamlss.tr", 
"gap", "gbev", "gbm", "gbs", "gcExplorer", "gcl", "gclus", "gcmrec", 
"gdata", "gee", "geepack", "geiger", "genalg", "gene2pathway", 
"genetics", "geoR", "geoRglm", "geomapdata", "geometry", "geonames", 
"geozoo", "getopt", "ggm", "ggplot", "ggplot2", "ghyp", "giRaph", 
"gibbs.met", "glasso", "gld", "glmc", "glmmAK", "glmmBUGS", "glmmML", 
"glmnet", "glmpath", "glpk", "gmaps", "gmm", "gmodels", "gmp", 
"gmt", "gmvalid", "gnm", "goalprog", "gof", "gogarch", "gpclib", 
"gplots", "gpls", "grImport", "grade", "granova", "graph", "graphicsQC", 
"grasp", "gregmisc", "gridBase", "grnnR", "grouped", "grplasso", 
"grpreg", "gsarima", "gsl", "gss", "gstat", "gsubfn", "gtm", 
"gtools", "gumbel", "gvlma", "HAPim", "HFWutils", "HH", "HI", 
"HSAUR", "HTMLapplets", "HadoopStreaming", "HaploSim", "HardyWeinberg", 
"HiddenMarkov", "Hmisc", "HydroMe", "HyperbolicDist", "hacks", 
"hapassoc", "haplo.ccs", "haplo.stats", "hapsim", "hash", "hbim", 
"hddplot", "hdeco", "hdf5", "hdrcde", "heatmap.plus", "helloJavaWorld", 
"heplots", "hett", "hexView", "hexbin", "hier.part", "hierfstat", 
"hints", "hlr", "hmm.discnp", "hoa", "homals", "homtest", "hopach", 
"hot", "howmany", "hsmm", "httpRequest", "hwde", "hwriter", "hybridHclust", 
"hydrogeo", "hydrosanity", "hyperdirichlet", "hypergeo", "IBrokers", 
"ICE", "ICEinfer", "ICS", "ICSNP", "IDPmisc", "ISA", "ISOcodes", 
"ISwR", "Icens", "Iso", "ibdreg", "ic.infer", "ic50", "icomp", 
"identity", "ifa", "ifs", "ifultools", "ig", "igraph", "iid.test", 
"imprProbEst", "impute", "imputeMDR", "ineq", "inetwork", "influence.ME", 
"inline", "intcox", "intervals", "introgress", "iplots", "ipptoolbox", 
"ipred", "irr", "irtProb", "irtoys", "ismev", "isotone", "its", 
"ivivc", "JADE", "JGR", "JM", "JavaGD", "JointGLM", "JointModeling", 
"JudgeIt", "jit", "jointDiag", "KMsurv", "Kendall", "KernSmooth", 
"kappalab", "kerfdr", "kernelPop", "kernlab", "kin.cohort", "kinship", 
"kknn", "klaR", "klin", "kml", "knnTree", "knncat", "knnflex", 
"knorm", "kohonen", "ks", "kst", "kza", "kzft", "kzs", "LDheatmap", 
"LDtests", "LIM", "LIStest", "LLAhclust", "LLN", "LMGene", "LambertW", 
"LearnBayes", "LearnEDA", "Lmoments", "LogConcDEAD", "LogicReg", 
"LoopAnalyst", "LowRankQP", "labdsv", "labeltodendro", "labstatR", 
"laercio", "lago", "lancet.iraqmortality", "languageR", "lars", 
"laser", "lasso2", "latentnet", "latentnetHRT", "lattice", "latticeExtra", 
"latticist", "lawstat", "lazy", "lcd", "lcda", "ldDesign", "lda.cv", 
"ldbounds", "leaps", "lga", "lgtdl", "lhs", "limSolve", "linprog", 
"ljr", "lme4", "lmeSplines", "lmec", "lmm", "lmodel2", "lmom", 
"lmomRFA", "lmomco", "lmtest", "lnMLE", "locfdr", "locfit", "locpol", 
"lodplot", "logcondens", "logilasso", "logistf", "loglognorm", 
"logregperm", "logspline", "lokern", "longRPart", "longitudinal", 
"longmemo", "lpSolve", "lpSolveAPI", "lpc", "lpridge", "lsa", 
"lspls", "lss", "ltm", "ltsa", "luca", "lvplot", "MAMSE", "MAclinical", 
"MBA", "MBESS", "MCAPS", "MCE", "MCMCglmm", "MCMCpack", "MCPAN", 
"MCPMod", "MChtest", "MDD", "MEMSS", "MFDA", "MIfuns", "MKLE", 
"MKmisc", "MLDA", "MLDS", "MLEcens", "MMG", "MNP", "MPV", "MSBVAR", 
"MSVAR", "MarkedPointProcess", "MasterBayes", "MatchIt", "Matching", 
"Matrix", "Metabonomic", "MiscPsycho", "ModelMap", "MultEq", 
"mAr", "mFilter", "maanova", "magic", "mapLD", "mapdata", "mapproj", 
"maps", "maptools", "maptree", "marelac", "marginTree", "marginalmodelplots", 
"markerSearchPower", "mathgraph", "matlab", "matrixcalc", "maxLik", 
"maxstat", "mblm", "mboost", "mc2d", "mcgibbsit", "mclust", "mclust02", 
"mcmc", "mco", "mda", "meboot", "mefa", "meifly", "memisc", "merror", 
"meta", "metaMA", "metacor", "mfp", "mgcv", "mhsmm", "mi", "micEcon", 
"mice", "mimR", "minet", "minpack.lm", "minxent", "mirf", "misc3d", 
"mitools", "mix", "mixPHM", "mixRasch", "mixdist", "mixer", "mixlow", 
"mixreg", "mixstock", "mixtools", "mlCopulaSelection", "mlbench", 
"mlegp", "mlica", "mlmRev", "mlogit", "mmcm", "mmlcr", "mnormt", 
"moc", "modeest", "modehunt", "modeltools", "moduleColor", "mokken", 
"mombf", "moments", "monoProc", "monomvn", "monreg", "moonsun", 
"mota", "mpm", "mprobit", "mra", "mratios", "mrdrc", "msBreast", 
"msDilution", "msProcess", "msProstate", "msm", "muS2RC", "muStat", 
"muUtil", "muhaz", "multcomp", "multcompView", "multic", "multicore", 
"multilevel", "multinomRob", "multipol", "multtest", "muscor", 
"mvbutils", "mvgraph", "mvna", "mvnmle", "mvnormtest", "mvoutlier", 
"mvpart", "mvtBinaryEP", "mvtnorm", "mvtnormpcs", "NADA", "NISTnls", 
"NMMAPSlite", "NMRS", "NORMT3", "NRAIA", "NestedCohort", "NetIndices", 
"nFDR", "nFactors", "ncdf", "ncf", "ncomplete", "negenes", "netmodels", 
"network", "networksis", "neural", "neuralnet", "nice", "nleqslv", 
"nlme", "nlmeODE", "nlrwr", "nls2", "nlstools", "nlt", "nltm", 
"nlts", "nnls", "noia", "nonbinROC", "nor1mix", "norm", "normalp", 
"normwn.test", "nortest", "noverlap", "np", "nparcomp", "npde", 
"nplplot", "npmc", "npmlreg", "nsRFA", "numDeriv", "nws", "OAIHarvester", 
"OPE", "ORMDR", "Oarray", "Oncotree", "OrdFacReg", "OrdMonReg", 
"obsSens", "oc", "oce", "odesolve", "odfWeave", "ofw", "onemap", 
"onion", "openNLP", "openNLPmodels", "opentick", "operators", 
"optmatch", "orientlib", "orloca", "orloca.es", "orth", "orthogonalsplinebasis", 
"orthopolynom", "ouch", "outliers", "oz", "PASWR", "PBSddesolve", 
"PBSmapping", "PBSmodelling", "PET", "PHYLOGR", "PK", "PKfit", 
"PKtools", "PMA", "POT", "PSAgraphics", "PSM", "PTAk", "PairViz", 
"Peaks", "PearsonICA", "PerformanceAnalytics", "PhViD", "PhySim", 
"PolynomF", "Pomic", "PredictiveRegression", "PresenceAbsence", 
"ProfessR", "PtProcess", "PwrGSD", "pARccs", "pack", "packClassic", 
"pairwiseCI", "paleoTS", "paltran", "pamr", "pan", "panel", "papply", 
"paran", "partitions", "partsm", "party", "pastecs", "pbatR", 
"pcaPP", "pcalg", "pcse", "pcurve", "pear", "pec", "pedigree", 
"penalized", "penalizedSVM", "peperr", "permax", "permtest", 
"perturb", "pga", "pgam", "pgirmess", "phangorn", "pheno", "phmm", 
"phpSerialize", "picante", "pinktoe", "pixmap", "plRasch", "playwith", 
"plink", "plm", "plotSEMM", "plotpc", "plotrix", "pls", "plsgenomics", 
"plspm", "plugdensity", "plyr", "pmg", "pmml", "poLCA", "poilog", 
"polspline", "polyapost", "polycor", "polydect", "polynom", "pomp", 
"popbio", "popgen", "poplab", "portfolio", "portfolioSim", "powell", 
"powerGWASinteraction", "powerpkg", "ppc", "ppls", "pps", "prabclus", 
"predbayescor", "predmixcor", "prefmod", "prettyR", "prim", "primer", 
"princurve", "prob", "prodlim", "profileModel", "profr", "proftools", 
"proj4", "proptest", "proto", "proxy", "pscl", "pseudo", "pspearman", 
"pspline", "psy", "psych", "psychometric", "psyphy", "pvclust", 
"pwr", "pwt", "QCA", "QCAGUI", "QRMlib", "QuantPsyc", "qAnalyst", 
"qcc", "qdg", "qgen", "qlspack", "qp", "qpcR", "qtl", "qtlDesign", 
"qtlbim", "qtlbook", "quadprog", "qualV", "quantchem", "quantmod", 
"quantreg", "quantregForest", "qvalue", "qvcalc", "R.cache", 
"R.huge", "R.matlab", "R.methodsS3", "R.oo", "R.rsp", "R.utils", 
"R2HTML", "R2WinBUGS", "R2jags", "RArcInfo", "RBGL", "RBloomberg", 
"RColorBrewer", "RCurl", "RDieHarder", "REQS", "RExcelInstaller", 
"RFA", "RFOC", "RFreak", "RGrace", "RGraphics", "RGtk2", "RHRV", 
"RHmm", "RII", "RItools", "RJDBC", "RJaCGH", "RKEA", "RLMM", 
"RLRsim", "RLadyBug", "RM2", "RMTstat", "RMySQL", "RNetCDF", 
"ROCR", "RODBC", "ROptEst", "ROptEstOld", "ROptRegTS", "ROracle", 
"RPMG", "RPostgreSQL", "RPyGeo", "RQDA", "RQuantLib", "RSAGA", 
"RSEIS", "RSQLite", "RSVGTipsDevice", "RScaLAPACK", "RSeqMeth", 
"RSurvey", "RSvgDevice", "RTOMO", "RTisean", "RUnit", "RWeka", 
"RWinEdt", "RXshrink", "RadioSonde", "RandVar", "RandomFields", 
"RankAggreg", "RaschSampler", "Ratings", "Rcapture", "Rcmdr", 
"RcmdrPlugin.Export", "RcmdrPlugin.FactoMineR", "RcmdrPlugin.HH", 
"RcmdrPlugin.IPSUR", "RcmdrPlugin.SurvivalT", "RcmdrPlugin.TeachingDemos", 
"RcmdrPlugin.epack", "RcmdrPlugin.orloca", "RcmdrPlugin.qcc", 
"RcmdrPlugin.survival", "Rcplex", "Rcpp", "Rcsdp", "Read.isi", 
"Reliability", "ResearchMethods", "ResistorArray", "Rfwdmv", 
"Rglpk", "RiboSort", "Rigroup", "Rlab", "Rlabkey", "Rlsf", "Rmpi", 
"RobAStBase", "RobLox", "RobRex", "Rpad", "Rsac", "Rserve", "Rsge", 
"Rsundials", "Rsymphony", "Runuran", "Rvelslant", "Rwave", "Ryacas", 
"r2lUniv", "rJava", "rPorta", "rSymPy", "race", "rake", "ramps", 
"randaes", "random", "randomForest", "randomLCA", "randomSurvivalForest", 
"randtoolbox", "rankreg", "rateratio.test", "rattle", "rbenchmark", 
"rbounds", "rbugs", "rcdd", "rcdk", "rcdklibs", "rcom", "rcompgen", 
"rconifers", "rda", "rdetools", "realized", "ref", "registry", 
"regress", "regsubseq", "regtest", "rela", "relaimpo", "relations", 
"relax", "relaxo", "reldist", "relimp", "relsurv", "remMap", 
"repolr", "reporttools", "reshape", "resper", "reweight", "rgcvpack", 
"rgdal", "rgenoud", "rggobi", "rgl", "rgr", "rgrs", "rhosp", 
"richards", "rimage", "rindex", "risksetROC", "rjacobi", "rjags", 
"rjson", "rlecuyer", "rmeta", "rmetasim", "rngwell19937", "robCompositions", 
"robfilter", "robust", "robustbase", "rootSolve", "roxygen", 
"rpanel", "rpart", "rpubchem", "rpvm", "rqmcmb2", "rrcov", "rrp", 
"rscproxy", "rsm", "rsprng", "rstream", "rtiff", "rtv", "runjags", 
"rv", "rwm", "rwt", "SASPECT", "SASmixed", "SASxport", "SDDA", 
"SDaA", "SGCS", "SGP", "SIN", "SLmisc", "SMC", "SMPracticals", 
"SMVar", "SNPMaP", "SNPMaP.cdm", "SNPassoc", "SNPmaxsel", "SQLiteDF", 
"SQLiteMap", "SRPM", "STAR", "ScottKnott", "SemiPar", "SenSrivastava", 
"SensoMineR", "SeqKnn", "SharedHT2", "SiZer", "SimComp", "SimHap", 
"SimpleTable", "Snowball", "SoDA", "SoPhy", "SparseM", "SpatialExtremes", 
"SpatialNP", "SpectralGEM", "SpherWave", "StatDA", "StatDataML", 
"StatFingerprints", "StatMatch", "Stem", "StreamMetabolism", 
"SubpathwayMiner", "SuppDists", "SweaveListingUtils", "SwissAir", 
"SyNet", "Synth", "s20x", "sabreR", "sac", "sampfling", "sampleSelection", 
"sampling", "samr", "sandwich", "sapa", "sbgcop", "sca", "scagnostics", 
"scaleboot", "scape", "scapeMCMC", "scatterplot3d", "schoolmath", 
"sciplot", "scout", "scrime", "scuba", "sda", "sdcMicro", "sdcTable", 
"sde", "sdtalt", "sdtoolkit", "seacarb", "seas", "seewave", "segclust", 
"segmented", "selectiongain", "sem", "sendplot", "sensR", "sensitivity", 
"seqinr", "seqmon", "seriation", "session", "setRNG", "sets", 
"sfsmisc", "sgeostat", "shape", "shapefiles", "shapes", "siar", 
"sigma2tools", "signal", "signalextraction", "simba", "simco", 
"simecol", "simex", "similarityRichards", "simone", "simpleboot", 
"singlecase", "sisus", "skewt", "sm", "sma", "smacof", "smatr", 
"smoothSurv", "smoothtail", "sn", "sna", "snow", "snowFT", "snowfall", 
"snp.plotter", "snpXpert", "som", "sound", "sp", "spBayes", "space", 
"spam", "sparseLDA", "spatclus", "spatgraphs", "spatialCovariance", 
"spatialkernel", "spatialsegregation", "spatstat", "spc", "spcosa", 
"spdep", "spe", "spectralGP", "spectrino", "spgrass6", "spgwr", 
"splancs", "spls", "splus2R", "spssDDI", "spsurvey", "spuRs", 
"sqldf", "ssanv", "ssize.fdr", "sspir", "sspline", "st", "staRt", 
"stab", "startupmsg", "stashR", "statmod", "statnet", "stepPlr", 
"stepwise", "stinepack", "stochasticGEM", "stochmod", "stream.net", 
"strucchange", "subplex", "subselect", "sudoku", "supclust", 
"superpc", "surv2sample", "survBayes", "survcomp", "surveillance", 
"survey", "surveyNG", "survival", "survivalROC", "survrec", "svGUI", 
"svIDE", "svMisc", "svSocket", "svcR", "svcm", "svmpath", "systemfit", 
"TIMP", "TRAMPR", "TRIANG", "TSA", "TSHRC", "TSMySQL", "TSP", 
"TSPostgreSQL", "TSSQLite", "TSdbi", "TSfame", "TShistQuote", 
"TSodbc", "TSpadi", "TTR", "TWIX", "TeachingDemos", "TeachingSampling", 
"TinnR", "TraMineR", "TwoWaySurvival", "TwslmSpikeWeight", "taskPR", 
"tawny", "tcltk2", "tdist", "tdm", "tdthap", "tensor", "tensorA", 
"termstrc", "tframe", "tframePlus", "tgp", "tiger", "tileHMM", 
"time", "timeDate", "timeSeries", "timereg", "timsac", "tis", 
"titan", "titecrm", "tkrgl", "tkrplot", "tlemix", "tlnise", "tm", 
"tmvtnorm", "topmodel", "tossm", "tpr", "trackObjs", "tradeCosts", 
"tree", "treelet", "triangle", "trimcluster", "trip", "tripEstimation", 
"tripack", "truncgof", "truncnorm", "truncreg", "trust", "tsDyn", 
"tsModel", "tseries", "tseriesChaos", "tsfa", "tslars", "tuneR", 
"tutoR", "twang", "tweedie", "twslm", "UNF", "USPS", "Umacs", 
"UsingR", "ucminf", "udunits", "ump", "unbalhaar", "uncompress", 
"uniCox", "untb", "urca", "urn", "uroot", "VDCutil", "VGAM", 
"VIM", "VLMC", "VR", "VaR", "VhayuR", "vabayelMix", "varSelRF", 
"varmixt", "vars", "vbmp", "vcd", "vegan", "verification", "verify", 
"vioplot", "vowels", "vrmlgen", "vrtest", "WINRPACK", "WWGbook", 
"WaveCGH", "WeedMap", "WhatIf", "WilcoxCV", "WriteXLS", "wasim", 
"waveclock", "waved", "wavelets", "waveslim", "wavethresh", "wccsom", 
"wgaim", "wikibooks", "wle", "wmtsa", "wnominate", "wombsoft", 
"wordnet", "write.snns", "XML", "XReg", "x12", "xgobi", "xtable", 
"xts", "YaleToolkit", "YourCast", "yaImpute", "yacca", "yaml", 
"yest", "ZIGP", "Zelig", "zipfR", "zoeppritz", "zoo", "zyp"))



[Rd] suggestion for R >= 3.0: computer-readable CHANGELOG
Brian Diggs