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) structure(c(FALSE, TRUE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, TRUE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, TRUE, FALSE, TRUE, TRUE, FALSE, 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"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")) ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
